Discussion of topics in Dynamics

Some significant current work

Technique issues

Wang, C., Rance, M., and Palmer, A. G. Mapping chemical exchange in proteins with MW > 50 kD. J Am Chem Soc 125, 8968-8969. LIBRARY:WangRance03.pdf

Ferrage, F., Pelupessey P., Cowburn D., Bodenhausen G. "Intra-residue dipolar cross-relaxation rates between 13Cα and 13C' as a measure of internal dynamics in proteins by NMR Spectroscopy" J. Am. Chem. Soc. 128 11072-8

Fushman, D., and Cowburn, D. (2001). Nuclear magnetic resonance relaxation in determination of residue-specific 15N chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol 339, 109-126. a, b

Solids/ dynamics

Related to membrane proteins in solution

Kamen, D.E., Cahill, S.M. and Girvin, M.E. (2007) Multiple alignment of membrane proteins for measuring residual dipolar couplings using lanthanide ions bound to a small metal chelator. Journal of the American Chemical Society, 129, 1846-1847. LIBRARY:KamenCahill07.pdf

General structure/dynamics studies

Del Rio, A., Dutta K., Chavez J., Ubarretxena-Belandia, I., Ghose, R., Solution Structure and Dynamics of the N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Pseudomonas aeruginosa: Insights into a Functional Role in Intramembrane Proteolysis. 2006 J Mol Biol 365: 109-122. a

Dutta K, Shi HH, Cruz-Chu ER, Kami K, Ghose R. (2004) Dynamic influences on a high-affinity, high-specificity interaction involving the C-terminal SH3 domain of P67(phox) Biochemistry 43 8094-8106

Joel A. Butterwick and Arthur G. Palmer, III "An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H" Protein Sci. 2006 15 2697-2707

Massi F, Wang C, Palmer AG. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 36 10787-94

Edwards , T.A., Butterwick, J.A., Zeng, L., Gupta, Y.K., Wang, X, Wharton, R.P., Palmer, A.G., Aggarwal, A.K. Solution Structure of the Vts1 SAM Domain in the Presence of RNA J. Mol. Biol. 356, 1065-1072. a

Tang Y, Grey MJ, McKnight^? J, Palmer AG, Raleigh DP 'Multistate Folding of the Villin Headpiece Domain.' J Mol Biol 355, 1066-1072. a

Grey, M.J., Tang, Y, Alexov, E, McKnight^?, C.J., Raleigh, D.P.,Palmer, A.G. (2006) Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain . Journal of Molecular Biology 355, 1078-1094. a

Valentine, E. R., and Palmer, A. G., 3rd. Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2 Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA. Biochemistry 44, 3410-3417

Wang, C., Karpowich, N., Hunt, J. F., Rance, M., and Palmer, A. G. Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters. J Mol Biol 342, 525-537.

Butterwick, J. A., Patrick Loria, J., Astrof, N. S., Kroenke, C. D., Cole, R., Rance, M., and Palmer, A. G., 3rd . Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J Mol Biol 339, 855-871.

Muralidharan V., Dutta K., Cho J., Vila-Perello M., Raleigh DP., Cowburn D., Muir TW 'Solution Structure and Folding Characteristics of the C-Terminal SH3 Domain of c-Crk-II' Biochemistry 45, 8874-8884 a

Kempf, J. G.; Jung, J-y.; Ragain, C.; Sampson, N. S.; Loria, J. P. Dynamic Requirements for a functional protein hinge. 2007 J. Mol. Biol 368: 131-149

Sung YH, Eliezer D 'Residual Structure, Backbone Dynamics, and Interactions within the Synuclein Family.' J Mol Biol 372:689-707

Sung, Y, Eliezer, D, Secondary structure and dynamics of micelle bound β- and γ-synuclein. Prot Sci, 15,1162-1174.

