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    Assays for nucleotide-competitive reversible and irreversible inhibitors of Ras GTPases.
    Biochemistry 2018 May 23. Epub 2018 May 23.
    Although the Ras protein has been seen as a potential target for cancer therapy for the past 30 years, there was a tendency to consider it undruggable until recently. This has changed with the demonstration that small molecules with specifcity for (disease related mutants of) Ras can indeed be found, and some of these molecules form covalent adducts. A subgroup of these molecules can be characterized as competing with binding of the natural ligands GTP and GDP. Read More

    Slow Starter Enzymes: Role of Active Site Architecture in the Catalytic Control in the Biosynthesis of Taxadiene by Taxadiene Synthase.
    Biochemistry 2018 May 23. Epub 2018 May 23.
    Taxadiene synthase (TXS) catalyzes the formation of the natural product Taxa-4(5),11(12)-diene (henceforth Taxadiene). Taxadiene is the precursor in the formation of Taxol, which is an important natural anti-cancer agent. In the current study, we present a detailed mechanistic view of the biosynthesis of Taxadiene by TXS, using a hybrid quantum mechanics-molecular mechanics potential in conjunction with free energy simulation methods. Read More

    Reassessment of the transport mechanism of the human zinc transporter SLC39A2.
    Biochemistry 2018 May 23. Epub 2018 May 23.
    The human zinc transporter SLC39A2, also known as ZIP2, was shown to mediate zinc transport that could be inhibited at pH values below 7.0 and stimulated by HCO3-, suggesting a Zn2+/HCO3- cotransport mechanism (1). In contrast, recent experiments in our laboratory indicated that the functional activity of ZIP2 increases at acidic pH (2). Read More

    Design, construction, and validation of histone-binding effectors in vitro and in cells.
    Biochemistry 2018 May 23. Epub 2018 May 23.
    Chromatin is a system of nuclear proteins and nucleic acids that plays a pivotal role in gene expression and cell behavior, and is therefore the subject of intense study for cell development and cancer research. Biochemistry, crystallography, and reverse genetics have elucidated the macromolecular interactions that drive chromatin regulation. One of the central mechanisms is the recognition of post translational modifications (PTMs) on histone proteins by a family of nuclear proteins known as "readers. Read More

    Hydrophobic Collapse of Ubiquitin Generates Rapid Protein-Water Motions.
    Biochemistry 2018 May 23. Epub 2018 May 23.
    We report time resolved measurements of the coupled protein-water modes of solvated ubiquitin during protein folding. Kinetic terahertz absorption (KITA) spectroscopy serves as a label-free technique to monitor large-scale conformational changes and folding of proteins subsequent to a sudden T-jump. Our KITA measurements reveal a significant change in the coupled ubiquitin-solvent dynamics even in the initial phase of hydrophobic collapse. Read More

    Structure-Function Relationships in the Oligomeric NADPH-Dependent Assimilatory Sulfite Reductase.
    Biochemistry 2018 May 22. Epub 2018 May 22.
    The central step in the assimilation of sulfur is a six-electron reduction of sulfite to sulfide, catalyzed by the oxidoreductase NADPH-dependent assimilatory Sulfite Reductase (SiR). SiR is composed of two subunits. One is a multi-domain flavin-binding reductase (SiRFP) and the other an iron-containing oxidase (SiRHP). Read More

    Investigation of Solvent Hydron Exchange in the Reaction Catalyzed by the Antibiotic Resistance Protein, Cfr.
    Biochemistry 2018 May 22. Epub 2018 May 22.
    Cfr is a radical S-adenosylmethionine (RS) methylase that appends methyl groups to C8 and C2 of adenosine 2503 in 23S ribosomal RNA. Methylation of C8 confers resistance to several classes of antibiotics that bind in or near the peptidyl transferase center of the bacterial ribosome, including the synthetic antibiotic linezolid. The Cfr reaction requires the action of five conserved cysteines, three of which ligate a required [4Fe-4S] cluster cofactor. Read More

