Interdisciplinary Bio Central
 
Etc. (Bioinformatics/Computational biology/Molecular modeling)

Local structural alignment and classification of TIM barrel domains
Changwon Keum1,*, Jihong Kim2 and Jongsun Jung2
1Department of BioSystems, KAIST, Daejeon, Korea
2NGRI, KNIH, Seoul, Korea
*Corresponding author
  Published : May 31, 2006
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Synopsis

TIM barrel domain is widely studied since it is one of most common structure and mediates diverse function maintaining overall structure. TIM barrel domain's function is determined by local structural environment at the C-terminal end of barrel structure. We classified TIM barrel domains by local structural alignment tool, LSHEBA, to understand characteristics of TIM barrel domain's functionalvariation. TIM barrel domains classified as the same cluster share common structure, function and ligands. Over 80% of TIM barrels in clusters share exactly the same catalytic function. Comparing clustering result with that of SCOP, we found that it's important to know local structural environment of TIM barrel domains rather than overallstructure to understand specific structural detail of TIM barrel function. Non TIM barrel domains were associated to make different domain combination to form a different function. The relationship between domain combination, we suggested expected evolutional history. We finally analyzed the characteristics of amino acids around ligand interface.

Keyword: TIM barrel, local structural alignment, functional diversity
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