Insights into the behaviour of phosphorylated DNA breaks from molecular dynamic simulations.

Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity-understanding how DNA sensor proteins recognize certain SSB types is crucial for studies of the DNA repair pathways. During repair of damaged DNA the final SSB that is to be ligated contains a 5'-phosphorylated end. The present work employed molecular simulation (MD) of DNA with a phosphorylated break in solution to address multiple questions regarding the dynamics of the break site.

Theoretical Investigations of a point mutation affecting H5 Hemagglutinin's receptor binding preference.

The avian influenza A H5N1 virus is a subtype of influenza A virus (IAV) that causes a highly infectious and severe respiratory illness in birds and poses significant economic losses in poultry farming. To infect host cell, the virus uses its surface glycoprotein named Hemagglutinin (HA) to recognize and to interact with the host cell receptor containing either α2,6- (SAα2,6 Gal) or α2,3-linked Sialic Acid (SAα2,3 Gal). The H5N1 virus has not yet acquired the capability for efficient human-to-human transmission.

An In Vivo and In Silico Approach Reveals Possible Sodium Channel Nav1.2 Inhibitors from as a Novel Treatment for Epilepsy.

Epilepsy is a neurological disease that affects approximately 50 million people worldwide. Despite an existing abundance of antiepileptic drugs, lifelong disease treatment is often required but could be improved with alternative drugs that have fewer side effects. Given that epileptic seizures stem from abnormal neuronal discharges predominately modulated by the human sodium channel Nav1.

Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities.

Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can nowadays be efficiently obtained via machine learning models trained on first-principles data. However, the transferability of the models trained on small molecules to larger structures is unclear, and direct training on large structures is prohibitively expensive.

Periplasmic chitooligosaccharide-binding protein requires a three-domain organization for substrate translocation.

Periplasmic solute-binding proteins (SBPs) specific for chitooligosaccharides, (GlcNAc) (n = 2, 3, 4, 5 and 6), are involved in the uptake of chitinous nutrients and the negative control of chitin signal transduction in Vibrios. Most translocation processes by SBPs across the inner membrane have been explained thus far by two-domain open/closed mechanism. Here we propose three-domain mechanism of the (GlcNAc) translocation based on experiments using a recombinant VcCBP, SBP specific for (GlcNAc) from Vibrio cholerae.

Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis β-oxidation trifunctional enzyme.

The Mycobacterium tuberculosis trifunctional enzyme (MtTFE) is an αβ tetrameric enzyme. The α-chain harbors the 2E-enoyl-CoA hydratase (ECH) and 3S-hydroxyacyl-CoA dehydrogenase (HAD) activities and the β-chain provides the 3-ketoacyl-CoA thiolase (KAT) activity. Enzyme kinetic data reported here show that medium and long chain enoyl-CoA molecules are preferred substrates for MtTFE.

Integrin α11β1 is a receptor for collagen XIII.

Collagen XIII is a conserved transmembrane collagen mainly expressed in mesenchymal tissues. Previously, we have shown that collagen XIII modulates tissue development and homeostasis. Integrins are a family of receptors that mediate signals from the environment into the cells and vice versa.

Structure-based classification of FAD binding sites: A comparative study of structural alignment tools.

A total of six different structural alignment tools (TM-Align, TriangleMatch, CLICK, ProBis, SiteEngine and GA-SI) were assessed for their ability to perform two particular tasks: (i) discriminating FAD (flavin adenine dinucleotide) from non-FAD binding sites, and (ii) performing an all-to-all comparison on a set of 883 FAD binding sites for the purpose of classifying them. For the first task, the consistency of each alignment method was evaluated, showing that every method is able to distinguish FAD and non-FAD binding sites with a high Matthews correlation coefficient. Additionally, GA-SI was found to provide alignments different from those of the other approaches.

Comparison of non-sequential sets of protein residues.

A methodology for performing sequence-free comparison of functional sites in protein structures is introduced. The method is based on a new notion of similarity among superimposed groups of amino acid residues that evaluates both geometry and physico-chemical properties. The method is specifically designed to handle disconnected and sparsely distributed sets of residues.

GSK3β-dependent phosphorylation alters DNA binding, transactivity and half-life of the transcription factor USF2.

The upstream stimulatory factor 2 (USF2) is a regulator of important cellular processes and is supposed to have also a role during tumor development. However, the knowledge about the mechanisms that control the function of USF2 is limited. The data of the current study show that USF2 function is regulated by phosphorylation and identified GSK3β as an USF2-phosphorylating kinase.

Interaction of di-N-acetylchitobiosyl moranoline with a family GH19 chitinase from moss, Bryum coronatum.

Tri-N-acetylchitotriosyl moranoline, (GlcNAc)3-M, was previously shown to strongly inhibit lysozyme (Ogata M, Umemoto N, Ohnuma T, Numata T, Suzuki A, Usui T, Fukamizo T. 2013. A novel transition-state analogue for lysozyme, 4-O-β-tri-Nacetylchitotriosyl moranoline, provided evidence supporting the covalent glycosyl-enzyme intermediate.

Phylogenetic relationships and classification of thiolases and thiolase-like proteins of Mycobacterium tuberculosis and Mycobacterium smegmatis.

Thiolases are enzymes involved in lipid metabolism. Thiolases remove the acetyl-CoA moiety from 3-ketoacyl-CoAs in the degradative reaction. They can also catalyze the reverse Claisen condensation reaction, which is the first step of biosynthetic processes such as the biosynthesis of sterols and ketone bodies.

