Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins.
Analysis on the three dimensional structures of (alpha/beta)(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/beta)(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 beta-strands of the (alpha/beta)(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/beta)(8) barrel proteins are proposed.
Selvaraj
S
S
Computational Biology Research Center (CBRC), Institute of Advanced Industrial Science and Technology (AIST) 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.
Gromiha
M Michael
MM
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013696:Temperature
D000596:Amino Acids; D011506:Proteins