Difference: ProteinNmrCourseSyllabus (1 vs. 4)

Revision 425 Jan 2007 - Main.DavidCowburn

 DRAFT 2 DC
Day
Module Title
 		Leceturer(s)
1
1 General Introduction -- What NMR can do. Complementarity to other methods. Additional information to other methods

1
2 Basic principles: Macroscopic and microscopic magnetization, spins, interaction of nuclear spins with a magnetic field, Boltzmann distribution in a magnetic field, the NMR signal
2
3 FT NMR: The one pulse experiment, Fourier transforms, sampling theorem and digitization, sensitivity of FT NMR
2
4 Properties of NMR spectra: Chemical shifts, J-couplings, linewidths, relaxation. The additivity of biopolymer spectra. Through space and through bond assignment principles
3
5 Spin evolution, Single dimension to multidimensional NMR using HMQC/ HSQC as illustration
3 6
Classical and quantum-mechanical description of NMR: Bloch equations to the master equation
4 7
The building blocks of multidimensional NMR, simple use of product operators
4
 8
 How multidimensional sequences work -- building with the blocks, phase cycling, experimental considerations, elementary analysis using product operators
5 9
Preparation of NMR samples. Elementary cloning example, growth on minimal media, isotope labeling, screening of sample conditions, stability
5 10
Advanced preparation issues -- Pichia, cell free, segmental labeling, statagy selection
6 11 Back to the spectrometer, using HSQC and variant sequences including TROSY for characterization
6 12 The through bond assignment strategy and triple res experiments. HNCO HN(CO)CA and how they work
7 13 Adding side chain typing and connectivities -- HNCACB/HNCOCACB and variants
7 14 Mid term quiz /exam
8 15 Analysing spectra for assignment etc. General review of approach. Use of NMRVIEW
8 16 Working examples and use of NMR VIEW for assignment ,
9 17 evaluation of assignment, automation issues for assignment, the assignment of side chains H's
9 18 Structural constraints. Introduction, experimental and inferred H bonds, and angles, through space (nOe) and dipolar constraints
10 19 Using programs for generating nOe assignments -- NMRVIEW , part automation, etc
10 20 Illustrative example of calculation flow using XPLOR/NIH and aria protocol
11 21 Examination of the refinement process and incremental additional assignment strategies for structure generation
11 22 Matching the derived structure and the input data -- accuracy, precision, reasonablness of interpretation
12 23 Objective(?) evalution and what the structure means. WHATIF, external bioinformatics uses , comparison with other structures, novelty of fold/ structure
12 24 Strategies for larger proteins , RDCs and other methods for molecular machines
13 25 Student presentations (1)
13 26 Advanced topics -- GFT NMR and related methods,
14 27 Student presentations (2)
14 28 Advanced topics -- NMR and mapping of small molecule interactions -- lead development for pharmaceuticals
15 29 Student presentations (3)
15 30 Advanced topic -- dynamics and the nature of the NMR
1

RG's draft

Biomolecular NMR Spectroscopy – Principles & Applications

Date: January 30th  May 15th

Presentations: May 22nd & May 29th.

Time: 1:30 – 4:30 pm on Tuesdays

Place: The New York Structural Biology Center

Take-home Midterm Exam (50 %) and Presentations (50 %)

15 Lectures (30 modules) (DRAFT 1 RG)

  1. Introduction (1)
  2. Basic principles: Macroscopic and microscopic magnetization, spins, interaction of nuclear spins with a magnetic field, Boltzmann distribution in a magnetic field, the NMR signal, CW NMR (1).
  3. FT NMR: The one pulse experiment, Fourier transforms, sampling theorem and digitization, sensitivity of FT NMR (1).
  4. Signal processing: Window functions, apodization, zero-filling, linear prediction (1).
  5. Properties of NMR spectra: Chemical shifts, J-couplings, linewidths (1).
  6. Classical and quantum-mechanical description of NMR: Bloch equations to the master equation (1).
  7. Product operators (2).
  8. Single dimension to multidimensional NMR (1).
  9. Preparation of labeled samples for biomolecular applications: E. coli expression, specific labeling, segmental labeling, cell-free expression. (2)
  10. HSQC and variants including TROSY. (2)
  11. A triple-resonance experiment: HNCO (1)
  12. HNCACB/HNCOCACB and variants. Strategies for sequential assignments. (3)
  13. Introduction to NMRView. (2)
  14. Generation of structural constraints: Dihedral angles, NOEs and orientational constraints from RDCs. (4)
  15. Calculation of Structures. (2)
  16. Introduction to ARIA (2).
  17. Evaluation of structures: Procheck, WHATIF, DALI. (1)
  18. NMR in drug discovery (2).
  19. Special strategies for large proteins (1).

