Etching of “Microwire-on-Insulator”-Type Structures

Plasma Physics Reports - Nanoribbons from different materials, such as graphene and topological insulators, are currently intensively studied as structures needed in nanoelectronics and spintronics...     

Regulation of Aggregation of Self-Associated Peptides,Including N-Terminal Fragments of the Alzheimer’s β-Amyloid Peptide,by Nitro Derivatives of Azoloazine

Russian Journal of Bioorganic Chemistry - The potential of the nitro compounds of the azoloazine class as regulators of aggregation of natural self-associating peptides was demonstrated by the...     

Comparative Study of the Action of Bovine Duodenal Proteinases (Duodenases) on Polypeptide Substrates

A comparative study of substrate specificity of bovine duodenal proteinases—chymotrypsin-like duodenase (ChlD) and dual-specificity duodenase (dsD)—was carried out using oligopeptide substrates (human proinsulin, glucagon, melittin, angiotensinogen fragment 1-14). ChlD displayed mainly chymotrypsin-like properties towards these substrates, hydrolyzing peptide bonds carboxy-terminally to bulky aliphatic or aromatic residues. In melittin, ChlD additionally cleaved peptide bonds after Thr and Ser residues. Dual-specificity duodenase (dsD) significantly restricted its specificity to only trypsin-like or only chymotrypsin-like or displayed full activity, combining both specificities, depending on substrate. Both ChlD and dsD efficiently hydrolyzed a single peptide bond (Phe8–His9) in angiotensinogen fragment 1-14. The kinetic parameters of angiotensinogen fragment 1-14 cleavage by ChlD and dsD were determined (k _cat/K _m = 80,500 M^-1·sec^-1 for ChlD and 103,000 M^-1·sec^-1 for dsD).     

Glucoamylase: structure/function relationships, and protein engineering

Glucoamylases are inverting exo-acting starch hydrolases releasing beta-glucose from the non-reducing ends of starch and related substrates. The majority of glucoamylases are multidomain enzymes consisting of a catalytic domain connected to a starch-binding domain by an O-glycosylated linker region. Three-dimensional structures have been determined of free and inhibitor complexed glucoamylases from Aspergillus awamori var. X100, Aspergillus niger, and Saccharomycopsis fibuligera. The catalytic domain folds as a twisted (alpha/alpha)(6)-barrel with a central funnel-shaped active site, while the starch-binding domain folds as an antiparallel beta-barrel and has two binding sites for starch or beta-cyclodextrin. Certain glucoamylases are widely applied industrially in the manufacture of glucose and fructose syrups. For more than a decade mutational investigations of glucoamylase have addressed fundamental structure/function relationships in the binding and catalytic mechanisms. In parallel, issues of relevance for application have been pursued using protein engineering to improve the industrial properties. The present review focuses on recent findings on the catalytic site, mechanism of action, substrate recognition, the linker region, the multidomain architecture, the engineering of specificity and stability, and roles of individual substrate binding subsites.     

CA10 regulates neurexin heparan sulfate addition via a direct binding in the secretory pathway

Neurexins are presynaptic adhesion molecules that shape the molecular composition of synapses. Diversification of neurexins in numerous isoforms is believed to confer synapse‐specific properties by engaging with distinct ligands. For example, a subset of neurexin molecules carry a heparan sulfate (HS) glycosaminoglycan that controls ligand binding, but how this post‐translational modification is controlled is not known. Here, we observe that CA10, a ligand to neurexin in the secretory pathway, regulates neurexin‐HS formation. CA10 is exclusively found on non‐HS neurexin and CA10 expressed in neurons is sufficient to suppress HS addition and attenuate ligand binding and synapse formation induced by ligands known to recruit HS. This effect is mediated by a direct interaction in the secretory pathway that blocks the primary step of HS biosynthesis: xylosylation of the serine residue. NMR reveals that CA10 engages residues on either side of the serine that can be HS‐modified, suggesting that CA10 sterically blocks xylosyltransferase access in Golgi. These results suggest a mechanism for the regulation of HS on neurexins and exemplify a new mechanism to regulate site‐specific glycosylations.     

Towards functional proteomics of minority component of honeybee royal jelly: The effect of post‐translational modifications on the antimicrobial activity of apalbumin2

This study illustrates multifunctionality of proteins of honeybee royal jelly (RJ) and how their neofunctionalization result from various PTMs of maternal proteins. Major proteins of RJ, designated as apalbumins belong to a protein family consisting of nine members with M_r of 49–87 kDa and they are accompanied by high number of minority homologs derived from maternal apalbumins. In spite of many data on diversity of apalbumins, the molecular study of their individual minority homologous is still missing. This work is a contribution to functional proteomics of second most abundant protein of RJ apalbumin2 (M_r 52.7 kDa). We have purified a minority protein from RJ; named as apalbumin2a, differ from apalbumin2 in M_r (48.6 kDa), in N‐terminal amino acids sequences – ENSPRN and in N‐linked glycans. Characterization of apalbumin2a by LC‐MALDI TOF/TOF MS revealed that it is a minority homolog of the major basic royal jelly protein, apalbumin2, carrying two fully occupied N‐glycosylation sites, one with high‐mannose structure, HexNAc2Hex9, and another carrying complex type antennary structures, HexNAc4Hex3 and HexNAc5Hex4. We have found that apalbumin2a inhibit growth of Paenibacillus larvae. The obtained data call attention to functional plasticity of RJ proteins with potential impact on functional proteomics in medicine.     

A direct introduction of <Superscript>18</Superscript>O isotopes into peptides and proteins for quantitative mass spectroscopy analysis

A method for direct introduction of ¹⁸O isotopes into carboxyl groups of peptides and proteins via the exchange with H₂ ¹⁸O in the presence of TFA is described. The isotope label is sufficiently stable in a wide pH range. Since the compounds labeled by this method retain their physicochemical characteristics, they can be used as an internal standard in quantitative assay of authentic compounds in the analyzed objects by means of mass spectrometry. This method is applicable to quantitative analysis of peptides and proteins in biological environments, as well as for quantitative kinetic studies of metabolism and enzyme activity. The quantitative analysis of polypeptides and proteins is combined with trypsinolysis. When necessary, the isotope label can be simultaneously introduced into all peptides and proteins in a control biosample, making it applicable as a standard for comparative analysis of experimental biosamples.