Essential dynamics of proteins Export

@article{citeulike:238187, abstract = {Analysis of extended molecular dynamics (MD) simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the configurational space into two subspaces: (1) an ldquoessentialrdquo subspace containing only a few degrees of freedom in which anharmonic motion occurs that comprises most of the positional fluctuations; and (2) the remaining space in which the motion has a narrow Gaussian distribution and which can be considered as ldquophysically constrained.rdquo If overall translation and rotation are eliminated, the two spaces can be constructed by a simple linear transformation in Cartesian coordinate space, which remains valid over several hundred picoseconds. The transformation follows from the covariance matrix of the positional deviations. The essential degrees of freedom seem to describe motions which are relevant for the function of the protein, while the physically constrained subspace merely describes irrelevant local fluctuations. The near-constraint behavior of the latter subspace allows the separation of equations of motion and promises the possibility of investigating independently the essential space and performing dynamic simulations only in this reduced space. {\copyright} 1993 Wiley-Liss, Inc.}, address = {Department of Biophysical Chemistry and BIOSON Research Institute, the University of Groningen, 9747 AG Groningen, The Netherlands}, author = {Amadei, Andrea and Linssen, Antonius B. M. and Berendsen, Herman J. C.}, citeulike-article-id = {238187}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/prot.340170408}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/8108382}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=8108382}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/107611161/ABSTRACT}, doi = {10.1002/prot.340170408}, issn = {0887-3585}, journal = {Proteins: Structure, Function, and Genetics}, keywords = {essential-dynamics}, month = {December}, number = {4}, pages = {412--425}, posted-at = {2005-11-29 18:39:29}, priority = {2}, title = {Essential dynamics of proteins}, url = {http://dx.doi.org/10.1002/prot.340170408}, volume = {17}, year = {1993} }

TY - JOUR ID - citeulike:238187 L3 - citeulike-article-id:238187 N2 - Analysis of extended molecular dynamics (MD) simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the configurational space into two subspaces: (1) an ldquoessentialrdquo subspace containing only a few degrees of freedom in which anharmonic motion occurs that comprises most of the positional fluctuations; and (2) the remaining space in which the motion has a narrow Gaussian distribution and which can be considered as ldquophysically constrained.rdquo If overall translation and rotation are eliminated, the two spaces can be constructed by a simple linear transformation in Cartesian coordinate space, which remains valid over several hundred picoseconds. The transformation follows from the covariance matrix of the positional deviations. The essential degrees of freedom seem to describe motions which are relevant for the function of the protein, while the physically constrained subspace merely describes irrelevant local fluctuations. The near-constraint behavior of the latter subspace allows the separation of equations of motion and promises the possibility of investigating independently the essential space and performing dynamic simulations only in this reduced space. © 1993 Wiley-Liss, Inc. IS - 4 JF - Proteins: Structure, Function, and Genetics SN - 0887-3585 AD - Department of Biophysical Chemistry and BIOSON Research Institute, the University of Groningen, 9747 AG Groningen, The Netherlands EP - 425 TI - Essential dynamics of proteins VL - 17 SP - 412 KW - essential-dynamics AU - Amadei, Andrea AU - Linssen, Antonius AU - Berendsen, Herman PY - 1993/12// UR - http://dx.doi.org/10.1002/prot.340170408 ER -