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Original Paper

The simulation approach to bacterial outer membrane proteins (Review)

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Pages 151-161 | Received 22 Jan 2004, Published online: 09 Jul 2009

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Read on this site (3)

Nabajyoti Goswami, Md. Iftikar Hussain & Probodh Borah. (2018) Molecular dynamics approach to probe the antigenicity of PagN – an outer membrane protein of Salmonella Typhi. Journal of Biomolecular Structure and Dynamics 36:8, pages 2131-2146.
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Syma Khalid & Mark S. P. Sansom. (2006) Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis. Molecular Membrane Biology 23:6, pages 499-508.
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Articles from other publishers (49)

Xianjing He, Jiao Liu, Kai Jiang, Shuai Lian, Yu Shi, Shan Fu, Pengyu Zhao, Jiawei Xiao, Dongbo Sun & Donghua Guo. (2023) The outer membrane protein of Fusobacterium necrophorum, 43K OMP, stimulates inflammatory cytokine production through nuclear factor kappa B activation. Anaerobe 82, pages 102768.
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Justin M. Hansen, Maarten F. de Jong, Qi Wu, Li-Shu Zhang, David B. Heisler, Laura T. Alto & Neal M. Alto. (2021) Pathogenic ubiquitination of GSDMB inhibits NK cell bactericidal functions. Cell 184:12, pages 3178-3191.e18.
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Biswajit Maiti, Saurabh Dubey, Hetron Mweemba Munang'andu, Iddya Karunasagar, Indrani Karunasagar & Øystein Evensen. (2020) Application of Outer Membrane Protein-Based Vaccines Against Major Bacterial Fish Pathogens in India. Frontiers in Immunology 11.
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Huilin Ma, Aliza Khan & Shikha Nangia. (2017) Dynamics of OmpF Trimer Formation in the Bacterial Outer Membrane of Escherichia coli . Langmuir 34:19, pages 5623-5634.
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Rajesh Vij, Zhonghua Lin, Nancy Chiang, Jean-Michel Vernes, Kelly M. Storek, Summer Park, Joyce Chan, Y. Gloria Meng, Laetitia Comps-Agrar, Peng Luan, Sophia Lee, Kellen Schneider, Jack BeversIIIIII, Inna Zilberleyb, Christine Tam, Christopher M. Koth, Min Xu, Avinash Gill, Marcy R. Auerbach, Peter A. Smith, Steven T. Rutherford, Gerald Nakamura, Dhaya Seshasayee, Jian Payandeh & James T. Koerber. (2018) A targeted boost-and-sort immunization strategy using Escherichia coli BamA identifies rare growth inhibitory antibodies. Scientific Reports 8:1.
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D. Jefferies & S. Khalid. 2017. Modeling of Microscale Transport in Biological Processes. Modeling of Microscale Transport in Biological Processes 1 18 .
Li L. Duan, Guo Q. Feng & Qing G. Zhang. (2016) Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy. Scientific Reports 6:1.
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Anna Pavlova, Hyea Hwang, Karl Lundquist, Curtis Balusek & James C. Gumbart. (2016) Living on the edge: Simulations of bacterial outer-membrane proteins. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858:7, pages 1753-1759.
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Karunakar R. Pothula, Carlos J.F. Solano & Ulrich Kleinekath?fer. (2016) Simulations of outer membrane channels and their permeability. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858:7, pages 1760-1771.
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Jamie Parkin, Matthieu Chavent & Syma Khalid. (2015) Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes. Biophysical Journal 109:3, pages 461-468.
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Philip C. Biggin & Peter J. Bond. 2015. Molecular Modeling of Proteins. Molecular Modeling of Proteins 91 108 .
G. Mayeli Estrada‐Villegas & Emilio Bucio. 2014. Advanced Sensor and Detection Materials. Advanced Sensor and Detection Materials 61 86 .
Angel Contreras‐García & Emilio Bucio. 2013. Nanomaterials in Drug Delivery, Imaging, and Tissue Engineering. Nanomaterials in Drug Delivery, Imaging, and Tissue Engineering 59 97 .
