(Q45964522)

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Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties.

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Europe PubMed Central

PubMed publication ID

18 December 2017

http://europepmc.org/abstract/MED/21910139

Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties. (English)

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Europe PubMed Central

PubMed publication ID

18 December 2017

http://europepmc.org/abstract/MED/21910139

1

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Arieh Warshel

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Europe PubMed Central

PubMed publication ID

18 December 2017

author name string

Anatoly Dryga

2

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Europe PubMed Central

PubMed publication ID

18 December 2017

http://europepmc.org/abstract/MED/21910139

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publication date

9 September 2011

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Europe PubMed Central

PubMed publication ID

18 December 2017

http://europepmc.org/abstract/MED/21910139

1 reference

Europe PubMed Central

PubMed publication ID

18 December 2017

http://europepmc.org/abstract/MED/21910139

79

1 reference

Europe PubMed Central

PubMed publication ID

18 December 2017

http://europepmc.org/abstract/MED/21910139

12

1 reference

Europe PubMed Central

PubMed publication ID

18 December 2017

http://europepmc.org/abstract/MED/21910139

3469-3484

1 reference

Europe PubMed Central

PubMed publication ID

18 December 2017

http://europepmc.org/abstract/MED/21910139

Electrostatic effects in proteins

1 reference

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21 January 2018

Electrostatic interactions in macromolecules: theory and applications

1 reference

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21 January 2018

Modeling electrostatic effects in proteins

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21 January 2018

Calculations of electrostatic interactions in biological systems and in solutions

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Roles of electrostatic interaction in proteins.

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Electrostatic effects in macromolecules: fundamental concepts and practical modeling

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21 January 2018

Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability

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21 January 2018

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

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Electrostatic Energy and Macromolecular Function

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21 January 2018

Polarizable Force Fields: History, Test Cases, and Prospects

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21 January 2018

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

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21 January 2018

Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels

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Renormalizing SMD: The Renormalization Approach and Its Use in Long Time Simulations and Accelerated PMF Calculations of Macromolecules

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

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21 January 2018

On the calculation of electrostatic interactions in proteins.

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

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Classical electrostatics in biology and chemistry

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21 January 2018

Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis

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Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties

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Energetics of electron-transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudomonas viridis.

1 reference

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21 January 2018

Calculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centers.

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Electrostatic models for computing protonation and redox equilibria in proteins.

1 reference

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21 January 2018

A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins.

1 reference

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21 January 2018

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

1 reference

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21 January 2018

Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects

1 reference

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Tuning heme redox potentials in the cytochrome C subunit of photosynthetic reaction centers.

1 reference

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21 January 2018

Are acidic and basic groups in buried proteins predicted to be ionized?

1 reference

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21 January 2018

Reorganization in apo- and holo-beta-lactoglobulin upon protonation of Glu89: molecular dynamics and pKa calculations

1 reference

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21 January 2018

Proton binding to proteins: a free-energy component analysis using a dielectric continuum model.

1 reference

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21 January 2018

Membrane-induced conformational changes of kyotorphin revealed by molecular dynamics simulations

1 reference

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21 January 2018

Acidic range titration of HEWL using a constant-pH molecular dynamics method.

1 reference

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21 January 2018

Microscopic theory of the dielectric properties of proteins

1 reference

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21 January 2018

Prediction of pH-dependent properties of proteins

1 reference

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21 January 2018

Electrostatic interactions in an integral membrane protein

1 reference

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21 January 2018

Probing protein electrostatics with a synthetic fluorescent amino acid.

1 reference

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21 January 2018

A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding.

1 reference

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21 January 2018

Experimental measurement of the effective dielectric in the hydrophobic core of a protein.

1 reference

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21 January 2018

A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins

1 reference

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21 January 2018

High apparent dielectric constants in the interior of a protein reflect water penetration

1 reference

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21 January 2018

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

1 reference

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21 January 2018

Using a charging coordinate in studies of ionization induced partial unfolding

1 reference

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21 January 2018

pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling.

1 reference

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21 January 2018

Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase.

1 reference

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21 January 2018

Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies

1 reference

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21 January 2018

Effects of Nonpolar Environments on the Redox Potentials of Heme Complexes

1 reference

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21 January 2018

Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins.

1 reference

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21 January 2018

Protein Control of Redox Potentials of Ironminus signSulfur Proteins

1 reference

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21 January 2018

Structural origins of redox potentials in Fe-S proteins: electrostatic potentials of crystal structures

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Insights into properties and energetics of iron-sulfur proteins from simple clusters to nitrogenase

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Dynamics of biochemical and biophysical reactions: insight from computer simulations

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21 January 2018

Electrostatic control of charge separation in bacterial photosynthesis

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21 January 2018

On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions

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Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

1 reference

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21 January 2018

Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility

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Computer simulation studies of the fidelity of DNA polymerases

1 reference

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Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water.

