Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics. (Q30353714)

20 June 2017

title

Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics. (English)

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molecular dynamics simulation

20 June 2017

main subject

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author name string

Iwona Siuda

series ordinal

1

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20 June 2017

Lea Thøgersen

series ordinal

2

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20 June 2017

publication date

19 September 2013

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Journal of Molecular Modeling

20 June 2017

published in

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20 June 2017

volume

19

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20 June 2017

issue

11

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20 June 2017

page(s)

4931-4945

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Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes

20 June 2017

cites work

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Periplasmic binding proteins: a versatile superfamily for protein engineering

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Structural mechanisms for domain movements in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Structure of the L-leucine-binding protein refined at 2.4 A resolution and comparison with the Leu/Ile/Val-binding protein structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

X-ray structures of the leucine-binding protein illustrate conformational changes and the basis of ligand specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Perspectives on the structure-function of ABC transporters: the Switch and Constant Contact models

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

ATP-binding cassette transporters in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Structural insights into ABC transporter mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Atomic structures of periplasmic binding proteins and the high-affinity active transport systems in bacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Comparative molecular dynamics--similar folds and similar motions?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Molecular dynamics simulations of the periplasmic ferric-hydroxamate binding protein FhuD.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Opening and closing motions in the periplasmic vitamin B12 binding protein BtuF.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Conformational dynamics of L-lysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Collective dynamics of periplasmic glutamine binding protein upon domain closure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Computing ensembles of transitions from stable states: Dynamic importance sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Analysis of domain movements in glutamine-binding protein with simple models

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Characterization of protein conformational states by normal-mode frequencies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Detection of functional modes in protein dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Multiscale modeling of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

The MARTINI force field: coarse grained model for biomolecular simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Martini Coarse-Grained Force Field: Extension to Carbohydrates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

GROMACS: fast, flexible, and free

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Development and testing of a general amber force field

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Automatic atom type and bond type perception in molecular mechanical calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Analysis of domain motions by approximate normal mode calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Mechanics and dynamics of B1 domain of protein G: role of packing and surface hydrophobic residues

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Simulations of the c-subunit of ATP-synthase reveal helix rearrangements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Release of content through mechano-sensitive gates in pressurized liposomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Mechanosensitive membrane channels in action

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

The natural history of protein domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

The anatomy and taxonomy of protein structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Multiple open forms of ribose-binding protein trace the path of its conformational change

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Crystal structures of the choline/acetylcholine substrate-binding protein ChoX from Sinorhizobium meliloti in the liganded and unliganded-closed states

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Partitioning protein structures into domains: why is it so difficult?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

CATH--a hierarchic classification of protein domain structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Data growth and its impact on the SCOP database: new developments

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

21 January 2018

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Toward consistent assignment of structural domains in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Prediction of novel and analogous folds using fragment assembly and fold recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

PDP: protein domain parser.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Improved Parameters for the Martini Coarse-Grained Protein Force Field.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Polarizable water model for the coarse-grained MARTINI force field

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Testing models for transport systems dependent on periplasmic binding proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Structure of an ABC transporter in complex with its binding protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Crystal structure of a catalytic intermediate of the maltose transporter

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Crystal structure of the maltose transporter in a pretranslocation intermediate state

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Mathematical treatment of the kinetics of binding protein dependent transport systems reveals that both the substrate loaded and unloaded binding proteins interact with the membrane components

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Simple models for the analysis of binding protein‐dependent transport systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Liganded and unliganded receptors interact with equal affinity with the membrane complex of periplasmic permeases, a subfamily of traffic ATPases

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

In vitro functional characterization of BtuCD-F, the Escherichia coli ABC transporter for vitamin B12 uptake.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

On the thermodynamic efficiency of Ca²⁺-ATPase molecular machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Energetics of kinesin-1 stepping mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

The ModFOLD server for the quality assessment of protein structural models

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS00894-013-1991-9

The histidine-binding protein undergoes conformational changes in the absence of ligand as analyzed with conformation-specific monoclonal antibodies

21 January 2018

1 reference

12 December 2020

Molecular dynamics simulations of the bacterial periplasmic heme binding proteins ShuT and PhuT

1 reference

12 December 2020

The mechanism of ligand binding to the periplasmic C4-dicarboxylate binding protein (DctP) from Rhodobacter capsulatus

1 reference

12 December 2020

The 1.9 A x-ray structure of a closed unliganded form of the periplasmic glucose/galactose receptor from Salmonella typhimurium

1 reference

12 December 2020

Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme

1 reference

12 December 2020

Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa

1 reference

12 December 2020

Periplasmic binding protein structure and function. Refined X-ray structures of the leucine/isoleucine/valine-binding protein and its complex with leucine

1 reference

12 December 2020

Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields

1 reference

12 December 2020

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

1 reference

12 December 2020

Reconstitution of the histidine periplasmic transport system in membrane vesicles. Energy coupling and interaction between the binding protein and the membrane complex

1 reference

12 December 2020

On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations.

1 reference

12 December 2020

10.1007/S00894-013-1991-9

Identifiers

DOI

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20 June 2017

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