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Analyzing the normal mode dynamics of macromolecules by the component synthesis method
Author(s) -
Hao MingHong,
Harvey Stephen C.
Publication year - 1992
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360321012
Subject(s) - normal mode , macromolecule , curse of dimensionality , eigenvalues and eigenvectors , harmonic , biomolecule , chemistry , molecule , component (thermodynamics) , space (punctuation) , dimension (graph theory) , range (aeronautics) , mode (computer interface) , molecular physics , biological system , statistical physics , classical mechanics , physics , quantum mechanics , mathematics , materials science , computer science , vibration , biochemistry , statistics , organic chemistry , composite material , pure mathematics , biology , operating system
Abstract This paper presents a general method for studying the harmonic dynamics of large biomolecules and molecular complexes. The performance and accuracy of the method applied to a number of molecules are also reported. The basic approach of the method is to divide a macromolecule into a number of smaller components. The local normal modes of the components are first calculated by treating individual components and the interactions between nearest neighboring components. The physical displacements of all atoms are then represented in the local normal mode space, in which a selected range of high‐frequency local modes is neglected. The equation of motion of the molecule in the local normal mode space will then have a smaller dimension, and consequently the normal modes of the whole structure, particularly for large molecules, can be solved much more easily. The normal modes of two polypeptides–(Ala) 6 and (Ala) 12− and a double‐helical DNA– d(ATATA) · d(TATAT)–are analyzed with this method. Reductions on the dimensions of harmonic dynamic equations for these molecules have been made, with the fraction of the deleted high‐frequency modes ranging from ½ to ⅚. The calculated low‐frequency normal modes are found to be very accurate as compared to the exact solutions by standard procedure. The major advantage of the present approach on macromolecule harmonic dynamics is that the reduction on the dimensionality of the eigenvalue problems can be varied according to the size of molecules, so the method can be easily applied to large macromolecules with controlled accuracy. © 1992 John Wiley & Sons, Inc.