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dc.contributor.authorLeo-Macías, Alejandra-
dc.contributor.authorLópez-Romero, Pedro-
dc.contributor.authorLupyan, Dmitry-
dc.contributor.authorZerbino, Daniel-
dc.contributor.authorOrtiz, Ángel R.-
dc.identifier.citationBiophysical Journal 88:1291-1299 (2005)en_US
dc.description.abstractAn 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 three-dimensional 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.en_US
dc.description.sponsorshipThis work was funded by grant BIO2001–3745 from the Spanish MCYT. A.L.M. is an FPI predoctoral fellow. D.L. is a predoctoral fellow of the PhD program of the Mount Sinai School of Medicine, New York. D.Z. is the recipient of a visiting fellowship from the Ecole Polytechnique (France). Research at Centro de Biología Molecular "Severo Ochoa" is facilitated by an institutional grant from Fundación Ramón Areces.en_US
dc.format.extent273275 bytes-
dc.format.extent333556 bytes-
dc.publisherBiophysical Societyen_US
dc.subjectProtein superfamiliesen_US
dc.titleAn Analysis of Core Deformations in Protein Superfamiliesen_US
dc.description.peerreviewedPeer revieweden_US
dc.contributor.funderMinisterio de Ciencia y Tecnología (España)-
dc.contributor.funderIcahn School of Medicine at Mount Sinai-
dc.contributor.funderÉcole Polytechnique (France)-
dc.contributor.funderFundación Ramón Areces-
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