OLD DRAFT

  1. Basic NMR formalism
    1. Pulse / fourier transform
    2. Elementary Spin Mechanics
    3. Frequency discrimination
    4. The spectrometer -- critical issues for protein NMR
    5. Elementary Data Processing
  2. NMR building blocks (COSY, TOCSY, NOESY/ROESY, INEPT, TROSY)
    1. Relaxation
  3. Advanced multidimensional NMR
    1. Experimental issues
    2. Data processing
    3. Data analysis
  4. Application of NMR to Structural Biology
    1. Sample Preparation
      • Expression and labeling strategies (uniform/selective/deuteration).
        1. In cell expression screening
      • Concentration and buffer conditions.
      • Initial checks (unfolded/aggregated/degraded).
      • Alignment media
    2. Data processing
      • TOPSPIN/XWINNMR + CARA
      • NMRPIPE + NMRView
    3. Resonance Assignments
      • Backbone and side chains (small proteins < 20 kDa).
      • Automated assignment routines in NMRView/CARA.
    4. Structural Restraints
      • Distance restraints (NOESY based experiments).
      • Manual Vs automated NOE assignments.
      • Hydrogen-Bonds.
      • Angle restraints (e.g. HNHA, HNHB).
      • Dipolar couplings.
    5. Structure Calculations
      • Secondary Structure determination (CSI, TALOS and NOE patterns).
      • Fold determination (CYANA, ARIA, X-PLOR-NIH).
      • Structure quality assessment (Procheck-NMR).
    6. Topics of special interest
      • Biomolecular interactions (filtered experiments, chemical shift perturbation).
      • Biomolecular complex structures (strategies).
      • Characterizing backbone side-chain dynamics.
      • NMR of Nucleic acids and Carbohydrates.
    7. Advanced NMR Techniques
      • Application of TROSY based methods to proteins > 20 kDa.
      • Membrane protein structures.
      • Direct carbon-detect experiments (application to paramagnetic systems, large proteins and unfolded proteins).
      • GFT/Reduced dimensionality in structural genomics.
      • Segmental labeling

Evaluation, Credit

  • Evaluation will be available by using worked examples, by class participation, by class presentation, or by essay. Students needing evaluation for credit will have priority for this course, although auditors are welcome if space is available.
  • Credit -- Graduate students should inquire at their institution, and may contact members of the NYSBC scientific committee. NYSBC cannot provide credit.

Lectures -- assume 13, some may be split between lecturers

Number Nominal date Faculty Topics Comments
1 30 Jan

6 Feb
13 Feb
20 Feb - - Week of Washington's b'day
27 Feb
6 Mar
13 Mar
20 Mar
7 27 Mar
8 3 Apr
9 10 Apr
10 17 Apr
11 24 Apr
12 1 May
13 8 May 

                     2007                                

       January               February                 March        
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa 
    1  2  3  4  5  6                1  2  3                1  2  3
 7  8  9 10 11 12 13    4  5  6  7  8  9 10    4  5  6  7  8  9 10
 14 15 16 17 18 19 20   11 12 13 14 15 16 17   11 12 13 14 15 16 17
 21 22 23 24 25 26 27   18 19 20 21 22 23 24   18 19 20 21 22 23 24
 28 29 30 31            25 26 27 28            25 26 27 28 29 30 31

        April                   May                   June         
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa 
 1  2  3  4  5  6  7          1  2  3  4  5                   1  2
 8  9 10 11 12 13 14    6  7  8  9 10 11 12    3  4  5  6  7  8  9
 15 16 17 18 19 20 21   13 14 15 16 17 18 19   10 11 12 13 14 15 16
 22 23 24 25 26 27 28   20 21 22 23 24 25 26   17 18 19 20 21 22 23
 29 30                  27 28 29 30 31         24 25 26 27 28 29 30
Changed:
<
<		Mark Girvin?'s course outline ...
>
>		Mark Girvin's course outline ...
 Lectures & Labs:

Introduction & Basic Principles of NMR

Signal Properties and Data Processing

Chemical Shift and Spin-Spin Coupling

A repertoire of one-dimensional methods

Product operator description & coherence transfer

Introduction to two-dimensional NMR (hsqc & EXSY/NOESY)

2D Heteronuclear & Homonuclear experiments Homonuclear Resonance assignments & Structural Constraints Structure calculation, refinement & evaluation Lab 3: 23 residue antibiotic peptide: 2D correlation spectra & assignments Representative Protein NMR structure determinations (homonuclear) Lab 4: 2D NOESY spectrum & analysis using NMRVIEW Structure Determination of Nucleic Acids & Other Macromolecules Representative Nucleic Acid NMR Structure Determinations Lab 5: Structure calculation & analysis Introduction to 3D NMR Triple resonance experiments Lab 6: 2D & 3D 1H15N spectra of labeled proteins New methods in NMR of larger proteins Lab 7: Triple resonance experiments "Fun with Enzymes:" kon, koff, Keq, Keq', PIX, etc. Water, hydration & hydrogen bonds Folding of proteins & nucleic acids Ionization states & pKa's + Lab 8: Titration of histidine pKa's in ribonuclease Conformation of ligands on macromolecules & NMR-Based Screening methods Lab 9: Substrate kon and koff from saturation transfer Heteronuclear relaxation & Macromolecular dynamics

Registered Students

Name Lab Institution Credit ?
Changed:
<
<
ErtanEryilmaz? Ronnie Ghose? cuny.gif ?
>
>
ErtanEryilmaz Ronnie Ghose cuny.gif ?
 

