Peptide tertiary structure nucleation by side-chain crosslinking with metal complexation and double "click" cycloaddition.
Ontology highlight
ABSTRACT:
SUBMITTER: Torres O
PROVIDER: S-EPMC2981402 | biostudies-literature | 2008 Jul
REPOSITORIES: biostudies-literature
Publications
Peptide tertiary structure nucleation by side-chain crosslinking with metal complexation and double "click" cycloaddition.
Torres Oscar O Yüksel Deniz D Bernardina Matt M Kumar Krishna K Bong Dennis D
Chembiochem : a European journal of chemical biology 20080701 11
Similar Datasets
Project description:We previously described potent inhibition of Ebola virus entry by a 'C-peptide' based on the GP2 C-heptad repeat region (CHR) targeted to endosomes ('Tat-Ebo'). Here, we report the synthesis and evaluation of C-peptides conjugated to cholesterol, and Tat-Ebo analogs containing covalent side chain-side chain crosslinks to promote α-helical conformation. We found that the cholesterol-conjugated C-peptides were potent inhibitors of Ebola virus glycoprotein (GP)-mediated cell entry (~10(3)-fold reduction in infection at 40 μM). However, this mechanism of inhibition is somewhat non-specific because the cholesterol-conjugated peptides also inhibited cell entry mediated by vesicular stomatitis virus glycoprotein G. One side chain-side chain crosslinked peptide had moderately higher activity than the parent compound Tat-Ebo. Circular dichroism revealed that the cholesterol-conjugated peptides unexpectedly formed a strong α-helical conformation that was independent of concentration. Side chain-side chain crosslinking enhanced α-helical stability of the Tat-Ebo variants, but only at neutral pH. These result provide insight into mechanisms of C-peptide inhibiton of Ebola virus GP-mediated cell entry.
| S-EPMC3822755 | biostudies-literature
Project description:The copper-catalyzed alkyne-azide cycloaddition (CuAAC) is one of the most powerful chemical strategies for selective fluorescent labeling of biomolecules in in vitro or biological systems. In order to accelerate the ligation process and ensure efficient formation of conjugates under diluted conditions, external copper(I) ligands or sophisticated copper(I)-chelating azides are used. This latter strategy, however, increases the bulkiness of the triazole linkage, thus perturbing the biological function or dynamic behavior of the conjugates. In a proof-of-concept study, we investigated the use of an extremely compact fluorophore-based copper(I) chelating azide in order to accelerate the CuAAC with concomitant fluorescence labeling; in our strategy, the fluorophore is able to complex copper(I) species while retaining its photophysical properties. It is believed that this unprecedented approach which was applied for the labeling of a short peptide molecule and the fluorescent labeling of live cells, could be extended to other families of nitrogen-based fluorophores in order to tune both the reaction rate and photophysical characteristics.
| S-EPMC7225998 | biostudies-literature
Project description:The metal-free reaction of 5-(2-arylethenyl)-3-aryl-1,2,4-oxadiazoles with arenes in neat triflic acid (TfOH, CF3SO3H), both under thermal and microwave conditions, leads to 5-(2,2-diarylethyl)-3-aryl-1,2,4-oxadiazoles. The products are formed through the regioselective hydroarylation of the side chain carbon-carbon double bond of the starting oxadiazoles in yields up to 97%. According to NMR data and DFT calculations, N4,C-diprotonated forms of oxadiazoles are the electrophilic intermediates in this reaction.
| S-EPMC5433146 | biostudies-literature
Project description:Observing the structures of proteins within the cell and tracking structural changes under different cellular conditions are the ultimate challenges for structural biology. This, however, requires an experimental technique that can generate sufficient data for structure determination and is applicable in the native environment of proteins. Crosslinking/mass spectrometry (CLMS) and protein structure determination have recently advanced to meet these requirements and crosslinking-driven de novo structure determination in native environments is now possible. In this opinion article, we highlight recent successes in the field of CLMS with protein structure modeling and challenges it still holds.
| S-EPMC5854373 | biostudies-other
Project description:Thin films formed by complexation of oppositely charged polyelectrolytes have significant potential in applications such as separation membranes, biocompatible or anticorrosion coatings, and drug delivery systems. While layer-by-layer deposition is a reliable method for producing conformal films, this multi-step process limits scalability. In this study, we functionalize polymers with photoactive protecting and crosslinking groups, allowing a one-step approach for preparing polyelectrolyte complex (PEC) films. To achieve this goal, we introduced o-nitrobenzyl and coumarin groups into a polyanion. The o-nitrobenzyl protecting groups can be selectively deprotected upon exposure to 365 nm light, revealing charged pendent groups that initiate polyelectrolyte complexation. Simultaneously, the coumarin units in the copolymers undergo dimerization, enhancing the solvochemical stability of the PEC films. Notably, short-wave UV irradiation (254 nm) enables retrocyclization of the coumarin dimers, returning the PEC film to its uncrosslinked state. These UV-driven deprotection, crosslinking, and de-crosslinking processes provide a versatile and tunable platform for fabricating reversibly crosslinked films. By integrating photoresponsive polymers and reversible covalent linkages, this approach offers new opportunities for designing PEC materials with tunable dynamic properties for advanced applications.