Bussell, R Jr, Ramlall, T F, Eliezer, D. Helix Periodicity, Topology and Dynamics of Membrane-Associated alpha-Synuclein. Prot Sci 14, 862-872. WEIL%

Naik, M.T., Lee, H., Bracken, C. and Breslow, E., NMR Investigation of Main-Chain Dynamics of the H80E Mutant of Bovine Neurophysin-I: Demonstration of Dimerization-Induced Changes at the Hormone-Binding Site, Biochemistry 44, 11766-11776

Ghose, R., Shekhtman, A., Goger, M. J., Ji, H., and Cowburn, D. (2001). A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat Struct Biol 8, 998-1004. a, b

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 08 May 2008

Discussion of topics in Dynamics

Some significant current work

Technique issues

Wang, C., Rance, M., and Palmer, A. G. Mapping chemical exchange in proteins with MW > 50 kD. J Am Chem Soc 125, 8968-8969. LIBRARY:WangRance03.pdf

Ferrage, F., Pelupessey P., Cowburn D., Bodenhausen G. "Intra-residue dipolar cross-relaxation rates between 13Cα and 13C' as a measure of internal dynamics in proteins by NMR Spectroscopy" J. Am. Chem. Soc. 128 11072-8

Fushman, D., and Cowburn, D. (2001). Nuclear magnetic resonance relaxation in determination of residue-specific 15N chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol 339, 109-126. a, b

Solids/ dynamics

Related to membrane proteins in solution

General structure/dynamics studies

Del Rio, A., Dutta K., Chavez J., Ubarretxena-Belandia, I., Ghose, R., Solution Structure and Dynamics of the N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Pseudomonas aeruginosa: Insights into a Functional Role in Intramembrane Proteolysis. 2006 J Mol Biol 365: 109-122. a

Dutta K, Shi HH, Cruz-Chu ER, Kami K, Ghose R. (2004) Dynamic influences on a high-affinity, high-specificity interaction involving the C-terminal SH3 domain of P67(phox) Biochemistry 43 8094-8106

Joel A. Butterwick and Arthur G. Palmer, III "An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H" Protein Sci. 2006 15 2697-2707

Massi F, Wang C, Palmer AG. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 36 10787-94

Edwards , T.A., Butterwick, J.A., Zeng, L., Gupta, Y.K., Wang, X, Wharton, R.P., Palmer, A.G., Aggarwal, A.K. Solution Structure of the Vts1 SAM Domain in the Presence of RNA J. Mol. Biol. 356, 1065-1072. a

Tang Y, Grey MJ, McKnight^? J, Palmer AG, Raleigh DP 'Multistate Folding of the Villin Headpiece Domain.' J Mol Biol 355, 1066-1072. a

Grey, M.J., Tang, Y, Alexov, E, McKnight^?, C.J., Raleigh, D.P.,Palmer, A.G. (2006) Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain . Journal of Molecular Biology 355, 1078-1094. a

Butterwick, J. A., Patrick Loria, J., Astrof, N. S., Kroenke, C. D., Cole, R., Rance, M., and Palmer, A. G., 3rd . Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J Mol Biol 339, 855-871.

Muralidharan V., Dutta K., Cho J., Vila-Perello M., Raleigh DP., Cowburn D., Muir TW 'Solution Structure and Folding Characteristics of the C-Terminal SH3 Domain of c-Crk-II' Biochemistry 45, 8874-8884 a

Kempf, J. G.; Jung, J-y.; Ragain, C.; Sampson, N. S.; Loria, J. P. Dynamic Requirements for a functional protein hinge. 2007 J. Mol. Biol 368: 131-149

Sung YH, Eliezer D 'Residual Structure, Backbone Dynamics, and Interactions within the Synuclein Family.' J Mol Biol 372:689-707

Sung, Y, Eliezer, D, Secondary structure and dynamics of micelle bound β- and γ-synuclein. Prot Sci, 15,1162-1174.

Bussell, R Jr, Ramlall, T F, Eliezer, D. Helix Periodicity, Topology and Dynamics of Membrane-Associated alpha-Synuclein. Prot Sci 14, 862-872. WEIL%

Naik, M.T., Lee, H., Bracken, C. and Breslow, E., NMR Investigation of Main-Chain Dynamics of the H80E Mutant of Bovine Neurophysin-I: Demonstration of Dimerization-Induced Changes at the Hormone-Binding Site, Biochemistry 44, 11766-11776

Ghose, R., Shekhtman, A., Goger, M. J., Ji, H., and Cowburn, D. (2001). A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat Struct Biol 8, 998-1004. a, b

