Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation (Q40150434)

17 September 2017

Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation (English)

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17 September 2017

Nilsson L

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17 September 2017

Sen S

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17 September 2017

language of work or name

English

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publication date

1 October 1999

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17 September 2017

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inferred from page(s)

published in

Biophysical Journal

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17 September 2017

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17 September 2017

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17 September 2017

1782-1800

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Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator

17 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Binding of the estrogen receptor to DNA. The role of waters

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

How hormone receptor-DNA binding affects nucleosomal DNA: the role of symmetry

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Hydration and DNA recognition by homeodomains

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Protein-DNA complexes: the cost of recognition

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Molecular recognition mediated by bound water. A mechanism for star activity of the restriction endonuclease EcoRI

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Structure of restriction endonuclease BamHI and its relationship to EcoRI.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Crystal structure analysis of a complete turn of B-DNA

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

The interpretation of protein structures: Estimation of static accessibility

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Crystal structure of trp repressor/operator complex at atomic resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Homeodomain-type DNA recognition

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

The energetic basis of specificity in the Eco RI endonuclease--DNA interaction.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300464

Molecular dynamics study of glucocorticoid receptor-DNA binding

4 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

Structure, thermodynamics and cooperativity of the glucocorticoid receptor DNA-binding domain in complex with different response elements. Molecular dynamics simulation and free energy perturbation studies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

Comparison of simple potential functions for simulating liquid water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

Solution structure of papain as studied by molecular mechanics and molecular dynamics techniques

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

All-atom empirical potential for molecular modeling and dynamics studies of proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977024-4

10.1016/S0006-3495(99)77024-4

7 January 2021

Identifiers

DOI

1 reference

release_7oovs2ninzdynoemjp6ygqhklm

17 September 2017

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Fatcat

https://api.fatcat.wiki/v0/release/7oovs2ninzdynoemjp6ygqhklm

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

17 September 2017

PubMed publication ID

10512803

1 reference