Hydrogenase enzymes and their synthetic models: the role of metal hydrides

D Schilter, JM Camara, MT Huynh… - Chemical …, 2016 - ACS Publications
Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or
Fe active sites. Synthetic modeling of the many H2ase states has provided insight into …

Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states

E Brunk, U Rothlisberger - Chemical reviews, 2015 - ACS Publications
The quantum nature of electrons and nuclei is manifested in countless biological events
including the rearrangements of electrons in biochemical reactions, electron and proton …

Self-consistent determination of long-range electrostatics in neural network potentials

A Gao, RC Remsing - Nature communications, 2022 - nature.com
Abstract Machine learning has the potential to revolutionize the field of molecular simulation
through the development of efficient and accurate models of interatomic interactions. Neural …

The molecular mechanism of the catalase reaction

M Alfonso-Prieto, X Biarnés, P Vidossich… - Journal of the …, 2009 - ACS Publications
Catalases are ubiquitous enzymes that prevent cell oxidative damage by degrading
hydrogen peroxide to water and oxygen (2H2O2→ 2 H2O+ O2) with high efficiency. The …

Metal–ligand interactions in drug design

L Riccardi, V Genna, M De Vivo - Nature Reviews Chemistry, 2018 - nature.com
The fast-growing body of experimental data on metalloenzymes and organometallic
compounds is fostering the exploitation of metal–ligand interactions for the design of new …

Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa

J Dreier, P Ruggerone - Frontiers in microbiology, 2015 - frontiersin.org
Pseudomonas aeruginosa infections are becoming increasingly difficult to treat due to
intrinsic antibiotic resistance and the propensity of this pathogen to accumulate diverse …

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

SF Sousa, AJM Ribeiro, RPP Neves… - Wiley …, 2017 - Wiley Online Library
Quantum mechanics/molecular mechanics (QM/MM) methods offer a very appealing option
for the computational study of enzymatic reaction mechanisms, by separating the problem …

Catalytic metal ions and enzymatic processing of DNA and RNA

G Palermo, A Cavalli, ML Klein… - Accounts of chemical …, 2015 - ACS Publications
Conspectus Two-metal-ion-dependent nucleases cleave the phosphodiester bonds of
nucleic acids via the two-metal-ion (2M) mechanism. Several high-resolution X-ray …

Modelling enzymatic mechanisms with QM/MM approaches: current status and future challenges

RP Magalhães, HS Fernandes… - Israel Journal of …, 2020 - Wiley Online Library
Quantum mechanics/molecular mechanics (QM/MM) methods are presently a well‐
established alternative for the study of enzymatic reaction mechanisms. They enable the …

Multiscale modeling of proteins

V Tozzini - Accounts of chemical research, 2010 - ACS Publications
The activity within a living cell is based on a complex network of interactions among
biomolecules, exchanging information and energy through biochemical processes. These …