Abstract
The electric field in the hydrogen-bond network of the active site of ketosteroid isomerase (KSI) has been experimentally measured using vibrational Stark effect (VSE) spectroscopy, and utilized to study the electrostatic contribution to catalysis. A large gap was found in the electric field between the computational simulation based on the Amber force field and the experimental measurement. In this work, quantum mechanical (QM) calculations of the electric field were performed using an ab initio QM/MM molecular dynamics (MD) simulation and electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. Our results demonstrate that the QM-derived electric field based on the snapshots from QM/MM MD simulation could give quantitative agreement with the experiment. The accurate calculation of the electric field inside the protein requires both the rigorous sampling of configurations, and a QM description of the electrostatic field. Based on the direct QM calculation of the electric field, we theoretically confirmed that there is a linear correlation relationship between the activation free energy and the electric field in the active site of wild-type KSI and its mutants (namely, D103N, Y16S, and D103L). Our study presents a computational protocol for the accurate simulation of the electric field in the active site of the protein, and provides a theoretical foundation that supports the link between electric fields and enzyme catalysis.
Highlights
It is still a controversial issue on the origin of the tremendous catalytic power of enzymes, it has been commonly accepted that the electrostatic field plays a key role in the enzyme’s high catalytic proficiency [1,2]
The ab initio quantum mechanical (QM)/Molecular mechanics (MM) molecular dynamics (MD) simulations were performed to calculate the electric field mainly exerted by H-bonds in the active site of ketosteroid isomerase (KSI)
By comparing with the simulations using the classical force field, we found that the H-bonds would be dynamically stabilized by the QM electronic polarization effect, which plays an important role in accurate calculations of the electric field
Summary
It is still a controversial issue on the origin of the tremendous catalytic power of enzymes, it has been commonly accepted that the electrostatic field plays a key role in the enzyme’s high catalytic proficiency [1,2]. The site-directed mutagenesis approach is widely used in studies on enzymes for altering their catalytic rate, while the point mutation is often created near the active site which may lead to unexpected structural rearrangement, change of the substrate binding state, and sometimes even introduction of excess water molecules This is usually imperceptible in macroscopic experimental measurement based on VSE spectroscopy. In the case of KSI, whose active site forms strong and short H-bonds with the substrate, the study [5] by Fried et al shows that there was a large gap in the electric fields between the calculated value based on a MD simulation using the standard Amber force field and the experimental measurement. Based on the fragment-based QM calculations on electric fields, the correlation between the electric field and the activation free energy is validated from the theoretical perspective, and new physical insights obtained from the accurate simulation of electric fields in proteins are discussed
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