Flier for course http://www.nysbc.net/library/ProteinNmrCourse07.pdf

  • Set ALLOWTOPICVIEW =
Changed:
<
<
  • Set ALLOWTOPICCHANGE = ProteinNmrCourseFacultyGroup?
>
>
 
Changed:
<
<		-- DavidCowburn? - 08 Jun 2006
>
>		-- DavidCowburn - 08 Jun 2006
  * Presentation2.ppt: Presentation2.ppt
Added:
>
>
META TOPICMOVED by="DavidCowburn" date="1169762062" from="Main.ProteinNmrCourseSyllabus" to="Staffarchive.ProteinNmrCourseSyllabus"
 

Revision 325 Jan 2007 - Main.DavidCowburn

 DRAFT 2 DC
Day
Module Title
 		Leceturer(s)
1
1 General Introduction -- What NMR can do. Complementarity to other methods. Additional information to other methods

1
2 Basic principles: Macroscopic and microscopic magnetization, spins, interaction of nuclear spins with a magnetic field, Boltzmann distribution in a magnetic field, the NMR signal
2
3 FT NMR: The one pulse experiment, Fourier transforms, sampling theorem and digitization, sensitivity of FT NMR
2
4 Properties of NMR spectra: Chemical shifts, J-couplings, linewidths, relaxation. The additivity of biopolymer spectra. Through space and through bond assignment principles
3
5 Spin evolution, Single dimension to multidimensional NMR using HMQC/ HSQC as illustration
3 6
Classical and quantum-mechanical description of NMR: Bloch equations to the master equation
4 7
The building blocks of multidimensional NMR, simple use of product operators
4
 8
 How multidimensional sequences work -- building with the blocks, phase cycling, experimental considerations, elementary analysis using product operators
5 9
Preparation of NMR samples. Elementary cloning example, growth on minimal media, isotope labeling, screening of sample conditions, stability
5 10
Advanced preparation issues -- Pichia, cell free, segmental labeling, statagy selection
6 11 Back to the spectrometer, using HSQC and variant sequences including TROSY for characterization
6 12 The through bond assignment strategy and triple res experiments. HNCO HN(CO)CA and how they work
7 13 Adding side chain typing and connectivities -- HNCACB/HNCOCACB and variants
7 14 Mid term quiz /exam
8 15 Analysing spectra for assignment etc. General review of approach. Use of NMRVIEW
8 16 Working examples and use of NMR VIEW for assignment ,
9 17 evaluation of assignment, automation issues for assignment, the assignment of side chains H's
9 18 Structural constraints. Introduction, experimental and inferred H bonds, and angles, through space (nOe) and dipolar constraints
10 19 Using programs for generating nOe assignments -- NMRVIEW , part automation, etc
10 20 Illustrative example of calculation flow using XPLOR/NIH and aria protocol
11 21 Examination of the refinement process and incremental additional assignment strategies for structure generation
11 22 Matching the derived structure and the input data -- accuracy, precision, reasonablness of interpretation
12 23 Objective(?) evalution and what the structure means. WHATIF, external bioinformatics uses , comparison with other structures, novelty of fold/ structure
12 24 Strategies for larger proteins , RDCs and other methods for molecular machines
13 25 Student presentations (1)
13 26 Advanced topics -- GFT NMR and related methods,
14 27 Student presentations (2)
14 28 Advanced topics -- NMR and mapping of small molecule interactions -- lead development for pharmaceuticals
15 29 Student presentations (3)
15 30 Advanced topic -- dynamics and the nature of the NMR
1

RG's draft

Biomolecular NMR Spectroscopy – Principles & Applications

Date: January 30th  May 15th

Presentations: May 22nd & May 29th.

Time: 1:30 – 4:30 pm on Tuesdays

Place: The New York Structural Biology Center

Take-home Midterm Exam (50 %) and Presentations (50 %)

15 Lectures (30 modules) (DRAFT 1 RG)

  1. Introduction (1)
  2. Basic principles: Macroscopic and microscopic magnetization, spins, interaction of nuclear spins with a magnetic field, Boltzmann distribution in a magnetic field, the NMR signal, CW NMR (1).
  3. FT NMR: The one pulse experiment, Fourier transforms, sampling theorem and digitization, sensitivity of FT NMR (1).
  4. Signal processing: Window functions, apodization, zero-filling, linear prediction (1).
  5. Properties of NMR spectra: Chemical shifts, J-couplings, linewidths (1).
  6. Classical and quantum-mechanical description of NMR: Bloch equations to the master equation (1).
  7. Product operators (2).
  8. Single dimension to multidimensional NMR (1).
  9. Preparation of labeled samples for biomolecular applications: E. coli expression, specific labeling, segmental labeling, cell-free expression. (2)
  10. HSQC and variants including TROSY. (2)
  11. A triple-resonance experiment: HNCO (1)
  12. HNCACB/HNCOCACB and variants. Strategies for sequential assignments. (3)
  13. Introduction to NMRView. (2)
  14. Generation of structural constraints: Dihedral angles, NOEs and orientational constraints from RDCs. (4)
  15. Calculation of Structures. (2)
  16. Introduction to ARIA (2).
  17. Evaluation of structures: Procheck, WHATIF, DALI. (1)
  18. NMR in drug discovery (2).
  19. Special strategies for large proteins (1).