Teresa Paramo, Diana Garzón, Daniel A. Holdbrook, Syma Khalid & Peter J. Bond. 2013. Lipid-Protein Interactions. Lipid-Protein Interactions 435 455 .
Syma Khalid & Peter J. Bond. 2013. Biomolecular Simulations. Biomolecular Simulations 635 657 .
Anton B Guliaev. (2012) Protein dynamics via computational microscope . World Journal of Methodology 2:6, pages 42.
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Saija Kiljunen, Neeta Datta, Svetlana V. Dentovskaya, Andrey P. Anisimov, Yuriy A. Knirel, José A. Bengoechea, Otto Holst & Mikael Skurnik. (2011) Identification of the Lipopolysaccharide Core of Yersinia pestis and Yersinia pseudotuberculosis as the Receptor for Bacteriophage φA1122. Journal of Bacteriology 193:18, pages 4963-4972.
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Ángel Piñeiro, Peter J. Bond & Syma Khalid. (2011) Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study. Biochimica et Biophysica Acta (BBA) - Biomembranes 1808:6, pages 1746-1752.
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Mehdi Damaghi, K. Tanuj Sapra, Stefan Köster, Özkan Yildiz, Werner Kühlbrandt & Daniel J. Muller. (2010) Dual energy landscape: The functional state of the β‐barrel outer membrane protein G molds its unfolding energy landscape. PROTEOMICS 10:23, pages 4151-4162.
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Syma Khalid & Marc Baaden. 2010. Molecular Simulations and Biomembranes. Molecular Simulations and Biomembranes 225 247 .
D. Peter Tieleman. 2010. Molecular Simulations and Biomembranes. Molecular Simulations and Biomembranes 1 25 .
Thuy Hien T. Nguyen, Niny Z. Rao, William M. Schroeder & Preston B. Moore. (2010) Coarse-grained molecular dynamics of tetrameric transmembrane peptide bundles within a lipid bilayer. Chemistry and Physics of Lipids 163:6, pages 530-537.
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Istv?n Bir?Soroosh Pezeshki, Helge Weingart, Mathias Winterhalter & Ulrich Kleinekath?fer. (2010) Comparing the Temperature-Dependent Conductance of the Two Structurally Similar E. coli Porins OmpC and OmpF. Biophysical Journal 98:9, pages 1830-1839.
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Kristian Dimitrievski & Bengt Kasemo. (2010) Simulations of lipid transfer between a supported lipid bilayer and adsorbing vesicles. Colloids and Surfaces B: Biointerfaces 75:2, pages 454-465.
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Szymon JarosÅawski, Katia Duquesne, James N. Sturgis & Simon Scheuring. (2009) High-resolution architecture of the outer membrane of the Gram-negative bacteria Roseobacter denitrificans . Molecular Microbiology 74:5, pages 1211-1222.
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Olivier Delalande, Nicolas Férey, Gilles Grasseau & Marc Baaden. (2009) Complex molecular assemblies at hand via interactive simulations. Journal of Computational Chemistry 30:15, pages 2375-2387.
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James Gumbart, Michael C. Wiener & Emad Tajkhorshid. (2009) Coupling of Calcium and Substrate Binding through Loop Alignment in the Outer-Membrane Transporter BtuB. Journal of Molecular Biology 393:5, pages 1129-1142.
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Soroosh Pezeshki, Catalin Chimerel, Andrey N. Bessonov, Mathias Winterhalter & Ulrich Kleinekathöfer. (2009) Understanding Ion Conductance on a Molecular Level: An All-Atom Modeling of the Bacterial Porin OmpF. Biophysical Journal 97:7, pages 1898-1906.
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David C. Young. 2009. Computational Drug Design. Computational Drug Design 253 257 .
Peter J. Bond, Daniel L. Parton, James F. Clark & Mark S.P. Sansom. (2008) Coarse-Grained Simulations of the Membrane-Active Antimicrobial Peptide Maculatin 1.1. Biophysical Journal 95:8, pages 3802-3815.
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Philip C. Biggin & Peter J. Bond. 2008. Molecular Modeling of Proteins. Molecular Modeling of Proteins 147 160 .
Valery G. Veresov & Alexander I. Davidovskii. (2007) Monte Carlo simulations of tBid association with the mitochondrial outer membrane. European Biophysics Journal 37:1, pages 19-33.