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 08 May 2008

Discussion of topics in Dynamics

Some significant current work

Technique issues

Wang, C., Rance, M., and Palmer, A. G. Mapping chemical exchange in proteins with MW > 50 kD. J Am Chem Soc 125, 8968-8969. LIBRARY:WangRance03.pdf

Ferrage, F., Pelupessey P., Cowburn D., Bodenhausen G. "Intra-residue dipolar cross-relaxation rates between 13Cα and 13C' as a measure of internal dynamics in proteins by NMR Spectroscopy" J. Am. Chem. Soc. 128 11072-8

Fushman, D., and Cowburn, D. (2001). Nuclear magnetic resonance relaxation in determination of residue-specific 15N chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol 339, 109-126. a, b

Solids/ dynamics

Related to membrane proteins in solution

Kamen, D.E., Cahill, S.M. and Girvin, M.E. (2007) Multiple alignment of membrane proteins for measuring residual dipolar couplings using lanthanide ions bound to a small metal chelator. Journal of the American Chemical Society, 129, 1846-1847. LIBRARY:KamenCahill07.pdf

General structure/dynamics studies

Del Rio, A., Dutta K., Chavez J., Ubarretxena-Belandia, I., Ghose, R., Solution Structure and Dynamics of the N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Pseudomonas aeruginosa: Insights into a Functional Role in Intramembrane Proteolysis. 2006 J Mol Biol 365: 109-122. a

Dutta K, Shi HH, Cruz-Chu ER, Kami K, Ghose R. (2004) Dynamic influences on a high-affinity, high-specificity interaction involving the C-terminal SH3 domain of P67(phox) Biochemistry 43 8094-8106

Joel A. Butterwick and Arthur G. Palmer, III "An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H" Protein Sci. 2006 15 2697-2707

Massi F, Wang C, Palmer AG. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 36 10787-94

Edwards , T.A., Butterwick, J.A., Zeng, L., Gupta, Y.K., Wang, X, Wharton, R.P., Palmer, A.G., Aggarwal, A.K. Solution Structure of the Vts1 SAM Domain in the Presence of RNA J. Mol. Biol. 356, 1065-1072. a

Tang Y, Grey MJ, McKnight^? J, Palmer AG, Raleigh DP 'Multistate Folding of the Villin Headpiece Domain.' J Mol Biol 355, 1066-1072. a

Grey, M.J., Tang, Y, Alexov, E, McKnight^?, C.J., Raleigh, D.P.,Palmer, A.G. (2006) Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain . Journal of Molecular Biology 355, 1078-1094. a

Valentine, E. R., and Palmer, A. G., 3rd. Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2^? Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA. Biochemistry 44, 3410-3417

Wang, C., Karpowich, N., Hunt, J. F., Rance, M., and Palmer, A. G. Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters. J Mol Biol 342, 525-537.

Butterwick, J. A., Patrick Loria, J., Astrof, N. S., Kroenke, C. D., Cole, R., Rance, M., and Palmer, A. G., 3rd . Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J Mol Biol 339, 855-871.

Sung YH, Eliezer D 'Residual Structure, Backbone Dynamics, and Interactions within the Synuclein Family.' J Mol Biol 372:689-707

Sung, Y, Eliezer, D, Secondary structure and dynamics of micelle bound β- and γ-synuclein. Prot Sci, 15,1162-1174.

Bussell, R Jr, Ramlall, T F, Eliezer, D. Helix Periodicity, Topology and Dynamics of Membrane-Associated alpha-Synuclein. Prot Sci 14, 862-872. WEIL%

Naik, M.T., Lee, H., Bracken, C. and Breslow, E., NMR Investigation of Main-Chain Dynamics of the H80E Mutant of Bovine Neurophysin-I: Demonstration of Dimerization-Induced Changes at the Hormone-Binding Site, Biochemistry 44, 11766-11776

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 08 May 2008

Discussion of topics in Dynamics

Some significant current work

Technique issues

Solids/ dynamics

Related to membrane proteins in solution

General structure/dynamics studies

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 08 May 2008

Discussion of topics in Dynamics

Some significant current work

Technique issues

Ferrage, F., Pelupessey P., Cowburn D., Bodenhausen G. "Intra-residue dipolar cross-relaxation rates between 13Cα and 13C' as a measure of internal dynamics in proteins by NMR Spectroscopy" J. Am. Chem. Soc. 128 11072-8

