Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration (Q30693903)

18 September 2017

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

1 reference

18 September 2017

Carolyn A Fitch

1

1 reference

18 September 2017

Daniel A Karp

2

1 reference

18 September 2017

Kelly K Lee

3

1 reference

18 September 2017

Wesley E Stites

4

1 reference

18 September 2017

Eaton E Lattman

5

1 reference

18 September 2017

Bertrand García-Moreno E

6

1 reference

18 September 2017

language of work or name

English

0 references

publication date

1 June 2002

1 reference

18 September 2017

1 reference

18 September 2017

82

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18 September 2017

6

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18 September 2017

3289-3304

1 reference

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

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Salt effects on ionization equilibria of histidines in myoglobin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Water penetration and escape in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Molecular basis for pH sensitivity and proton transfer in green fluorescent protein: protonation and conformational substates from electrostatic calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Tanford-Kirkwood electrostatics for protein modeling.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Calculation of electron transfer reorganization energies using the finite difference Poisson-Boltzmann model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Temperature dependence of histidine ionization constants in myoglobin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Charge density-dependent strength of hydration and biological structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Explicit solvent models in protein pKa calculations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

1H, 13C and 15N chemical shift referencing in biomolecular NMR

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Prediction of pH-dependent properties of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Calculations of electrostatic interactions in biological systems and in solutions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

pH-dependent processes in proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

How do serine proteases really work?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Protein hydration and function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

In a staphylococcal nuclease mutant the side-chain of a lysine replacing valine 66 is fully buried in the hydrophobic core

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Linkage of thioredoxin stability to titration of ionizable groups with perturbed pKa.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

The crystal structure of staphylococcal nuclease refined at 1.7 A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Structural comparison of apomyoglobin and metaquomyoglobin: pH titration of histidines by NMR spectroscopy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Protein control of iron-sulfur cluster redox potentials

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Electrostatic models for computing protonation and redox equilibria in proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

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

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

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

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Electrostatic effects in macromolecules: fundamental concepts and practical modeling

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Electrostatics of proteins: description in terms of two dielectric constants simultaneously.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Polar fluctuations in proteins: molecular-dynamic studies of cytochrome c in aqueous solution

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Modeling of protein conformational fluctuations in pKa predictions

25 November 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

25 November 2018

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

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

7 January 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

The determinants of pKas in proteins

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

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

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302117

NMR assignments of the four histidines of staphylococcal nuclease in native and denatured states

25 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

Hydrogen-1 NMR evidence for three interconverting forms of staphylococcal nuclease: effects of mutations and solution conditions on their distribution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

Protein hydration dynamics in aqueous solution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

A magnetization-transfer nuclear magnetic resonance study of the folding of staphylococcal nuclease

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

Multiple conformations of a protein demonstrated by magnetization transfer NMR spectroscopy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

Water penetration and escape in proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

Comparison of simple potential functions for simulating liquid water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

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

7 January 2021

1 reference

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Family of G protein alpha chains: amphipathic analysis and predicted structure of functional domains

7 January 2021

1 reference

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Structural features of the protoporphyrin-apomyoglobin complex: a proton NMR spectroscopy study

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

The role of hydrophobic microenvironments in modulating pKa shifts in proteins.

7 January 2021

1 reference

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Simulation of activation free energies in molecular systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

In a staphylococcal nuclease mutant the side-chain of a lysine replacing valine 66 is fully buried in the hydrophobic core

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

What about protein polarity?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

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

7 January 2021

1 reference

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pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

On the calculation of pKas in proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975670-1

Dielectric relaxation spectra of water adsorbed on lysozyme

7 January 2021

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12023252

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(02)75670-1

1 reference

18 September 2017

1 reference

18 September 2017

PubMed publication ID

12023252

1 reference