Impact of divalent metal cations on the catalysis of peptide bonds: a DFT study

Within the ATP-grasp family of enzymes, divalent alkaline earth metals are proposed to chelate terminal ATP phosphates and facilitate the formation of peptide bonds. Density functional theory methods are used to explore the impact of metal ions on peptide bond formation, providing an insight into experimental metal substitution studies. Calculations show that alkaline earth and transition metal cations coordinate with an acylphosphate reactant and aid in the separation of the phosphate leaving group. The critical biochemical reaction is proposed to proceed through the formation of a six-membered transition state in the relatively nonpolar active site of human glutathione synthetase, an ATP-grasp enzyme. While the identity of the metal ion has a moderate impact on the thermodynamics of peptide bond formation, kinetic differences are much sharper. Simulations indicate that several transition metal ions, most notably Cu²⁺, may be particularly advantageous for catalysis. The detailed mechanistic study serves to elucidate the vital role of coordination chemistry in the formation of peptide bonds.     

Diastereoselective synthesis of the 5-hydroxy-pyrrolidinone amino acid of the microsclerodermins and model studies for an end-game strategy for microsclerodermin B

The first diastereoselective synthesis of the 5-hydroxy-pyrrolidinone amino acid common to eight members of the microsclerodermin family is presented. Our strategy involves formal hydration of an unsaturated precursor via the use of a two-step hydroxybromination-debromination protocol; this procedure provides exclusively the requisite 4,5-cis-pyrrolidinone. Furthermore model studies are presented that indicated the potential viability of this hydration strategy in the context of a synthesis of microsclerodermin B.     

Peptide Property Modeling by Cluj Indices

Abstract

The novel Cluj property indices are used for modeling the biological properties of dipeptides: the ACE inhibition activity of a set of 58 dipeptides and the bitter tasting activity of a set of 48 dipeptides, taken from the literature. The results are compared to those reported in some previous works.     

Adapting the Glaser Reaction for Bioconjugation: Robust Access to Structurally Simple,Rigid Linkers

Copper‐mediated coupling between alkynes to generate a structurally rigid, linear 1,3‐diyne linkage has been known for over a century. However, the mechanistic requirement to simultaneously maintain Cu^I and an oxidant has limited its practical utility, especially for complex functional molecules in aqueous solution. We find that addition of a specific bpy‐diol ligand protects unprotected peptides from Cu^II‐mediated oxidative damage through the formation of an insoluble Cu^II gel which solves the critical challenge of applying Glaser coupling to substrates that are degraded by Cu^II. The generality of this method is illustrated through the conjugation of a series of polar and nonpolar labels onto a fully unprotected GLP‐1R agonist through a linear 7 Å diynyl linker.     

Resolving quantum dots and peptide assembly and disassembly using bending capillary electrophoresis

Despite the numerous techniques developed for the studying nanoparticle and peptide interaction nowadays, sensitive and convenient assay in the process of flow, especially to simulate the self‐assembly of quantum dots (QDs) and peptide inflow in blood vessels, still remains big challenges. Here, we report a novel assay for studying the self‐assembly of QDs and peptide, based on CE using a bending capillary. We demonstrate that the semicircles numbers of the bending capillary affect the self‐assembly kinetics of CdSe/ZnS QDs and ATTO‐D₃LVPRGSGP₉G₂H₆ peptide. Moreover, benefitting from this novel assay, the effect of the position on the self‐assembly has also been realized. More importantly, we also demonstrate that this novel assay can be used for studying the stability of the QDs–peptide complex inflow. We believe that our novel assay proposed in this work could be further used as a general strategy for the studying nanoparticle–biomolecule interaction or biomolecule–biomolecule interaction.