OLD DRAFT

  1. Basic NMR formalism
    1. Pulse / fourier transform
    2. Elementary Spin Mechanics
    3. Frequency discrimination
    4. The spectrometer -- critical issues for protein NMR
    5. Elementary Data Processing
  2. NMR building blocks (COSY, TOCSY, NOESY/ROESY, INEPT, TROSY)
    1. Relaxation
  3. Advanced multidimensional NMR
    1. Experimental issues
    2. Data processing
    3. Data analysis
  4. Application of NMR to Structural Biology
    1. Sample Preparation
      • Expression and labeling strategies (uniform/selective/deuteration).
        1. In cell expression screening
      • Concentration and buffer conditions.
      • Initial checks (unfolded/aggregated/degraded).
      • Alignment media
    2. Data processing
      • TOPSPIN/XWINNMR + CARA
      • NMRPIPE + NMRView
    3. Resonance Assignments
      • Backbone and side chains (small proteins < 20 kDa).
      • Automated assignment routines in NMRView/CARA.
    4. Structural Restraints
      • Distance restraints (NOESY based experiments).
      • Manual Vs automated NOE assignments.
      • Hydrogen-Bonds.
      • Angle restraints (e.g. HNHA, HNHB).
      • Dipolar couplings.
    5. Structure Calculations
      • Secondary Structure determination (CSI, TALOS and NOE patterns).
      • Fold determination (CYANA, ARIA, X-PLOR-NIH).
      • Structure quality assessment (Procheck-NMR).
    6. Topics of special interest
      • Biomolecular interactions (filtered experiments, chemical shift perturbation).
      • Biomolecular complex structures (strategies).
      • Characterizing backbone side-chain dynamics.
      • NMR of Nucleic acids and Carbohydrates.
    7. Advanced NMR Techniques
      • Application of TROSY based methods to proteins > 20 kDa.
      • Membrane protein structures.
      • Direct carbon-detect experiments (application to paramagnetic systems, large proteins and unfolded proteins).
      • GFT/Reduced dimensionality in structural genomics.
      • Segmental labeling

Evaluation, Credit

  • Evaluation will be available by using worked examples, by class participation, by class presentation, or by essay. Students needing evaluation for credit will have priority for this course, although auditors are welcome if space is available.
  • Credit -- Graduate students should inquire at their institution, and may contact members of the NYSBC scientific committee. NYSBC cannot provide credit.

Lectures -- assume 13, some may be split between lecturers

Number Nominal date Faculty Topics Comments
1 30 Jan

6 Feb
13 Feb
20 Feb - - Week of Washington's b'day
27 Feb
6 Mar
13 Mar
20 Mar
7 27 Mar
8 3 Apr
9 10 Apr
10 17 Apr
11 24 Apr
12 1 May
13 8 May 

                     2007                                

       January               February                 March        
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa 
    1  2  3  4  5  6                1  2  3                1  2  3
 7  8  9 10 11 12 13    4  5  6  7  8  9 10    4  5  6  7  8  9 10
 14 15 16 17 18 19 20   11 12 13 14 15 16 17   11 12 13 14 15 16 17
 21 22 23 24 25 26 27   18 19 20 21 22 23 24   18 19 20 21 22 23 24
 28 29 30 31            25 26 27 28            25 26 27 28 29 30 31

        April                   May                   June         
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa 
 1  2  3  4  5  6  7          1  2  3  4  5                   1  2
 8  9 10 11 12 13 14    6  7  8  9 10 11 12    3  4  5  6  7  8  9
 15 16 17 18 19 20 21   13 14 15 16 17 18 19   10 11 12 13 14 15 16
 22 23 24 25 26 27 28   20 21 22 23 24 25 26   17 18 19 20 21 22 23
 29 30                  27 28 29 30 31         24 25 26 27 28 29 30
Mark Girvin?'s course outline ...

Lectures & Labs:

Introduction & Basic Principles of NMR

Signal Properties and Data Processing

Chemical Shift and Spin-Spin Coupling

A repertoire of one-dimensional methods

Product operator description & coherence transfer

Introduction to two-dimensional NMR (hsqc & EXSY/NOESY)

