(Q31796804)

18 September 2017

Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dynamics contrasted with NMR (English)

1 reference

molecular dynamics simulation

18 September 2017

0 references

author name string

Derreumaux S

series ordinal

1

1 reference

PMCID

1300966

18 September 2017

Fermandjian S

series ordinal

2

1 reference

PMCID

1300966

18 September 2017

language of work or name

English

0 references

publication date

1 August 2000

1 reference

18 September 2017

1 reference

18 September 2017

79

1 reference

18 September 2017

2

1 reference

18 September 2017

656-669

1 reference

An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA found by combined NMR and molecular modelling studies

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Molecular dynamics simulations of DNA in solutions with different counter-ions.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

DNA bending determines Fos-Jun heterodimer orientation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

DNA bending by small, mobile multivalent cations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Sequence determinants of the intrinsic bend in the cyclic AMP response element

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

DNA bending: the prevalence of kinkiness and the virtues of normality

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Characterization of the ATF/CREB site and its complex with GCN4.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

DNA-binding domains of Fos and Jun do not induce DNA curvature: an investigation with solution and gel methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Sensitivity of NMR internucleotide distances to B-DNA conformation: underlying mechanics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Solution structure of the ATF-2 recognition site and its interaction with the ATF-2 peptide

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Solution structure of the CpG containing d(CTTCGAAG)2 oligonucleotide: NMR data and energy calculations are compatible with a BI/BII equilibrium at CpG.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Statistical analysis of DNA duplex structural features

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Transcription factors. 1: bZIP proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

BI-BII transitions in B-DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

DNA targets for certain bZIP proteins distinguished by an intrinsic bend

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Determinants of half-site spacing preferences that distinguish AP-1 and ATF/CREB bZIP domains

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Stereochemical basis of DNA bending by transcription factors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Temperature and salt dependence of the gel migration anomaly of curved DNA fragments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

c-JUN, JUN B, and JUN D differ in their binding affinities to AP-1 and CRE consensus sequences: effect of FOS proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Cross-family dimerization of transcription factors Fos/Jun and ATF/CREB alters DNA binding specificity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Conformational sub-states in B-DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Minimum length of a sequence-specific DNA binding peptide

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

A General Approach to the Optimization of the Conformation of Ring Molecules with an Application to Valinomycin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300966

Optimised parameters for A-DNA and B-DNA

31 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

Molecular dynamics with coupling to an external bath

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

Effect of distortions in the phosphate backbone conformation of six related octanucleotide duplexes on CD and 31P NMR spectra

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

Comparison of simple potential functions for simulating liquid water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

The flexibility of the nucleic acids: (II). The calculation of internal energy and applications to mononucleotide repeat DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

Structural behavior of the CpG step in two related oligonucleotides reflects its malleability in solution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

Divalent cations stabilize unstacked conformations of DNA and RNA by interacting with base pi systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

Electrostatic mechanism for DNA bending by bZIP proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

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%2800%2976324-7

Molecular dynamics studies of axis bending in d(G5-(GA4T4C)2-C5) and d(G5-(GT4A4C)2-C5): effects of sequence polarity on DNA curvature

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

A “Hydrat-Ion” Spine in a B-DNA Minor Groove

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

Inherent DNA curvature and flexibility correlate with TATA box functionality

7 January 2021

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/10920000

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A smooth particle mesh Ewald method

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2800%2976324-7

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(00)76324-7

1 reference

18 September 2017

1 reference

18 September 2017

1 reference

PMCID

1300966