Protein-DNA interactions: a structural analysis

Jones, Susan R.; Heyningen, Paul van; Berman, Helen M.; Thornton, Janet M.

doi:10.1006/jmbi.1999.2659

Cited by 399 publications

(372 citation statements)

References 96 publications

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“…That is, the deformations of helical structure occur in the context of the water molecules, proteins, and other species in direct contact with the double helix. Prior to our work, analyses of such interactions were literal and statistical in the sense of counting the number of different contacts in known structures 13,14 , or protein-centric in the sense of cataloging the various amino acids and folding motifs in close contact with nucleic acid [15][16][17][18] . Many of the tools developed to visualize protein-DNA complexes, e.g., NUCPLOT 19 , similarly focus on the identities of amino acids or secondary structural elements with respect to DNA primary structure.…”

Section: Introductionmentioning

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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Section: Introductionmentioning

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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“…Non-specific interactions between proteins and DNA are poorly documented, but the predominance of electrostatic undeniable [14,15,16,17,18,19]. Proteins that bind to DNA are most often positively charged.…”

Section: Proteins 421 Chargementioning

confidence: 99%

“…This supports the idea that electrostatics is involved to some extent in the intermittent behavior, with a probable role for the dissolved salt ions. Electrostatics plays indeed a major role in the protein-DNA interaction [14,15,16,17,18,19,20]. The reason is that DNA is very strongly negatively charged (-2 charges per base pair).…”

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confidence: 99%

“…The reason is that DNA is very strongly negatively charged (-2 charges per base pair). On the other hand, DNA-binding proteins are most often positively charged on the surface that faces DNA, so to be attracted onto it [14,15].…”

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confidence: 99%

“…This reading can be performed, besides other interactions, by the formation of hydrogen bonds between the protein and the side of the base pairs exposed toward the major groove, without opening the double helix [14,15]. Since the patterns of hydrogen bonds that may be formed on each base pair is different, a protein can discriminate precisely a target site by looking for the formation of the good hydrogen bond pattern along the entire sequence visited.…”

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confidence: 99%

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Protein–DNA Electrostatics

Barbi¹,

Paillusson²

2013

Dynamics of Proteins and Nucleic Acids

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Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any active process. It has been rapidly recognized that to achieve this task these proteins should be efficient at both searching (i.e. sampling fast relevant parts of DNA) and finding (i.e. recognizing the specific site).A two-mode search and variants of it have been suggested since the 70s to explain either a fast search or an efficient recognition. Combining these two properties at a phenomenological level is however more difficult as they appear to have antagonist roles. To overcome this difficulty, one may simply need to drop the dichotomic view inherent to the two-mode search and look more thoroughly at the set of interactions between DNA-binding proteins and a given 1 arXiv:1311.7496v1 [physics.bio-ph] 29 Nov 2013 DNA segment either specific or non-specific. This chapter demonstrates that, in doing so in a very generic way, one may indeed find a potential reconciliation between a fast search and an efficient recognition. Although a lot remains to be done, this could be the time for a change of paradigm.

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Comparison of molecular dynamics and harmonic mode calculations on RNA

Zacharias

2000

Biopolymers

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Conformational fluctuations of a double‐stranded RNA oligonucleotide have been calculated from a two nanosecond molecular dynamics simulation including explicit waters and ions and from a harmonic mode analysis. The harmonic mode analysis was performed in the absence of solvent using various effective dielectric screening functions. RNA flexiblity was analyzed and compared at the level of atomic position fluctuations, helical base‐pair descriptor fluctuations and global helix bending, stretching, and twisting flexibilities. Although quantitative differences were found, the qualitative pattern of atomic position and helical descriptor fluctuations along the sequence was similar for both methods. For the helical descriptor flexibility, the largest differences were observed for base‐pair roll and rise that showed two times larger fluctuations in the molecular dynamics simulation. A significant overlap between the subspace spanned by soft principal components calculated from the molecular dynamics simulation and harmonic modes was found. Both approaches predict a negative covariation for most helical base‐pair step descriptors of neighboring base pair steps (with the exception of rise), which tend to stiffen the RNA at the global level. The RNA persistence length extracted from the molecular dynamics simulation (350–600 Å) is smaller than the experimental value (∼720 Å) and estimates based on the harmonic mode approach (1100–1700 Å). © 2000 John Wiley & Sons, Inc. Biopoly 54: 547–560, 2000

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Protein-DNA interactions: a structural analysis

Cited by 399 publications

References 96 publications

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

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

Protein–DNA Electrostatics

Comparison of molecular dynamics and harmonic mode calculations on RNA

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