Cargando…

Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target

Undecaprenyl pyrophosphate synthase is a cis-prenyltransferase enzyme, which is required for cell wall biosynthesis in bacteria. Undecaprenyl pyrophosphate synthase is an attractive target for antimicrobial therapy. We performed long molecular dynamics simulations and docking studies on undecaprenyl...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sinko, William, de Oliveira, César, Williams, Sarah, Van Wynsberghe, Adam, Durrant, Jacob D, Cao, Rong, Oldfield, Eric, McCammon, J Andrew
Formato:	Texto
Lenguaje:	English
Publicado:	Blackwell Publishing Ltd 2011
Materias:	Research Articles
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095679/ https://www.ncbi.nlm.nih.gov/pubmed/21294851 http://dx.doi.org/10.1111/j.1747-0285.2011.01101.x

Ejemplares similares

Undecaprenyl Diphosphate Synthase Inhibitors: Antibacterial Drug Leads
por: Sinko, William, et al.
Publicado: (2014)

Species Differences in Alternative Substrate Utilization by the Antibacterial Target Undecaprenyl Pyrophosphate Synthase
por: Dodbele, Samantha, et al.
Publicado: (2014)

Biophysical Investigation of the Mode of Inhibition of Tetramic Acids, the Allosteric Inhibitors of Undecaprenyl Pyrophosphate Synthase
por: Lee, Lac V., et al.
Publicado: (2010)

Anthranilic Acid Inhibitors of Undecaprenyl Pyrophosphate Synthase (UppS), an Essential Enzyme for Bacterial Cell Wall Biosynthesis
por: Jukič, Marko, et al.
Publicado: (2019)

Structure-Based Inhibitors Exhibit Differential Activities against Helicobacter pylori and Escherichia coli Undecaprenyl Pyrophosphate Synthases
por: Kuo, Chih-Jung, et al.
Publicado: (2008)

Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis
por: El Ghachi, Meriem, et al.
Publicado: (2018)

Membrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase
por: Manat, Guillaume, et al.
Publicado: (2015)

Towards discovery of inhibitors of the undecaprenyl-pyrophosphate phosphatase BacA by virtual high-throughput screening
por: Jukič, Marko, et al.
Publicado: (2022)

HupA, the main undecaprenyl pyrophosphate and phosphatidylglycerol phosphate phosphatase in Helicobacter pylori is essential for colonization of the stomach
por: Gasiorowski, Elise, et al.
Publicado: (2019)

NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function
por: Durrant, Jacob D., et al.
Publicado: (2011)

NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein−Ligand Complexes
por: Durrant, Jacob D., et al.
Publicado: (2010)

Pyrone-Based Inhibitors of Metalloproteinase Types 2 and 3 May Work as Conformation-Selective Inhibitors
por: Durrant, Jacob D, et al.
Publicado: (2011)

Toward Understanding the Conformational Dynamics of RNA Ligation
por: Swift, Robert V., et al.
Publicado: (2009)

LigMerge: A Fast Algorithm to Generate Models of Novel Potential Ligands from Sets of Known Binders
por: Lindert, Steffen, et al.
Publicado: (2012)

w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
por: Arrar, Mehrnoosh, et al.
Publicado: (2012)

Farnesyl Diphosphate Synthase Inhibitors from In Silico Screening
por: Lindert, Steffen, et al.
Publicado: (2013)

Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations
por: Kaus, Joseph W., et al.
Publicado: (2015)

Undecaprenyl phosphate translocases confer conditional microbial fitness
por: Sit, Brandon, et al.
Publicado: (2022)

AutoClickChem: Click Chemistry in Silico
por: Durrant, Jacob D., et al.
Publicado: (2012)

Molecular dynamics simulations and drug discovery
por: Durrant, Jacob D, et al.
Publicado: (2011)

Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors
por: Durrant, Jacob D, et al.
Publicado: (2011)

Periplasmic phosphorylation of lipid A is linked to the synthesis of undecaprenyl phosphate
por: Touzé, Thierry, et al.
Publicado: (2008)

Structures of Fission Yeast Inositol Pyrophosphate Kinase Asp1 in Ligand-Free, Substrate-Bound, and Product-Bound States
por: Benjamin, Bradley, et al.
Publicado: (2022)

Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design
por: Durrant, Jacob D, et al.
Publicado: (2011)

Population Based Reweighting of Scaled Molecular Dynamics
por: Sinko, William, et al.
Publicado: (2013)

Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme’s active site closure
por: Park, Jaeok, et al.
Publicado: (2012)

Functional Characterization of the Xanthophyllomyces dendrorhous Farnesyl Pyrophosphate Synthase and Geranylgeranyl Pyrophosphate Synthase Encoding Genes That Are Involved in the Synthesis of Isoprenoid Precursors
por: Alcaíno, Jennifer, et al.
Publicado: (2014)

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics
por: Grant, Barry J., et al.
Publicado: (2009)

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations
por: Sinko, William, et al.
Publicado: (2011)

Water in Cavity−Ligand Recognition
por: Baron, Riccardo, et al.
Publicado: (2010)

Molecular mechanism for conformational activation of SARS-CoV-2 RNA polymerase by nucleoside triphosphate
por: Ma, Wen, et al.
Publicado: (2022)

Discovery of Small Molecule Inhibitors of the PH Domain Leucine-Rich Repeat Protein Phosphatase (PHLPP) by Chemical and Virtual Screening
por: Sierecki, Emma, et al.
Publicado: (2010)

Computational Insights into Binding of Bisphosphates to Farnesyl Pyrophosphate Synthase
por: Ohno, K, et al.
Publicado: (2011)

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations
por: Wereszczynski, Jeff, et al.
Publicado: (2010)

Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach
por: Ishizuka, Ryosuke, et al.
Publicado: (2010)

Computational Identification of Uncharacterized Cruzain Binding Sites
por: Durrant, Jacob D., et al.
Publicado: (2010)

Functional Analysis of H(+)-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum
por: Kuil, Teun, et al.
Publicado: (2022)

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration
por: Fajer, Mikolai, et al.
Publicado: (2008)

Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening
por: Durrant, Jacob D., et al.
Publicado: (2013)

Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein
por: Bucher, Denis, et al.
Publicado: (2011)

Cannot write session to /tmp/vufind_sessions/sess_0g8v0pglgqcc1rok1cbpl41g70