MRS Proceedings

Articles

Long-Range Structural Regularities and Collectivity of Folded Proteins

2009 MRS Fall Meeting.

Canan Atilgana1, Ibrahim Inanca2 and Ali Rana Atilgana3

a1 canan@sabanciuniv.edu, Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, Turkey

a2 iinanc@su.sabanciuniv.edu, Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, Turkey

a3 atilgan@sabanciuniv.edu, Sabanci University, Faculty of Engineering and Natural Sciences, Istanbul, Turkey

Abstract

Coarse-grained network models of proteins successfully predict equilibrium properties related to collective modes of motion. In this study, the network construction strategies and their systematic application to proteins are used to explain the role of network models in defining the collective properties of the system. The analysis is based on the radial distribution function, a newly defined angular distribution function and the spectral dimensions of a large set of globular proteins. Our analysis shows that after reaching a certain threshold for cut-off distance, network construction has negligible effect on the collective motions and the fluctuation patterns of the residues.

(Received December 10 2009)

(Accepted March 16 2010)

Key Words

  • macromolecular structure;
  • structural;
  • biological
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