Difference: AnnMcDermott (1 vs. 22)

Revision 2213 Nov 2009 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"


Public information on Grants associated with NYSBC

Grant Number: 1R01GM088724-0109 Project Title: Structural and Functional Studies of Channels and Pumps by Solid State NMR PI Information: Name Email Title MCDERMOTT, ANN E. aem5@columbia.edu PROFESSOR

Abstract: This abstract is not available.

Public Health Relevance: This Public Health Relevance is not available.

Thesaurus Terms:

There are no thesaurus terms on file for this project.

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE Research Administration NEW YORK, NY 100277003 Fiscal Year: 2009 Department: CHEMISTRY Project Start: 30-SEP-2009 Project End: 31-AUG-2013 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBM

Changed:
<
<
_
>
>

 Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project , the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 2113 Nov 2009 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"

 Personal Preferences (details in TWikiVariables)
  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Added:
>
>
-->
 
Added:
>
>

 Public information on Grants associated with NYSBC
Added:
>
>
Grant Number: 1R01GM088724-0109 Project Title: Structural and Functional Studies of Channels and Pumps by Solid State NMR PI Information: Name Email Title MCDERMOTT, ANN E. aem5@columbia.edu PROFESSOR

Abstract: This abstract is not available.

Public Health Relevance: This Public Health Relevance is not available.

Thesaurus Terms:

There are no thesaurus terms on file for this project.

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE Research Administration NEW YORK, NY 100277003 Fiscal Year: 2009 Department: CHEMISTRY Project Start: 30-SEP-2009 Project End: 31-AUG-2013 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBM

_

 Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project , the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 2013 Nov 2009 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project , the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 1917 Nov 2008 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project , the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 1817 Nov 2008 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"
Changed:
<
<
  • Comment: NYSBC NMR Park Bldg 900 Magnet 2128548393
>
>
  • Comment: NYSBC NMR Park Bldg 900 Magnet (212)854-8393
 

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project , the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 1717 Nov 2008 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"
Changed:
<
<
  • Comment: NYSBC NMR Park Bldg 900 Magnet
>
>
  • Comment: NYSBC NMR Park Bldg 900 Magnet 2128548393
Added:
>
>
 

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project , the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 1601 Apr 2008 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

Changed:
<
<
In this projectyiyiu the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this projectyiyiu, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.
>
>
In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project , the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.
 

META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 1521 Mar 2008 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

Changed:
<
<
In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.
>
>
In this projectyiyiu the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this projectyiyiu, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.
 

META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 1419 Feb 2008 - Main.JasperShahn

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 1330 Jul 2007 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"
Deleted:
<
<
 

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 1205 Dec 2006 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"
Changed:
<
<

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


>
>

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

Added:
>
>
In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.
 
META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 1114 Feb 2006 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.

Deleted:
<
<

Application pending from NYSBC -- NIH 1 S10 RR022986-01 ZRF1 BCMB-L (30) I. Review to complete by end Mar 06, National Advisory Group meet May 06.

 

META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 1009 Feb 2006 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"
Added:
>
>
 Personal Preferences (details in TWikiVariables)
  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


Application pending from NYSBC -- NIH 1 S10 RR022986-01 ZRF1 BCMB-L (30) I. Review to complete by end Mar 06, National Advisory Group meet May 06.

Changed:
<
<

>
>

 
META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 930 Nov 2005 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB


NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR
Changed:
<
<
NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla
>
>
NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla
 MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences
Changed:
<
<
Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University
>
>
Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University
 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851
Changed:
<
<
NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144
>
>
NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144
 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.

Added:
>
>

Application pending from NYSBC -- NIH 1 S10 RR022986-01 ZRF1 BCMB-L (30) I. Review to complete by end Mar 06, National Advisory Group meet May 06.

 

META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 820 Jun 2005 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB

Added:
>
>

NSF Award Abstract - #0316248 Assignment and Structural Characterization of Uniformly Labeled Proteins by Solid State NMR

NSF Org MCB Intial Amendment Date July 28, 2003 Latest Amendment Date May 15, 2005 Award Number 0316248 Award Instrument Continuing grant Program Manager Kamal Shukla MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences Start Date July 15, 2003 Expires June 30, 2006 (Estimated) Awarded Amount to Date $477914 Investigator(s) AnnMcDermott aem5@columbia.edu(Principal Investigator) Sponsor Columbia University 1210 Amsterdam Avenue; MC 2205 New York, NY 10027 212/854-6851 NSF Program(s) BIOMOLECULAR SYSTEMS Field Application(s) Program Reference Code(s) BIOT,9183,1164 Program Element Code(s) 1144 Abstract

In this project the PI will develop new solid state NMR methods to study protein structure. In the previous grant period, the PI has largely completed the site-specific NMR resonance assignments for microcrystalline human Ubiquitin, providing proof of principle for the first stage in denovo structure determination by solid state NMR. In this project, the PI will confirm the existing assignments, and locate signals for the mobile portions. With the recent availability of high magnetic field strengths, her group intends to attempt more challenging and biologically interesting targets; two additional proteins would be assigned as solid phase precipitates: Calmodulin and Triosephosphate Isomerase. Finally, the PI will determine the 3D structure of Ubiquitin based on solid-state NMR data, utilizing several sources of experimental data. Torsional constraints are available from the chemical shifts themselves, which will be analyzed using statistical databases from solution NMR as well as from computed shifts. Hydrogen bond correlations will be measured via N-H...C correlations. Tertiary contacts will be measured using spin diffusion as well as selective recoupling experiments. Structures would be calculated using commercially available software. While structural genomics proceeds apace, many important non-soluble proteins are not readily characterized; the PI's laboratory will attempt characterization of some of the non-soluble targets when the methods are established through this work. The PI is involved with collaborations with several academic and industrial labs that will facilitate transfer of the information obtained through this research. The core effort, however, is the training of outstanding graduate students. High school and undergraduate students will be trained and exposed to structural biology and magnetic resonance in the PI's laboratory.


