Density Functional Theory Calculations to Investigate the Role Played by an Aspartate Dyad in Hsp60-Catalyzed ATP Hydrolysis

TL;DR

This paper uses computational methods to study how a pair of aspartate residues in Hsp60 influence ATP hydrolysis, a key process in protein folding.

Contribution

The study provides new insights into the mechanism of ATP hydrolysis in Hsp60 by analyzing the role of an aspartate dyad using DFT calculations.

Findings

Hydrolysis is favored when the aspartate dyad is deprotonated.

Dyad closure increases ATPase activity in the V72I Hsp60 mutant.

Protonation state significantly affects the reaction barrier for ATP hydrolysis.

Abstract

Adenosine 5′-triphosphate
(ATP) hydrolysis is one of the
most significant reactions in biochemistry. In chaperone proteins,
energy released by hydrolysis enables them to carry out their function
and help other proteins (called “clients”) to fold into
their functional form. Here, we run Density Functional Theory calculations
on three cluster models of the Hsp60 active site extracted from our
previous molecular dynamics simulations of the 14-meric Hsp60 double-ring
complex: our aim is to qualitatively investigate the mechanisms of
ATP hydrolysis in different scenarios where the chaperone closes a
dyad composed of catalytic aspartates Asp50 and Asp397. Since dyad
closure raises Asp pK
a values and increases
likelihood of protonation, we modeled the active site both in the
presence and absence of a proton. Comparison of reaction barriers
suggests that hydrolysis is favored when aspartates become deprotonated,
explaining increased ATPase activity observed in V72I mutant Hsp60
(known to favor dyad closure).

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