Search results for "protein"

Three-dimensional crystallization of the light-harvesting complex from Mantoniella squamata (Prasinophyceae) requires an adequate purification proced…

1995

Abstract We present a new purification procedure for the light-harvesting complex of Mantoniella squamata whereupon three-dimensional crystallization succeeded. Previous purification methods were based on density centrifugations as the only separating principle. We have extended this preparation procedure by applying anion-exchange and molecular-sieve chromatography techniques. Purity and stability of the complex were proved by denaturing and non-denaturing polyacrylamide-gel electrophoresis, and spectroscopic measurements. With respect to contaminating lipids the purified pigment-protein complex was examined by thin-layer chromatography and the aggregation and/or oligomeric states were inv…

The Greenland shark Somniosus microcephalus—Hemoglobins and ligand-binding properties

2017

A large amount of data is currently available on the adaptive mechanisms of polar bony fish hemoglobins, but structural information on those of cartilaginous species is scarce. This study presents the first characterisation of the hemoglobin system of one of the longest-living vertebrate species (392 +/- 120 years), the Arctic shark Somniosus microcephalus. Three major hemoglobins are found in its red blood cells and are made of two copies of the same a globin combined with two copies of three very similar beta subunits. The three hemoglobins show very similar oxygenation and carbonylation properties, which are unaffected by urea, a very important compound in marine elasmobranch physiology.…

Cryo-EM structure of ssDNA bacteriophage ΦCjT23 provides insight into early virus evolution.

2022

AbstractThe origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid protein structures facilitate the study of distant evolutionary relationships. Here we characterize the lipid-containing ssDNA temperate bacteriophage ΦCjT23, which infects Flavobacterium sp. (Bacteroidetes). We report ΦCjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy reveals similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses wit…

Filament sets and decompositions of homogeneous continua

2007

Abstract This paper applies the concepts introduced in the article: Filament sets and homogeneous continua [J.R. Prajs, K. Whittington, Filament sets and homogeneous continua, Topology Appl. 154 (8) (2007) 1581–1591, doi:10.1016/j.topol.2006.12.005 ] to decompositions of homogeneous continua. Several new or strengthened results on aposyndesis are given. Newly defined decompositions are discussed. A proposed classification scheme for homogeneous continua is shown to be mostly invariant under Jones' aposyndetic decomposition.

Origin of Enzymatic Kinetic Isotope Effects in Human Purine Nucleoside Phosphorylase

2017

Here we report a study of the effect of heavy isotope labeling on the reaction catalyzed by human purine nucleoside phosphorylase (hPNP) to elucidate the origin of its catalytic effect and of the enzymatic kinetic isotope effect (EKIE). Using quantum mechanical and molecular mechanical (QM/MM) molecular dynamics (MD) simulations, we study the mechanism of the hPNP enzyme and the dynamic effects by means of the calculation of the recrossing transmission coefficient. A free energy surface (FES), as a function of both a chemical and an environmental coordinate, is obtained to show the role of the environment on the chemical reaction. Analysis of reactive and nonreactive trajectories allows us …

MD Simulation Investigation on the Binding Process of Smoke-Derived Germination Stimulants to Its Receptor

2019

Karrikins (KARs) are a class of smoke-derived seed germination stimulants with great significance in both agriculture and plant biology. By means of direct binding to the receptor protein KAI2, the compounds can initiate the KAR signal transduction pathway, hence triggering germination of the dormant seeds in the soil. In the research, several molecular dynamics (MD) simulation techniques were properly integrated to investigate the binding process of KAR1 to KAI2 and reveal the details of the whole binding event. The calculated binding free energy, -7.00 kcal/mol, is in good agreement with the experimental measurement, -6.83 kcal/mol. The obtained PMF profile indicates the existence of thre…

Oxidovanadium(V) amine bisphenolates as epoxidation, sulfoxidation and catechol oxidation catalysts

2017

Air-stable oxidovanadium(V) complexes with tetradentate amine bisphenolate ligands were made by the reaction of VOSO4·xH2O and ligand precursors in MeOH solutions. Isolated compounds were studied as catechol oxidase models as well as catalysts for epoxidation and sulfoxidation reactions. All compounds can catalyse such oxidation reactions without notable structure-activity correlations. The 51V NMR studies indicate that the complexes turn to the number of different species during the catalytic experiments. peerReviewed

Heavy enzymes and the rational redesign of protein catalysts

2019

Abstract An unsolved mystery in biology concerns the link between enzyme catalysis and protein motions. Comparison between isotopically labelled “heavy” dihydrofolate reductases and their natural‐abundance counterparts has suggested that the coupling of protein motions to the chemistry of the catalysed reaction is minimised in the case of hydride transfer. In alcohol dehydrogenases, unnatural, bulky substrates that induce additional electrostatic rearrangements of the active site enhance coupled motions. This finding could provide a new route to engineering enzymes with altered substrate specificity, because amino acid residues responsible for dynamic coupling with a given substrate present…

2020

Teraryl-based alpha-helix mimetics have resulted in efficient inhibitors of protein-protein interactions (PPIs). Extending the concept to even longer oligoarene systems would allow for the mimicking of even larger interaction sites. We present a highly efficient synthetic modular access to quateraryl alpha-helix mimetics, in which, at first, two phenols undergo electrooxidative dehydrogenative cross-coupling. The resulting 4,4′-biphenol is then activated by conversion to nonaflates, which serve as leaving groups for iterative Pd-catalyzed Suzuki-cross-coupling reactions with suitably substituted pyridine boronic acids. This work, for the first time, demonstrates the synthetic efficiency of …

Effect of different concentrations of specific inhibitor of matrix metalloproteinases on the shear bond strength of self-adhesive resin cements to de…

2017

Background Considering the probability of chemical and enzymatic reactions between matrix metalloproteinases (MMPs) in the dentin structure and their specific inhibitors, the aim of the present study was to evaluate the effect of different concentrations of specific inhibitor of MMPs (galardin) on the shear bond strength of self-adhesive resin cements to dentin. Material and Methods Forty-eight sound human premolars were mounted in self-cured acrylic resin after removal of the enamel on the buccal and lingual surfaces. The dentin surfaces achieved were polished and prepared with 600-grit silicon carbide paper. The samples were divided into 3 groups (n=16) based on the concentration of galar…