A decapeptide motif for binding to the minor groove of DNA A proposal

Turnell, William G.; Satchwell, Sandra C.; Travers, Andrew

doi:10.1016/0014-5793(88)80750-6

Cited by 39 publications

(13 citation statements)

References 23 publications

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“…3) shows that PepA is generally alkaline, perhaps inviting electrostatic attraction of the DNA, and three potential binding sites have been surmised from a detailed examination. Helix 2 lies along the apex of the molecule (Figs 2 and 3) and bears a superficial resemblance to histone helices thought to bind across the minor groove of DNA wrapping around a protein core (Turnell et al, 1988). The N-terminus and the 10-residue insertion have sequences with a weak similarity to proline-rich, DNA binding motifs (Churchill and Travers, 1991).…”

Section: Resultsmentioning

confidence: 99%

Nucleoprotein architecture and ColE1 dimer resolution: a hypothesis

Hodgman

Griffiths

Summers

1998

Molecular Microbiology

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SummaryDimers of plasmid ColE1 are converted to monomers by site-specific recombination, a process that requires 240 bp of DNA (cer ) and four host-encoded proteins (XerC, XerD, ArgR and PepA). Here, we propose structures for nucleoprotein complexes involved in cer -Xer recombination based upon existing knowledge of the structures of component proteins and computational analyses of protein structure and DNA curvature. We propose that, in the nucleoprotein complex at a single cer site, a PepA hexamer acts as an adaptor, connecting the heterodimeric recombinase (XerCD) to an ArgR hexamer. This provides a protein core around which the cer site wraps, its exact path being defined by strong sequence-specific interactions with ArgR and XerCD, weak interactions with PepA and sequencedependent flexibility of cer. The initial association of single-site complexes (pairing) is proposed to occur via an ArgR-PepA interaction. Pairing between sites in a plasmid dimer is stabilized by DNA supercoiling and is followed by a structural isomerization to form a recombination-proficient synaptic complex. We propose that paired structures formed between sites in trans are too short-lived to permit synaptic complex formation. There is thus an energetic barrier to inappropriate recombination reactions. Our proposals are consistent with a wide range of experimental observations.

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Section: Resultsmentioning

confidence: 99%

Nucleoprotein architecture and ColE1 dimer resolution: a hypothesis

Hodgman

Griffiths

Summers

1998

Molecular Microbiology

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“…Miller et al, 1985;Brennan and Mathews, 1989;Knight et al, 1989), the types of putative structural motifs that a protein might use for minor groove binding are relatively undefined. However, motifs for minor groove binding have been proposed, including an ce-helix for protamine (Warrant and Kim, 1978) and for a decapeptide IRL Press sequence found in the globular domain of histone HI (Turnell et al, 1988), an anti-parallel fl-ribbon (Kim, 1983), and a special type of fl-turn structure for the sequence motifs SPK(R)K(R) ('SPKK') and SPXX (Suzuki, 1988a(Suzuki, , 1989a. Here we show that the 'SPKK' motif, found primarily in histones, binds to the minor groove of DNA with a degree of sequence specificity for A/T-rich sites.…”

Section: Introductionmentioning

confidence: 99%

‘SPKK’ motifs prefer to bind to DNA at A/T-rich sites.

1989

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The termini of histone H1 and sea urchin spermatogenous H1 and H2B, which are essential for correct chromatin condensation, often contain repeats of the sequence SPK(R)K(R). A special type of beta‐turn structural motif has been proposed for this sequence, and it has been shown that a segment of the sea urchin sperm H1 N terminus, which has six repeats of the motif (S6 peptide), binds to DNA and competes with the DNA binding drug Hoechst 33258. Here, we demonstrate by quantitative analysis of hydroxyl radical footprints that the synthetic oligopeptide, SPRKSPRK (S2), and the S6 peptide prefer to bind to the minor groove of DNA at the same A/T‐rich sites. The locations of these binding sites are similar to Hoechst, but the sequence specificity of the oligopeptides is lower than that of Hoechst, and the detailed protection patterns differ slightly. We suggest that these small peptides and Hoechst recognize similar sequence‐dependent features of the local architecture of DNA.

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“…This glycoprotein, derived from the chemically and antigenically indistinguishable circulating serum amyloid P-component (SAP) [6], is invariably present in all forms of amyloid known [2]. It shares an extensive cDNA and amino acid sequence homology with C-reactive protein (CRP) [7,8] as well as a structural motif homologous with histones H 1 and H4 [9], possibly responsible for its reported DNA-binding properties [10,11]. The protein, a member of the pentraxin family, is calcium-dependently associated with the amyloid fibrils [12,13], and citrate or EDTA is thus used to remove it.…”

Section: Introductionmentioning

confidence: 99%

On the association between amyloid fibrils and glycosaminoglycans; possible interactive role of Ca2+ and amyloid P-component

Stenstad

Magnus

Syse

et al. 1993

Clinical and Experimental Immunology

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SUMMARYWe have previously reported the specific association of glycosaminoglycans (GAG) and proteoglycans (PG) with amyloid fibrils and characterized the polysaccharides directly extracted from amyloid-laden tissues. In the present study we further elucidate the association between purified amyloid fibrils and GAG/PG with special reference to those GAG/PG associated with amyloid Pcomponent (AP) and the interactive role of Ca2+ ions. Amyloid fibrils were isolated from human hepatic AA amyloid employing water extraction with and without preceding removal of AP, an extrafibrillar protein component of all amyloids, using sodium citrate. GAG/PG co-isolated with the amyloid extracts, with and without AP, were isolated and characterized. Agarose-affinity chromatography of extracts containing AP was performed, and the GAG associated with this extrafibrillary protein were characterized as well. Several different GAG/PG populations were demonstrated in the various extracts. The abolition of calcium-dependent binding markedly influenced the amount of GAG/PG recovered in the fibril extracts, as well as the total amount of amyloid material obtained. Thus, it seems that calcium plays an important role in the association between the fibrils and the sugar moieties, and that a significant fraction of the GAG found in amyloid exhibits a Ca2+-dependent fibril-GAG interaction. No significant difference in the proportion between galactosaminoglycans and glucosamines was, however, disclosed when the two extraction protocols were compared, suggesting that no particular GAG species has a higher affinity for the fibrils themselves. Both dermatan/chondroitin sulphate and heparan sulphate identified in the present study exhibited a Ca2+-dependent interaction with AP, supporting previous findings. However, the amyloid-associated galactosaminoglycans found, especially the large PG appearing in small amounts, seemed to have a higher affinity for the extrafibrillar AP than the other GAG.

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A decapeptide motif for binding to the minor groove of DNA A proposal

Cited by 39 publications

References 23 publications

Nucleoprotein architecture and ColE1 dimer resolution: a hypothesis

Nucleoprotein architecture and ColE1 dimer resolution: a hypothesis

‘SPKK’ motifs prefer to bind to DNA at A/T-rich sites.

On the association between amyloid fibrils and glycosaminoglycans; possible interactive role of Ca2+ and amyloid P-component

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