2D Heteronuclear & Homonuclear experiments Homonuclear Resonance assignments & Structural Constraints Structure calculation, refinement & evaluation Lab 3: 23 residue antibiotic peptide: 2D correlation spectra & assignments Representative Protein NMR structure determinations (homonuclear) Lab 4: 2D NOESY spectrum & analysis using NMRVIEW Structure Determination of Nucleic Acids & Other Macromolecules Representative Nucleic Acid NMR Structure Determinations Lab 5: Structure calculation & analysis Introduction to 3D NMR Triple resonance experiments Lab 6: 2D & 3D 1H15N spectra of labeled proteins New methods in NMR of larger proteins Lab 7: Triple resonance experiments "Fun with Enzymes:" kon, koff, Keq, Keq', PIX, etc. Water, hydration & hydrogen bonds Folding of proteins & nucleic acids Ionization states & pKa's + Lab 8: Titration of histidine pKa's in ribonuclease Conformation of ligands on macromolecules & NMR-Based Screening methods Lab 9: Substrate kon and koff from saturation transfer Heteronuclear relaxation & Macromolecular dynamics

Registered Students

Name Lab Institution Credit ?up
ErtanEryilmaz? Ronnie Ghose? cuny.gif ?

Flier for course http://www.nysbc.net/library/ProteinNmrCourse07.pdf

  • Set ALLOWTOPICVIEW =
Changed:
<
<
  • Set ALLOWTOPICCHANGE = ProteinNmrCourseGroup?
>
>
  • Set ALLOWTOPICCHANGE = ProteinNmrCourseFacultyGroup?
 -- DavidCowburn? - 08 Jun 2006 * Presentation2.ppt: Presentation2.ppt

Revision 207 Nov 2006 - Main.DavidCowburn

 DRAFT 2 DC
Day
Module Title
 		Leceturer(s)
1
1 General Introduction -- What NMR can do. Complementarity to other methods. Additional information to other methods

1
2 Basic principles: Macroscopic and microscopic magnetization, spins, interaction of nuclear spins with a magnetic field, Boltzmann distribution in a magnetic field, the NMR signal
2
3 FT NMR: The one pulse experiment, Fourier transforms, sampling theorem and digitization, sensitivity of FT NMR
2
4 Properties of NMR spectra: Chemical shifts, J-couplings, linewidths, relaxation. The additivity of biopolymer spectra. Through space and through bond assignment principles
3
5 Spin evolution, Single dimension to multidimensional NMR using HMQC/ HSQC as illustration
3 6
Classical and quantum-mechanical description of NMR: Bloch equations to the master equation
4 7
The building blocks of multidimensional NMR, simple use of product operators
4
 8
 How multidimensional sequences work -- building with the blocks, phase cycling, experimental considerations, elementary analysis using product operators
5 9
Preparation of NMR samples. Elementary cloning example, growth on minimal media, isotope labeling, screening of sample conditions, stability
5 10
Advanced preparation issues -- Pichia, cell free, segmental labeling, statagy selection
6 11 Back to the spectrometer, using HSQC and variant sequences including TROSY for characterization
6 12 The through bond assignment strategy and triple res experiments. HNCO HN(CO)CA and how they work
7 13 Adding side chain typing and connectivities -- HNCACB/HNCOCACB and variants
7 14 Mid term quiz /exam
8 15 Analysing spectra for assignment etc. General review of approach. Use of NMRVIEW
8 16 Working examples and use of NMR VIEW for assignment ,
9 17 evaluation of assignment, automation issues for assignment, the assignment of side chains H's
9 18 Structural constraints. Introduction, experimental and inferred H bonds, and angles, through space (nOe) and dipolar constraints
10 19 Using programs for generating nOe assignments -- NMRVIEW , part automation, etc
10 20 Illustrative example of calculation flow using XPLOR/NIH and aria protocol
11 21 Examination of the refinement process and incremental additional assignment strategies for structure generation
11 22 Matching the derived structure and the input data -- accuracy, precision, reasonablness of interpretation
12 23 Objective(?) evalution and what the structure means. WHATIF, external bioinformatics uses , comparison with other structures, novelty of fold/ structure
12 24 Strategies for larger proteins , RDCs and other methods for molecular machines
13 25 Student presentations (1)
13 26 Advanced topics -- GFT NMR and related methods,
14 27 Student presentations (2)
14 28 Advanced topics -- NMR and mapping of small molecule interactions -- lead development for pharmaceuticals
15 29 Student presentations (3)
15 30 Advanced topic -- dynamics and the nature of the NMR
1

Added:
>
>		RG's draft

Biomolecular NMR Spectroscopy – Principles & Applications

Date: January 30th  May 15th

Presentations: May 22nd & May 29th.

Time: 1:30 – 4:30 pm on Tuesdays

Place: The New York Structural Biology Center

Take-home Midterm Exam (50 %) and Presentations (50 %)