| S-EPMC11886613 | biostudies-literature
Project description:The synthesis of a 4-dibenzocyclooctynol (DIBO) functionalized polyethylene glycol (PEG) and fabrication of hydrogels via strain-promoted, metal-free, azide-alkyne cycloaddition is reported. The resulting hydrogel materials provide a versatile alternative in which to encapsulate cells that are sensitive to photochemical or chemical crosslinking mechanisms.
| S-EPMC3507357 | biostudies-literature
Project description:The development of constrained peptides for inhibition of protein-protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine (hCys) amino acids spaced at i and i + 4 positions by double substitution. The constraint can be readily removed by displacement of the maleimide using excess thiol. This new constraining methodology results in enhanced α-helical conformation (BID and RNase S peptide) as demonstrated by circular dichroism and molecular dynamics simulations, resistance to proteolysis (BID) as demonstrated by trypsin proteolysis experiments and retained or enhanced potency of inhibition for Bcl-2 family protein-protein interactions (BID), or greater capability to restore the hydrolytic activity of the RNAse S protein (RNase S peptide). Finally, use of a dibromomaleimide functionalized with an alkyne permits further divergent functionalization through alkyne-azide cycloaddition chemistry on the constrained peptide with fluorescein, oligoethylene glycol or biotin groups to facilitate biophysical and cellular analyses. Hence this methodology may extend the scope and accessibility of peptide stapling.
| S-EPMC5618791 | biostudies-literature
Project description:Genetic code expansion is a powerful tool for the study of protein interactions, as it allows for the site-specific incorporation of a photoreactive group via non-canonical amino acids. Recently, several groups have published bifunctional amino acids that carry a handle for click chemistry in addition to the photo-crosslinker. This allows for the specific labeling of crosslinked proteins and therefore the pulldown of peptides for further analysis. This review describes the properties and advantages of different bifunctional amino acids, and gives an overview about current and future applications.
| S-EPMC7226127 | biostudies-literature
Project description:Creating atomic defects in nanomaterials is an effective approach to promote the catalytic performance of a catalyst, but the defective catalysts are often prone to mechanical collapse if not properly synthesized. The uncontrollably formed defects also make it difficult to systematically investigate their effects on the catalytic performance. Herein, we report an efficient method of ionic reductive complexation extraction (IRCE) to fabricate atomic vacancies in a transition metal based nanomaterial without damaging its nanostructure, turning the otherwise catalytically inactive material to an advanced catalyst towards water oxidation in alkaline electrolyte. Here nickel based layered double hydroxide mixed with Cu(ii) is used to demonstrate the concept. With a tunable content and uniform dispersion of Cu(ii) on the brucite layer of the LDH, a suitable complexing agent could specifically combine with and remove the target Cu(ii), thereby creating the desired vacancies. The resulting vacancy rich TM LDH is found to be an excellent OER electrocatalyst with a low overpotential and small Tafel slope, due to the purposely modulated geometric and electronic structures of the active sites, and the greatly decreased charge transfer resistance.
| S-EPMC6839596 | biostudies-literature
Project description:Cholesterol is a ubiquitous hydrocarbon compound that can serve as substrate for microbial growth. This steroid and related cyclic compounds are recalcitrant due to their low solubility in water, complex ring structure, the presence of quaternary carbon atoms, and the low number of functional groups. Aerobic metabolism therefore makes use of reactive molecular oxygen as co-substrate of oxygenases to hydroxylate and cleave the sterane ring system. Consequently, anaerobic metabolism must substitute oxygenase-catalyzed steps by O(2)-independent hydroxylases. Here we show that one of the initial reactions of anaerobic cholesterol metabolism in the β-proteobacterium Sterolibacterium denitrificans is catalyzed by an unprecedented enzyme that hydroxylates the tertiary C25 atom of the side chain without molecular oxygen forming a tertiary alcohol. This steroid C25 dehydrogenase belongs to the dimethyl sulfoxide dehydrogenase molybdoenzyme family, the closest relative being ethylbenzene dehydrogenase. It is a heterotrimer, which is probably located at the periplasmic side of the membrane and contains one molybdenum cofactor, five [Fe-S] clusters, and one heme b. The draft genome of the organism contains several genes coding for related enzymes that probably replace oxygenases in steroid metabolism.
| S-EPMC3481293 | biostudies-literature