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Combining Evolutionary Conservation and Quantum Topological Analyses to Determine QM Subsystems for Biomolecular QM/MM Simulations

preprint
submitted on 30.03.2021, 20:27 and posted on 31.03.2021, 12:59 by Mark A. Hix, Emmett M. Leddin, G. Andres Cisneros
We present an approach that combines protein sequence/structure evolution and electron localization function (ELF) analyses. The combination of these two analysis allows the determination of whether a residue needs to be included in the QM subsystem, or can be represented by the MM environment. We have applied this approach on two systems previously investigated by QM/MM simulations, 4{oxalocrotonate tautomerase (4OT), and ten-eleven translocation-2 (TET2), that provide examples where fragments may or may not need to be included in the QM subsystem. Subsequently, we present the use of this approach to determine the appropriate QM subsystem to calculate the minimum energy path (MEP) for the reaction catalyzed by human DNA polymerase lambda? with a third cation in the active site.

Funding

NIH RO1GM108583

NSF CHE-1856162

NSF CHE-1531468

History

Email Address of Submitting Author

andres@unt.edu

Institution

University of North Texas

Country

USA

ORCID For Submitting Author

0000-0001-6629-3430

Declaration of Conflict of Interest

no conflicts

Version Notes

version 1.0

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ChemRxiv

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