Fushman, D., and Cowburn, D. (2001). Nuclear magnetic resonance relaxation in determination of residue-specific 15N chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol 339, 109-126. a, b

Solids/ dynamics

Related to membrane proteins in solution

Kamen, D.E., Cahill, S.M. and Girvin, M.E. (2007) Multiple alignment of membrane proteins for measuring residual dipolar couplings using lanthanide ions bound to a small metal chelator. Journal of the American Chemical Society, 129, 1846-1847. LIBRARY:KamenCahill07.pdf

General structure/dynamics studies

Del Rio, A., Dutta K., Chavez J., Ubarretxena-Belandia, I., Ghose, R., Solution Structure and Dynamics of the N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Pseudomonas aeruginosa: Insights into a Functional Role in Intramembrane Proteolysis. 2006 J Mol Biol 365: 109-122. a

Dutta K, Shi HH, Cruz-Chu ER, Kami K, Ghose R. (2004) Dynamic influences on a high-affinity, high-specificity interaction involving the C-terminal SH3 domain of P67(phox) Biochemistry 43 8094-8106

Joel A. Butterwick and Arthur G. Palmer, III "An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H" Protein Sci. 2006 15 2697-2707

Massi F, Wang C, Palmer AG. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 36 10787-94 Edwards , T.A., Butterwick, J.A., Zeng, L., Gupta, Y.K., Wang, X, Wharton, R.P., Palmer, A.G., Aggarwal, A.K. Solution Structure of the Vts1 SAM Domain in the Presence of RNA J. Mol. Biol. 356, 1065-1072. a

Tang Y, Grey MJ, McKnight^? J, Palmer AG, Raleigh DP 'Multistate Folding of the Villin Headpiece Domain.' J Mol Biol 355, 1066-1072. a

Grey, M.J., Tang, Y, Alexov, E, McKnight^?, C.J., Raleigh, D.P.,Palmer, A.G. (2006) Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain . Journal of Molecular Biology 355, 1078-1094. a

Valentine, E. R., and Palmer, A. G., 3rd. Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2^? Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA. Biochemistry 44, 3410-3417

Wang, C., Karpowich, N., Hunt, J. F., Rance, M., and Palmer, A. G. Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters. J Mol Biol 342, 525-537.

Butterwick, J. A., Patrick Loria, J., Astrof, N. S., Kroenke, C. D., Cole, R., Rance, M., and Palmer, A. G., 3rd . Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J Mol Biol 339, 855-871.

Muralidharan V., Dutta K., Cho J., Vila-Perello M., Raleigh DP., Cowburn D., Muir TW 'Solution Structure and Folding Characteristics of the C-Terminal SH3 Domain of c-Crk-II' Biochemistry 45, 8874-8884 a

Kempf, J. G.; Jung, J-y.; Ragain, C.; Sampson, N. S.; Loria, J. P. Dynamic Requirements for a functional protein hinge. 2007 J. Mol. Biol 368: 131-149

Sung YH, Eliezer D 'Residual Structure, Backbone Dynamics, and Interactions within the Synuclein Family.' J Mol Biol 372:689-707

Sung, Y, Eliezer, D, Secondary structure and dynamics of micelle bound β- and γ-synuclein. Prot Sci, 15,1162-1174.

Bussell, R Jr, Ramlall, T F, Eliezer, D. Helix Periodicity, Topology and Dynamics of Membrane-Associated alpha-Synuclein. Prot Sci 14, 862-872.

