Localization of protein-binding sites within families of proteins.

@article{citeulike:909583, abstract = {We address the question of whether or not the positions of protein-binding sites on homologous protein structures are conserved irrespective of the identities of their binding partners. First, for each domain family in the Structural Classification of Proteins (SCOP), protein-binding sites are extracted from our comprehensive database of structurally defined binary domain interactions (PIBASE). Second, the binding sites within each family are superposed using a structural alignment of its members. Finally, the degree of localization of binding sites within each family is quantified by comparing it with localization expected by chance. We found that 72\% of the 1847 SCOP domain families in PIBASE have binding sites with localization values greater than expected by chance. Moreover, 554 (30\%) of these families have localizations that are statistically significant (i.e., more than four standard deviations away from the mean expected by chance). In contrast, only 144 (8\%) families have significantly low localization. The absence of a significant correlation of the binding site localization with the average sequence and structural conservations in a family suggests that localization can be helpful for describing the functional diversity of protein-protein interactions, complementing measures of sequence and structural conservation. Consideration of the binding site localization may also result in spatial restraints for the modeling of protein assembly structures.}, address = {Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143-2552, USA.}, author = {Korkin, D. and Davis, F. P. and Sali, A. }, citeulike-article-id = {909583}, doi = {10.1110/ps.051571905}, issn = {0961-8368}, journal = {Protein Sci}, keywords = {ppi, scop}, month = {September}, number = {9}, pages = {2350--2360}, posted-at = {2008-05-16 10:19:45}, priority = {2}, title = {Localization of protein-binding sites within families of proteins.}, url = {http://dx.doi.org/10.1110/ps.051571905}, volume = {14}, year = {2005} }

TY - JOUR ID - citeulike:909583 L3 - citeulike-article-id:909583 TI - Localization of protein-binding sites within families of proteins. JF - Protein Sci VL - 14 IS - 9 SP - 2350 EP - 2360 AD - Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143-2552, USA. SN - 0961-8368 N2 - We address the question of whether or not the positions of protein-binding sites on homologous protein structures are conserved irrespective of the identities of their binding partners. First, for each domain family in the Structural Classification of Proteins (SCOP), protein-binding sites are extracted from our comprehensive database of structurally defined binary domain interactions (PIBASE). Second, the binding sites within each family are superposed using a structural alignment of its members. Finally, the degree of localization of binding sites within each family is quantified by comparing it with localization expected by chance. We found that 72% of the 1847 SCOP domain families in PIBASE have binding sites with localization values greater than expected by chance. Moreover, 554 (30%) of these families have localizations that are statistically significant (i.e., more than four standard deviations away from the mean expected by chance). In contrast, only 144 (8%) families have significantly low localization. The absence of a significant correlation of the binding site localization with the average sequence and structural conservations in a family suggests that localization can be helpful for describing the functional diversity of protein-protein interactions, complementing measures of sequence and structural conservation. Consideration of the binding site localization may also result in spatial restraints for the modeling of protein assembly structures. KW - ppi KW - scop AU - Korkin, D AU - Davis, FP AU - Sali, A PY - 2005/09// UR - http://dx.doi.org/10.1110/ps.051571905 ER -