QM/MM Study of a VIM-1 Metallo-β-Lactamase Enzyme: The Catalytic Reaction Mechanism

Insights into the Catalytic Mechanism of Domains CD1 and CD2 in Histone Deacetylase 6 from Quantum Calculations

(2021) Mario Prejanò et al.   ACS Catalysis

Water Molecules Allow the Intramolecular Activation of the Thiamine Di-Phosphate Cofactor in Human Transketolase: Mechanistic Insights into a Famous Proposal

(2021) Fabiola E. Medina et al.   ACS Catalysis

Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design

(2021) Guillermo Bahr et al.   CHEMICAL REVIEWS

Animal Fatty Acid Synthase: A Chemical Nanofactory

(2021) Pedro Paiva et al.   CHEMICAL REVIEWS

The urgent need for metallo-β-lactamase inhibitors: an unattended global threat

(2021) Maria F Mojica et al.   LANCET INFECTIOUS DISEASES

Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase

(2020) Rimsha Mehmood et al.   Journal of Chemical Theory and Computation

The ORCA quantum chemistry program package

(2020) Frank Neese et al.   JOURNAL OF CHEMICAL PHYSICS

Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase

(2020) John Z Chen et al.   eLife

Metallo-β-Lactamase Inhibitors Inspired on Snapshots from the Catalytic Mechanism

(2020) Antonela R. Palacios et al.   Biomolecules

Frontiers of metal-coordinating drug design

(2020) Giulia Palermo et al.   Expert Opinion on Drug Discovery

Interplay between β-lactamases and new β-lactamase inhibitors

(2019) Karen Bush et al.   NATURE REVIEWS MICROBIOLOGY

Contemporary approaches to site-selective protein modification

(2019) Emily A. Hoyt et al.   Nature Reviews Chemistry

Evaluating Transition Metal Barrier Heights with the Latest Density Functional Theory Exchange–Correlation Functionals: The MOBH35 Benchmark Database

(2019) Mark A. Iron et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview

(2019) Henrique S. Fernandes et al.   MOLECULES

Protein determinants of dissemination and host specificity of metallo-β-lactamases

(2019) Carolina López et al.   Nature Communications

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

(2019) Chuan Tian et al.   Journal of Chemical Theory and Computation

Cyclobutanone Mimics of Intermediates in Metallo-β-Lactamase Catalysis

(2018) Martine I. Abboud et al.   CHEMISTRY-A EUROPEAN JOURNAL

Communication: An improved linear scaling perturbative triples correction for the domain based local pair-natural orbital based singles and doubles coupled cluster method [DLPNO-CCSD(T)]

(2018) Yang Guo et al.   JOURNAL OF CHEMICAL PHYSICS

Toward Accurate QM/MM Reaction Barriers with Large QM Regions Using Domain Based Pair Natural Orbital Coupled Cluster Theory

(2018) Giovanni Bistoni et al.   Journal of Chemical Theory and Computation

In Silico Fragment-Based Design Identifies Subfamily B1 Metallo-β-lactamase Inhibitors

(2018) Ricky Cain et al.   JOURNAL OF MEDICINAL CHEMISTRY

Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-β-lactamases

(2018) Ramya Salimraj et al.   FEBS Journal

QM/MM Study of the Reaction Mechanism of the Dehydratase Domain from Mammalian Fatty Acid Synthase

(2018) Fabiola E. Medina et al.   ACS Catalysis

Structural/mechanistic insights into the efficacy of nonclassical β-lactamase inhibitors against extensively drug resistant Stenotrophomonas maltophilia clinical isolates

(2017) Karina Calvopiña et al.   MOLECULAR MICROBIOLOGY

KPC: Klebsiella pneumoniae carbapenemasa, principal carbapenemasa en enterobacterias

(2017) Alejandra Vera-Leiva et al.   Revista Chilena de Infectologia

A general reaction mechanism for carbapenem hydrolysis by mononuclear and binuclear metallo-β-lactamases

(2017) María-Natalia Lisa et al.   Nature Communications

Software update: the ORCA program system, version 4.0

(2017) Frank Neese   Wiley Interdisciplinary Reviews-Computational Molecular Science

Kinetic Study of Laboratory Mutants of NDM-1 Metallo-β-Lactamase and the Importance of an Isoleucine at Position 35

