Amino acid pair interchanges at spatially conserved locations

Journal of Molecular Biology
D NaorR Nussinov

Abstract

Here we study the pattern of amino acid interchanges at spatially, locally conserved regions in globally dissimilar and unrelated proteins. By using a method which completely separates the amino acid sequence from its respective structure, this work addresses the question of which properties of the amino acids are the most crucial for the stability of conserved structural motifs. The proteins are taken from a structurally non-redundant dataset. The spatially conserved substructural motifs are defined as consisting of a "large enough" number of Calpha atoms found to provide a geometric match between two proteins, regardless of the order of the Calpha atoms in the sequence, or of the sequence composition of the substructures. This approach can apply to proteins with little or no sequence similarity but with sufficient structural similarity, and is unique in its ability to handle local, non-topological matches between pairs of dissimilar proteins. The method uses a computer-version based algorithm, the Geometric Hashing. Since the Geometric Hashing ignores sequence information it lends itself to answer the question posed above. The interchanges at geometrically similar positions that have been obtained with our method demonstrate ...Continue Reading

Citations

Jan 1, 1997·Protein Science : a Publication of the Protein Society·C J Tsai, R Nussinov
Aug 1, 1997·Protein Science : a Publication of the Protein Society·A WallqvistD G Covell
Jan 16, 2002·Protein Science : a Publication of the Protein Society·Iddo Friedberg, Hanah Margalit
Nov 15, 2007·Theoretical Biology & Medical Modelling·Jan C Biro
Mar 8, 2007·Annals of the New York Academy of Sciences·Jan C Biro
Jul 12, 2007·Proteins·Piotr PokarowskiAndrzej Kolinski
Jan 14, 2010·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·J Dennis PollackDennis K Pearl
Sep 22, 2020·Protein Science : a Publication of the Protein Society·Rakesh Trivedi, Hampapathalu Adimurthy Nagarajaram
Feb 26, 2008·Analytical Biochemistry·Andrew J MurphyJohn Love
Apr 23, 2009·Biochimie·Guilhem FaureAlexandre G de Brevern

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