Rationalization of the difference in lifetime of two covalent sialosyl-enzyme intermediates of Trypanosoma rangeli sialidase.

The difference in lifetime with respect to hydrolysis of two covalent syalosyl-enzyme intermediates of two difluorinated sialic acid analogues ( 1 and 2) bound to Trypanosoma rangeli sialidase is rationalized based on quantum mechanical calculations. The two intermediates differ only in a single functional group, acetamide in the sialidase- 1 complex and hydroxyl in the sialidase- 2 complex. It is shown that the acetamide group, which is also present in the natural substrate, increases the pKa of a catalytic base (Asp60) through electrostatic repulsion with the carbonyl oxygen on the ligand.

Cooperative hydrogen bonding effects are key determinants of backbone amide proton chemical shifts in proteins.

A computational methodology for backbone amide proton chemical shift (delta(H)) predictions based on ab initio quantum mechanical treatment of part of the protein is presented. The method is used to predict and interpret 13 delta(H) values in protein G and ubiquitin. The predicted amide-amide delta(H) values are within 0.