Contribution of cation-π interactions to the stability of protein-DNA complexes 1 1Edited by J. Thornton

Wintjens, René; Liévin, Jacques; Rooman, Marianne; Buisine, Eric

doi:10.1006/jmbi.2000.4040

Cited by 219 publications

(237 citation statements)

References 57 publications

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“…However, the reorientation of the nucleobase positions the six-membered heterocycle above Arg-587 (Fig. 2, B and D), a less favored arrangement observed only in rare cases (47). In summary, the distance between 3Ј-OH and the ␣-phosphate increases in the following direction KlenTaq F-A Ͻ KlenTaq F-G-II Ͻ KlenTaq F-G-I that are all longer than the one observed in the canonical case (Fig.…”

Section: Klentaq With Ddgtp Opposite An Abasic Site (Klentaq F-g-i mentioning

confidence: 77%

“…However, in KlenTaq F-G-I , ddGTP is stabilized by cation-interaction with Arg-587. Because this type of interaction strongly depends on the distribution of the electron density in the aromatic ring system, there is in the case of purines a clear preference for arginine to position itself below or above the imidazole five-atom ring system (47). Indeed, this is observed in KlenTaq F-G-I for Arg-587 (Fig.…”

Section: Klentaq With Ddgtp Opposite An Abasic Site (Klentaq F-g-i mentioning

confidence: 93%

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Amino Acid Templating Mechanisms in Selection of Nucleotides Opposite Abasic Sites by a Family A DNA Polymerase

Obeid

Welte

Diederichs

et al. 2012

Journal of Biological Chemistry

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Background: Abasic sites are the most frequent DNA lesions and are often bypassed by incorporating an adenosine opposite that lesion. Results: We determined structures of DNA polymerase in complex with different nucleotides opposite an abasic site. Conclusion: Interaction of the incoming nucleotide with a single amino acid governs nucleotide selection opposite abasic sites. Significance: This work furthers the understanding of the bypass of a mutagenic lesion by DNA polymerases.

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Section: Klentaq With Ddgtp Opposite An Abasic Site (Klentaq F-g-i mentioning

confidence: 77%

Section: Klentaq With Ddgtp Opposite An Abasic Site (Klentaq F-g-i mentioning

confidence: 93%

Amino Acid Templating Mechanisms in Selection of Nucleotides Opposite Abasic Sites by a Family A DNA Polymerase

Obeid

Welte

Diederichs

et al. 2012

Journal of Biological Chemistry

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show abstract

“…analysis of spatial distances, atom-atom interaction angles) (Mandel-Gutfreund et al, 1998a) or statistical/probabilistic considerations (Luscombe et al, 2000;Reddy et al, 2001). Other types of interactions between amino acids and bases in the major or minor grooves, including the effect of water molecules (Luscombe et al, 2001;Morávek et al, 2002) cation-p (Wintjens et al, 2000;Rooman et al, 2002) and stacking interactions (Rooman et al, 2002;Biot et al, 2004) were investigated. Consequently, databases with these interactions were created, such as Protein-Side Chain Interactions database and Protein-Nucleic Acid Interaction server (Flocco and Mowbray, 1994) which allowed predicting common rules that assign the recognition process.…”

Section: Protein-dna Interactionsmentioning

confidence: 99%

“…Wintjens et al (2000) showed the existence of cation-p interactions by analysing 48 highresolution X-ray structures of protein-DNA complexes and by quantum mechanics energy calculations. They found frequent proximity of aromatic rings of nucleotides bases and positively charged groups of amino acid side chains.…”

Section: Stair Motifs In Protein/dna Complexesmentioning

confidence: 99%

Amino acids–nucleotides biomolecular recognition: from biological occurrence to affinity chromatography

Sousa

Cruz

Queiroz

2010

J of Molecular Recognition

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aIn this review, the protein-DNA interactions are discussed considering different perspectives, and the biological occurrence of this interaction is explained at atomic level. The evaluation of the amino acid-nucleotide recognition has been investigated analysing datasets for predicting the association preferences and the geometry that favours the interaction.Based on this knowledge, an affinity chromatographic method was developed also exploiting this biological favoured contact. In fact, the implementation of this technique brings the possibility to apply the concept of molecular interactions to the development of new purification methodologies. In addition, the integration of the information recovered by all the different perspectives can bring new insights about some biological mechanisms, though not totally clarified.

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“…This increasing trend has driven the development of a variety of improvements in protein expression and stability analysis. The stability can be determined by several interactions such as salt bridge, di-sulfide bond, conventional hydrogen bonds electrostatic interaction, Van crucial in many areas of modern chemistry, especially in the field of molecular recognition and for structural stability (Hunter et al, 1990;Wintjens et al, 2000). In addition cation-π interaction (Dougherty, 1996; Ma and Dougherty, 1997; Scrutton and Raine, 1996) is increasingly recognized as an important noncovalent binding interaction relevant to structural biology.…”

Section: Introductionmentioning

confidence: 99%

Role of the Cation-π Interaction in Therapeutic Proteins: A Comparative Study with Conventional Stabilizing Forces

Shanthi¹,

Ramanathan²

2009

J Comput Sci Syst Biol

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The cation-π interaction is an important, general force for molecular recognition in biological receptors. In this study, we have analyzed the energy contribution resulting from cation-π interactions in the set of therapeutic proteins. The contribution of cation-π interacting residues in secondary structure involvement, solvent accessibility, stabilization centers, stabilizing residues and conservation score has been evaluated. Secondary structure of the cation-π involving residues shows that, Arg and Lys prefers to be in strand. Among the π residues, Phe prefer to be in coil, Tyr prefers to be in strand and Trp prefer to be in helix. Among the cation-π interacting residues Arg and Lys were in the exposed regions. Phe and Tyr were in the partially buried region and Trp in the fully buried region. Stabilization centers for these proteins showed that all the five residues found in cation-π interactions are important in locating one or more of such centers. The contribution of stabilizing residues in the cation-π interactions was analyzed. Further, the study shows that, 43 percent of the amino acid residues that are involved in cation-π interactions might be conserved in therapeutic proteins. The comparison between the conventional and nonconventional interactions in the data set, clearly depict the significance of cation-π interaction in the stability of therapeutic proteins. On the whole, the results presented in this work will be very useful for understanding the contribution of cation-π interaction to the stability of therapeutic proteins.

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Contribution of cation-π interactions to the stability of protein-DNA complexes 1 1Edited by J. Thornton

Cited by 219 publications

References 57 publications

Amino Acid Templating Mechanisms in Selection of Nucleotides Opposite Abasic Sites by a Family A DNA Polymerase

Amino Acid Templating Mechanisms in Selection of Nucleotides Opposite Abasic Sites by a Family A DNA Polymerase

Amino acids–nucleotides biomolecular recognition: from biological occurrence to affinity chromatography

Role of the Cation-π Interaction in Therapeutic Proteins: A Comparative Study with Conventional Stabilizing Forces

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