Naik, M.T., Lee, H., Bracken, C. and Breslow, E., NMR Investigation of Main-Chain Dynamics of the H80E Mutant of Bovine Neurophysin-I: Demonstration of Dimerization-Induced Changes at the Hormone-Binding Site, Biochemistry 44, 11766-11776

Ghose, R., Shekhtman, A., Goger, M. J., Ji, H., and Cowburn, D. (2001). A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat Struct Biol 8, 998-1004. a, b

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 08 May 2008

Discussion of topics in Dynamics

Some significant current work

Technique issues

Wang, C., Rance, M., and Palmer, A. G. Mapping chemical exchange in proteins with MW > 50 kD. J Am Chem Soc 125, 8968-8969. LIBRARY:WangRance03.pdf

Ferrage, F., Pelupessey P., Cowburn D., Bodenhausen G. "Intra-residue dipolar cross-relaxation rates between 13Cα and 13C' as a measure of internal dynamics in proteins by NMR Spectroscopy" J. Am. Chem. Soc. 128 11072-8

Fushman, D., and Cowburn, D. (2001). Nuclear magnetic resonance relaxation in determination of residue-specific 15N chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol 339, 109-126. a, b

Solids/ dynamics

Related to membrane proteins in solution

General structure/dynamics studies

Del Rio, A., Dutta K., Chavez J., Ubarretxena-Belandia, I., Ghose, R., Solution Structure and Dynamics of the N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Pseudomonas aeruginosa: Insights into a Functional Role in Intramembrane Proteolysis. 2006 J Mol Biol 365: 109-122. a

Dutta K, Shi HH, Cruz-Chu ER, Kami K, Ghose R. (2004) Dynamic influences on a high-affinity, high-specificity interaction involving the C-terminal SH3 domain of P67(phox) Biochemistry 43 8094-8106

Joel A. Butterwick and Arthur G. Palmer, III "An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H" Protein Sci. 2006 15 2697-2707

Massi F, Wang C, Palmer AG. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 36 10787-94 Edwards , T.A., Butterwick, J.A., Zeng, L., Gupta, Y.K., Wang, X, Wharton, R.P., Palmer, A.G., Aggarwal, A.K. Solution Structure of the Vts1 SAM Domain in the Presence of RNA J. Mol. Biol. 356, 1065-1072. a

Tang Y, Grey MJ, McKnight^? J, Palmer AG, Raleigh DP 'Multistate Folding of the Villin Headpiece Domain.' J Mol Biol 355, 1066-1072. a

Grey, M.J., Tang, Y, Alexov, E, McKnight^?, C.J., Raleigh, D.P.,Palmer, A.G. (2006) Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain . Journal of Molecular Biology 355, 1078-1094. a

Valentine, E. R., and Palmer, A. G., 3rd. Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2^? Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA. Biochemistry 44, 3410-3417

Wang, C., Karpowich, N., Hunt, J. F., Rance, M., and Palmer, A. G. Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters. J Mol Biol 342, 525-537.

Butterwick, J. A., Patrick Loria, J., Astrof, N. S., Kroenke, C. D., Cole, R., Rance, M., and Palmer, A. G., 3rd . Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J Mol Biol 339, 855-871.

Muralidharan V., Dutta K., Cho J., Vila-Perello M., Raleigh DP., Cowburn D., Muir TW 'Solution Structure and Folding Characteristics of the C-Terminal SH3 Domain of c-Crk-II' Biochemistry 45, 8874-8884 a

Kempf, J. G.; Jung, J-y.; Ragain, C.; Sampson, N. S.; Loria, J. P. Dynamic Requirements for a functional protein hinge. 2007 J. Mol. Biol 368: 131-149

Sung YH, Eliezer D 'Residual Structure, Backbone Dynamics, and Interactions within the Synuclein Family.' J Mol Biol 372:689-707

Sung, Y, Eliezer, D, Secondary structure and dynamics of micelle bound β- and γ-synuclein. Prot Sci, 15,1162-1174.

Bussell, R Jr, Ramlall, T F, Eliezer, D. Helix Periodicity, Topology and Dynamics of Membrane-Associated alpha-Synuclein. Prot Sci 14, 862-872.

Naik, M.T., Lee, H., Bracken, C. and Breslow, E., NMR Investigation of Main-Chain Dynamics of the H80E Mutant of Bovine Neurophysin-I: Demonstration of Dimerization-Induced Changes at the Hormone-Binding Site, Biochemistry 44, 11766-11776

Ghose, R., Shekhtman, A., Goger, M. J., Ji, H., and Cowburn, D. (2001). A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat Struct Biol 8, 998-1004. a, b

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 08 May 2008

Discussion of topics in Dynamics

Some significant current work

Technique issues

Fushman, D., and Cowburn, D. (2001). Nuclear magnetic resonance relaxation in determination of residue-specific 15N chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol 339, 109-126. a, b

Solids/ dynamics

Related to membrane proteins in solution

Kamen, D.E., Cahill, S.M. and Girvin, M.E. (2007) Multiple alignment of membrane proteins for measuring residual dipolar couplings using lanthanide ions bound to a small metal chelator. Journal of the American Chemical Society, 129, 1846-1847.

