Slow normal modes of proteins are accurately reproduced across different platforms

Physical Biology
Hyuntae NaM M Tirion

Abstract

The Protein data bank (PDB) (Berman et al 2000 Nucl. Acids Res. 28 235-42) contains the atomic structures of over 105 biomolecules with better than 2.8 Å resolution. The listing of the identities and coordinates of the atoms comprising each macromolecule permits an analysis of the slow-time vibrational response of these large systems to minor perturbations. 3D video animations of individual modes of oscillation demonstrate how regions interdigitate to create cohesive collective motions, providing a comprehensive framework for and familiarity with the overall 3D architecture. Furthermore, the isolation and representation of the softest, slowest deformation coordinates provide opportunities for the development of mechanical models of enzyme function. The eigenvector decomposition, therefore, must be accurate, reliable as well as rapid to be generally reported upon. We obtain the eigenmodes of a 1.2 Å 34 kDa PDB entry using either exclusively heavy atoms or partly or fully reduced atomic sets; Cartesian or internal coordinates; interatomic force fields derived either from a full Cartesian potential, a reduced atomic potential or a Gaussian distance-dependent potential; and independently developed software. These varied technologie...Continue Reading

References

Aug 16, 1979·Nature·P J ArtymiukM J Sternberg
Apr 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·J Kuriyan, W I Weis
Aug 15, 1983·Journal of Molecular Biology·M Levitt
Jun 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·N GoT Nishikawa
Nov 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·B Brooks, M Karplus
Apr 1, 1995·Biophysical Journal·D ben-Avraham, M M Tirion
Mar 5, 1993·Journal of Molecular Biology·M M Tirion, D ben-Avraham
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Jan 7, 1998·Protein Science : a Publication of the Protein Society·S Parthasarathy, M R Murthy
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Feb 13, 2001·Biophysical Journal·A R AtilganI Bahar
Jun 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Dengming MingJianpeng Ma
Oct 31, 2003·Proceedings of the National Academy of Sciences of the United States of America·Wenjun Zheng, Sebastian Doniach
Sep 29, 2004·Journal of Structural Biology·Yongmei WangRobert L Jernigan
Mar 16, 2005·Structure·A J RaderIvet Bahar
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Apr 12, 2006·Physical Review Letters·S Nicolay, Y-H Sanejouand
May 10, 2006·Proceedings of the National Academy of Sciences of the United States of America·Wenjun ZhengD Thirumalai
May 16, 2009·Journal of Computational Chemistry·B R BrooksM Karplus
Apr 3, 2014·Proteins·Hyuntae Na, Guang Song
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus
Apr 15, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Monique M Tirion, Daniel ben-Avraham

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