Results 91 to 100 of about 295,113 (307)

Integrative Modeling in the Age of Machine Learning: A Summary of HADDOCK Strategies in CAPRI Rounds 47–55

Proteins: Structure, Function, and Bioinformatics, EarlyView.
ABSTRACT The HADDOCK team participated in CAPRI rounds 47–55 as server, manual predictor, and scorers. Throughout these CAPRI rounds, we used a plethora of computational strategies to predict the structure of protein complexes. Of the 10 targets comprising 24 interfaces, we achieved acceptable or better models for 3 targets in the human category and 1 ...
Victor Reys, Marco Giulini, Vlad Cojocaru, Anna Engel, Xiaotong Xu, Jorge Roel‐Touris, Cunliang Geng, Francesco Ambrosetti, Brian Jiménez‐García, Zuzana Jandova, Panagiotis I. Koukos, Charlotte van Noort, João M. C. Teixeira, Siri C. van Keulen, Manon Réau, Rodrigo V. Honorato, Alexandre M. J. J. Bonvin   +16 more
wiley   +1 more source

The Variety in the Common Theme of Translation Inhibition by Type II Toxin–Antitoxin Systems

Frontiers in Genetics, 2020
Type II Toxin–antitoxin (TA) modules are bacterial operons that encode a toxic protein and its antidote, which form a self-regulating genetic system. Antitoxins put a halter on toxins in many ways that distinguish different types of TA modules.
D. Jurėnas, L. Van Melderen
semanticscholar   +1 more source

Characterization of HicAB toxin-antitoxin module of Sinorhizobium meliloti

BMC Microbiology, 2019
Background Toxin-antitoxin (TA) systems are little genetic units generally composed of two genes encoding antitoxin and toxin. These systems are known to be involved in many functions that can lead to growth arrest and cell death.
Manon Thomet, Annie Trautwetter, Gwennola Ermel, Carlos Blanco   +3 more
doaj   +1 more source

Crystal Structure and Functional Characterization of YjgK From Salmonella Typhimurium

Proteins: Structure, Function, and Bioinformatics, EarlyView.
ABSTRACT The YhcH/YjgK/YiaL (DUF386) family, widely conserved across bacterial species, is involved in essential cellular processes yet remains poorly characterized. YjgK from Salmonella enterica serovar Typhimurium has drawn attention because of its potential role in biofilm formation associated with metal homeostasis, which may be critical for ...
Su‐Yeon Choi, Eunsuk Kim, Hyunjin Yoon, Ha‐Neul Kim, Ji‐Hun Kim, Seung‐Hyeon Seok, Min‐Duk Seo   +6 more
wiley   +1 more source

hipBA toxin-antitoxin systems mediate persistence in Caulobacter crescentus

Scientific Reports, 2020
Antibiotic persistence is a transient phenotypic state during which a bacterium can withstand otherwise lethal antibiotic exposure or environmental stresses. In Escherichia coli, persistence is promoted by the HipBA toxin-antitoxin system. The HipA toxin
Charles Y. Huang, Carlos Gonzalez-Lopez, C. Henry, I. Mijakovic, K. Ryan   +4 more
semanticscholar   +1 more source

Identification of type II toxin-antitoxin modules in Burkholderia pseudomallei [PDF]

, 2014
© 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reservedThis is an open access article that is freely available in ORE or from the publisher's web site. Please cite the published version.Type II
Butt, Aaron Trevor, Harmer, Nicholas, Müller, C, Titball, Richard W.   +3 more
core   +1 more source

Evaluating the Potential for Cross-Interactions of Antitoxins in Type II TA Systems

Toxins, 2020
The diversity of Type-II toxin–antitoxin (TA) systems in bacterial genomes requires tightly controlled interaction specificity to ensure protection of the cell, and potentially to limit cross-talk between toxin–antitoxin pairs of the same family of TA ...
Chih-Han Tu, Michelle Holt, Shengfeng Ruan, Christina Bourne   +3 more
doaj   +1 more source

Biomolecular Interaction Prediction in the Pre‐ and Post‐AlphaFold Era: The 8th CAPRI Evaluation

Proteins: Structure, Function, and Bioinformatics, EarlyView.
ABSTRACT We report on the 8th CAPRI Evaluation period, capturing the assessment of CAPRI Rounds 47 to 55 (excluding the CASP and COVID‐related Rounds), which have witnessed the transition to AI‐driven prediction tools such as AlphaFold and related alternatives. The prediction Rounds in this evaluation are characterized by a high level of difficulty due
Marc F. Lensink, Nessim Raouraoua, Guillaume Brysbaert, Sameer Velankar, Shoshana J. Wodak, Alexandre M. J. J. Bonvin   +5 more
wiley   +1 more source

The Toxin-Antitoxin MazEF Drives Staphylococcus aureus Biofilm Formation, Antibiotic Tolerance, and Chronic Infection

mBio, 2019
Surgical infections are one of the most common types of infections encountered in a hospital. Staphylococcus aureus is the most common pathogen associated with this infection.
Dongzhu Ma, Jonathan B Mandell, N. Donegan, A. Cheung, Wanyan Ma, S. Rothenberger, R. Shanks, A. Richardson, K. Urish   +8 more
semanticscholar   +1 more source

Bacterial retrons encode tripartite toxin/antitoxin systems

bioRxiv, 2020
Retrons are genetic retroelements, commonly found in bacterial genomes and recently repurposed as genome editing tools. Their encoded reverse transcriptase (RT) produces a multi-copy single-stranded DNA (msDNA). Despite our understanding of their complex
Jacob Bobonis, A. Mateus, Birgit Pfalz, Sarela García-Santamarina, Marco Galardini, C. Kobayashi, F. Stein, M. Savitski, J. Elfenbein, H. Andrews-Polymenis, Athanasios Typas   +10 more
semanticscholar   +1 more source