Exploring the common dynamics of homologous proteins. Application to the globin family

¹ Universidad Nacional de Quilmes
² Universidad Nacional de Quilmes

^* To whom correspondence should be addressed. E-mail: seba{at}unq.edu.ar.

Submitted on September 17, 2004
Revised on October 8, 2004
Accepted on 15 February 2005

	Abstract

We present a procedure to explore the global dynamics shared between members of the same protein family. The method allows the comparison of patterns of vibrational motion obtained by Gaussian Network Model (GNM) analysis. Following the identification of collective coordinates that were conserved during evolution, we quantify the common dynamics within a family. Representative vectors that describe this dynamics are defined using a singular value decomposition approach. As a test case, the globin heme-binding family is considered. The two lowest normal modes are shown to be conserved within this family. Our results encourage the development of models for protein evolution that take into account the conservation of dynamical features.

Key Words: Collective vibrational motion, Gaussian Network Model, Normal Modes, Singular Value Decomposition

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