Development of the force field parameters for phosphoimidazole and phosphohistidine. Export

@article{citeulike:440126, abstract = {Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule--a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent.}, address = {M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, Moscow V-437, 117997 GSP, Russia.}, author = {Kosinsky, Y. A. and Volynsky, P. E. and Lagant, P. and Vergoten, G. and Suzuki, E. and Arseniev, A. S. and Efremov, R. G.}, citeulike-article-id = {440126}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.20055}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15185324}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15185324}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/108564197/ABSTRACT}, doi = {10.1002/jcc.20055}, issn = {0192-8651}, journal = {J Comput Chem}, keywords = {ab-initio, development, force-field, gromacs, imidazole, methodology, pho-his}, month = {August}, number = {11}, pages = {1313--1321}, posted-at = {2005-12-16 22:28:57}, priority = {0}, title = {Development of the force field parameters for phosphoimidazole and phosphohistidine.}, url = {http://dx.doi.org/10.1002/jcc.20055}, volume = {25}, year = {2004} }

TY - JOUR ID - citeulike:440126 L3 - citeulike-article-id:440126 N2 - Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule--a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent. IS - 11 JF - J Comput Chem SN - 0192-8651 AD - M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, Moscow V-437, 117997 GSP, Russia. EP - 1321 TI - Development of the force field parameters for phosphoimidazole and phosphohistidine. VL - 25 SP - 1313 KW - ab-initio KW - development KW - force-field KW - gromacs KW - imidazole KW - methodology KW - pho-his AU - Kosinsky, YA AU - Volynsky, PE AU - Lagant, P AU - Vergoten, G AU - Suzuki, E AU - Arseniev, AS AU - Efremov, RG PY - 2004/08// UR - http://dx.doi.org/10.1002/jcc.20055 ER -