@article{ ISI:000088503900018,
Author = {Doruker, P and Atilgan, AR and Bahar, I},
Title = {{Dynamics of proteins predicted by molecular dynamics simulations and
   analytical approaches: Application to alpha-amylase inhibitor}},
Journal = {{PROTEINS-STRUCTURE FUNCTION AND GENETICS}},
Year = {{2000}},
Volume = {{40}},
Number = {{3}},
Pages = {{512-524}},
Month = {{AUG 15}},
Abstract = {{The dynamics of alpha-amylase inhibitors has been investigated using
   molecular dynamics (IUD) simulations and two analytical approaches, the
   Gaussian network model (GNM) and anisotropic network model (ANM). MD
   simulations use a full atomic approach with empirical force fields,
   while the analytical approaches are based on a coarse-grained
   single-site-per-residue model with a single-parameter harmonic potential
   between sufficiently close (r less than or equal to 7 Angstrom) residue
   pairs. The major difference between the GNM and the ANM is that no
   directional preferences can be obtained in the GNM, all residue
   fluctuations being theoretically isotropic, while ANM does incorporate
   directional preferences. The dominant modes of motions are identified by
   (i) the singular value decomposition (SVD) of the MD trajectory
   matrices, and (ii) the similarity transformation of the Kirchhoff
   matrices of interresidue contacts in the GNM or ANM. The mean-square
   fluctuations of individual residues and the cross-correlations between
   domain movements retain the same characteristics, in all
   approaches-although the dispersion of modes and detailed amplitudes of
   motion obtained in the ANM conform more closely with MD results. The
   major weakness of the analytical approaches appears, on the other hand,
   to be their inadequacy to account for the anharmonic motions or
   multimeric transitions driven by the slowest collective mode observed in
   MD. Such motions usually suffer, however, from MD sampling
   inefficiencies, and multiple independent runs should be tested before
   making conclusions about their validity and detailed mechanisms. Overall
   this study invites attention to (i) the robustness of the average
   properties (mean-square fluctuations, cross-correlations) controlled by
   the low frequency motions, which are invariably reproduced in all
   approaches, and (ii) the utility and efficiency of the ANM, the
   computational time cost of which is of the order of ``minutes{''} (real
   time), as opposed to ``days{''} for MD simulations. Proteins
   2000;40:512-524. (C) 2000 Wiley-Liss, Inc.}},
Publisher = {{WILEY-LISS}},
Address = {{DIV JOHN WILEY \& SONS INC, 605 THIRD AVE, NEW YORK, NY 10158-0012 USA}},
Type = {{Article}},
Language = {{English}},
Affiliation = {{Bahar, I (Reprint Author), Bogazici Univ, Sch Engn, Ctr Polymer Res, TR-80815 Bebek, Istanbul, Turkey.
   Bogazici Univ, Sch Engn, Ctr Polymer Res, TR-80815 Bebek, Istanbul, Turkey.
   TUBITAK Adv Polymer Mat Res Ctr, Istanbul, Turkey.}},
DOI = {{10.1002/1097-0134(20000815)40:3<512::AID-PROT180>3.0.CO;2-M}},
ISSN = {{0887-3585}},
Keywords = {{correlated fluctuations; molecular dynamics simulations; beta-proteins;
   Gaussian network model; anisotropic effects; principal component
   analysis}},
Keywords-Plus = {{NORMAL-MODE ANALYSIS; X-RAY-DIFFRACTION; COLLECTIVE MOTIONS;
   CONFIGURATIONAL ENTROPY; VIBRATIONAL DYNAMICS; COMPUTER-SIMULATION;
   SINGLE-PARAMETER; GLOBULAR PROTEIN; DOMAIN MOTIONS; LYSOZYME}},
Research-Areas = {{Biochemistry \& Molecular Biology; Biophysics}},
Web-of-Science-Categories  = {{Biochemistry \& Molecular Biology; Biophysics}},
ResearcherID-Numbers = {{Atilgan, Ali Rana/A-7805-2011}},
Number-of-Cited-References = {{55}},
Times-Cited = {{160}},
Usage-Count-(Last-180-days) = {{2}},
Usage-Count-Since-2013 = {{18}},
Journal-ISO = {{Proteins}},
Doc-Delivery-Number = {{339XV}},
Unique-ID = {{ISI:000088503900018}},
}