Atomic resolution view into the structure-function relationships of the human myelin peripheral membrane protein P2.

P2 is a fatty acid-binding protein expressed in vertebrate peripheral nerve myelin, where it may function in bilayer stacking and lipid transport. P2 binds to phospholipid membranes through its positively charged surface and a hydrophobic tip, and accommodates fatty acids inside its barrel structure. The structure of human P2 refined at the ultrahigh resolution of 0.

The structure of the CD3ζζ transmembrane dimer in lipid bilayers.

Virtually every aspect of the human adaptive immune response is controlled by T cells. The T cell receptor (TCR) complex is responsible for the recognition of foreign peptide sequences, forming the initial step in the elimination of germ-infected cells. The recognition leads to an extracellular conformational change that is transmitted intracellularly through the Cluster of Differentiation 3 (CD3) subunits of the TCR-CD3 complex.

The first identification of carbohydrate binding modules specific to chitosan.

Two carbohydrate binding modules (DD1 and DD2) belonging to CBM32 are located at the C terminus of a chitosanase from Paenibacillus sp. IK-5. We produced three proteins, DD1, DD2, and tandem DD1/DD2 (DD1+DD2), and characterized their binding ability.

An atomistic model for assembly of transmembrane domain of T cell receptor complex.

The T cell receptor (TCR) together with accessory cluster of differentiation 3 (CD3) molecules (TCR-CD3 complex) is a key component in the primary function of T cells. The nature of association of the transmembrane domains is of central importance to the assembly of the complex and is largely unknown. Using multiscale molecular modeling and simulations, we have investigated the structure and assembly of the TCRα-CD3ε-CD3δ transmembrane domains both in membrane and in micelle environments.

Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae.

Post-translational modification of proteins by lysine acetylation plays important regulatory roles in living cells. The budding yeast Saccharomyces cerevisiae is a widely used unicellular eukaryotic model organism in biomedical research. S.

The enolization chemistry of a thioester-dependent racemase: the 1.4 Å crystal structure of a reaction intermediate complex characterized by detailed QM/MM calculations.

In the active site of the bacterial α-methylacyl-CoA racemase of Mycobacterium tuberculosis (MCR), the chirality of the 2-methyl branched C2-atom is interconverted between (S) and (R) isomers. Protein crystallographic data and quantum mechanics/molecular mechanics (QM/MM) computational approaches show that this interconversion is achieved via a planar enolate intermediate. The crystal structure, at 1.

High-temperature cultivation and 5' mRNA optimization are key factors for the efficient overexpression of thermostable Deinococcus geothermalis purine nucleoside phosphorylase in Escherichia coli.

Overexpression of genes from thermophiles in Escherichia coli is an attractive approach towards the large-scale production of thermostable biocatalysts. However, various factors can challenge efficient heterologous protein expression--one example is the formation of stable 5' mRNA secondary structures that can impede an efficient translation initiation. In this work, we describe the expression optimization of purine nucleoside phosphorylase from the thermophilic microbe Deinococcus geothermalis in E.

A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis.

Expression of a class V chitinase gene (At4g19810, AtChiC) in Arabidopsis thaliana was examined by quantitative real-time PCR and by analyzing microarray data available at Genevestigator. The gene expression was induced by the plant stress-related hormones abscisic acid (ABA) and jasmonic acid (JA) and by the stress resulting from the elicitor flagellin, NaCl, and osmosis. The recombinant AtChiC protein was produced in E.

Dimerization of human lysyl hydroxylase 3 (LH3) is mediated by the amino acids 541-547.

Lysyl hydroxylases (LH), which catalyze the post-translational modifications of lysines in collagen and collagen-like proteins, function as dimers. However, the amino acids responsible for dimerization and the role of dimer formation in the enzymatic activities of LH have not yet been identified. We have localized the region responsible for the dimerization of lysyl hydroxylase 3 (LH3), a multifunctional enzyme of collagen biosynthesis, to a sequence of amino acids between the glycosyltransferase activity and the lysyl hydroxylase activity domains.

Hydrolysis of phosphohistidine in water and in prostatic acid phosphatase.

Calculation of the free energy profile for hydrolysis of phosphohistidine using ONIOM methodology indicates a much tighter transition state in the enzyme active site compared to that in explicit water and elucidates the role of active site residues in catalysis.

A flexible loop controlling the enzymatic activity and specificity in a glycosyl hydrolase family 19 endochitinase from barley seeds (Hordeum vulgare L.).

To examine the role of the loop structure consisting of residues 70-82 (70-82 loop) localized to +3/4 subsite of the substrate binding cleft of a family GH-19 endochitinase from barley seeds, Trp72 and Trp82 were mutated, and the mutated enzymes (W72A, W82A, and W72A/W82A) were characterized. Thermal stability and specific activities toward glycol chitin and chitin hexasaccharide were significantly affected by the individual mutations. When N-acetylglucosamine hexamer was hydrolyzed by the wild type, the beta-anomer of the substrate was preferentially hydrolyzed, producing the trimer predominantly and the dimer and tetramer in lesser amounts.

Inclusion of ionization states of ligands in affinity calculations.

When estimating binding affinities of a ligand, which can exists in multiple forms, for a target molecule, one must consider all possible competing equilibria. Here, a method is presented that estimates the contribution of the protonation equilibria of a ligand in solution to the measured or calculated binding affinity. The method yields a correction to binding constants that are based on the total concentration of inhibitor (the sum of all ionized forms of the inhibitor in solution) to account for the complexed form of the inhibitor only.