 
META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 713 Jun 2005 - Main.LisaHickey

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Added:
>
>
Public information on Grants associated with NYSBC

Grant Number: 5R01GM066388-02 PI Name: MCDERMOTT, ANN E. PI Email: aem5@columbia.edu PI Title: PROFESSOR Project Title: Solid State Nuclear Magnetic Resonance Studies of TIM

Abstract: DESCRIPTION (provided by applicant): Triosephosphate isomerase, an isomerase catalyzing an uphill reaction, offers a prime opportunity to stabilize and probe key kinetic and structural features of a Michaelis complex. This proposal capitalizes on our recent advances in stabilizing the Michaelis complex, and our optimization of a range of biophysical probes for the system, so that individual kinetic events and intermediate(s) can be studied. X-ray diffraction at 1.2Angstroms of the Michaelis complex shows a highly compressed active site with unusually short hydrogen bonds and an unexpected substrate torsional state. Recent data, utilizing three spectroscopic methods, indicate that loop opening and product release is rate determining for enzymatic throughput, and invite the hypothesis that loop opening may be triggered by the completion of the enzymatic reaction. The following issues are now ripe for pursuit. (1) Mutants in which the general base glutamic acid 165 and the general acid histidine 95 are replaced with alternative hydrogen bond partners are catalytically inactive. How does selection of the active site amino acids influence compression in the Michaelis complex and polarization of the substrate? (2) What are the chemical species in the Michaelis complex, and how do their concentrations depend upon temperature? Does the proposed enediolate chemical intermediate have a significant population, as might be expected based upon isotope washout? The substrate, while "pinned" through hydrogen bonds to the active site, appears to be mobile at the carbon centers, suggestive of an active rearrangement. Are the chemical reaction rates faster than the loop's motion, as suggested by the minimal primary isotope effects? (3) What are the conformational and ionization changes in the active site of the protein for the Michaelis complex, and what changes accompany the progress along the chemical reaction coordinate? How is the general base E165 positioned for the initial stage of the reaction? (4) What implications would changes in the ligand or mutations in the strongly conserved loop residues have for loop opening rates and for catalysis? These questions would be pursued through solid state NMR, vibrational spectroscopy and X-ray diffraction experiments, both static and dynamic .

Thesaurus Terms: active site, aminoacid, chemical kinetics, enzyme complex, triose phosphate isomerase catalyst, compression, conformation, fungal protein, gene mutation, solid state, temperature Raman spectrometry, X ray crystallography, infrared spectrometry, nuclear magnetic resonance spectroscopy, protein purification

Institution: COLUMBIA UNIV NEW YORK MORNINGSIDE 1210 AMSTERDAM AVE, MC 2205 NEW YORK, NY 10027 Fiscal Year: 2004 Department: CHEMISTRY Project Start: 01-AUG-2002 Project End: 31-JUL-2006 ICD: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES IRG: BBCB

 
META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 627 May 2005 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"
Changed:
<
<
>
>
 

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"

Revision 503 May 2005 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Added:
>
>
  • Tag for 05 ubiquitin paper:
    aem05.gif

META FILEATTACHMENT attr="" comment="Tag for 05 ubiquitin paper" date="1115147150" name="aem05.gif" path="aem05.gif" size="19741" user="DavidCowburn" version="1.1"
 

Revision 418 Apr 2005 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"
Changed:
<
<
  • Company Name: Columbia University
>
>
  • Company Name: Columbia University ColumbiaUniversityintheCityofNewYorkcopy.gif
 

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Revision 311 Apr 2005 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"
Changed:
<
<
  • Comment:
>
>
  • Comment: NYSBC NMR Park Bldg %9%
 Personal Preferences (details in TWikiVariables)
  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Revision 225 Jan 2005 - Main.DavidCowburn

 
META TOPICPARENT name="TWikiUsers"
Changed:
<
<
>
>
  • Name: Ann McDermott
Deleted:
<
<
 

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

Revision 124 Jan 2005 - Main.AnnMcDermott

 
META TOPICPARENT name="TWikiUsers"

Personal Preferences (details in TWikiVariables)

  • Horizontal size of text edit box:
    • Set EDITBOXWIDTH = 70
  • Vertical size of text edit box:
    • Set EDITBOXHEIGHT = 17
  • Style of text edit box. width: 99% for full window width (default), width: auto to disable.
    • Set EDITBOXSTYLE = width: 99%
  • Optionally write protect your home page: (set it to your WikiName)
    • Set ALLOWTOPICCHANGE =

Related topics

 
Copyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding this intranet, Send feedback