(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/S0006-3495(98)77671-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(98)77671-4

The price of lost freedom: entropy of bimolecular complex formation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(98)77671-4

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/S0006-3495(98)77671-4

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/S0006-3495(98)77671-4

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/S0006-3495(98)77671-4

Electrostatic complementarity at protein/protein interfaces

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(98)77671-4

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/S0006-3495(98)77671-4

Dynamics of DNA oligomers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(98)77671-4

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/S0006-3495(98)77671-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(98)77671-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(98)77671-4

On the calculation of pKas in proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/S0006-3495(98)77671-4

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