4.6 Article

Identification of AHL Synthase in Desulfovibrio vulgaris Hildenborough Using an In-Silico Methodology

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Environmental Sciences

Degradation of n-hexanoyl homoserine lactone with quorum quenching bacteria immobilised magnetic nanocomposite beads

Jaskiran Kaur et al.

Summary: This study investigated the potential of immobilized quorum quenching bacteria on magnetic nanocomposite beads for degrading the signal molecule C6-HSL. The results showed that the QQ bacteria immobilized on the IMN beads successfully degraded C6-HSL, offering possibilities for controlling biofilm formation on membrane surfaces during wastewater treatment processes.

ENVIRONMENTAL TECHNOLOGY (2022)

Article Biochemistry & Molecular Biology

Enhancement of Methane Catalysis Rates in Methylosinus trichosporium OB3b

Dipayan Samanta et al.

Summary: By modeling and docking experiments, the active sites and the impact of mutants on methane oxidation rates in particulate methane monooxygenase (pMMO) were determined.

BIOMOLECULES (2022)

Article Biochemical Research Methods

The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects

Alessandro Pedretti et al.

Summary: This article provides an overview of the latest release of the VEGA suite of programs, which has been developed and freely released for the past 20 years, gaining about 22,500 registered users. In addition to drug design studies, VEGA package also includes cheminformatics and modeling features for various computational chemistry contexts. The flexible architecture of VEGA program allows for expansion and customization, with a focus on the highly optimized HyperDrive library.

BIOINFORMATICS (2021)

Article Limnology

Sampling, separation, and quantification of N-acyl homoserine lactones from marine intertidal sediments

Frederike Stock et al.

Summary: N-acyl homoserine lactones (AHLs) are signaling molecules produced by Gram-negative bacteria for cell-cell communication, influencing marine bacterial processes and interactions with microalgae. Measuring AHL concentrations is challenging but important for ecological research and biofilm control. A novel sampling and analysis method has been developed to detect and quantify AHLs in marine sediment samples efficiently.

LIMNOLOGY AND OCEANOGRAPHY-METHODS (2021)

Article Limnology

Simultaneous recording of filtration and respiration in marine organisms in response to short-term environmental variability

Jahangir Vajedsamiei et al.

Summary: This paper introduces an empirical method using FOFS to enhance understanding of benthic filter feeders' performance under changing environmental conditions. Through online data recording and Python script processing, researchers can adjust experimental procedures in different environments to provide a detailed description of stress-response relationships and detect species' tolerance limits.

LIMNOLOGY AND OCEANOGRAPHY-METHODS (2021)

Article Biology

Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells

Seongjin Park et al.

Summary: RNA-binding protein Hfq plays a crucial role in post-transcriptional gene regulation in bacteria, with widespread mRNA-binding activity. Short RNAs can either form a ternary complex with mRNA on Hfq or displace mRNA from Hfq in a binding face-dependent manner. Hfq binding to certain mRNAs through its distal face can recruit RNase E to promote mRNA turnover.
Review Microbiology

Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion

Abhilash Kumar Tripathi et al.

Summary: Sulfate-reducing bacteria (SRB) are bacteria that can respire under anaerobic conditions using sulfate as a terminal electron acceptor, potentially causing issues such as pipeline corrosion and fouling. Understanding the molecular mechanisms of biofilm formation and corrosion by SRB is crucial for effectively addressing the challenges they pose.

FRONTIERS IN MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

Structure-Guided Biochemical Analysis of Quorum Signal Synthase Specificities

Shi-Hui Dong et al.

ACS CHEMICAL BIOLOGY (2020)

Article Chemistry, Physical

Scalable molecular dynamics on CPU and GPU architectures with NAMD

James C. Phillips et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Materials Science, Multidisciplinary

Accelerated low water corrosion: the microbial sulfur cycle in microcosm

Martin Smith et al.

NPJ MATERIALS DEGRADATION (2019)

Article Biochemistry & Molecular Biology

MolProbity: More and better reference data for improved all-atom structure validation

Christopher J. Williams et al.

PROTEIN SCIENCE (2018)

Article Multidisciplinary Sciences

Molecular basis for the substrate specificity of quorum signal synthases

Shi-Hui Dong et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Microbiology

Activity, Abundance, and Localization of Quorum Sensing Receptors in Vibrio harveyi

Nicola Lorenz et al.

FRONTIERS IN MICROBIOLOGY (2017)

Article Neurosciences

Peptides as Quorum Sensing Molecules: Measurement Techniques and Obtained Levels In vitro and In vivo

Frederick Verbeke et al.

FRONTIERS IN NEUROSCIENCE (2017)

Article Biochemistry & Molecular Biology

Effective protein model structure refinement by loop modeling and overall relaxation

Gyu Rie Lee et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2016)

Review Microbiology

Quorum sensing signal-response systems in Gram-negative bacteria

Kai Papenfort et al.

