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Biophysical Journal 84:1919-1925 (2003)
© 2003 The Biophysical Society

Role of Hydrophobic Clusters and Long-Range Contact Networks in the Folding of ({alpha}/ß)8 Barrel Proteins

S. Selvaraj* and M. Michael Gromiha

Computational Biology Research Center (CBRC), Institute of Advanced Industrial Science and Technology (AIST) 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan; and * Department of Physics, Bharathidasan University, Tiruchirapalli 620 024, Tamilnadu, India

Correspondence: Address reprint requests to M. Michael Gromiha, Tel.: +81-3-3599-8046; Fax: +81-3-3599-8081; E-mail: michael-gromiha{at}aist.go.jp.

Analysis on the three dimensional structures of ({alpha}/ß)8 barrel proteins provides ample light to understand the factors that are responsible for directing and maintaining their common fold. In this work, the hydrophobically enriched clusters are identified in 92% of the considered ({alpha}/ß)8 barrel proteins. The residue segments with hydrophobic clusters have high thermal stability. Further, these clusters are formed and stabilized through long-range interactions. Specifically, a network of long-range contacts connects adjacent ß-strands of the ({alpha}/ß)8 barrel domain and the hydrophobic clusters. The implications of hydrophobic clusters and long-range networks in providing a feasible common mechanism for the folding of ({alpha}/ß)8 barrel proteins are proposed.




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[Abstract] [Full Text] [PDF]


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