NDLI: Energy based approach for understanding the recognition mechanism in protein

Content Provider	Royal Society of Chemistry (RSC)
Author	Yokota, Kiyonobu Gromiha, M. Michael Fukui, Kazuhiko
Copyright Year	2009
Abstract	Protein–protein interactions play an essential role in the regulation of various cellular processes. Understanding the recognition mechanism of protein–protein complexes is a challenging task in molecular and computational biology. In this work, we have developed an energy based approach for identifying the binding sites and important residues for binding in protein–protein complexes. The new approach is different from the traditional distance based contacts in which the repulsive interactions are treated as binding sites as well as the contacts within a specific cutoff have been treated in the same way. We found that the residues and residue-pairs with charged and aromatic side chains are important for binding. These residues influence to form cation–π, electrostatic and aromatic interactions. Our observation has been verified with the experimental binding specificity of protein–protein complexes and found good agreement with experiments. Based on these results we have proposed a novel mechanism for the recognition of protein–protein complexes: the charged and aromatic residues in receptor and ligand initiate recognition by making suitable interactions between them; the neighboring hydrophobic residues assist the stability of complex along with other hydrogen bonding partners by the polar residues. Further, the propensity of residues in the binding sites of receptors and ligands, atomic contributions and the influence on secondary structure will be discussed.
Starting Page	1779
Ending Page	1786
Page Count	8
File Format	HTM / HTML PDF
ISSN	1742206X
Volume Number	5
Issue Number	12
Journal	Molecular BioSystems
DOI	10.1039/b904161n
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Cell surface receptor Ligand Hydrophobic effect Biomolecular structure Computational biology Hydrogen bond
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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