NATURE REVIEWS MICROBIOLOGY (2016)

Review Biotechnology & Applied Microbiology

Microbial extracellular electron transfer and its relevance to iron corrosion

Souichiro Kato

MICROBIAL BIOTECHNOLOGY (2016)

Article Infectious Diseases

Quorum Sensing and the Use of Quorum Quenchers as Natural Biocides to Inhibit Sulfate-Reducing Bacteria

Giantommaso Scarascia et al.

ANTIBIOTICS-BASEL (2016)

Article Biochemical Research Methods

DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment

Erik S. Wright

BMC BIOINFORMATICS (2015)

Article Biotechnology & Applied Microbiology

Role of LuxIR Homologue AnoIR in Acinetobacter nosocomialis and the Effect of Virstatin on the Expression of anoR Gene

Man Hwan Oh et al.

JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY (2015)

Review Microbiology

Biofilm dispersion and quorum sensing

Cristina Solano et al.

CURRENT OPINION IN MICROBIOLOGY (2014)

Article Biochemistry & Molecular Biology

Pfam: the protein families database

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Evolution of Acyl-Substrate Recognition by a Family of Acyl-Homoserine Lactone Synthases

Quin H. Christensen et al.

PLOS ONE (2014)

Article Chemistry, Multidisciplinary

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

David Sehnal et al.

JOURNAL OF CHEMINFORMATICS (2013)

Article Medicine, Research & Experimental

Bacterial Quorum Sensing: Its Role in Virulence and Possibilities for Its Control

Steven T. Rutherford et al.

COLD SPRING HARBOR PERSPECTIVES IN MEDICINE (2012)

Review Chemistry, Multidisciplinary

Structural Basis of Acyl-homoserine Lactone-Dependent Signaling

Mair E. A. Churchill et al.

CHEMICAL REVIEWS (2011)

Article Multidisciplinary Sciences

Small-molecule inhibitor binding to an N-acyl-homoserine lactone synthase

Jiwoung Chung et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Isovaleryl-homoserine lactone, an unusual branched-chain quorum-sensing signal from the soybean symbiont Bradyrhizobium japonicum

Andrea Lindemann et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Chemistry, Multidisciplinary

Open Babel: An open chemical toolbox

Noel M. O'Boyle et al.

JOURNAL OF CHEMINFORMATICS (2011)

Review Biochemistry & Molecular Biology

Quorum sensing in natural environments: emerging views from microbial mats

Alan W. Decho et al.

TRENDS IN MICROBIOLOGY (2010)

Review Chemistry, Multidisciplinary

CHARMM: The Biomolecular Simulation Program

B. R. Brooks et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Biotechnology & Applied Microbiology

Rapid screening of quorum-sensing signal N-acyl homoserine lactones by an in vitro cell-free assay

Tomohiro Kawaguchi et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2008)

Article Biotechnology & Applied Microbiology

The RAST server: Rapid annotations using subsystems technology

Ramy K. Aziz et al.

BMC GENOMICS (2008)

Article Biochemistry & Molecular Biology

Quorum-sensing system affects gall development incited by Pantoea agglomerans pv. gypsophilae

Laura Chalupowicz et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2008)

Article Multidisciplinary Sciences

A new class of homoserine lactone quorum-sensing signals

Amy L. Schaefer et al.

NATURE (2008)

Review Microbiology

The ecology and biotechnology of sulphate-reducing bacteria

Gerard Muyzer et al.

NATURE REVIEWS MICROBIOLOGY (2008)

Article Biochemistry & Molecular Biology

NCBIBLAST: a better web interface

Mark Johnson et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Microbiology

Control of quorum sensing by a Burkholderia pseudomallei multidrug efflux pump

Ying Ying Chan et al.

JOURNAL OF BACTERIOLOGY (2007)

Article Biochemistry & Molecular Biology

InterProScan: protein domains identifier

E Quevillon et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

Structure of the Pseudomonas aeruginosa acyl-homoserinelactone synthase LasI

TA Gould et al.

MOLECULAR MICROBIOLOGY (2004)

Article Biochemistry & Molecular Biology

Refinement of homology-based protein structures by molecular dynamics simulation techniques

H Fan et al.

PROTEIN SCIENCE (2004)

Review Microbiology

Quorum-sensing in gram-negative bacteria

NA Whitehead et al.

FEMS MICROBIOLOGY REVIEWS (2001)

Article Biotechnology & Applied Microbiology

Synthesis of multiple N-acylhomoserine lactones is wide-spread among the members of the Burkholderia cepacia complex

A Gotschlich et al.

SYSTEMATIC AND APPLIED MICROBIOLOGY (2001)

Article Multidisciplinary Sciences

Acyl-homoserine lactone quorum sensing in Gram-negative bacteria: A signaling mechanism involved in associations with higher organisms

MR Parsek et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)