help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
Biophys. J. BioFAST: First Published November 12, 2004. doi:10.1529/biophysj.104.052449
© 2004 by the Biophysical Society.

A more recent version of this article appeared on February 1, 2005.
This Article
Right arrow Full Text (Rapid PDF)
Right arrow supplemental file
Right arrow All Versions of this Article:
biophysj.104.052449v1
88/2/1291    most recent
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow Author home page(s):
Angel R. Ortiz
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Leo-Macias, A.
Right arrow Articles by Ortiz, A. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Leo-Macias, A.
Right arrow Articles by Ortiz, A. R.

PROTEINS

AN ANALYSIS OF CORE DEFORMATIONS IN PROTEIN SUPERFAMILIES

Alejandra Leo-Macias 1, Pedro Lopez-Romero 1, Daniel Zerbino 2, Dmitry Lupyan 3 and Angel R. Ortiz 1*

1 Consejo Superior de Investigaciones Cientificas
2 Ecole Polytechnique
3 Mount Sinai School of Medicine

* To whom correspondence should be addressed. E-mail: aro{at}cbm.uam.es.

Submitted on September 14, 2004
Revised on October 15, 2004
Accepted on 2 November 2004


  Abstract
An analysis is presented on how structural cores modify their shape across homologous proteins, and whether or not a relationship exists between these structural changes and the vibrational normal modes that proteins experiment as a result of the topological constraints imposed by the fold. A set of 35 representative, well populated protein familiees is studied. The evolutionary directions of deformation are obtained by using multiple structural alignments to superimpose the structures and extract a conserved core, together with Principal Components Analysis (PCA) to extract the main deformation modes from the three-dimensional superimposition. In parallel, a low-resolution Normal Mode Analysis (NMA) technique is employed to study the properties of the mechanical core plasticity of these same families. We show that the evolutionary deformations span a low dimensional space, of 4-5 dimensions on average. A statistically significant correspondence exists between these principal deformations and the ~20 slowest vibrational modes accessible to a particular topology. We conclude that, to a significant extent, the structural response of a protein topology to sequence changes takes place by means of collective deformations along combinations of a small number of low-frequency modes. The findings have implications in structure prediction by homology modeling.

Key Words: comparative modeling, normal mode analysis, principal component analysis, protein conformational motions, structural alignments




This article has been cited by other articles:


Home page
 J. Virol.Home page
Q. Wang, F. Cheng, M. Lu, X. Tian, and J. Ma
Crystal Structure of Unliganded Influenza B Virus Hemagglutinin
J. Virol., March 15, 2008; 82(6): 3011 - 3020.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L.-W. Yang, A. J. Rader, X. Liu, C. J. Jursa, S. C. Chen, H. A. Karimi, and I. Bahar
oGNM: online computation of structural dynamics using the Gaussian Network Model.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W24 - W31.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
Copyright © 2004 by the Biophysical Society.