Publication

ESSENTIAL DYNAMICS OF PROTEINS

AMADEI, A., LINSSEN, ABM. & BERENDSEN, HJC., Dec-1993, In : Proteins-Structure Function and Bioinformatics. 17, 4, p. 412-425 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

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 ''essential'' 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 ''physically constrained.'' 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. (C) 1993 Wiley-Liss, Inc.

Original languageEnglish
Pages (from-to)412-425
Number of pages14
JournalProteins-Structure Function and Bioinformatics
Volume17
Issue number4
Publication statusPublished - Dec-1993

    Keywords

  • NORMAL MODES, CONSTRAINT DYNAMICS, MOLECULAR DYNAMICS, LYSOZYME, MOLECULAR-DYNAMICS, COLLECTIVE MOTIONS, SIMULATIONS, POLYPEPTIDE, ENTROPY

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