15 Lectures (30 modules) (DRAFT 1 RG)

  1. Introduction (1)
  2. Basic principles: Macroscopic and microscopic magnetization, spins, interaction of nuclear spins with a magnetic field, Boltzmann distribution in a magnetic field, the NMR signal, CW NMR (1).
  3. FT NMR: The one pulse experiment, Fourier transforms, sampling theorem and digitization, sensitivity of FT NMR (1).
  4. Signal processing: Window functions, apodization, zero-filling, linear prediction (1).
  5. Properties of NMR spectra: Chemical shifts, J-couplings, linewidths (1).
  6. Classical and quantum-mechanical description of NMR: Bloch equations to the master equation (1).
  7. Product operators (2).
  8. Single dimension to multidimensional NMR (1).
  9. Preparation of labeled samples for biomolecular applications: E. coli expression, specific labeling, segmental labeling, cell-free expression. (2)
  10. HSQC and variants including TROSY. (2)
  11. A triple-resonance experiment: HNCO (1)
  12. HNCACB/HNCOCACB and variants. Strategies for sequential assignments. (3)
  13. Introduction to NMRView. (2)
  14. Generation of structural constraints: Dihedral angles, NOEs and orientational constraints from RDCs. (4)
  15. Calculation of Structures. (2)
  16. Introduction to ARIA (2).
  17. Evaluation of structures: Procheck, WHATIF, DALI. (1)
  18. NMR in drug discovery (2).
  19. Special strategies for large proteins (1).
 

OLD DRAFT

  1. Basic NMR formalism
    1. Pulse / fourier transform
    2. Elementary Spin Mechanics
    3. Frequency discrimination
    4. The spectrometer -- critical issues for protein NMR
    5. Elementary Data Processing
  2. NMR building blocks (COSY, TOCSY, NOESY/ROESY, INEPT, TROSY)
    1. Relaxation
  3. Advanced multidimensional NMR
    1. Experimental issues
    2. Data processing
    3. Data analysis
  4. Application of NMR to Structural Biology
    1. Sample Preparation
      • Expression and labeling strategies (uniform/selective/deuteration).
        1. In cell expression screening
      • Concentration and buffer conditions.
      • Initial checks (unfolded/aggregated/degraded).
      • Alignment media
    2. Data processing
      • TOPSPIN/XWINNMR + CARA
      • NMRPIPE + NMRView
    3. Resonance Assignments
      • Backbone and side chains (small proteins < 20 kDa).
      • Automated assignment routines in NMRView/CARA.
    4. Structural Restraints
      • Distance restraints (NOESY based experiments).
      • Manual Vs automated NOE assignments.
      • Hydrogen-Bonds.
      • Angle restraints (e.g. HNHA, HNHB).
      • Dipolar couplings.
    5. Structure Calculations
      • Secondary Structure determination (CSI, TALOS and NOE patterns).
      • Fold determination (CYANA, ARIA, X-PLOR-NIH).
      • Structure quality assessment (Procheck-NMR).
    6. Topics of special interest
      • Biomolecular interactions (filtered experiments, chemical shift perturbation).
      • Biomolecular complex structures (strategies).
      • Characterizing backbone side-chain dynamics.
      • NMR of Nucleic acids and Carbohydrates.
    7. Advanced NMR Techniques
      • Application of TROSY based methods to proteins > 20 kDa.
      • Membrane protein structures.
      • Direct carbon-detect experiments (application to paramagnetic systems, large proteins and unfolded proteins).
      • GFT/Reduced dimensionality in structural genomics.
      • Segmental labeling

Evaluation, Credit

  • Evaluation will be available by using worked examples, by class participation, by class presentation, or by essay. Students needing evaluation for credit will have priority for this course, although auditors are welcome if space is available.
  • Credit -- Graduate students should inquire at their institution, and may contact members of the NYSBC scientific committee. NYSBC cannot provide credit.

Lectures -- assume 13, some may be split between lecturers

Number Nominal date Faculty Topics Comments
1 30 Jan

6 Feb
13 Feb
20 Feb - - Week of Washington's b'day
27 Feb
6 Mar
13 Mar
20 Mar
7 27 Mar
8 3 Apr
9 10 Apr
10 17 Apr
11 24 Apr
12 1 May
13 8 May 

                     2007                                

       January               February                 March        
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa 
    1  2  3  4  5  6                1  2  3                1  2  3
 7  8  9 10 11 12 13    4  5  6  7  8  9 10    4  5  6  7  8  9 10
 14 15 16 17 18 19 20   11 12 13 14 15 16 17   11 12 13 14 15 16 17
 21 22 23 24 25 26 27   18 19 20 21 22 23 24   18 19 20 21 22 23 24
 28 29 30 31            25 26 27 28            25 26 27 28 29 30 31

        April                   May                   June         
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa 
 1  2  3  4  5  6  7          1  2  3  4  5                   1  2
 8  9 10 11 12 13 14    6  7  8  9 10 11 12    3  4  5  6  7  8  9
 15 16 17 18 19 20 21   13 14 15 16 17 18 19   10 11 12 13 14 15 16
 22 23 24 25 26 27 28   20 21 22 23 24 25 26   17 18 19 20 21 22 23
 29 30                  27 28 29 30 31         24 25 26 27 28 29 30
Mark Girvin?'s course outline ...

