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...

Descripció completa

Dades bibliogràfiques
Autors principals:	Domański, J, Hedger, G, Best, R, Stansfield, P, Sansom, M
Format:	Journal article
Publicat:	American Chemical Society 2016

Ítems similars

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Membrane proteins: a tale of barrels and corks
per: Sansom, M
Publicat: (1999)

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

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

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

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

Membrane proteins: molecular dynamics simulations.
per: Lindahl, E, et al.
Publicat: (2008)

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

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

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

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

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

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

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

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

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