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Influence of medium- and long-range interactions in different folding types of globular proteins.

Authors
  • Kumarevel, T S
  • Gromiha, M Michael
  • Selvaraj, S
  • Gayatri, K
  • Kumar, P K R
Type
Published Article
Journal
Biophysical Chemistry
Publisher
Elsevier
Publication Date
Oct 16, 2002
Volume
99
Issue
2
Pages
189–198
Identifiers
PMID: 12377369
Source
Medline
License
Unknown

Abstract

Recognition of protein fold from amino acid sequence is a challenging task. The structure and stability of proteins from different fold are mainly dictated by inter-residue interactions. In our earlier work, we have successfully used the medium- and long-range contacts for predicting the protein folding rates, discriminating globular and membrane proteins and for distinguishing protein structural classes. In this work, we analyze the role of inter-residue interactions in commonly occurring folds of globular proteins in order to understand their folding mechanisms. In the medium-range contacts, the globin fold and four-helical bundle proteins have more contacts than that of DNA-RNA fold although they all belong to all-alpha class. In long-range contacts, only the ribonuclease fold prefers 4-10 range and the other folding types prefer the range 21-30 in alpha/beta class proteins. Further, the preferred residues and residue pairs influenced by these different folds are discussed. The information about the preference of medium- and long-range contacts exhibited by the 20 amino acid residues can be effectively used to predict the folding type of each protein.

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