(Q34190132)

31 July 2017

title

Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences (English)

1 reference

31 July 2017

Surjit B Dixit

1

1 reference

31 July 2017

David Q Andrews

series ordinal

2

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31 July 2017

D L Beveridge

series ordinal

3

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31 July 2017

language of work or name

English

0 references

publication date

24 February 2005

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31 July 2017

number of pages

11

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inferred from page(s)

published in

Biophysical Journal

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31 July 2017

volume

88

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31 July 2017

issue

5

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31 July 2017

page(s)

3147-3157

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Structure and axis curvature in two dA6 x dT6 DNA oligonucleotides: comparison of molecular dynamics simulations with results from crystallography and NMR spectroscopy

31 July 2017

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation

5 July 2018

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Solution structure of an A-tract DNA bend

5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Transcription activation by catabolite activator protein (CAP)

5 July 2018

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5 July 2018

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

5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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The DNA binding domain and bending angle of E. coli CAP protein.

5 July 2018

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5 July 2018

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NH2-terminal arm of phage lambda repressor contributes energy and specificity to repressor binding and determines the effects of operator mutations

5 July 2018

1 reference

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Free energy via molecular simulation: applications to chemical and biomolecular systems

5 July 2018

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Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site

5 July 2018

1 reference

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Domain communication in the dynamical structure of human immunodeficiency virus 1 protease

5 July 2018

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DNA recognition by proteins with the helix-turn-helix motif

5 July 2018

1 reference

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The DNA binding arm of lambda repressor: critical contacts from a flexible region

5 July 2018

1 reference

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

5 July 2018

1 reference

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

5 July 2018

1 reference

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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

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Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level.

5 July 2018

1 reference

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Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility

28 October 2018

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Molecular dynamics simulation reveals sequence-intrinsic and protein-induced geometrical features of the OL1 DNA operator

28 October 2018

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The meaning of component analysis: decomposition of the free energy in terms of specific interactions.

28 October 2018

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Cooperative protein-DNA interactions: effects of potassium chloride on .lambda. cI binding to OR

28 October 2018

1 reference

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Estimating entropies from molecular dynamics simulations

28 October 2018

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Entropy calculations on the molten globule state of a protein: Side-chain entropies of α-lactalbumin

28 October 2018

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Decomposition of the Free Energy of a System in Terms of Specific Interactions

28 October 2018

1 reference

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Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations

28 October 2018

1 reference

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Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants

28 October 2018

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12 December 2020

Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution

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12 December 2020

Calorimetric analysis of lambda cI repressor binding to DNA operator sites

1 reference

12 December 2020

One nanosecond molecular dynamics simulation of the N-terminal domain of the lambda repressor protein

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12 December 2020

Protein-DNA recognition: new perspectives and underlying themes

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12 December 2020

Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity?

1 reference

12 December 2020

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

1 reference

12 December 2020

NMR relaxation studies of the role of conformational entropy in protein stability and ligand binding

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12 December 2020

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

1 reference

12 December 2020

Protein dynamics from NMR

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12 December 2020

The Nucleic Acid Database

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12 December 2020

Structural and thermodynamic strategies for site-specific DNA binding proteins

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12 December 2020

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

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12 December 2020

Topological measurement of protein-induced DNA bend angles

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12 December 2020

10.1529/BIOPHYSJ.104.053843

Identifiers

DOI

1 reference

31 July 2017

1 reference

31 July 2017

1 reference