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Importance of hydrophobic cluster formation through long‐range contacts in the folding transition state of two‐state proteins
Author(s) -
Selvaraj S.,
Gromiha M. Michael
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20109
Subject(s) - contact order , protein folding , lattice protein , folding (dsp implementation) , chemistry , hydrophobic effect , crystallography , phi value analysis , chemical physics , phase transition , cluster (spacecraft) , protein structure , state (computer science) , biophysics , native state , biochemistry , physics , thermodynamics , biology , computer science , programming language , electrical engineering , engineering , algorithm
Understanding the folding pathways of proteins is a challenging task. The Φ value approach provides a detailed understanding of transition‐state structures of folded proteins. In this work, we have computed the hydrophobicity associated with each residue in the folded state of 16 two‐state proteins and compared the Φ values of each mutant residue. We found that most of the residues with high Φ value coincide with local maximum in surrounding hydrophobicity, or have nearby residues that show such maximum in hydrophobicity, indicating the importance of hydrophobic interactions in the transition state. We have tested our approach to different structural classes of proteins, such as α‐helical, SH3 domains of all‐β proteins, β‐sandwich, and α/β proteins, and we observed a good agreement with experimental results. Further, we have proposed a hydrophobic contact network pattern to relate the Φ values with long‐range contacts, which will be helpful to understand the transition‐state structures of folded proteins. The present approach could be used to identify potential hydrophobic clusters that may form through long‐range contacts during the transition state. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.