Molecular simulations of a dynamic protein complex: role of salt-bridges and polar interactions in configurational transitions (Q37337992)

19 August 2017

Molecular simulations of a dynamic protein complex: role of salt-bridges and polar interactions in configurational transitions (English)

1 reference

19 August 2017

Matthias Buck

2

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author name string

Liqun Zhang

series ordinal

1

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PMCID

3838735

19 August 2017

language of work or name

English

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publication date

1 November 2013

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19 August 2017

6

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based on heuristic

inferred from page(s)

published in

Biophysical Journal

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19 August 2017

105

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19 August 2017

10

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19 August 2017

2412-2417

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Starting-structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD-derived order parameters

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Refinement of protein structure homology models via long, all-atom molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

NMR structure of a heterodimeric SAM:SAM complex: characterization and manipulation of EphA2 binding reveal new cellular functions of SHIP2.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

A direct coupling between global and internal motions in a single domain protein? MD investigation of extreme scenarios

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Protein-protein docking tested in blind predictions: the CAPRI experiment

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

The role of dynamic conformational ensembles in biomolecular recognition

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Segmented transition pathway of the signaling protein nitrogen regulatory protein C

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Fundamental aspects of protein-protein association kinetics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

NMR Studies of a Heterotypic Sam−Sam Domain Association: The Interaction between the Lipid Phosphatase Ship2 and the EphA2 Receptor † , ‡

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Solution NMR Structures of Productive and Non-productive Complexes between the A and B Domains of the Cytoplasmic Subunit of the Mannose Transporter of the Escherichia coli Phosphotransferase System

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Scalable molecular dynamics with NAMD

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

The role of alpha-, 3(10)-, and pi-helix in helix-->coil transitions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

A simple physical model for binding energy hot spots in protein-protein complexes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Electrostatic aspects of protein-protein interactions.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Kinetics of desolvation-mediated protein-protein binding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Folding funnels, binding funnels, and protein function

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

The atomic structure of protein-protein recognition sites

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Principles of protein-protein interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

The Src SH2 domain interacts dynamically with the focal adhesion kinase binding site as demonstrated by paramagnetic NMR spectroscopy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Novel modulation factor quantifies the role of water molecules in protein interactions.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

On the contribution of water-mediated interactions to protein-complex stability.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Wordom: a program for efficient analysis of molecular dynamics simulations.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Hydrogen bonds and salt bridges across protein-protein interfaces

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Mechanism of Helix Nucleation and Propagation: Microscopic View from Microsecond Time Scale MD Simulations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3838735

Role of protein-water hydrogen bond dynamics in the protein dynamical transition

3 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24268153

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Hydration of protein-protein interfaces

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24268153

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2013.09.052

1 reference

19 August 2017

1 reference

19 August 2017

1 reference

PMCID

3838735