Structure of the CAP-DNA Complex at 2.5 Å Resolution: A Complete Picture of the Protein-DNA Interface

Parkinson, Gary N.; Wilson, Christopher; Gunasekera, Angelo; Ebright, Yon W.; Ebright, Richard E.; Berman, Helen M.

doi:10.1006/jmbi.1996.0409

Cited by 263 publications

(206 citation statements)

References 52 publications

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“…The structural changes, and their relationship to cAMP binding and DNA binding, are remarkably clear and simple. The present results, together with previously reported structures of CAP in the presence of cAMP (6)(7)(8), complete the structural basis for understanding the allosteric control of CAP, a prototypic transcriptional regulatory factor.…”

supporting

confidence: 78%

“…CAP was the first transcription regulatory protein to have its 3D structure determined (5). The 3D structures of CAP have been determined in its cAMP-bound state (6) and in its cAMP-bound state in complex with DNA (7,8). Nevertheless, the structural basis of the cAMP-mediated allosteric transition in CAP has remained unclear, because the structure of CAP in the absence of cAMP was unknown.…”

mentioning

confidence: 99%

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Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

Popovych

Tzeng

Tonelli

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

203

278

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supporting

confidence: 78%

mentioning

confidence: 99%

Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

Popovych

Tzeng

Tonelli

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

203

278

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“…2). (B) Determination of DNA curvature associated with different roll distributions -DNA is not a monotonous, regular straight helix, but rather deforms in response to external stresses in a sequence-dependent manner 9,[52][53][54][55][56] . For example, the catabolic activator protein (CAP) introduces two sharp kinks at pyrimidine-purine (YR) steps in its binding site, bending the DNA at these steps into the major groove via large positive roll 57,58 . By contrast, the DNA wrapped tightly around the assembly of histone proteins on the surface of the nucleosome core particle deforms via both positive and negative roll, with pronounced bending into the minor groove occurring at regularly spaced YR steps 59 .…”

Section: Sample Applications Of 3dnamentioning

confidence: 99%

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

2008

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We present a set of protocols showing how to use the 3DNA suite of programs to analyze, rebuild, and visualize three-dimensional nucleic-acid structures. The software determines a wide range of conformational parameters, including the identities and rigid-body parameters of interacting bases and base-pair steps, the nucleotides comprising helical fragments, the area of overlap of stacked bases, etc. The reconstruction of three-dimensional structure takes advantage of rigorously defined rigid-body parameters, producing rectangular block representations of the nucleic-acid bases and base pairs and all-atom models with approximate sugar-phosphate backbones. The visualization components create vector-based drawings and scenes that can be rendered as raster-graphics images, allowing for easy generation of publication-quality figures. The utility programs use geometric variables to control the view and scale of an object, for comparison of related structures. The commands run in seconds even for large structures. The software and related information are available at http://3dna.rutgers.edu/.

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“…Travers [19] categorized the recognition as (a) digital or direct code, i.e., direct hydrogen bonding between protein side chains and exposed edges of the base pairs mainly in the major and to a lesser extent in the minor groove, providing complementarity to correct sequence (van der Waals interactions between the protein and the DNA are included under direct code in subsequent discussions in the literature), and (b) analog or indirect code, i.e., structural deformation of the DNA to provide sequence selectivity by virtue of the ability of the nucleotide base sequence to assume a particular conformation (intrinsic or induced), required for binding to a protein at lower free energy cost than other sequences. The recent structures of IHF-DNA [34] and CAP-DNA [35,36] complexes vividly illustrate the extent of deformation achieved by DNA to accomplish specific binding.…”

Section: Introductionmentioning

confidence: 96%

Free Energy Analysis of Protein–DNA Binding: The EcoRI Endonuclease–DNA Complex

Jayaram

McConnell

Dixit

et al. 1999

Journal of Computational Physics

107

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A detailed theoretical analysis of the thermodynamics and functional energetics of protein-DNA binding in the EcoRI endonuclease-DNA complex is presented. The standard free energy of complexation is considered in terms of a thermodynamic cycle of seven distinct steps decomposed into a total of 24 well-defined components. The model we employ involves explicit all-atom accounts of the energetics of structural adaptation of the protein and the DNA upon complex formation; the van der Waals and electrostatic interactions between the protein and the DNA; and the electrostatic polarization and screening effects, van der Waals components, and cavitation effects of solvation. The ion atmosphere of the DNA is described in terms of a counterion condensation model combined with a Debye-Huckel treatment of added salt effects. Estimates of entropy loss due to decreased translational and rotational degrees of freedom in the complex relative to the unbound species based on classical statistical mechanics are included, as well as corresponding changes in the vibrational and configurational entropy. The magnitudes and signs of the various components are estimated from the AMBER parm94 force field, generalized Born theory, solvent accessibility measures, and empirical estimates of quantities related to ion release.The calculated standard free energy of formation, −11.5 kcal/mol, agrees with experiment to within 5 kcal/mol. This net binding free energy is discerned to be the resultant of a balance of several competing contributions associated with chemical forces as conventionally defined, with 10 out of 24 terms favoring complexation. Contributions to binding compounded from subsets of the 24 components provide a basis for advancing a molecular perspective of binding in terms of structural adaptation, electrostatics, van der Waals interactions, hydrophobic effects, and small ion reorganization and release upon complexation. The van der Waals interactions and water release favor complexation, while electrostatic interactions, considering both intramolecular and solvation effects, prove unfavorable. Analysis of individual contributions to the standard free energy of complexation at the nucleotide and amino

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Structure of the CAP-DNA Complex at 2.5 Å Resolution: A Complete Picture of the Protein-DNA Interface

Cited by 263 publications

References 52 publications

Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

Free Energy Analysis of Protein–DNA Binding: The EcoRI Endonuclease–DNA Complex

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