ArticleJournal of chemical theory and computation2021
Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 19 citations in OpenAlex.
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- Plant fucosyltransferase FUT11 distorts the sugar acceptor to catalyze via a transient oxocarbenium intermediate mechanism.Nature communications · 2026Article
- Comparison of Magnesium and Manganese Ions on the Structural and Catalytic Properties of Human DNA Polymerase Gamma.Journal of chemical theory and computation · 2025Article
- Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations.The Journal of chemical physics · 2024Article
- The Impact of Inflammation-Induced Tumor Plasticity during Myeloid Transformation.Cancer discovery · 2022Article
- Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families.Physical chemistry chemical physics : PCCP · 2021Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Selection of residues and other molecular fragments for inclusion in the quantum mechanics (QM) region for QM/molecular mechanics (MM) simulations is an important step for these calculations. Here, we present an approach that combines protein sequence/structure evolution and electron localization function (ELF) analyses. The combination of these two analyses 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 λ (Polλ) with a third cation in the active site. Our results suggest that the combination of protein evolutionary and ELF analyses provides insights into residue/molecular fragment selection for QM/MM simulations.
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