Lectures & Labs:

Introduction & Basic Principles of NMR

Signal Properties and Data Processing

Chemical Shift and Spin-Spin Coupling

A repertoire of one-dimensional methods

Product operator description & coherence transfer

Introduction to two-dimensional NMR (hsqc & EXSY/NOESY)

2D Heteronuclear & Homonuclear experiments Homonuclear Resonance assignments & Structural Constraints Structure calculation, refinement & evaluation Lab 3: 23 residue antibiotic peptide: 2D correlation spectra & assignments Representative Protein NMR structure determinations (homonuclear) Lab 4: 2D NOESY spectrum & analysis using NMRVIEW Structure Determination of Nucleic Acids & Other Macromolecules Representative Nucleic Acid NMR Structure Determinations Lab 5: Structure calculation & analysis Introduction to 3D NMR Triple resonance experiments Lab 6: 2D & 3D 1H15N spectra of labeled proteins New methods in NMR of larger proteins Lab 7: Triple resonance experiments "Fun with Enzymes:" kon, koff, Keq, Keq', PIX, etc. Water, hydration & hydrogen bonds Folding of proteins & nucleic acids Ionization states & pKa's + Lab 8: Titration of histidine pKa's in ribonuclease Conformation of ligands on macromolecules & NMR-Based Screening methods Lab 9: Substrate kon and koff from saturation transfer Heteronuclear relaxation & Macromolecular dynamics

Registered Students

Name Lab Institution Credit ?
ErtanEryilmaz? Ronnie Ghose? cuny.gif ?

Flier for course http://www.nysbc.net/library/ProteinNmrCourse07.pdf

  • Set ALLOWTOPICVIEW =
  • Set ALLOWTOPICCHANGE = ProteinNmrCourseGroup?

-- DavidCowburn? - 08 Jun 2006 * Presentation2.ppt: Presentation2.ppt

Revision 107 Nov 2006 - Main.DavidCowburn

 DRAFT 2 DC
Day
Module Title
 		Leceturer(s)
1
1 General Introduction -- What NMR can do. Complementarity to other methods. Additional information to other methods

1
2 Basic principles: Macroscopic and microscopic magnetization, spins, interaction of nuclear spins with a magnetic field, Boltzmann distribution in a magnetic field, the NMR signal
2
3 FT NMR: The one pulse experiment, Fourier transforms, sampling theorem and digitization, sensitivity of FT NMR
2
4 Properties of NMR spectra: Chemical shifts, J-couplings, linewidths, relaxation. The additivity of biopolymer spectra. Through space and through bond assignment principles
3
5 Spin evolution, Single dimension to multidimensional NMR using HMQC/ HSQC as illustration
3 6
Classical and quantum-mechanical description of NMR: Bloch equations to the master equation
4 7
The building blocks of multidimensional NMR, simple use of product operators
4
 8
 How multidimensional sequences work -- building with the blocks, phase cycling, experimental considerations, elementary analysis using product operators
5 9
Preparation of NMR samples. Elementary cloning example, growth on minimal media, isotope labeling, screening of sample conditions, stability
5 10
Advanced preparation issues -- Pichia, cell free, segmental labeling, statagy selection
6 11 Back to the spectrometer, using HSQC and variant sequences including TROSY for characterization
6 12 The through bond assignment strategy and triple res experiments. HNCO HN(CO)CA and how they work
7 13 Adding side chain typing and connectivities -- HNCACB/HNCOCACB and variants
7 14 Mid term quiz /exam
8 15 Analysing spectra for assignment etc. General review of approach. Use of NMRVIEW
8 16 Working examples and use of NMR VIEW for assignment ,
9 17 evaluation of assignment, automation issues for assignment, the assignment of side chains H's
9 18 Structural constraints. Introduction, experimental and inferred H bonds, and angles, through space (nOe) and dipolar constraints
10 19 Using programs for generating nOe assignments -- NMRVIEW , part automation, etc
10 20 Illustrative example of calculation flow using XPLOR/NIH and aria protocol
11 21 Examination of the refinement process and incremental additional assignment strategies for structure generation
11 22 Matching the derived structure and the input data -- accuracy, precision, reasonablness of interpretation
12 23 Objective(?) evalution and what the structure means. WHATIF, external bioinformatics uses , comparison with other structures, novelty of fold/ structure
12 24 Strategies for larger proteins , RDCs and other methods for molecular machines
13 25 Student presentations (1)
13 26 Advanced topics -- GFT NMR and related methods,
14 27 Student presentations (2)
14 28 Advanced topics -- NMR and mapping of small molecule interactions -- lead development for pharmaceuticals
15 29 Student presentations (3)
15 30 Advanced topic -- dynamics and the nature of the NMR
1

