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Solvent effects in the slow dynamics of proteins
Author(s) -
Hinsen Konrad,
Kneller Gerald R.
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21655
Subject(s) - solvent , dynamics (music) , molecular dynamics , chemical physics , protein dynamics , chemistry , solvent exposure , lysozyme , solvent effects , computational chemistry , crystallography , physics , organic chemistry , biochemistry , acoustics
The influence of solvent on the slow internal dynamics of proteins is studied by comparing molecular dynamics simulations of solvated and unsolvated lysozyme. The dynamical trajectories are projected onto the protein's normal modes in order to obtain a separate analysis for each of the associated time scales. The results show that solvent effects are important for the slowest motions (below ≈ 1 ps −1 ) but negligible for faster motions. The damping effects seen in the latter show that the principal source of friction in protein dynamics is not the solvent, but the protein itself. Proteins 2008. © 2007 Wiley‐Liss, Inc.