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QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues

Myrosinase from Sinapis alba hydrolyzes glycosidic bonds of β-d-S-glucosides. The enzyme shows an enhanced activity in the presence of l-ascorbic acid. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics simulations to study the catalytic reaction of wild-type myrosinase and its E464A, Q187A, and Q187E mutants. Test calculation

Crystal structure of reduced protein R2 of ribonucleotide reductase : The structural basis for oxygen activation at a dinuclear iron site

Background: Ribonucleotide reductases (RNRs) catalyze the formation of the deoxyribonucleotides that are essential for DNA synthesis. The R2 subunit of Escherichia coli RNR is a homodimer containing one dinuclear iron centre per monomer. A tyrosyl radical is essential for catalysis, and is formed via a reaction in which the reduced, diferrous form of the iron centre activates dioxygen. To help und

Direct Visualisation of the Surface Atomic Active Sites of Carbon-Supported Co3O4 Nanocrystals via High-Resolution Phase Restoration

The atomic arrangement of the terminating facets on spinel Co3O4 nanocrystals is strongly linked to their catalytic performance. However, the spinel crystal structure offers multiple possible surface terminations depending on the synthesis. Thus, understanding the terminating surface atomic structure is essential in developing high-performance Co3O4 nanocrystals. In this work, we present direct at

Multi-year statistical and modeling analysis of submicrometer aerosol number size distributions at a rain forest site in Amazonia

The Amazon Basin is a unique region to study atmospheric aerosols, given their relevance for the regional hydrological cycle and the large uncertainty of their sources. Multi-year datasets are crucial when contrasting periods of natural conditions and periods influenced by anthropogenic emissions. In the wet season, biogenic sources and processes prevail, and the Amazonian atmospheric composition

Holocene Hydrographic Variations From the Baltic-North Sea Transitional Area (IODP Site M0059)

Deoxygenation affects many continental shelf seas across the world today and results in increasing areas of hypoxia (dissolved oxygen concentration ([O2]) <1.4 ml/L). The Baltic Sea is increasingly affected by deoxygenation. Deoxygenation correlates with other environmental variables such as changing water temperature and salinity and is directly linked to ongoing global climate change. To place t

Early diagenesis of foraminiferal calcite under anoxic conditions : A case study from the Landsort Deep, Baltic Sea (IODP Site M0063)

The chemical composition of foraminiferal calcite is widely used for studying past environmental conditions and biogeochemistry. However, high rates of microbial organic matter degradation and abundant dissolved metal sources in sediments and pore waters may impede the application of foraminifera-based proxies due to formation of secondary carbonates or other authigenic minerals on and/or inside o

Assessment of groundwater safety surrounding contaminated water storage sites using multivariate statistical analysis and Heckman selection model: a case study of Kazakhstan

Petrochemical enterprises in Kazakhstan discharge polluted wastewater into special recipients. Contaminants infiltrate through the soil into the groundwater, which potentially affects public health and environment safety. This paper presents the evaluation of a 7-year monitoring program from one of the factories and includes nineteen variables from nine wells during 2013–2019. Several multivariate

Synchrotron radiation X-ray absorption fine structure and magnetization improvement of A-site Ce3+ doped LaFeO3

Synchrotron radiation (SR) is an interesting tool for probing the properties of the matter in various domains such as nanotechnology, energy materials, catalysis and the cultural heritage. Herein, we synthesized nanomultiferroic samples La1−xCexFeO3 (0.00 ≤ x ≤ 0.15) using auto combustion method and glycine as a fuel. The magnetic behavior was studied and interrelated with the results of synchrotr

Site-specific antibodies distinguish single amino acid substitutions in position 57 in HLA-DQ β-chain alleles associated with insulin-dependent diabetes

The HLA-DQ β-chain gene shows a close association with susceptibility or resistance to autoimmune insulin-dependent diabetes mellitus (IDDM) and it has been suggested that the amino acid in position 57 may be of pathogenetic importance. To study the expression of the IDDM associated HLA-DQ β-chain alleles, we immunized rabbits with 12 to 13 amino acid long peptides representing HLA-DQw7 and -DQw8

The effects of changing the site of activating phosphorylation in CDK2 from threonine to serine

Cyclin-dependent kinases (CDKs) that control cell cycle progression are regulated in many ways, including activating phosphorylation of a conserved threonine residue. This essential phosphorylation is carried out by the CDK-activating kinase (CAK). Here we examine the effects of replacing this threonine residue in human CDK2 by serine. We found that cyclin A bound equally well to wild-type CDK2 (C