Model for crankshaft motion of protein backbone in nonspecific binding site of serine proteases

TL;DR

This study models how hydrogen bond strengthening in serine proteases' binding sites affects peptide backbone motion, revealing that low-barrier bonds significantly increase crankshaft motion frequency.

Contribution

It introduces a realistic microscopic model showing how low-barrier hydrogen bonds alter peptide backbone dynamics in serine proteases.

Findings

Hydrogen bond transformation doubles crankshaft motion frequency.

Coupling interaction in the peptide chain is weak and repulsive.

Effective on-site potential is steeper than harmonic.

Abstract

The consequences of recent experimental finding that hydrogen bonds of the anti-parallel $\beta $-sheet in nonspecific binding site of serine proteases become significantly shorter and stronger synchronously with the catalytic act are examined. We investigate the effect of the transformation of an ordinary hydrogen bond into a low-barrier one on the crankshaft motion a peptide group in the anti-parallel $\beta $-sheet. For this purpose we make use of a realistic model of the peptide chain with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction characterizing the peptide chain rigidity is found to be surprisingly weak and repulsive in character. The effective on-site potential is found to be a hard one, i.e., goes more steep than a harmonic one. At transformation of the ordinary hydrogen bond into the low-barrier one the frequency of crankshaft motion of the corresponding peptide group in the anti-parallel $\beta $-sheet is roughly doubled.