Characterization of Protein Conformational States by Normal-Mode Frequencies Export

@article{citeulike:1588128, abstract = {Abstract: Conformational change in polymers including proteins is central to many molecular processes. Defining conformational states, however, remains a difficult and increasingly common problem, with many existing methods based on arbitrary or potentially unrepresentative measures. Furthermore, the expanding length of molecular dynamics simulations and direct observation of transitions between different energy basins suggest that this issue will only become evermore important. Methods commonly used to characterize conformational states include principal component analysis, root-mean-square deviation-based clustering, and geometric measurements such as hinge angles and distances. Here we present a method where the eigenvector frequencies derived from a Gaussian network model (Bahar, I.; Atilgan, A. R.; Erman, B. Folding Des. 1997, 2, 173-181) of a trajectory of structures from a molecular dynamics simulation are used to describe the state of the protein at each time point. We apply the method to three proteins that share the same fold as the type II periplasmic binding proteins: The lysine-arginine-ornithine-binding protein, the glutamine-binding protein, and the ligand-binding domain from the NR1 N-methyl-D-aspartate receptor. We find that the method can distinguish different states in good agreement with a variety of previous analyses and additionally provides information on the dynamic properties of that system at a given time point.}, address = {Contribution from the Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Department of Primary Care, University of Oxford, Rosemary Rue Building, Old Road Campus, Headington, Oxford OX3 7LF, U.K.}, author = {Hall, B. A. and Kaye, S. L. and Pang, A. and Perera, R. and Biggin, P. C.}, citeulike-article-id = {1588128}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ja071797y}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ja071797y}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17715919}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17715919}, day = {23}, doi = {10.1021/ja071797y}, journal = {J. Am. Chem. Soc.}, keywords = {flexibility, normal\_modes, proteins}, month = {August}, posted-at = {2008-04-25 14:35:56}, priority = {2}, title = {Characterization of Protein Conformational States by Normal-Mode Frequencies}, url = {http://dx.doi.org/10.1021/ja071797y}, year = {2007} }

TY - JOUR ID - citeulike:1588128 L3 - citeulike-article-id:1588128 N2 - Abstract: Conformational change in polymers including proteins is central to many molecular processes. Defining conformational states, however, remains a difficult and increasingly common problem, with many existing methods based on arbitrary or potentially unrepresentative measures. Furthermore, the expanding length of molecular dynamics simulations and direct observation of transitions between different energy basins suggest that this issue will only become evermore important. Methods commonly used to characterize conformational states include principal component analysis, root-mean-square deviation-based clustering, and geometric measurements such as hinge angles and distances. Here we present a method where the eigenvector frequencies derived from a Gaussian network model (Bahar, I.; Atilgan, A. R.; Erman, B. Folding Des. 1997, 2, 173-181) of a trajectory of structures from a molecular dynamics simulation are used to describe the state of the protein at each time point. We apply the method to three proteins that share the same fold as the type II periplasmic binding proteins: The lysine-arginine-ornithine-binding protein, the glutamine-binding protein, and the ligand-binding domain from the NR1 N-methyl-D-aspartate receptor. We find that the method can distinguish different states in good agreement with a variety of previous analyses and additionally provides information on the dynamic properties of that system at a given time point. JF - J. Am. Chem. Soc. AD - Contribution from the Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Department of Primary Care, University of Oxford, Rosemary Rue Building, Old Road Campus, Headington, Oxford OX3 7LF, U.K. TI - Characterization of Protein Conformational States by Normal-Mode Frequencies KW - flexibility KW - normal_modes KW - proteins AU - Hall, BA AU - Kaye, SL AU - Pang, A AU - Perera, R AU - Biggin, PC PY - 2007/08/23/ UR - http://dx.doi.org/10.1021/ja071797y ER -