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Development and Validation of the Quantum Mechanical Bespoke Protein Force Field.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Allen, Alice EA 
Robertson, Michael J 
Payne, Michael C 
Cole, Daniel J 

Abstract

Molecular mechanics force field parameters for macromolecules, such as proteins, are traditionally fit to reproduce experimental properties of small molecules, and thus, they neglect system-specific polarization. In this paper, we introduce a complete protein force field that is designed to be compatible with the quantum mechanical bespoke (QUBE) force field by deriving nonbonded parameters directly from the electron density of the specific protein under study. The main backbone and sidechain protein torsional parameters are rederived in this work by fitting to quantum mechanical dihedral scans for compatibility with QUBE nonbonded parameters. Software is provided for the preparation of QUBE input files. The accuracy of the new force field, and the derived torsional parameters, is tested by comparing the conformational preferences of a range of peptides and proteins with experimental measurements. Accurate backbone and sidechain conformations are obtained in molecular dynamics simulations of dipeptides, with NMR J coupling errors comparable to the widely used OPLS force field. In simulations of five folded proteins, the secondary structure is generally retained, and the NMR J coupling errors are similar to standard transferable force fields, although some loss of the experimental structure is observed in certain regions of the proteins. With several avenues for further development, the use of system-specific nonbonded force field parameters is a promising approach for next-generation simulations of biological molecules.

Description

Keywords

34 Chemical Sciences, 3406 Physical Chemistry, 3407 Theoretical and Computational Chemistry, Bioengineering

Journal Title

ACS Omega

Conference Name

Journal ISSN

2470-1343
2470-1343

Volume Title

4

Publisher

American Chemical Society (ACS)
Sponsorship
Engineering and Physical Sciences Research Council (EP/P034616/1)
Engineering and Physical Sciences Research Council (EP/L015552/1)
Engineering and Physical Sciences Research Council (EP/J017639/1)
Engineering and Physical Sciences Research Council (EP/P020259/1)