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An Analysis of Core Deformations in Protein Superfamilies (2005)
| Citations: | 13 - 0 self |
BibTeX
@MISC{Leo-macias05ananalysis,
author = {Ra Leo-macias and Pedro Lopez-romero and Dmitry Lupyan and Y Daniel Zerbino and Angel R. Ortiz},
title = {An Analysis of Core Deformations in Protein Superfamilies},
year = {2005}
}
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Abstract
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 experience as a result of the topological constraints imposed by the fold. A set of 35 representative, well-populated protein families 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 to extract the main deformation modes from the threedimensional superimposition. In parallel, a low-resolution normal mode analysis 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.
Keyphrases
core deformation protein superfamily threedimensional superimposition structural change mechanical core plasticity evolutionary deformation main deformation mode structural core low-frequency mode evolutionary direction principal component analysis vibrational normal mode low-resolution normal mode analysis technique particular topology collective deformation vibrational mode protein topology topological constraint well-populated protein family conserved core significant extent significant correspondence exists structure prediction small number homologous protein low dimensional space structural response homology modeling multiple structural alignment principal deformation
