ArticleMethods in enzymology2016
Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions.
Article in Methods in enzymology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Dynamic shift of internal electric field accelerates enzymatic polyethylene terephthalate depolymerization.Communications chemistry · 2026Article
- Special Issue: "Advanced Research on Molecular Modeling of Protein Structure and Functions".International journal of molecular sciences · 2025Article
- Mining coral-derived terpene synthases and mechanistic studies of the coral biflorane synthase.Science advances · 2025Article
- HydE Catalytic Mechanism Is Powered by a Radical Relay with Redox-Active Fe(I)-Containing Intermediates.Journal of the American Chemical Society · 2025Article
- Nuclear-Electronic Orbital Quantum Mechanical/Molecular Mechanical Real-Time Dynamics.The journal of physical chemistry letters · 2023Article
- Discovering a uniform functional trade-off of the CBC-type 2,3-oxidosqualene cyclases and deciphering its chemical logic.Science advances · 2023Article
- Catalytic deAMPylation in AMPylation-inhibitory/assistant forms of FICD protein.Frontiers in chemistry · 2023Article
- Review on the QM/MM Methodologies and Their Application to Metalloproteins.Molecules (Basel, Switzerland) · 2022Review
- Quantum Chemical Study of a Radical Relay Mechanism for the HydG-Catalyzed Synthesis of a Fe(II)(CO)Biochemistry · 2021Article
- A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations.The Journal of chemical physics · 2021Article
- Differences in the Nature of the Phosphoryl Transfer Transition State in Protein Phosphatase 1 and Alkaline Phosphatase: Insights from QM Cluster Models.The journal of physical chemistry. B · 2020Article
- Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate.Nature catalysis · 2019Article
- Two symmetric arginine residues play distinct roles inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations.Molecules (Basel, Switzerland) · 2018Article
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Authors and funding
4 authors.
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Abstract
There are two key requirements for reliably simulating enzyme reactions: one is a reasonably accurate potential energy surface to describe the bond-forming/breaking process as well as to adequately model the heterogeneous enzyme environment; the other is to perform extensive sampling since an enzyme system consists of at least thousands of atoms and its energy landscape is very complex. One attractive approach to meet both daunting tasks is Born-Oppenheimer ab initio QM/MM molecular dynamics (aiQM/MM-MD) simulation with umbrella sampling. In this chapter, we describe our recently developed pseudobond Q-Chem-Amber interface, which employs a combined electrostatic-mechanical embedding scheme with periodic boundary condition and the particle mesh Ewald method for long-range electrostatics interactions. In our implementation, Q-Chem and the sander module of Amber are combined at the source code level without using system calls, and all necessary data communications between QM and MM calculations are achieved via computer memory. We demonstrate the applicability of this pseudobond Q-Chem-Amber interface by presenting two examples, one reaction in aqueous solution and one enzyme reaction. Finally, we describe our established aiQM/MM-MD enzyme simulation protocol, which has been successfully applied to study more than a dozen enzymes.
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