Title: Analysis of protein dynamics using local-DME calculations

Authors: Di Wu, Stephen Smith, Hannah Mahan, Robert L. Jernigan, Zhijun Wu

Addresses: Department of Mathematics, Western Kentucky University, Bowling Green, KY 42101, USA. ' NSF-REU Summer Program in Mathematics, Iowa State University, Ames, IA 50010, USA. ' NSF-REU Summer Program in Mathematics, Iowa State University, Ames, IA 50010, USA. ' Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50010, USA. ' Department of Mathematics, Iowa State University, Ames, IA 50010, USA

Abstract: Flexibility and dynamics of protein structures are reflected in the B-factors and order parameters obtained experimentally with X-ray crystallography and Nuclear Magnetic Resonance (NMR). Methods such as Normal Mode Analysis (NMA) and Elastic Network Models (ENM) can be used to predict the fluctuations of protein structures for either atomic level or coarse-grained structures. Here, we introduce the Local-Distance Matrix Error (DME), an efficient and simple analytic method to study the fluctuations of protein structures, especially for the ensembles of NMR-determined protein structures. Comparisons with the fluctuations obtained by experiments and other by computations show strong correlations.

Keywords: protein dynamics; NMR structure modelling; GNM; elastic network model; DME; distance matrix errors; protein structures; bioinformatics.

DOI: 10.1504/IJBRA.2011.040093

International Journal of Bioinformatics Research and Applications, 2011 Vol.7 No.2, pp.146 - 161

Accepted: 08 Jul 2010
Published online: 13 May 2011 *

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