(Q42736099)

6 November 2017

Free energy simulations of a GTPase: GTP and GDP binding to archaeal initiation factor 2. (English)

1 reference

6 November 2017

Carine Clavaguéra

2

0 references

Thomas Simonson

object named as

Thomas Simonson

series ordinal

4

0 references

Gilles Ohanessian

object named as

Gilles Ohanessian

series ordinal

3

0 references

author name string

Priyadarshi Satpati

series ordinal

1

1 reference

PMC publication ID

3097523

6 November 2017

language of work or name

English

0 references

publication date

2 May 2011

1 reference

Journal of Physical Chemistry B

6 November 2017

1 reference

6 November 2017

115

1 reference

6 November 2017

20

1 reference

6 November 2017

6749-6763

1 reference

Polarizable Force Fields: History, Test Cases, and Prospects

6 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Conformational selection in G-proteins: lessons from Ras and Rho.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Prediction of reorganization free energies for biological electron transfer: a comparative study of Ru-modified cytochromes and a 4-helix bundle protein

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

The distinct conformational dynamics of K-Ras and H-Ras A59G

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Current status of the AMOEBA polarizable force field

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Large conformational changes in proteins: signaling and other functions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase A.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

The role of dynamic conformational ensembles in biomolecular recognition

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Alchemical free energy simulations for biological complexes: powerful but temperamental....

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Structure-function insights into prokaryotic and eukaryotic translation initiation.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

CHARMM: the biomolecular simulation program

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

PROCAIN: protein profile comparison with assisting information.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Cyclopiazonic Acid Is Complexed to a Divalent Metal Ion When Bound to the Sarcoplasmic Reticulum Ca2+-ATPase

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Allosteric communication in myosin V: from small conformational changes to large directed movements

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born model.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Variable atomic radii for continuum-solvent electrostatics calculation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Extensive conformational transitions are required to turn on ATP hydrolysis in myosin.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Calculation of protein-ligand binding free energy by using a polarizable potential

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Comparison of multiple Amber force fields and development of improved protein backbone parameters

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Scalable molecular dynamics with NAMD

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Structural mechanism of the recovery stroke in the myosin molecular motor

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Accurate description of van der Waals complexes by density functional theory including empirical corrections

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

The many roles of computation in drug discovery

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Force fields for protein simulations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

The missing link between thermodynamics and structure in F1-ATPase

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Molecular dynamics simulations of biomolecules

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Free energy simulations come of age: protein-ligand recognition

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Unraveling hot spots in binding interfaces: progress and challenges

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

The guanine nucleotide-binding switch in three dimensions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Macromolecular electrostatics: continuum models and their growing pains

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Electrostatic contributions to molecular free energies in solution

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

G proteins, effectors and GAPs: structure and mechanism

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Concentration of MgATP2- and other ions in solution. Calculation of the true concentrations of species present in mixtures of associating ions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Role of the arginine finger in Ras.RasGAP revealed by QM/MM calculations

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Semiempirical GGA-type density functional constructed with a long-range dispersion correction.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Structural switch of the gamma subunit in an archaeal aIF2 alpha gamma heterodimer.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Quantum mechanical continuum solvation models.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Dissection of the GTPase mechanism of Ras protein by MD analysis of Ras mutants

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

The conformational states of Mg.ATP in water

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Theory of biomolecular recognition

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Free energy simulations: the meaning of the individual contributions from a component analysis.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Molecular Dynamics Simulations Show That Bound Mg2+Contributes to Amino Acid and Aminoacyl Adenylate Binding Specificity in Aspartyl-tRNA Synthetase through Long Range Electrostatic Interactions

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3097523

Standard thermodynamic formation properties for the adenosine 5'-triphosphate series

1 December 2018

1 reference

12 December 2020

Density functional calculations of ATP systems. 1. Crystalline ATP hydrates and related molecules

1 reference

12 December 2020

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

1 reference

12 December 2020

Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations

1 reference

12 December 2020

The structural coupling between ATPase activation and recovery stroke in the myosin II motor

1 reference

12 December 2020

Why an A-loop phospho-mimetic fails to activate PAK1: understanding an inaccessible kinase state by molecular dynamics simulations

1 reference

12 December 2020

ATP Synthesis by Rotary Catalysis (Nobel lecture)

1 reference

12 December 2020

Energy, Life, and ATP (Nobel Lecture)

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP201934P

1 reference

6 November 2017

1 reference

PMC publication ID

3097523

6 November 2017

PubMed publication ID

21534562

1 reference

PMC publication ID

3097523