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Timothy Carpenter, Syma Khalid & Mark S.P. Sansom. (2007) A multidomain outer membrane protein from Pasteurella multocida: Modelling and simulation studies of PmOmpA. Biochimica et Biophysica Acta (BBA) - Biomembranes 1768:11, pages 2831-2840.
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Syma Khalid, John Holyoake & Mark S. P. Sansom. 2007. Biophysical Analysis of Membrane Proteins. Biophysical Analysis of Membrane Proteins 159 185 .
Peter J. Bond, Jeremy P. Derrick & Mark S.P. Sansom. (2007) Membrane Simulations of OpcA: Gating in the Loops?. Biophysical Journal 92:2, pages L23-L25.
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Concei??o A.S.A. Minetti & David P. Remeta. (2006) Energetics of membrane protein folding and stability. Archives of Biochemistry and Biophysics 453:1, pages 32-53.
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Peter J. Bond, José D. Faraldo-Gómez, Sundeep S. Deol & Mark S. P. Sansom. (2006) Membrane protein dynamics and detergent interactions within a crystal: A simulation study of OmpA. Proceedings of the National Academy of Sciences 103:25, pages 9518-9523.
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Stewart A. Adcock & J. Andrew McCammon. (2006) Molecular Dynamics:  Survey of Methods for Simulating the Activity of Proteins. Chemical Reviews 106:5, pages 1589-1615.
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Marilisa Neri, Claudio Anselmi, Vincenzo Carnevale, Attilio V Vargiu & Paolo Carloni. (2006) Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential . Journal of Physics: Condensed Matter 18:14, pages S347-S355.
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Syma Khalid, Peter J. Bond, Sundeep S. Deol & Mark S. P. Sansom. (2006) Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa. Proteins: Structure, Function, and Bioinformatics 63:1, pages 6-15.
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Sundeep S. Deol, Carmen Domene, Peter J. Bond & Mark S.P. Sansom. (2006) Anionic Phospholipid Interactions with the Potassium Channel KcsA: Simulation Studies. Biophysical Journal 90:3, pages 822-830.
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Peter J. Bond, Jonathan Cuthbertson, Sundeep S. Deol, Lucy R. Forrest, Jennifer Johnston, George Patargias & Mark S.P. Sansom. 2006. New Algorithms for Macromolecular Simulation. New Algorithms for Macromolecular Simulation 3 20 .
Virak VisudtipholeMatthew B. ThomasDavid A. ChaltonJeremy H. Lakey. (2005) Refolding of Escherichia coli outer membrane protein F in detergent creates LPS-free trimers and asymmetric dimers. Biochemical Journal 392:2, pages 375-381.
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M.S.P. SansomP.J. BondS.S. DeolA. GrottesiS. HaiderZ.A. Sands. (2005) Molecular simulations and lipid–protein interactions: potassium channels and other membrane proteins. Biochemical Society Transactions 33:5, pages 916-920.
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P.J. BondJ. CuthbertsonM.S.P. Sansom. (2005) Simulation studies of the interactions between membrane proteins and detergents. Biochemical Society Transactions 33:5, pages 910-912.
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Christine Peter & Gerhard Hummer. (2005) Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations. Biophysical Journal 89:4, pages 2222-2234.
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Emad Tajkhorshid, Jordi Cohen, Aleksij Aksimentiev, Marcos Sotomayor & Klaus Schulten. 2005. Bacterial Ion Channels and Their Eukaryotic Homologs. Bacterial Ion Channels and Their Eukaryotic Homologs 153 190 .
Rainer A. Böckmann & Amedeo Caflisch. (2005) Spontaneous Formation of Detergent Micelles around the Outer Membrane Protein OmpX. Biophysical Journal 88:5, pages 3191-3204.
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Marc Baaden & Mark S.P. Sansom. (2004) OmpT: Molecular Dynamics Simulations of an Outer Membrane Enzyme. Biophysical Journal 87:5, pages 2942-2953.
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