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1: Biophys Chem. 2002 Oct 16;99(2):189-98.
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Influence of medium- and long-range interactions in different folding types of globular proteins.

Kumarevel TS, Gromiha MM, Selvaraj S, Gayatri K, Kumar PK.

National Institute of Advanced Industrial Science and Technology (AIST), Institute of Molecular and Cell Biology, Functional Nucleic Acids Group, Tsukuba Central 6, 1-1 Higashi, Tsukuba Science City, Ibaraki, Japan. kumarevel-thirumananseri@aist.go.jp

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.

PMID: 12377369 [PubMed - indexed for MEDLINE]