OLD DRAFT

  1. Basic NMR formalism
    1. Pulse / fourier transform
    2. Elementary Spin Mechanics
    3. Frequency discrimination
    4. The spectrometer -- critical issues for protein NMR
    5. Elementary Data Processing
  2. NMR building blocks (COSY, TOCSY, NOESY/ROESY, INEPT, TROSY)
    1. Relaxation
  3. Advanced multidimensional NMR
    1. Experimental issues
    2. Data processing
    3. Data analysis
  4. Application of NMR to Structural Biology
    1. Sample Preparation
      • Expression and labeling strategies (uniform/selective/deuteration).
        1. In cell expression screening
      • Concentration and buffer conditions.
      • Initial checks (unfolded/aggregated/degraded).
      • Alignment media
    2. Data processing
      • TOPSPIN/XWINNMR + CARA
      • NMRPIPE + NMRView
    3. Resonance Assignments
      • Backbone and side chains (small proteins < 20 kDa).
      • Automated assignment routines in NMRView/CARA.
    4. Structural Restraints
      • Distance restraints (NOESY based experiments).
      • Manual Vs automated NOE assignments.
      • Hydrogen-Bonds.
      • Angle restraints (e.g. HNHA, HNHB).
      • Dipolar couplings.
    5. Structure Calculations
      • Secondary Structure determination (CSI, TALOS and NOE patterns).
      • Fold determination (CYANA, ARIA, X-PLOR-NIH).
      • Structure quality assessment (Procheck-NMR).
    6. Topics of special interest
      • Biomolecular interactions (filtered experiments, chemical shift perturbation).
      • Biomolecular complex structures (strategies).
      • Characterizing backbone side-chain dynamics.
      • NMR of Nucleic acids and Carbohydrates.
    7. Advanced NMR Techniques
      • Application of TROSY based methods to proteins > 20 kDa.
      • Membrane protein structures.
      • Direct carbon-detect experiments (application to paramagnetic systems, large proteins and unfolded proteins).
      • GFT/Reduced dimensionality in structural genomics.
      • Segmental labeling

Evaluation, Credit

  • Evaluation will be available by using worked examples, by class participation, by class presentation, or by essay. Students needing evaluation for credit will have priority for this course, although auditors are welcome if space is available.
  • Credit -- Graduate students should inquire at their institution, and may contact members of the NYSBC scientific committee. NYSBC cannot provide credit.

Lectures -- assume 13, some may be split between lecturers

Number Nominal date Faculty Topics Comments
1 30 Jan

6 Feb
13 Feb
20 Feb - - Week of Washington's b'day
27 Feb
6 Mar
13 Mar
20 Mar
7 27 Mar
8 3 Apr
9 10 Apr
10 17 Apr
11 24 Apr
12 1 May
13 8 May 

                     2007                                

       January               February                 March        
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa 
    1  2  3  4  5  6                1  2  3                1  2  3
 7  8  9 10 11 12 13    4  5  6  7  8  9 10    4  5  6  7  8  9 10
 14 15 16 17 18 19 20   11 12 13 14 15 16 17   11 12 13 14 15 16 17
 21 22 23 24 25 26 27   18 19 20 21 22 23 24   18 19 20 21 22 23 24
 28 29 30 31            25 26 27 28            25 26 27 28 29 30 31

        April                   May                   June         
Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa   Su Mo Tu We Th Fr Sa 
 1  2  3  4  5  6  7          1  2  3  4  5                   1  2
 8  9 10 11 12 13 14    6  7  8  9 10 11 12    3  4  5  6  7  8  9
 15 16 17 18 19 20 21   13 14 15 16 17 18 19   10 11 12 13 14 15 16
 22 23 24 25 26 27 28   20 21 22 23 24 25 26   17 18 19 20 21 22 23
 29 30                  27 28 29 30 31         24 25 26 27 28 29 30
Mark Girvin?'s course outline ...

Lectures & Labs:

Introduction & Basic Principles of NMR

Signal Properties and Data Processing

Chemical Shift and Spin-Spin Coupling

A repertoire of one-dimensional methods

Product operator description & coherence transfer

Introduction to two-dimensional NMR (hsqc & EXSY/NOESY)

2D Heteronuclear & Homonuclear experiments Homonuclear Resonance assignments & Structural Constraints Structure calculation, refinement & evaluation Lab 3: 23 residue antibiotic peptide: 2D correlation spectra & assignments Representative Protein NMR structure determinations (homonuclear) Lab 4: 2D NOESY spectrum & analysis using NMRVIEW Structure Determination of Nucleic Acids & Other Macromolecules Representative Nucleic Acid NMR Structure Determinations Lab 5: Structure calculation & analysis Introduction to 3D NMR Triple resonance experiments Lab 6: 2D & 3D 1H15N spectra of labeled proteins New methods in NMR of larger proteins Lab 7: Triple resonance experiments "Fun with Enzymes:" kon, koff, Keq, Keq', PIX, etc. Water, hydration & hydrogen bonds Folding of proteins & nucleic acids Ionization states & pKa's + Lab 8: Titration of histidine pKa's in ribonuclease Conformation of ligands on macromolecules & NMR-Based Screening methods Lab 9: Substrate kon and koff from saturation transfer Heteronuclear relaxation & Macromolecular dynamics

Registered Students

Name Lab Institution Credit ?
ErtanEryilmaz? Ronnie Ghose? cuny.gif ?

Flier for course http://www.nysbc.net/library/ProteinNmrCourse07.pdf

  • Set ALLOWTOPICVIEW =
  • Set ALLOWTOPICCHANGE = ProteinNmrCourseGroup?

-- DavidCowburn? - 08 Jun 2006 * Presentation2.ppt: Presentation2.ppt

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