General structure/dynamics studies

Del Rio, A., Dutta K., Chavez J., Ubarretxena-Belandia, I., Ghose, R., Solution Structure and Dynamics of the N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Pseudomonas aeruginosa: Insights into a Functional Role in Intramembrane Proteolysis. 2006 J Mol Biol 365: 109-122. a

Dutta K, Shi HH, Cruz-Chu ER, Kami K, Ghose R. (2004) Dynamic influences on a high-affinity, high-specificity interaction involving the C-terminal SH3 domain of P67(phox) Biochemistry 43 8094-8106

Joel A. Butterwick and Arthur G. Palmer, III "An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H" Protein Sci. 2006 15 2697-2707

Massi F, Wang C, Palmer AG. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 36 10787-94 Edwards , T.A., Butterwick, J.A., Zeng, L., Gupta, Y.K., Wang, X, Wharton, R.P., Palmer, A.G., Aggarwal, A.K. Solution Structure of the Vts1 SAM Domain in the Presence of RNA J. Mol. Biol. 356, 1065-1072. a

Tang Y, Grey MJ, McKnight^? J, Palmer AG, Raleigh DP 'Multistate Folding of the Villin Headpiece Domain.' J Mol Biol 355, 1066-1072. a

Grey, M.J., Tang, Y, Alexov, E, McKnight^?, C.J., Raleigh, D.P.,Palmer, A.G. (2006) Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain . Journal of Molecular Biology 355, 1078-1094. a

Valentine, E. R., and Palmer, A. G., 3rd. Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2^? Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA. Biochemistry 44, 3410-3417

Wang, C., Karpowich, N., Hunt, J. F., Rance, M., and Palmer, A. G. Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters. J Mol Biol 342, 525-537.

Butterwick, J. A., Patrick Loria, J., Astrof, N. S., Kroenke, C. D., Cole, R., Rance, M., and Palmer, A. G., 3rd . Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J Mol Biol 339, 855-871.

Muralidharan V., Dutta K., Cho J., Vila-Perello M., Raleigh DP., Cowburn D., Muir TW 'Solution Structure and Folding Characteristics of the C-Terminal SH3 Domain of c-Crk-II' Biochemistry 45, 8874-8884 a

Kempf, J. G.; Jung, J-y.; Ragain, C.; Sampson, N. S.; Loria, J. P. Dynamic Requirements for a functional protein hinge. 2007 J. Mol. Biol 368: 131-149

Sung YH, Eliezer D 'Residual Structure, Backbone Dynamics, and Interactions within the Synuclein Family.' J Mol Biol 372:689-707

Sung, Y, Eliezer, D, Secondary structure and dynamics of micelle bound β- and γ-synuclein. Prot Sci, 15,1162-1174.

Bussell, R Jr, Ramlall, T F, Eliezer, D. Helix Periodicity, Topology and Dynamics of Membrane-Associated alpha-Synuclein. Prot Sci 14, 862-872.

Naik, M.T., Lee, H., Bracken, C. and Breslow, E., NMR Investigation of Main-Chain Dynamics of the H80E Mutant of Bovine Neurophysin-I: Demonstration of Dimerization-Induced Changes at the Hormone-Binding Site, Biochemistry 44, 11766-11776

Ghose, R., Shekhtman, A., Goger, M. J., Ji, H., and Cowburn, D. (2001). A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat Struct Biol 8, 998-1004. a, b

• Set ALLOWTOPICVIEW =

-- DavidCowburn - 08 May 2008

Discussion of topics in Dynamics

Some significant current work

Technique issues

Fushman, D., and Cowburn, D. (2001). Nuclear magnetic resonance relaxation in determination of residue-specific 15N chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol 339, 109-126. a, b

Solids/ dynamics

Related to membrane proteins in solution

Kamen, D.E., Cahill, S.M. and Girvin, M.E. (2007) Multiple alignment of membrane proteins for measuring residual dipolar couplings using lanthanide ions bound to a small metal chelator. Journal of the American Chemical Society, 129, 1846-1847.

