(Q36026093)

11 August 2017

Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease (English)

1 reference

11 August 2017

Daniel A Karp

1

1 reference

11 August 2017

Mary R Stahley

series ordinal

2

1 reference

11 August 2017

Bertrand García-Moreno

series ordinal

3

1 reference

11 August 2017

language of work or name

English

0 references

publication date

1 May 2010

1 reference

11 August 2017

1 reference

11 August 2017

49

1 reference

11 August 2017

19

1 reference

11 August 2017

4138-4146

1 reference

Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

The origin of the electrostatic perturbation in acetoacetate decarboxylase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

The pKa Values of Acidic and Basic Residues Buried at the Same Internal Location in a Protein Are Governed by Different Factors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

High tolerance for ionizable residues in the hydrophobic interior of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein-water interface as a determinant of pKavalues

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Crystallographic Study of Hydration of an Internal Cavity in Engineered Proteins with Buried Polar or Ionizable Groups

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

High Apparent Dielectric Constant Inside a Protein Reflects Structural Reorganization Coupled to the Ionization of an Internal Asp

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Modeling electrostatic effects in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Toward the accurate first-principles prediction of ionization equilibria in proteins.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Constant pH molecular dynamics with proton tautomerism

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Stabilization of internal charges in a protein: water penetration or conformational change?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Structural clues to the mechanism of ion pumping in bacteriorhodopsin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Crystallographic studies of the conformational changes that drive directional transmembrane ion movement in bacteriorhodopsin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Conformational substates in different crystal forms of the photoactive yellow protein-Correlation with theoretical and experimental flexibility

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Structural changes linked to proton translocation by subunit c of the ATP synthase

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

A local electrostatic change is the cause of the large-scale protein conformation shift in bacteriorhodopsin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Prediction of pH-dependent properties of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Calculation of protein extinction coefficients from amino acid sequence data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Improved methods for building protein models in electron density maps and the location of errors in these models

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of T4 lysozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Electrostatic control of charge separation in bacterial photosynthesis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Using a charging coordinate in studies of ionization induced partial unfolding

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Local stability identification and the role of a key aromatic amino acid residue in staphylococcal nuclease refolding

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Elucidation of information encoded in tryptophan 140 of staphylococcal nuclease

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Calculation of proton transfers in Bacteriorhodopsin bR and M intermediates

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

The structural basis for the perturbed pKa of the catalytic base in 4-oxalocrotonate tautomerase: kinetic and structural effects of mutations of Phe-50.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Global conformational changes upon receptor stimulation in photoactive yellow protein.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

The determinants of pKas in proteins

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Dielectric studies of protein hydration and hydration-induced flexibility

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373020

Dielectric relaxation spectra of water adsorbed on lysozyme

21 October 2018

1 reference

12 December 2020

Dielectric studies of the binding of water to lysozyme

1 reference

12 December 2020

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

1 reference

12 December 2020

Environments and mechanistic roles of the tyrosine residues of delta 5-3-ketosteroid isomerase

1 reference

12 December 2020

Energetic contribution of side chain hydrogen bonding to the stability of staphylococcal nuclease

1 reference

12 December 2020

Monitoring the sizes of denatured ensembles of staphylococcal nuclease proteins: implications regarding m values, intermediates, and thermodynamics

1 reference

12 December 2020

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

1 reference

12 December 2020

Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: comparing experimental with computed pK(a)s

1 reference

12 December 2020

Identifiers

DOI

10.1021/BI902114M

1 reference

11 August 2017

1 reference

11 August 2017

PubMed publication ID

20329780

1 reference