Elements of a DNA-polypeptide recognition code: Electrostatic potential around the double helix, and a stereospecific model for purine recognition

Rein, Robert; Garduno, Raymon; Egan, John T.; Columbano, Silvano; Coeckelenbergh, Yves; Macelroy, R. D.

doi:10.1016/0303-2647(77)90022-3

Cited by 17 publications

(4 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…If DNA and RNA double helices rather than individual nucleic acid bases are considered, the situation changes because several hydrogen-bonding recognition sites on the bases are now hidden by Watson-Crick-type base-pairing (Figure 18-3). Model building (1204,1205) and theoretical studies (1206) indicate that, as mentioned above, specific association between base-pairs embedded in double helices and amino acid side chains (or peptide groups) requires again the simultaneous formation of at least two hydrogen bonds. The minor (small) groove has the potential for distinguishing only between guanine and other bases (due to the unique guanine N2 amino group).…”

Section: General Considerations About Protein-nucleic Acid Interactionsmentioning

confidence: 89%

Principles of Nucleic Acid Structure

Saenger

1984

Springer Advanced Texts in Chemistry

5,985

312

6,279

View full text Add to dashboard Cite

Section: General Considerations About Protein-nucleic Acid Interactionsmentioning

confidence: 89%

Principles of Nucleic Acid Structure

Saenger

1984

Springer Advanced Texts in Chemistry

5,985

312

6,279

View full text Add to dashboard Cite

“…-Instrumental in the recognition of the guanine bases is an Arg residue on each arm, because of the well-documented possibilities of bidentate interactions occurring with 06 and N7 (16)(17)(18)(19)(20)(21). In the ~-sheet conformation, with Arg occurring as the first residue in the sequence, a L configuration of theCa carbon is necessary to orient the side chain towards the major groove whilst avoiding steric clashes.…”

Section: Discussionmentioning

confidence: 99%

“…a) The recourse to Arg rather than Lys or Orn as a cationic residue, on account of the well-documented capacity of this base to recognize guanine bases in the major groove (16)(17)(18)(19)(20)(21); energy balances including desolvation at the site of interaction resulted in a more favorable binding energetics for arginine rather than lysine binding to guanine (21).…”

Section: 'mentioning

confidence: 99%

Theoretical Design of a Bistetrapeptide Derivative of Mitoxantrone Targeted Towards the Double-Stranded Hexanucleotide Sequence d(GGCGCC)₂

Gresh

Kahn

1991

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

The hexanucleotide d(GGCGCC)2 is encountered in recurrent fashion within transcriptional activating sequences in retroviruses and protooncogenes. Our first theoretical design of novel oligopeptide derivatives of mitoxantrone, MTX (1), had enabled us to predict derivatives depsiGly-Lys(L) and depsiGly-Gly-Orn(D) to preferentially target the tetrameric core d(CCGG)2. Owing to the crucial importance of hexamer d(GGCGCC)2, we have attempted to extend the realm of our approach by now targeting this specific hexanucleotide. For that purpose, we undertook the design of further oligopeptide derivatives of MTX, in which each arm was identically amidated (rather than esterified as in (1)) by tri- or tetrapeptides of varying sequences and individual residue configurations. The binding affinities of these derivatives to the palindromic sequences d(GGCGCC)2, d(CGCGCG)2, d(GCCGGC)2 and d(CCCGGG)2, were compared by energy-minimization. We report here the results obtained with the most promising derivative, having the sequence Arg(L)-Gly-Val(L)-Glu(L), and displaying a considerable energy preference for d(GGCGCC)2 over the other candidate hexameric sites (referred to as I). In the corresponding complexes, the two arms are in two mutually antiparallel directions in the major groove, and adopt a beta-sheet like arrangement stabilized by two H-bonds involving the carbonyl and amide groups of the Gly residues. Each Arg side chain on a given arm chelates O6 and N7 atoms of G1, G2/G1', G2' with its imino and cis amino hydrogen, and is simultaneously bound through two amino hydrogens in a bidentate interaction with the Glu residue.

show abstract

“…Selectivity can only be possible if the electrostatic forces can cooperate with additional forces, which are governed by the 'conformation fit mechanism', existing only in the case of oligomers. Interactions governed by conformation have also been postulated by other authors as essential elements of the protein-DNA interaction [23,24]. In this paper the existence of such intcractions is proved experimentally and measured for the first time.…”

