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Specificity of Trypsin and Chymotrypsin: Loop-Motion-Controlled Dynamic Correlation as a Determinant

Wenzhe Ma ^* , Chao Tang ^*  and Luhua Lai ^* 

^* Center for Theoretical Biology, and State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China; and California Institute for Quantitative Biomedical Research, Departments of Biopharmaceutical Sciences and Biochemistry and Biophysics, University of California, San Francisco, California 94143-2540

Correspondence: Address reprint requests to Luhua Lai, E-mail: lhlai{at}pku.edu.cn.

Trypsin and chymotrypsin are both serine proteases with high sequence and structural similarities, but with different substrate specificity. Previous experiments have demonstrated the critical role of the two loops outside the binding pocket in controlling the specificity of the two enzymes. To understand the mechanism of such a control of specificity by distant loops, we have used the Gaussian network model to study the dynamic properties of trypsin and chymotrypsin and the roles played by the two loops. A clustering method was introduced to analyze the correlated motions of residues. We have found that trypsin and chymotrypsin have distinct dynamic signatures in the two loop regions, which are in turn highly correlated with motions of certain residues in the binding pockets. Interestingly, replacing the two loops of trypsin with those of chymotrypsin changes the motion style of trypsin to chymotrypsin-like, whereas the same experimental replacement was shown necessary to make trypsin have chymotrypsin's enzyme specificity and activity. These results suggest that the cooperative motions of the two loops and the substrate-binding sites contribute to the activity and substrate specificity of trypsin and chymotrypsin.