Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components (Q34779522)

4 August 2017

2 references

2 August 2019

11 December 2019

Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components (English)

1 reference

4 August 2017

1 reference

2 August 2019

1 reference

11 December 2019

Peter L Privalov

1

1 reference

4 August 2017

Anatoly I Dragan

series ordinal

2

1 reference

4 August 2017

Colyn Crane-Robinson

series ordinal

3

1 reference

4 August 2017

language of work or name

English

0 references

publication date

10 November 2010

1 reference

4 August 2017

1 April 2011

2 references

2 August 2019

11 December 2019

Nucleic Acids Research

3 references

4 August 2017

2 August 2019

11 December 2019

39

1 reference

4 August 2017

issue

7

1 reference

4 August 2017

page(s)

2483-2491

1 reference

Creative Commons Attribution-NonCommercial 2.5 Generic

4 August 2017

copyright license

2 references

2 August 2019

The role of DNA shape in protein-DNA recognition

11 December 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

What drives proteins into the major or minor grooves of DNA?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

The extended arms of DNA-binding domains: a tale of tails

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Fluorescence anisotropy studies on the Ku-DNA interaction: anion and cation effects

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

The three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex by NMR spectroscopy.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Kinetics of DNA hydration

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Grand canonical Monte Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation (L8+) to the center of DNA oligomers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Structural basis for DNA bending by the architectural transcription factor LEF-1

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Ion effects on ligand-nucleic acid interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions I. Colligative Properties

7 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ984

Thermodynamic signature of GCN4-bZIP binding to DNA indicates the role of water in discriminating between the AP-1 and ATF/CREB sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ984

Forces driving the binding of homeodomains to DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ984

The energetics of specific binding of AT-hooks from HMGA1 to target DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ984

DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ984

Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ984

Biochemistry. Completing the view of transcriptional regulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ984

Pentalysine-deoxyribonucleic acid interactions: a model for the general effects of ion concentrations on the interactions of proteins with nucleic acids.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ984

21 January 2018

The cost of DNA bending

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ984

Stability and DNA-binding ability of the bZIP dimers formed by the ATF-2 and c-Jun transcription factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKQ984

Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

Salt effects on polyelectrolyte-ligand binding: comparison of Poisson-Boltzmann, and limiting law/counterion binding models

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3074165

DNA binding and bending by HMG boxes: energetic determinants of specificity

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21071403

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The energetics of HMG box interactions with DNA: thermodynamics of the DNA binding of the HMG box from mouse sox-5

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21071403

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKQ984

1 reference

4 August 2017

1 reference

4 August 2017

1 reference