Section: Discussionmentioning

confidence: 64%

Studies on Interactions between Immobilized Lysine Residues and Oligomers of Thymidylic and Deoxyadenylic Acids

Schott

Eckstein

1980

European Journal of Biochemistry

View full text Add to dashboard Cite

Two groups of crosslinked polyacrylic gels with immobilized lysine and lysine peptides (Lys)~ and ( L y~)~-P r o have been used as models for the chromatographic investigation of lysine-peptide -oligonucleotide interactions. One group carries carboxylic groups in addition to the peptide residues in the gel matrix; the other gel type contains no such carboxylic groups in the gel matrix.Nucleotides of the series (dT)2-5, p(dT)l -4, p(dT)l -4p, (dA)2 -5 , p(dA)1-5 and p(dA)1-4p were chromatographed on these gels under various conditions in an aqueous buffer. On the gels of the first group the nucleotides were retarded only slighly, the positive charges of the &-amino groups being compensated partially or totally by the negatively charged carboxyl groups of the polymer matrix. On the gels of the second group, however, the oligonucleotides underwent specific interactions. These interactions were based primarily upon electrostatic forces between the positively charged E-amino groups of the immobilized peptides and the negatively charged phosphate groups of the oligonucleotides.Our results indicate that, in addition to the electrostatic interaction, the conformation plays a crucial role. We explain the selectivity of the interaction with a conformation-fit mechanism. The origin of this mechanism, which creates specific interactions from unspecific forces, is discussed.The organization of DNA and protein in chromatin is at present largely unknown and there is intense research activity in this area [l]. In order to evaluate and interpret histone-DNA interactions for example, model studies have been pursued using synthetic polypeptides [2-61, synthetic histone fragments [7] or histone [8-131 all complexed with DNA. Analysis of these interactions indicates a preferential binding of polylysine and lysine-rich histone to dA . dT-rich DNA. It was also found that the main characteristics which govern the interaction with DNA are located in the very lysine-rich part of the histone molecules In order to obtain more information about the elements of specificity in histone-DNA interactions, simple model systemes are required which allow one to characterize the individual interactions separately. To investigate the binding specificity between a DNA and a histone region, it ought to be profitable to apply [8,121. Abbreviations. The abbreviations for the nucleotides follow CBN Recommendations, see Eur. J . Biochem. 15,203-208 (1970). Note that (dN), has no terminal phosphates, p(dN), only the 5'-termlnal phosphate, p(dN).p both 3' and 5'-terminal phosphates.oligonucleotide-oligopeptide models. Until now, such analyses have not been performed, because convenient methods for the characterization of oligonucleotideoligopeptide interactions have not been available.Recently two methods have been published which make it possible to investigate the oligonucleotideoligopeptide interactions. One method uses the fieldjump technique [14]. The other, a very simple chromatographic approach [15,16], allows one to determine directly the strength...

show abstract

Elements of a DNA-polypeptide recognition code: Electrostatic potential around the double helix, and a stereospecific model for purine recognition

Cited by 17 publications

References 16 publications

Principles of Nucleic Acid Structure

Principles of Nucleic Acid Structure

Theoretical Design of a Bistetrapeptide Derivative of Mitoxantrone Targeted Towards the Double-Stranded Hexanucleotide Sequence d(GGCGCC)₂

Studies on Interactions between Immobilized Lysine Residues and Oligomers of Thymidylic and Deoxyadenylic Acids

Contact Info

Product

Resources

About

Elements of a DNA-polypeptide recognition code: Electrostatic potential around the double helix, and a stereospecific model for purine recognition

Cited by 17 publications

References 16 publications

Principles of Nucleic Acid Structure

Principles of Nucleic Acid Structure

Theoretical Design of a Bistetrapeptide Derivative of Mitoxantrone Targeted Towards the Double-Stranded Hexanucleotide Sequence d(GGCGCC)2

Studies on Interactions between Immobilized Lysine Residues and Oligomers of Thymidylic and Deoxyadenylic Acids

Contact Info

Product

Resources

About

Theoretical Design of a Bistetrapeptide Derivative of Mitoxantrone Targeted Towards the Double-Stranded Hexanucleotide Sequence d(GGCGCC)₂