PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 420847

Netropsin, a DNA-binding oligopeptide structural and binding studies.

H M Berman·S Neidle·C Zimmer·H Thrum
View original source ↗Export metadata ↓

Abstract

The crystal structure of netropsin, an oligopeptide which binds to DNA, has been determined. The molecule is bowed with the amide groups on the concave side, and the carbonyl and methyl groups on the convex side. The amide groups participate in extensive hydrogen bonding with water molecules; the charged amino end groups interact with the sulfate anions. Binding of netropsin to poly(dA) . poly(dT) under conditions of different ionic strength was also studied. Utilizing the crystallographic as well as the binding data, it is possible to build a model which explains the specificity of this antibiotic.

Explore related subjects

Circular DichroismCrystallographyGuanidinesNetropsinNucleic Acid ConformationPoly dA-dTPolydeoxyribonucleotidesProtein ConformationJournal ArticleResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

H M Berman, S Neidle, C Zimmer, H Thrum. 1979-01-26. Netropsin, a DNA-binding oligopeptide structural and binding studies.. https://doi.org/10.1016/0005-2787(79)90496-9

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

Deciphering the Function and Structure of PA1216 as an S-Adenosyl-l-Methionine Binding Protein Using Differential Scanning Fluorimetry and Circular Dichroism.

Microbes produce bioactive secondary metabolites as toxins, pigments, or virulence factors. These specialized compounds are produced by nonribosomal peptide synthetases (NRPS), polyketide synthases (PKS), or hybrid NRPS/PKS pathways. The genes encoding NRPS and PKS reside in biosynthetic gene clusters (BGCs), some of which have no identified metabolite associated with them. Characterization of these orphan BGCs could provide insights into potential bioactive compounds that have yet to be discovered. Here, we characterize PA1216, a putative methyltransferase embedded within an NRPS BGC in Pseudomonas aeruginosa strain PAO1. We cloned, expressed, and purified PA1216, and developed an optimized differential scanning fluorimetry assay to measure its thermal stability, demonstrating concentration-dependent stabilization in the presence of established methyltransferase cofactors and inhibitors. We then adapted this assay for high-throughput screening of potential PA1216 substrates, identifying destabilizing compounds, including glycyl-glycine dipeptides, amino esters with aromatic or basic side chains, and N-Boc-protected amino acids. In contrast, sodium salts of organic acids stabilized PA1216. Lastly, we employed AlphaFold to construct a predictive model, revealing that PA1216 contains a Rossmann-like fold and a glycine-rich loop, typical of class I methyltransferases, and we corroborated these secondary structural elements using circular dichroism spectroscopy. Overall, these studies illuminate PA1216 function and establish a platform for characterizing cryptic gene clusters within secondary metabolic pathways.

Circular Dichroism↗
PubMed1992

Synthesis and interaction studies of watersoluble nucleic acid analogs containing serine as a spacer.

Watersoluble nucleic acid analogs containing L- or D-serine as a spacer were synthesized. Thymine was used as nucleic acid bases of these analogs. The base contents of these analogs were 93-94%. These analogs were found to form stable polymer complexes with Poly A or DNA by specific base-base interaction, which were observed from hypochromicity of UV spectra. In both cases, the maximum hypochromicity values of PEI-L-Ser-Thy were higher than that of PEI-D-Ser-Thy.

Circular Dichroism↗