A Unification of the Elastic Network Model and the Gaussian Network Model for Optimal Description of Protein Conformational Motions and Fluctuations

¹ University at Buffalo

^* To whom correspondence should be addressed. E-mail: wjzheng{at}buffalo.edu.

Submitted on November 15, 2007
Revised on December 10, 2007
Accepted on 10 January 2008

	Abstract

Coarse grained elastic models with a C only representation and harmonic interactions have been increasingly used to describe the conformational motions and flexibility of various proteins. In this work, we will unify two complementary elastic models - the Elastic Network Model (ENM) and the Gaussian Network Model (GNM), in the framework of a Generalized Anisotropic Network Model (G-ANM) with a new anisotropy parameter f_anm. The G-ANM is reduced to GNM at f_anm=1, and ENM at f_anm=0. By analyzing a list of protein crystal structure pairs using G-ANM, we have attained optimal descriptions of both the isotropic thermal fluctuations and the crystallographically observed conformational changes with a small f_anm (f_anm0.1) and a physically realistic cutoff distance R_c~8Å. Thus the G-ANM improves the performance of GNM and ENM while preserving their simplicity. The properly parameterized G-ANM will enable more accurate and realistic modeling of protein conformational motions and flexibility.

Key Words: B factor, Gaussian network model, conformational change, elastic network model, normal mode analysis