(2016) Francesca Marcoccia et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

MCPB.py: A Python Based Metal Center Parameter Builder

(2016) Pengfei Li et al.   Journal of Chemical Information and Modeling

Structural basis of metallo-β-lactamase, serine-β-lactamase and penicillin-binding protein inhibition by cyclic boronates

(2016) Jürgen Brem et al.   Nature Communications

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

(2016) Sérgio Filipe Sousa et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

The ONIOM Method and Its Applications

(2015) Lung Wa Chung et al.   CHEMICAL REVIEWS

Structural and biochemical characterization of VIM-26 shows that Leu224 has implications for the substrate specificity of VIM metallo-β-lactamases

(2015) Hanna-Kirsti S. Leiros et al.   FEBS Journal

Overcoming differences: The catalytic mechanism of metallo-β-lactamases

(2015) María-Rocío Meini et al.   FEBS LETTERS

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds

(2015) Giuliano Malloci et al.   MOLECULES

Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease

(2015) António J. M. Ribeiro et al.   ACS Catalysis

Mechanism of Meropenem Hydrolysis by New Delhi Metallo β-Lactamase

(2015) Ravi Tripathi et al.   ACS Catalysis

His224 Alters the R2 Drug Binding Site and Phe218 Influences the Catalytic Efficiency of the Metallo-β-Lactamase VIM-7

(2014) Hanna-Kirsti S. Leiros et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Spectroscopic and Mechanistic Studies of Heterodimetallic Forms of Metallo-β-lactamase NDM-1

(2014) Hao Yang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular mechanisms of antibiotic resistance

(2014) Jessica M. A. Blair et al.   NATURE REVIEWS MICROBIOLOGY

New β-Lactamase Inhibitors: a Therapeutic Renaissance in an MDR World

(2013) Sarah M. Drawz et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism

(2013) Youngchang Kim et al.   FASEB JOURNAL

A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1

(2013) Kongkai Zhu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Global spread of antibiotic resistance: the example of New Delhi metallo-β-lactamase (NDM)-mediated carbapenem resistance

(2013) Alan P. Johnson et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Assay Platform for Clinically Relevant Metallo-β-lactamases

(2013) Sander S. van Berkel et al.   JOURNAL OF MEDICINAL CHEMISTRY

New Delhi Metallo-β-Lactamase I: Substrate Binding and Catalytic Mechanism

(2013) Min Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

“Stormy waters ahead”: global emergence of carbapenemases

(2013) Gopi Patel et al.   Frontiers in Microbiology

Binuclear Metallohydrolases: Complex Mechanistic Strategies for a Simple Chemical Reaction

(2012) Gerhard Schenk et al.   ACCOUNTS OF CHEMICAL RESEARCH

Metallo-β-lactamase structure and function

(2012) Timothy Palzkill   Annals of the New York Academy of Sciences

Libxc: A library of exchange and correlation functionals for density functional theory

(2012) Miguel A.L. Marques et al.   COMPUTER PHYSICS COMMUNICATIONS

Metallo-β-lactamases withstand low Zn(II) conditions by tuning metal-ligand interactions

(2012) Javier M González et al.   Nature Chemical Biology

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Effect of the damping function in dispersion corrected density functional theory

(2011) Stefan Grimme et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The ONIOM method: its foundation and applications to metalloenzymes and photobiology

(2011) Lung Wa Chung et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Artificial Metalloenzymes

(2010) Fiora Rosati et al.   ChemCatChem

Three Decades of  -Lactamase Inhibitors

(2010) S. M. Drawz et al.   CLINICAL MICROBIOLOGY REVIEWS

Role of changes in the L3 loop of the active site in the evolution of enzymatic activity of VIM-type metallo- -lactamases

(2010) M. Merino et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)

(2010) Martin B. Peters et al.   Journal of Chemical Theory and Computation

Mechanistic Basis for the Emergence of Catalytic Competence against Carbapenem Antibiotics by the GES Family of β-Lactamases

(2009) Hilary Frase et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Mechanisms of Catalysis by Metallo -Lactamases

(2008) Michael I. Page et al.   BIOINORGANIC CHEMISTRY AND APPLICATIONS

Role of the Zn1and Zn2sites in Metallo-β-lactamase L1

(2008) Zhenxin Hu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY