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Prediction of protein conformational freedom from distance constraints
Author(s) -
de Groot B.L.,
van Aalten D.M.F.,
Scheek R.M.,
Amadei A.,
Vriend G.,
Berendsen H.J.C.
Publication year - 1997
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/(sici)1097-0134(199710)29:2<240::aid-prot11>3.0.co;2-o
Subject(s) - degrees of freedom (physics and chemistry) , domain (mathematical analysis) , simple (philosophy) , set (abstract data type) , protein structure , statistical physics , calmodulin , biological system , frequency domain , physics , chemistry , computer science , mathematics , biology , mathematical analysis , quantum mechanics , enzyme , philosophy , epistemology , programming language , nuclear magnetic resonance
A method is presented that generates random protein structures that fulfil a set of upper and lower interatomic distance limits. These limits depend on distances measured in experimental structures and the strength of the interatomic interaction. Structural differences between generated structures are similar to those obtained from experiment and from MD simulation. Although detailed aspects of dynamical mechanisms are not covered and the extent of variations are only estimated in a relative sense, applications to an IgG‐binding domain, an SH3 binding domain, HPr, calmodulin, and lysozyme are presented which illustrate the use of the method as a fast and simple way to predict structural variability in proteins. The method may be used to support the design of mutants, when structural fluctuations for a large number of mutants are to be screened. The results suggest that motional freedom in proteins is ruled largely by a set of simple geometric constraints. Proteins 29:240–251, 1997. © 1997 Wiley‐Liss, Inc.