Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

In the current report, we provide a quantitative analysis of the convergence of the sampling of conformational space accomplished in molecular dynamics simulations of membrane proteins of duration in the order of 10 nanoseconds. A set of proteins of diverse size and topology is considered, ranging f...

Fuld beskrivelse

Bibliografiske detaljer
Main Authors:	Faraldo-Gómez, J, Forrest, L, Baaden, M, Bond, P, Domene, C, Patargias, G, Cuthbertson, J, Sansom, MS
Format:	Journal article
Sprog:	English
Udgivet:	2004

Lignende værker

Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment.
af: Patargias, G, et al.
Udgivet: (2005)

Membrane protein structure quality in molecular dynamics simulation.
af: Law, R, et al.
Udgivet: (2005)

Simulations of bacterial outer membrane proteins: Towards an e-outer membrane
af: Baaden, M, et al.
Udgivet: (2003)

Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.
af: Durrieu, M, et al.
Udgivet: (2009)

Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.
af: Bond, P, et al.
Udgivet: (2006)

Simulation studies of the interactions between membrane proteins and detergents.
af: Bond, P, et al.
Udgivet: (2005)

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

OmpT: molecular dynamics simulations of an outer membrane enzyme.
af: Baaden, M, et al.
Udgivet: (2004)

MD simulations of spontaneous membrane protein/detergent micelle formation.
af: Bond, P, et al.
Udgivet: (2004)

Water in ion channels and pores--simulation studies.
af: Sansom, MS, et al.
Udgivet: (2002)

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

OmpA: a pore or not a pore? Simulation and modeling studies.
af: Bond, P, et al.
Udgivet: (2002)

Lipid-protein interactions of integral membrane proteins: a comparative simulation study.
af: Deol, S, et al.
Udgivet: (2004)

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.
af: Cox, K, et al.
Udgivet: (2008)

Lipid/protein interactions and the membrane/water interfacial region.
af: Domene, C, et al.
Udgivet: (2003)

OmpT: Molecular dynamics simulations of an outer membrane enzyme.
af: Baaden, M, et al.
Udgivet: (2005)

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)

Conformational dynamics of OmpA: MD simulations of a bacterial outer membrane protein
af: Bond, P, et al.
Udgivet: (2004)

Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function.
af: Grottesi, A, et al.
Udgivet: (2005)

Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer.
af: Cuthbertson, J, et al.
Udgivet: (2006)

A molecular dynamics investigation of mono and dimeric states of the outer membrane enzyme OMPLA.
af: Baaden, M, et al.
Udgivet: (2003)

Molecular dynamics simulations of outer membrane phospholipase A
af: Baaden, M, et al.
Udgivet: (2004)

Membrane simulations: bigger and better?
af: Forrest, L, et al.
Udgivet: (2000)

Coarse-grained simulation: a high-throughput computational approach to membrane proteins.
af: Sansom, MS, et al.
Udgivet: (2008)

MD simulations of Mistic: conformational stability in detergent micelles and water.
af: Psachoulia, E, et al.
Udgivet: (2006)

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)

Barrels and corks in a computer - Modelling bacterial iron transport systems
af: Baaden, M, et al.
Udgivet: (2002)

Membrane simulations of OpcA: gating in the loops?
af: Bond, P, et al.
Udgivet: (2007)

Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations.
af: Grottesi, A, et al.
Udgivet: (2005)

Anionic phospholipid interactions with the potassium channel KcsA: simulation studies.
af: Deol, S, et al.
Udgivet: (2006)

BioSimGRID: Application to analysis of membrane protein simulations
af: Sansom, M, et al.
Udgivet: (2005)

Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.
af: Bond, P, et al.
Udgivet: (2003)

Extending the structure of an ABC transporter to atomic resolution: modeling and simulation studies of MsbA.
af: Campbell, J, et al.
Udgivet: (2003)

Conformational change in an MFS protein: MD simulations of LacY.
af: Holyoake, J, et al.
Udgivet: (2007)

Coarse-grained simulations of the membrane-active antimicrobial Peptide maculatin 1.1.
af: Bond, P, et al.
Udgivet: (2008)

Coarse-grained molecular dynamics simulations of membrane proteins and peptides.
af: Bond, P, et al.
Udgivet: (2007)

Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study.
af: Johnston, J, et al.
Udgivet: (2008)

Acquisition of siderophores in gram-negative bacteria.
af: Faraldo-Gómez, J, et al.
Udgivet: (2003)

Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa.
af: Khalid, S, et al.
Udgivet: (2006)