Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters

Computational modelling of efflux pumps and their inhibitors

(2017) Venkata Krishnan Ramaswamy et al.   Essays in Biochemistry

Evidence of a Substrate-Discriminating Entrance Channel in the Lower Porter Domain of the Multidrug Resistance Efflux Pump AcrB

(2016) Sabine Schuster et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Insights into the Inhibitory Mechanism of D13-9001 to the Multidrug Transporter AcrB through Molecular Dynamics Simulations

(2016) Zhicheng Zuo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives

(2016) Hanno Sjuts et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Fluorescent Microplate Assay Quantifies Bacterial Efflux and Demonstrates Two Distinct Compound Binding Sites in AcrB

(2015) Ramkumar Iyer et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Challenge of Efflux-Mediated Antibiotic Resistance in Gram-Negative Bacteria

(2015) Xian-Zhi Li et al.   CLINICAL MICROBIOLOGY REVIEWS

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

(2015) Chad W. Hopkins et al.   Journal of Chemical Theory and Computation

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

Molecular architecture of the bacterial tripartite multidrug efflux pump focusing on the adaptor bridging model

(2015) Saemee Song et al.   JOURNAL OF MICROBIOLOGY

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

(2015) Dima Kozakov et al.   Nature Protocols

AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity

(2015) Jessica M. A. Blair et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stepwise substrate translocation mechanism revealed by free energy calculations of doxorubicin in the multidrug transporter AcrB

(2015) Zhicheng Zuo et al.   Scientific Reports

Architecture and roles of periplasmic adaptor proteins in tripartite efflux assemblies

(2015) Martyn F. Symmons et al.   Frontiers in Microbiology

Mechanism of coupling drug transport reactions located in two different membranes

(2015) Helen I. Zgurskaya et al.   Frontiers in Microbiology

Structural basis of RND-type multidrug exporters

(2015) Akihito Yamaguchi et al.   Frontiers in Microbiology

Switch-Loop Flexibility Affects Transport of Large Drugs by the Promiscuous AcrB Multidrug Efflux Transporter

(2014) Hi-jea Cha et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Molecular Mechanism of MBX2319 Inhibition of Escherichia coli AcrB Multidrug Efflux Pump and Comparison with Other Inhibitors

(2014) Attilio V. Vargiu et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

β-Lactam Selectivity of Multidrug Transporters AcrB and AcrD Resides in the Proximal Binding Pocket

(2014) Naoki Kobayashi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lipid14: The Amber Lipid Force Field

(2014) Callum J. Dickson et al.   Journal of Chemical Theory and Computation

MLP Tools: a PyMOL plugin for using the molecular lipophilicity potential in computer-aided drug design

(2014) Nils Oberhauser et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structure of the AcrAB–TolC multidrug efflux pump

(2014) Dijun Du et al.   NATURE

Molecular mechanisms of antibiotic resistance

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

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

(2014) Sergio Ruiz-Carmona et al.   PLoS Computational Biology

Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB

(2014) Thomas Eicher et al.   eLife

RND Efflux Pumps: Structural Information Translated into Function and Inhibition Mechanisms

(2013) Paolo Ruggerone et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Structural basis for the inhibition of bacterial multidrug exporters

(2013) Ryosuke Nakashima et al.   NATURE

MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS

(2013) Paolo Ruggerone et al.   Computational and Structural Biotechnology Journal

Porter domain opening and closing motions in the multi-drug efflux transporter AcrB

(2012) Nadine Fischer et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Recognition of Imipenem and Meropenem by the RND-Transporter MexB Studied by Computer Simulations

(2012) Francesca Collu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations

(2012) A. V. Vargiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop

(2012) T. Eicher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Essential dynamics: foundation and applications

(2012) Isabella Daidone et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Vestibules Are Part of the Substrate Path in the Multidrug Efflux Transporter AcrB of Escherichia coli

(2011) F. Husain et al.   JOURNAL OF BACTERIOLOGY

Functionality Mapping on Internal Surfaces of Multidrug Transporter AcrB Based on Molecular Theory of Solvation: Implications for Drug Efflux Pathway

(2011) Takashi Imai et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Role of Water during the Extrusion of Substrates by the Efflux Transporter AcrB

(2011) Robert Schulz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations

(2011) Attilio V. Vargiu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket

(2011) Ryosuke Nakashima et al.   NATURE

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

Three ways in, one way out: Water dynamics in the trans-membrane domains of the inner membrane translocase AcrB

(2011) Nadine Fischer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations

(2010) Robert Schulz et al.   PLoS Computational Biology

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Assembly and transport mechanism of tripartite drug efflux systems

(2009) Rajeev Misra et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Regulation and physiological function of multidrug efflux pumps in Escherichia coli and Salmonella

(2009) Kunihiko Nishino et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Drug transport mechanism of the AcrB efflux pump

(2009) Klaas M. Pos   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

The assembled structure of a complete tripartite bacterial multidrug efflux pump

(2009) M. F. Symmons et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multidrug efflux transporter, AcrB—the pumping mechanism

(2008) S MURAKAMI   CURRENT OPINION IN STRUCTURAL BIOLOGY

Site-Directed Mutagenesis Reveals Putative Substrate Binding Residues in the Escherichia coli RND Efflux Pump AcrB

(2008) J. A. Bohnert et al.   JOURNAL OF BACTERIOLOGY

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY