Traceless synthesis of protein thioesters using enzyme-mediated hydrazinolysis and subsequent self-editing of cysteinyl prolyl sequence

A traceless thioester-producing protocol featuring carboxypeptidase Y-mediated hydrazinolysis of cysteinyl prolyl leucine-tagged peptides has been developed. The hydrazinolysis followed by thioesterification affords cysteinyl prolyl thioesters. Self-editing of the tag and subsequent trans-thioesterification yields peptide thioesters. The developed protocol was successfully applied to conversion of recombinant proteins to thioesters

An affordable and customizable wave buoy for the study of wave-ice interactions: design concept and results from field deployments

In the polar regions, the interaction between waves and ice has a crucial impact on the seasonal change in the sea ice extent. However, our comprehension of this phenomenon is restricted by a lack of observations, which, in turn, results in the exclusion of associated processes from numerical models. In recent years, availability of the low-cost and accurate Inertial Motion Units has enabled the development of affordable wave research devices. Despite advancements in designing innovative open-source instruments optimized for deployment on ice floes, their customizability and survivability remain limited, especially in open waters. This study presents a novel design concept for an affordable and customizable wave buoy, aimed for wave measurements in marginal ice zones. The central focus of this wave buoy design is the application of 3D printing as rapid prototyping technology. By utilizing the high customizability offered by 3D printing, the previously developed solar-powered wave buoy was customized to install a battery pack to continue the measurements in the high latitudes for more than several months. Preliminary results from field deployments in the Pacific and Arctic Oceans demonstrate that the performance of the instruments is promising. The accuracy of frequency wave spectra measurements is found to be comparable to that of considerably more expensive instruments. Finally, the study concludes with a general evaluation of using rapid prototyping technologies for buoy designs and proposes recommendations for future designs

Simulating Assembly Landscapes for Comprehensive Understanding of Supramolecular Polymer-Solvent Systems

Complexity in supramolecular polymer systems arises from interactions between different components, including solvent molecules. By varying their concentration or temperature in such multicomponent systems, complex phenomena can occur such as thermally bisignate and dilution-induced assembly of supramolecular polymers. Herein, we demonstrate that both these phenomena emerge from the same underlying interaction mechanism between the components. As a model system, amide-decorated supramolecular polymers of porphyrins were investigated in combination with aliphatic alcohols as hydrogen-bond scavengers, and thermodynamic mass-balance models were applied to map the three-dimensional assembly landscapes. These studies unveiled that the interaction between hydrogen-bond scavengers and monomers is temperature-dependent and becomes dominant at high monomer concentrations. With these insights, we could exploit competitive monomer-alcohol interactions to prompt the dilution-induced assembly of various common monomers as well as bisignate assembly events. Moreover, kinetic insights were obtained by navigating through the assembly landscape. Similar to phase diagrams of covalent polymers, these assembly landscapes provide a comprehensive picture of supramolecular polymerizations, which helps to precisely regulate the system properties. The generality of this approach using assembly landscapes makes it relevant for any supramolecular system, and this enhanced control will open the door to build complex and functional supramolecular polymer systems.</p

Development of a 1,3a,6a-triazapentalene derivative as a compact and thiol-specific fluorescent labeling reagent

For the fluorescence imaging of biologically active small compounds, the development of compact fluorophores that do not perturb bioactivity is required. Here we report a compact derivative of fluorescent 1,3a,6a-triazapentalenes, 2-isobutenylcarbonyl-1,3a,6a-triazapentalene (TAP-VK1), as a fluorescent labeling reagent. The reaction of TAP-VK1 with various aliphatic thiols proceeds smoothly to afford the corresponding 1,4-adducts in high yields, and nucleophiles other than thiols do not react. After the addition of thiol groups in dichloromethane, the emission maximum of TAP-VK1 shifts to a shorter wavelength and the fluorescence intensity is substantially increased. The utility of TAP-VK1 as a compact fluorescent labeling reagent is clearly demonstrated by the labeling of Captopril, which is a small molecular drug for hypertension. The successful imaging of Captopril, one of the most compact drugs, in this study demonstrates the usefulness of compact fluorophores for mechanistic studies

N-Sulfanylethylanilide-based traceable linker for enrichment and selective labelling of target proteins

An N-sulfanylethylanilide-based traceable linker, developed to facilitate identification of target proteins of bioactive compounds, was introduced into an alkynylated target protein. Subsequent adsorption onto streptavidin beads allowed it to be treated with a cysteine-fluorophore conjugate in the presence of phosphate. This induced the N-S acyl transfer reaction of the N-sulfanylethylanilide unit. The subsequent native chemical ligation of the fluorophore resulted in cleavage of the linker for target elution and fluorescent labelling of the target, allowing it to be distinguished from non-target proteins

Tailored Synthesis of 162-Residue S-Monoglycosylated GM2-Activator Protein (GM2AP) Analogues that Allows Facile Access to Protein Library

A synthetic protocol has been developed for the preparation of 162-residue S-monoglycosylated GM2-activator protein (GM2AP) analogues bearing various amino acid substitutions for Thr69. The facile incorporation of the replacements into the protein was achieved by a one-pot/N–to–C-directed sequential ligation strategy using readily accessible middle N-sulfanylethylanilide (SEAlide) peptides consisting of seven amino acid residues. A kinetically-controlled ligation protocol was successfully applied to the assembly of three peptide segments covering the GM2AP. The native chemical ligation (NCL) reactivities of the SEAlide can be tuned by the presence or absence of phosphate salts. Furthermore, the NCL of the alkyl thioester fragment (GM2AP (1–31)) with the N-terminal cysteinyl prolyl thioester (GM2AP (32–67)) proceeded smoothly to yield the 67-residue prolyl thioester, with the prolyl thioester moiety remaining intact. This newly developed strategy enabled the facile synthesis of GM2AP analogues. Thus, we refered this synthetic protocol as “Tailored Synthesis” for the construction of a GM2AP library

Ribosome binding protein GCN1 regulates the cell cycle and cell proliferation and is essential for the embryonic development of mice.

Amino acids exert many biological functions, serving as allosteric regulators and neurotransmitters, as constituents in proteins and as nutrients. GCN2-mediated phosphorylation of eukaryotic initiation factor 2 alpha (elF2α) restores homeostasis in response to amino acid starvation (AAS) through the inhibition of the general translation and upregulation of amino acid biosynthetic enzymes and transporters by activating the translation of Gcn4 and ATF4 in yeast and mammals, respectively. GCN1 is a GCN2-binding protein that possesses an RWD binding domain (RWDBD) in its C-terminus. In yeast, Gcn1 is essential for Gcn2 activation by AAS; however, the roles of GCN1 in mammals need to be established. Here, we revealed a novel role of GCN1 that does not depend on AAS by generating two Gcn1 mutant mouse lines: Gcn1-knockout mice (Gcn1 KO mice (Gcn1-/-)) and RWDBD-deleted mutant mice (Gcn1ΔRWDBD mice). Both mutant mice showed growth retardation, which was not observed in the Gcn2 KO mice, such that the Gcn1 KO mice died at the intermediate stage of embryonic development because of severe growth retardation, while the Gcn1ΔRWDBD embryos showed mild growth retardation and died soon after birth, most likely due to respiratory failure. Extension of pregnancy by 24 h through the administration of progesterone to the pregnant mothers rescued the expression of differentiation markers in the lungs and prevented lethality of the Gcn1ΔRWDBD pups, indicating that perinatal lethality of the Gcn1ΔRWDBD embryos was due to simple growth retardation. Similar to the yeast Gcn2/Gcn1 system, AAS- or UV irradiation-induced elF2α phosphorylation was diminished in the Gcn1ΔRWDBD mouse embryonic fibroblasts (MEFs), suggesting that GCN1 RWDBD is responsible for GCN2 activity. In addition, we found reduced cell proliferation and G2/M arrest accompanying a decrease in Cdk1 and Cyclin B1 in the Gcn1ΔRWDBD MEFs. Our results demonstrated, for the first time, that GCN1 is essential for both GCN2-dependent stress response and GCN2-independent cell cycle regulation

Development of a Chemical Methodology for the Preparation of Peptide Thioesters Applicable to Naturally Occurring Peptides Using a Sequential Quadruple Acyl Transfer System

Peptide thioesters are very useful in protein chemistry, and chemistry- and biochemistry-based protocols are used for the preparation of thioesters. Among such protocols, only a few biochemistry-based approaches have been use for naturally occurring peptide sequences. The development of chemistry-based protocols applicable to natural sequences remains a challenge, and the development of such methods would be a major contribution to protein science. Here, we describe the preparation of peptide thioesters using innovative methodology that features nickel(II)-mediated alcoholysis of a naturally occurring peptide sequence, followed by O-N and N-S acyl transfers. This protocol involves sequential quadruple acyl transfer, termed SQAT. Notably, the SQAT system consists of sequential chemical reactions that allow naturally occurring peptide sequences to be converted to thioesters without requiring an artificial chemical unit