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Biophys J, November 2002, p. 2457-2474, Vol. 83, No. 5
Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, Wisconsin 53706 USA
A block normal mode (BNM) algorithm, originally proposed
by Tama et al., (Proteins Struct. Func. Genet. 41:1-7, 2000)
was implemented into the simulation program CHARMM. The BNM
approach projects the hessian matrix into local translation/rotation
basis vectors and, therefore, dramatically reduces the size of the
matrix involved in diagonalization. In the current work, by
constructing the atomic hessian elements required in the projection
operation on the fly, the memory requirement for the BNM approach has
been significantly reduced from that of standard normal mode analysis and previous implementation of BNM. As a result, low frequency modes,
which are of interest in large-scale conformational changes of large
proteins or protein-nucleic acid complexes, can be readily obtained.
Comparison of the BNM results with standard normal mode analysis for a
number of small proteins and nucleic acids indicates that many
properties dominated by low frequency motions are well reproduced by
BNM; these include atomic fluctuations, the displacement covariance
matrix, vibrational entropies, and involvement coefficients for
conformational transitions. Preliminary application to a fairly large
system, Ca2+-ATPase (994 residues), is described as an
example. The structural flexibility of the cytoplasmic domains
(especially domain N), correlated motions among residues on domain
interfaces and displacement patterns for the transmembrane helices
observed in the BNM results are discussed in relation to the function
of Ca2+-ATPase. The current implementation of the BNM
approach has paved the way for developing efficient sampling algorithms
with molecular dynamics or Monte Carlo for studying long-time scale
dynamics of macromolecules.
Biophys J, November 2002, p. 2457-2474, Vol. 83, No. 5
© 2002 by the Biophysical Society 0006-3495/02/11/2457/18 $2.00
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