Self-guided Langevin dynamics study of regulatory interactions in NtrC. (Q42198361)

18 October 2017

Self-guided Langevin dynamics study of regulatory interactions in NtrC. (English)

1 reference

18 October 2017

Ana Damjanović

1

1 reference

18 October 2017

Bertrand García-Moreno E

series ordinal

2

1 reference

18 October 2017

Bernard R Brooks

series ordinal

3

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18 October 2017

language of work or name

English

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publication date

1 September 2009

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18 October 2017

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18 October 2017

76

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18 October 2017

4

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18 October 2017

1007-1019

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

18 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study

26 October 2017

1 reference

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Finding transition pathways using the string method with swarms of trajectories

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

Molecular dynamics simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin.

26 October 2017

1 reference

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The role of phosphorylation on the structure and dynamics of phospholamban: a model from molecular simulations

26 October 2017

1 reference

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Advances in methods and algorithms in a modern quantum chemistry program package.

26 October 2017

1 reference

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The structural basis for regulated assembly and function of the transcriptional activator NtrC.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.

26 October 2017

1 reference

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Long-timescale simulation methods

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration

26 October 2017

1 reference

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The origins of protein phosphorylation

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

Structural basis for control by phosphorylation

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

What are the dielectric "constants" of proteins and how to validate electrostatic models?

26 October 2017

1 reference

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Structure of a transiently phosphorylated switch in bacterial signal transduction

26 October 2017

1 reference

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Beryllofluoride mimics phosphorylation of NtrC and other bacterial response regulators

26 October 2017

1 reference

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Canonical dynamics: Equilibrium phase-space distributions

26 October 2017

1 reference

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VMD: visual molecular dynamics

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

Three-dimensional solution structure of the N-terminal receiver domain of NTRC

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

How good are predictions of protein secondary structure?

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

Protein phosphorylation and regulation of adaptive responses in bacteria

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

Coarse-grained dynamics of the receiver domain of NtrC: fluctuations, correlations and implications for allosteric cooperativity.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373014

Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles.

17 August 2018

1 reference

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Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY).

17 August 2018

1 reference

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Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces

17 August 2018

1 reference

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Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.

17 August 2018

1 reference

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Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure.

17 August 2018

1 reference

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The determinants of pKas in proteins

17 August 2018

1 reference

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Two-state allosteric behavior in a single-domain signaling protein

17 August 2018

1 reference

12 December 2020

Molecular dynamic simulations of the N-terminal receiver domain of NtrC reveal intrinsic conformational flexibility in the inactive state

1 reference

12 December 2020

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

1 reference

12 December 2020

Pathways for conformational change in nitrogen regulatory protein C from discrete path sampling

1 reference

12 December 2020

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.22439

1 reference

18 October 2017

1 reference

18 October 2017

PubMed publication ID

19384996

1 reference