Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association

Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association

Potential of mean force (PMF) calculations are used to characterize the free energy landscape of protein-lipid and protein-protein association within membranes. Coarse-grained simulations allow binding free energies to be determined with reasonable statistical error. This accuracy relies on defining...

Fuld beskrivelse

Bibliografiske detaljer
Main Authors:	Domański, J, Hedger, G, Best, R, Stansfield, P, Sansom, M
Format:	Journal article
Udgivet:	American Chemical Society 2016

Lignende værker

Free energy landscape of lipid interactions with regulatory binding sites on the transmembrane domain of the EGF receptor
af: Sansom, M, et al.
Udgivet: (2016)

The free energy landscape of dimerization of a membrane protein, NanC.
af: Thomas A Dunton, et al.
Udgivet: (2014-01-01)

Lipid loving ANTs: Molecular simulations of cardiolipin interactions and the organization of the adenine nucleotide translocase in model mitochondrial membranes
af: Sansom, M, et al.
Udgivet: (2016)

Balancing force field protein-lipid interactions to capture transmembrane helix-helix association
af: Domański, J, et al.
Udgivet: (2018)

Association of peripheral membrane proteins with membranes: free energy of binding of GRP1 PH domain with phosphatidylinositol phosphate-containing model bilayers
af: Naughton, F, et al.
Udgivet: (2016)

The free energy landscape of dimerization of a membrane protein‚ NanC
af: M., D, et al.
Udgivet: (2014)

Insights into membrane protein-lipid interactions from free energy calculations
af: Corey, R, et al.
Udgivet: (2019)

Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes
af: Domański, J, et al.
Udgivet: (2020)

Conformational Dynamics Govern the Free-Energy Landscape of a Membrane-Interacting Protein
af: Erik Frotscher, et al.
Udgivet: (2018-09-01)

Molecular simulations of glycolipids: Towards mammalian cell membrane models
af: Shorthouse, D, et al.
Udgivet: (2015)

Interactions of the EphA2 kinase domain with PIPs in membranes: implications for receptor function
af: Chavent, M, et al.
Udgivet: (2018)

Atomistic mechanism of transmembrane helix association.
af: Jan Domański, et al.
Udgivet: (2020-06-01)

Lipid interaction sites on channels, transporters and receptors: recent insights from molecular dynamics simulations
af: Sansom, M, et al.
Udgivet: (2016)

Energetics of protein interactions in the membrane via computer simulations
af: Domanski, J
Udgivet: (2017)

Outer membrane protein folding from an energy landscape perspective
af: Bob Schiffrin, et al.
Udgivet: (2017-12-01)

Energy Landscape for the Membrane Fusion Pathway in Influenza A Hemagglutinin From Discrete Path Sampling
af: David F. Burke, et al.
Udgivet: (2020-09-01)

A generalized born implicit-membrane representation compared to experimental insertion free energies.
af: Ulmschneider, M, et al.
Udgivet: (2007)

Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations
af: Domański, J, et al.
Udgivet: (2010)

Lipidbook: a public repository for force-field parameters used in membrane simulations.
af: Domański, J, et al.
Udgivet: (2010)

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.
af: Faraldo-Gómez, J, et al.
Udgivet: (2004)

Membrane protein simulations: ion channels and bacterial outer membrane proteins.
af: Domene, C, et al.
Udgivet: (2003)

Final configuration files for umbrella sampling in "Characterizing the free-energy landscapes of DNA origamis"
af: Doye, J
Udgivet: (2021)

Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.
af: Kei Moritsugu, et al.
Udgivet: (2014-10-01)

The Landscape of <i>Pseudomonas aeruginosa</i> Membrane-Associated Proteins
af: Sara Motta, et al.
Udgivet: (2020-11-01)

Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states.
af: Faraldo-Gómez, J, et al.
Udgivet: (2003)

Membrane proteins: a tale of barrels and corks
af: Sansom, M
Udgivet: (1999)

Epididymitis: revelations at the convergence of clinical and basic sciences
af: Vera Michel, et al.
Udgivet: (2015-01-01)

Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class
af: Parton, D, et al.
Udgivet: (2011)

Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class.
af: Parton, D, et al.
Udgivet: (2011)

A cell-free assay to determine the stoichiometry of plasma membrane proteins
af: Cesar Trigo, et al.
Udgivet: (2013-04-01)

Membrane proteins: molecular dynamics simulations.
af: Lindahl, E, et al.
Udgivet: (2008)

Molecular simulation approaches to membrane proteins.
af: Stansfeld, P, et al.
Udgivet: (2011)

Characterisation of lipid-protein interactions through computational modelling
af: Hedger, G
Udgivet: (2017)

An Energy Landscape Treatment of Decoy Selection in Template-Free Protein Structure Prediction
af: Nasrin Akhter, et al.
Udgivet: (2018-06-01)

The free energy landscape of retroviral integration
af: Willem Vanderlinden, et al.
Udgivet: (2019-10-01)

Memprotmd: adding the grease to membrane protein structures
af: Stansfeld, P, et al.
Udgivet: (2012)

The simulation approach to bacterial outer membrane proteins.
af: Bond, P, et al.
Udgivet: (2004)

Insertion and assembly of membrane proteins via simulation.
af: Bond, P, et al.
Udgivet: (2006)

Membrane proteins: Aquaporins--channels without ions.
af: Sansom, MS, et al.
Udgivet: (2001)

Setting up and optimization of membrane protein simulations.
af: Faraldo-Gómez, J, et al.
Udgivet: (2002)