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Protein Engineering, Vol. 12, No. 12, 1075-1086, December 1999
© 1999 Oxford University Press

Exploring the conformational diversity of loops on conserved frameworks

Weizhong Li, Shide Liang, Renxiao Wang, Luhua Lai1 and Yuzhen Han

Institute of Physical Chemistry, Peking University, Beijing 100871, China

Loops are structurally variable regions, but the secondary structural elements bracing loops are often conserved. Motifs with similar secondary structures exist in the same and different protein families. In this study, we made an all-PDB-based analysis and produced 495 motif families accessible from the Internet. Every motif family contains some variable loops spanning a common framework (a pair of secondary structures). The diversity of loops and the convergence of frameworks were examined. In addition, we also identified 119 loops with conformational changes in different PDB files. These materials can give some directions for functional loop design and flexible docking.

Keywords: database/loop/loop conformation/loop modeling/loop structure/motif

1 To whom correspondence should be addressed


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