Clustering of protein structural fragments reveals modular building block approach of nature
DSpace at IIT Bombay
View Archive InfoField | Value | |
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
|
|