Journal ArticleDOI
A “Drug Sweeping” State of the TriABC Triclosan Efflux Pump from Pseudomonas aeruginosa
Lucien Fabre,Abigail T. Ntreh,Amira Yazidi,Inga V. Leus,Jon W. Weeks,Sudipta Bhattacharyya,Sudipta Bhattacharyya,Jakob Ruickoldt,Isabelle Rouiller,Isabelle Rouiller,Helen I. Zgurskaya,Jurgen Sygusch +11 more
TLDR
It is proposed that selective substrate translocation involves conformational gating at the tunnel narrowing that, together with conformational ordering of TriA and TriB, creates an engaged state capable of mediating substrate efflux.About:
This article is published in Structure.The article was published on 2021-03-04. It has received 7 citations till now. The article focuses on the topics: Membrane fusion protein & Periplasmic space.read more
Citations
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Journal ArticleDOI
Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria
Ilyas Alav,Jessica Kobylka,Miriam S. Kuth,Klaas M. Pos,Martin Picard,Jessica M A Blair,Vassiliy N. Bavro +6 more
TL;DR: In this article, the authors summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of periplasmic adaptor proteins (PAPs) in providing a common architectural scaffold across diverse families of transporters.
Journal ArticleDOI
Disinfectant resistance in bacteria: Mechanisms, spread, and resolution strategies.
TL;DR: In this article, a review focused on the resistance mechanisms of disinfectant resistant bacteria on biofilms, cell membrane permeability, efflux pumps, degradable enzymes, and disinfectant targets.
Journal ArticleDOI
Ever-Adapting RND Efflux Pumps in Gram-Negative Multidrug-Resistant Pathogens: A Race against Time.
Martijn Zwama,Kunihiko Nishino +1 more
TL;DR: In this article, the authors take a closer look at clinically, environmentally and laboratory-evolved Gram-negative bacterial strains and their decreased drug sensitivity as a result of mutations directly in the RND-type pumps themselves (from Escherichia coli, Salmonella-enterica, Neisseria gonorrhoeae, Pseudomonas aeruginosa, Acinetobacter baumannii and Legionella pneumophila).
Journal ArticleDOI
The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux.
Valentin V. Rybenkov,Helen I. Zgurskaya,Chhandosee Ganguly,Inga V. Leus,Zhen Zhang,Mohammad Moniruzzaman +5 more
TL;DR: In this paper, the authors present a review of key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery.
Journal ArticleDOI
Multidrug Efflux Pumps and the Two-Faced Janus of Substrates and Inhibitors.
TL;DR: In this article, the authors discuss intriguing relationships between substrates and inhibitors of efflux pumps, as these two types of ligands face similar barriers and binding sites in the transporters and accessory proteins and both types of activities often occur with the same chemical scaffold.
References
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Real-space refinement in PHENIX for cryo-EM and crystallography.
Pavel V. Afonine,Pavel V. Afonine,Billy K. Poon,Randy J. Read,Oleg V. Sobolev,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Paul D. Adams,Paul D. Adams +9 more
TL;DR: In this article, the authors describe the implementation of real-space refinement in the phenixreal_space-refine program from the PHENIX suite, which makes use of extra information such as secondary-structure and rotamer-specific restraints.
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Virtual computational chemistry laboratory - design and description
Igor V. Tetko,Johann Gasteiger,Roberto Todeschini,Andrea Mauri,David J. Livingstone,Peter Ertl,Vladimir A. Palyulin,Eugene V. Radchenko,Nikolai S. Zefirov,Alexander S. Makarenko,Vsevolod Yu. Tanchuk,Volodymyr V. Prokopenko +11 more
TL;DR: The main features and statistics of the developed system, Virtual Computational Chemistry Laboratory, allowing the computational chemist to perform a comprehensive series of molecular indices/properties calculations and data analysis are reviewed.
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Crystal structure of bacterial multidrug efflux transporter AcrB
TL;DR: In this article, the crystal structure of AcrB at 3.5 A resolution was determined, which implies that substrates translocated from the cell interior through the transmembrane region and from the periplasm through the vestibules are collected in the central cavity and then actively transported through the pore into the TolC tunnel.
Journal ArticleDOI
Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6
Tim Grant,Nikolaus Grigorieff +1 more
TL;DR: A method of using optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions that should benefit cryo-EM work on all types of samples, especially those of relatively low-molecular mass.
Journal ArticleDOI
How significant is a protein structure similarity with TM-score = 0.5?
Jinrui Xu,Yang Zhang +1 more
TL;DR: This article makes an all-to-all gapless structural match on 6684 non-homologous single-domain proteins in the PDB and finds that the TM-scores follow an extreme value distribution, and examines the posterior probability of the same fold proteins from three datasets SCOP, CATH and the consensus of SCOP and CATH to indicate that TM-score can be used as an approximate but quantitative criterion for protein topology classification.