General structure/dynamics studies

Del Rio, A., Dutta K., Chavez J., Ubarretxena-Belandia, I., Ghose, R., Solution Structure and Dynamics of the N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Pseudomonas aeruginosa: Insights into a Functional Role in Intramembrane Proteolysis. 2006 J Mol Biol 365: 109-122. a

Dutta K, Shi HH, Cruz-Chu ER, Kami K, Ghose R. (2004) Dynamic influences on a high-affinity, high-specificity interaction involving the C-terminal SH3 domain of P67(phox) Biochemistry 43 8094-8106

Joel A. Butterwick and Arthur G. Palmer, III "An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H" Protein Sci. 2006 15 2697-2707

Massi F, Wang C, Palmer AG. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 36 10787-94 Edwards , T.A., Butterwick, J.A., Zeng, L., Gupta, Y.K., Wang, X, Wharton, R.P., Palmer, A.G., Aggarwal, A.K. Solution Structure of the Vts1 SAM Domain in the Presence of RNA J. Mol. Biol. 356, 1065-1072. a

Tang Y, Grey MJ, McKnight^? J, Palmer AG, Raleigh DP 'Multistate Folding of the Villin Headpiece Domain.' J Mol Biol 355, 1066-1072. a

Grey, M.J., Tang, Y, Alexov, E, McKnight^?, C.J., Raleigh, D.P.,Palmer, A.G. (2006) Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain . Journal of Molecular Biology 355, 1078-1094. a

Valentine, E. R., and Palmer, A. G., 3rd. Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2^? Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA. Biochemistry 44, 3410-3417

Wang, C., Karpowich, N., Hunt, J. F., Rance, M., and Palmer, A. G. Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters. J Mol Biol 342, 525-537.

Butterwick, J. A., Patrick Loria, J., Astrof, N. S., Kroenke, C. D., Cole, R., Rance, M., and Palmer, A. G., 3rd . Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J Mol Biol 339, 855-871.

Muralidharan V., Dutta K., Cho J., Vila-Perello M., Raleigh DP., Cowburn D., Muir TW 'Solution Structure and Folding Characteristics of the C-Terminal SH3 Domain of c-Crk-II' Biochemistry 45, 8874-8884 a

Kempf, J. G.; Jung, J-y.; Ragain, C.; Sampson, N. S.; Loria, J. P. Dynamic Requirements for a functional protein hinge. 2007 J. Mol. Biol 368: 131-149

Sung YH, Eliezer D 'Residual Structure, Backbone Dynamics, and Interactions within the Synuclein Family.' J Mol Biol 372:689-707

Sung, Y, Eliezer, D, Secondary structure and dynamics of micelle bound β- and γ-synuclein. Prot Sci, 15,1162-1174.

Bussell, R Jr, Ramlall, T F, Eliezer, D. Helix Periodicity, Topology and Dynamics of Membrane-Associated alpha-Synuclein. Prot Sci 14, 862-872.

Naik, M.T., Lee, H., Bracken, C. and Breslow, E., NMR Investigation of Main-Chain Dynamics of the H80E Mutant of Bovine Neurophysin-I: Demonstration of Dimerization-Induced Changes at the Hormone-Binding Site, Biochemistry 44, 11766-11776

Ghose, R., Shekhtman, A., Goger, M. J., Ji, H., and Cowburn, D. (2001). A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat Struct Biol 8, 998-1004. a, b

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-- DavidCowburn - 08 May 2008

Discussion of topics in Dynamics

Some significant current work

Technique issues

Wang, C., Rance, M., and Palmer, A. G. Mapping chemical exchange in proteins with MW > 50 kD. J Am Chem Soc 125, 8968-8969.

Ferrage, F., Pelupessey P., Cowburn D., Bodenhausen G. "Intra-residue dipolar cross-relaxation rates between 13Cα and 13C' as a measure of internal dynamics in proteins by NMR Spectroscopy" J. Am. Chem. Soc. 128 11072-8

Fushman, D., and Cowburn, D. (2001). Nuclear magnetic resonance relaxation in determination of residue-specific 15N chemical shift tensors in proteins in solution: protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol 339, 109-126. a, b

Solids/ dynamics

Related to membrane proteins in solution

Kamen, D.E., Cahill, S.M. and Girvin, M.E. (2007) Multiple alignment of membrane proteins for measuring residual dipolar couplings using lanthanide ions bound to a small metal chelator. Journal of the American Chemical Society, 129, 1846-1847.

General structure/dynamics studies

Del Rio, A., Dutta K., Chavez J., Ubarretxena-Belandia, I., Ghose, R., Solution Structure and Dynamics of the N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Pseudomonas aeruginosa: Insights into a Functional Role in Intramembrane Proteolysis. 2006 J Mol Biol 365: 109-122. a

Dutta K, Shi HH, Cruz-Chu ER, Kami K, Ghose R. (2004) Dynamic influences on a high-affinity, high-specificity interaction involving the C-terminal SH3 domain of P67(phox) Biochemistry 43 8094-8106

Joel A. Butterwick and Arthur G. Palmer, III "An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H" Protein Sci. 2006 15 2697-2707

Massi F, Wang C, Palmer AG. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 36 10787-94 Edwards , T.A., Butterwick, J.A., Zeng, L., Gupta, Y.K., Wang, X, Wharton, R.P., Palmer, A.G., Aggarwal, A.K. Solution Structure of the Vts1 SAM Domain in the Presence of RNA J. Mol. Biol. 356, 1065-1072. a

Tang Y, Grey MJ, McKnight^? J, Palmer AG, Raleigh DP 'Multistate Folding of the Villin Headpiece Domain.' J Mol Biol 355, 1066-1072. a

Grey, M.J., Tang, Y, Alexov, E, McKnight^?, C.J., Raleigh, D.P.,Palmer, A.G. (2006) Characterizing a Partially Folded Intermediate of the Villin Headpiece Domain Under Non-denaturing Conditions: Contribution of His41 to the pH-dependent Stability of the N-terminal Subdomain . Journal of Molecular Biology 355, 1078-1094. a

Valentine, E. R., and Palmer, A. G., 3rd. Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2^? Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA. Biochemistry 44, 3410-3417

Wang, C., Karpowich, N., Hunt, J. F., Rance, M., and Palmer, A. G. Dynamics of ATP-binding cassette contribute to allosteric control, nucleotide binding and energy transduction in ABC transporters. J Mol Biol 342, 525-537.

Butterwick, J. A., Patrick Loria, J., Astrof, N. S., Kroenke, C. D., Cole, R., Rance, M., and Palmer, A. G., 3rd . Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J Mol Biol 339, 855-871.

Muralidharan V., Dutta K., Cho J., Vila-Perello M., Raleigh DP., Cowburn D., Muir TW 'Solution Structure and Folding Characteristics of the C-Terminal SH3 Domain of c-Crk-II' Biochemistry 45, 8874-8884 a

Kempf, J. G.; Jung, J-y.; Ragain, C.; Sampson, N. S.; Loria, J. P. Dynamic Requirements for a functional protein hinge. 2007 J. Mol. Biol 368: 131-149

Sung YH, Eliezer D 'Residual Structure, Backbone Dynamics, and Interactions within the Synuclein Family.' J Mol Biol 372:689-707

Sung, Y, Eliezer, D, Secondary structure and dynamics of micelle bound β- and γ-synuclein. Prot Sci, 15,1162-1174.

Bussell, R Jr, Ramlall, T F, Eliezer, D. Helix Periodicity, Topology and Dynamics of Membrane-Associated alpha-Synuclein. Prot Sci 14, 862-872.

Naik, M.T., Lee, H., Bracken, C. and Breslow, E., NMR Investigation of Main-Chain Dynamics of the H80E Mutant of Bovine Neurophysin-I: Demonstration of Dimerization-Induced Changes at the Hormone-Binding Site, Biochemistry 44, 11766-11776

Ghose, R., Shekhtman, A., Goger, M. J., Ji, H., and Cowburn, D. (2001). A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat Struct Biol 8, 998-1004. a, b

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-- DavidCowburn - 08 May 2008