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How important are entropic contributions to enzyme catalysis?

1 reference

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21 January 2018

What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?

1 reference

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Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies

1 reference

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Computer simulations of enzyme catalysis: methods, progress, and insights

1 reference

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21 January 2018

Simulating enzyme reactions: challenges and perspectives

1 reference

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21 January 2018

Computer modelling of enzyme catalysed reaction mechanisms.

1 reference

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21 January 2018

Energetics of enzyme catalysis

1 reference

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Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites

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Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

1 reference

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Electrostatic basis for enzyme catalysis

1 reference

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21 January 2018

Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole

1 reference

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21 January 2018

Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

1 reference

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21 January 2018

Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase

1 reference

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21 January 2018

Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase

1 reference

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21 January 2018

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization

1 reference

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21 January 2018

Structural distribution of stability in a thermophilic enzyme

1 reference

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Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability

1 reference

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Do salt bridges stabilize proteins? A continuum electrostatic analysis.

1 reference

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21 January 2018

Electrostatic contributions to the stability of hyperthermophilic proteins.

1 reference

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21 January 2018

Increasing protein stability by altering long-range coulombic interactions

1 reference

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21 January 2018

Electrostatic contributions to protein stability and folding energy

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Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models

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Effective approach for calculations of absolute stability of proteins using focused dielectric constants

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Electrostatic basis for bioenergetics.

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Aquaporin water channels: molecular mechanisms for human diseases

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21 January 2018

Structural determinants of water permeation through aquaporin-1

1 reference

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21 January 2018

Structural basis of water-specific transport through the AQP1 water channel

1 reference

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21 January 2018

Climatic impact of tropical lowland deforestation on nearby montane cloud forests

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1 reference

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Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels

1 reference

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21 January 2018

Control of the selectivity of the aquaporin water channel family by global orientational tuning

1 reference

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21 January 2018

The dynamics and energetics of water permeation and proton exclusion in aquaporins

1 reference

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21 January 2018

Structural determinants of proton blockage in aquaporins

1 reference

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21 January 2018

On the origin of the electrostatic barrier for proton transport in aquaporin

1 reference

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21 January 2018

What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals

1 reference

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21 January 2018

Water and ion permeation in bAQP1 and GlpF channels: a kinetic Monte Carlo study

1 reference

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21 January 2018

The Grotthuss mechanism

1 reference

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21 January 2018

The mechanism of proton exclusion in aquaporin channels

1 reference

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Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium

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1 reference

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21 January 2018

Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Structure and function of channels and channelogs as studied by computational chemistry

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Simulations of ion current in realistic models of ion channels: the KcsA potassium channel

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Energetic optimization of ion conduction rate by the K+ selectivity filter

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Molecular dynamics study of the KcsA potassium channel

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Ion permeation mechanism of the potassium channel

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

K(+)/Na(+) selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Exploring the origin of the ion selectivity of the KcsA potassium channel

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Computer simulation of protein folding

1 reference

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21 January 2018

Theoretical Studies of Protein Folding

1 reference

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21 January 2018

Toward an outline of the topography of a realistic protein-folding funnel

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Simulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design?

1 reference

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21 January 2018

Dominant forces in protein folding

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

The MARTINI force field: coarse grained model for biomolecular simulations

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

On the relationship between thermal stability and catalytic power of enzymes

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes

1 reference

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21 January 2018

The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Closing in on the resting state of the Shaker K(+) channel.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

The electrostatics of VDAC: implications for selectivity and gating

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton Transfer Reaction

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Free Energy of Ionic Hydration

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Molecular dynamics at constant pH and reduction potential: application to cytochrome c(3)

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

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Are unit charges always negligible?

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

Control of reduction potential by protein matrix: lesson from a spherical protein model

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23125

21 January 2018

A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

On the calculation of pKas in proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Improving macromolecular electrostatics calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

On the energetics of conformational changes and pH dependent redox behaviour of electron transfer proteins

1 reference

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https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

A theoretical model for the effects of local nonpolar heme environments on the redox potentials in cytochromes

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Solvation, reorganization energy, and biological catalysis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Small Molecule Docking and Scoring

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Constant-pH Molecular Dynamics Simulations Reveal a β-Rich Form of the Human Prion Protein

1 reference

11 October 2022

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Computer simulation and analysis of the reaction pathway of triosephosphate isomerase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Buried, charged, non-ion-paired aspartic acid 76 contributes favorably to the conformational stability of ribonuclease T1

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

The dielectric constant of a folded protein

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PROT.23125

Identifiers

10.1002/PROT.23125

1 reference

Europe PubMed Central

PubMed publication ID

18 December 2017

http://europepmc.org/abstract/MED/21910139

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

18 December 2017

http://europepmc.org/abstract/MED/21910139

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