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Analysis of domain motions by approximate normal mode calculations
Author(s) -
Hinsen Konrad
Publication year - 1998
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(19981115)33:3<417::aid-prot10>3.0.co;2-8
Subject(s) - normal mode , frequency domain , rigidity (electromagnetism) , domain (mathematical analysis) , computer science , identification (biology) , algorithm , mode (computer interface) , statistical physics , physics , mathematics , mathematical analysis , acoustics , vibration , botany , quantum mechanics , computer vision , biology , operating system
The identification of dynamical domains in proteins and the description of the low‐frequency domain motions are one of the important applications of numerical simulation techniques. The application of these techniques to large proteins requires a substantial computational effort and therefore cannot be performed routinely, if at all. This article shows how physically motivated approximations permit the calculation of low‐frequency normal modes in a few minutes on standard desktop computers. The technique is based on the observation that the low‐frequency modes, which describe domain motions, are independent of force field details and can be obtained with simplified mechanical models. These models also provide a useful measure for rigidity in proteins, allowing the identification of quasi‐rigid domains. The methods are validated by application to three well‐studied proteins, crambin, lysozyme, and ATCase. In addition to being useful techniques for studying domain motions, the success of the approximations provides new insight into the relevance of normal mode calculations and the nature of the potential energy surface of proteins. Proteins 33:417–429, 1998. © 1998 Wiley‐Liss, Inc.