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Clustering of protein structural fragments reveals modular building block approach of nature

DSpace at IIT Bombay

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Title Clustering of protein structural fragments reveals modular building block approach of nature
 
Creator TENDULKAR, ASHISH V
JOSHI, ANAND A
SOHONI, MILIND
WANGIKAR, PRAMOD P
 
Subject geometric invariants
protein structure comparison
secondary structure
loop
 
Description Structures of peptide fragments drawn from a protein can potentially occupy a vast conformational continuum. We co-ordinatize this conformational space with the help of geometric invariants and demonstrate that the peptide conformations of the currently available protein structures are heavily biased in favor of a finite number of conformational types or structural building blocks. This is achieved by representing a peptides' backbone structure with geometric invariants and then clustering peptides based on closeness of the geometric invariants. This results in 12,903 clusters, of which 2207 are made up of peptides drawn from functionally and/or structurally related proteins. These are termed “functional” clusters and provide clues about potential functional sites. The rest of the clusters, including the largest few, are made up of peptides drawn from unrelated proteins and are termed “structural” clusters. The largest clusters are of regular secondary structures such as helices and beta strands as well as of beta hairpins. Several categories of helices and strands are discovered based on geometric differences. In addition to the known classes of loops, we discover several new classes, which will be useful in protein structure modeling. Our algorithm does not require assignment of secondary structure and, therefore, overcomes the limitations in loop classification due to ambiguity in secondary structure assignment at loop boundaries.
 
Publisher Elsevier
 
Date 2009-03-17T10:05:45Z
2011-11-25T19:15:46Z
2011-12-26T13:07:24Z
2011-12-27T05:55:27Z
2009-03-17T10:05:45Z
2011-11-25T19:15:46Z
2011-12-26T13:07:24Z
2011-12-27T05:55:27Z
2004
 
Type Article
 
Identifier Journal of Molecular Biology 338(3), 611-629
0022-2836
http://dx.doi.org/10.1016/j.jmb.2004.02.047
http://hdl.handle.net/10054/957
http://dspace.library.iitb.ac.in/xmlui/handle/10054/957
 
Language en