Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA. (Q34169304)

31 July 2017

title

Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA. (English)

1 reference

31 July 2017

V K Misra

1

1 reference

31 July 2017

J L Hecht

series ordinal

2

1 reference

31 July 2017

A S Yang

series ordinal

3

1 reference

31 July 2017

B Honig

series ordinal

4

1 reference

31 July 2017

language of work or name

English

0 references

publication date

1 November 1998

1 reference

31 July 2017

1 reference

31 July 2017

volume

75

1 reference

31 July 2017

issue

5

1 reference

31 July 2017

page(s)

2262-2273

1 reference

Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

The statistical-thermodynamic basis for computation of binding affinities: a critical review

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Entropy in protein folding and in protein-protein interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Explicit solvent models in protein pKa calculations.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

A free energy analysis of nucleic acid base stacking in aqueous solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Dielectric response of triplex DNA in ionic solution from simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Empirical scale of side-chain conformational entropy in protein folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Coupling of local folding to site-specific binding of proteins to DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

A thermodynamic study of the trp repressor-operator interaction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Prediction of pH-dependent properties of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Determinants of repressor/operator recognition from the structure of the trp operator binding site.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Electrostatic activation of Escherichia coli methionine repressor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Do salt bridges stabilize proteins? A continuum electrostatic analysis.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

A negative electrostatic determinant mediates the association between the Escherichia coli trp repressor and its operator DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

On the magnitude of the electrostatic contribution to ligand-DNA interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Salt effects on ligand-DNA binding. Minor groove binding antibiotics.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Protein denaturation. C. Theoretical models for the mechanism of denaturation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

On the calculation of electrostatic interactions in proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Lambda repressor mutations that increase the affinity and specificity of operator binding.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

The electrostatic potential of B-DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Cooperative tandem binding of met repressor of Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Role of the hydrophobic effect in stability of site-specific protein-DNA complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

A demonstration of the intrinsic importance of stabilizing hydrophobic binding and non-covalent van der Waals contacts dominant in the non-covalent CC-1065/B-DNA binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Sequence-selective, pH-dependent binding to DNA of benzophenanthridine alkaloids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Lambda repressor: a model system for understanding protein-DNA interactions and protein stability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Ion distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Electrostatic interactions in macromolecules: theory and applications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Comparison of operator-specific and nonspecific DNA binding of the .lambda. cI repressor: [KCl] and pH effects

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

16 Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Poisson-Boltzmann analysis of the lambda repressor-operator interaction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Binding of DNA to large fragment of DNA polymerase I: identification of strong and weak electrostatic forces and their biological implications.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Refined 1.8 A crystal structure of the lambda repressor-operator complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

The determinants of pKas in proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

The electrostatic contribution to the B to Z transition of DNA.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

On the pH dependence of protein stability.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Linkage of pH, anion and cation effects in protein-nucleic acid equilibria. Escherichia coli SSB protein-single stranded nucleic acid interactions.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

A computer-assisted analysis of conserved residues in the three-dimensional structures of the polymerase domains of Escherichia coli DNA polymerase I and HIV-1 reverse transcriptase.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

The dielectric constant of a folded protein

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299901

Sodium-23 NMR studies of cation-DNA interactions

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

The price of lost freedom: entropy of bimolecular complex formation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

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

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

Thermodynamics of the glucocorticoid receptor-DNA interaction: Binding of wild-type GR DBD to different response elements

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

Electrostatic complementarity at protein/protein interfaces

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

Proton-linked contributions to site-specific interactions of lambda cI repressor and OR

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

Dynamics of DNA oligomers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

Electrostatic field of the large fragment of Escherichia coli DNA polymerase I

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

An all atom force field for simulations of proteins and nucleic acids

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

On the calculation of pKas in proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977671-4

Coordinate ion pair formation between EcoRI endonuclease and DNA

7 January 2021

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/9788922

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structure of an immunoglobulin Fab fragment specific for poly(dG).poly(dC)

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/9788922

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structure of an immunoglobulin Fab fragment specific for triple-stranded DNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/9788922

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(98)77671-4

1 reference

31 July 2017

1 reference

31 July 2017

1 reference