    Benchmark analysis of native and artificial NAD+-dependent enzymes generated by a sequence based design method with or without phylogenetic data.
    Biochemistry 2018 May 22. Epub 2018 May 22.
    The expansion of protein sequence databases has enabled us to design artificial proteins by sequence-based design methods, such as full consensus design (FCD) and ancestral sequence reconstruction (ASR). Artificial proteins with enhanced activity levels compared with native ones can potentially be generated by such methods, but successful design is rare because preparing a sequence library by curating the database and selecting a method is difficult. Utilizing a curated library prepared by reducing conservation energies, we successfully designed two artificial L-threonine 3-dehydrogenase (SDR-TDH) with higher activity levels than native SDR-TDH, FcTDH-N1 and AncTDH, using FCD and ASR, respectively. Read More

    Membrane Topology of Trafficking Regulator of GLUT4 1 (TRARG1).
    Biochemistry 2018 May 22. Epub 2018 May 22.
    Trafficking regulator of GLUT4 1 (TRARG1) was recently identified to localise to glucose transporter type 4 (GLUT4) storage vesicles (GSVs) and to positively regulate GLUT4 trafficking. Our knowledge of TRARG1 structure and membrane topology is limited to predictive models, hampering efforts to further our mechanistic understanding of how it carries out its functions. Here, we use a combination of bioinformatics prediction tools and biochemical assays to define the membrane topology of the 173-amino acid mouse TRARG1. Read More

    Sulfonium Ion Condensation: the Burden Borne by SAM Synthetase.
    Biochemistry 2018 May 22. Epub 2018 May 22.
    S-Adenosylmethionine (SAM+) serves as the prin-cipal methylating agent in biological systems, but the thermodynamic basis of its reactivity does not appear to have been established. Here, we show that methionine, methanol and H+ combine to form S-methylmethionine (SMM+) with a temperature-independent equilibrium constant of 9.9 M-2. Read More

    Catalytic bases and stereo-control in Lamiaceae class II diterpene cyclases.
    Biochemistry 2018 May 22. Epub 2018 May 22.
    Plants from the widespread Lamiaceae family produce many labdane-related diterpenoids, a number of which serve medicinal roles, and whose biosynthesis is initiated by class II diterpene cyclases (DTCs). These enzymes utilize a general acid-base catalyzed cyclo-isomerization reaction to produce various stereoisomers of the eponymous labdaenyl carbocation intermediate, which can then undergo rearrangement and/or the addition of water prior to terminating deprotonation. Identification of the pair of residues that cooperatively serve as the catalytic base in the DTCs that produce ent-copalyl diphosphate (CPP) required for gibberellin phytohormone biosynthesis in all vascular plants has led to insight into the addition of water as well as rearrangement. Read More

    Cyanylated Cysteine Reports Site-Specific Changes at Protein-Protein Binding Interfaces Without Perturbation.
    Biochemistry 2018 May 22. Epub 2018 May 22.
    To investigate the cyanylated cysteine vibrational probe group's ability to report on binding-induced changes along a protein-protein interface, the probe group was incorporated at several sites in a peptide of the calmodulin (CaM) binding domain of skeletal muscle myosin light chain kinase. Isothermal titration calorimetry was used to determine the binding thermodynamics between calmodulin and each peptide. For all probe positions, the binding affinity was nearly identical to that of the unlabeled peptide. Read More

    RNA Modulates the Interaction Between Influenza A Virus NS1 and Human PABP1.
    Biochemistry 2018 May 21. Epub 2018 May 21.
    Non-Structural Protein 1 (NS1) is a multifunctional protein involved in preventing host-interferon response in Influenza A Virus (IAV). Previous studies have indicated that NS1 also stimulates the translation of viral mRNA by binding to conserved sequences in the viral 5'-UTR. Additionally, NS1 binds to Poly (A) Binding Protein (PABP1) and eukaryotic Initiation Factor 4G (eIF4G). Read More

    Entropy as a Driver of Selectivity for Inhibitor Binding to Histone Deacetylase 6.
    Biochemistry 2018 May 18. Epub 2018 May 18.
    Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States.
    Among the metal-dependent histone deacetylases, the class IIb isozyme HDAC6 is remarkable because of its role in the regulation of microtubule dynamics in the cytosol. Selective inhibition of HDAC6 results in microtubule hyperacetylation, leading to cell cycle arrest and apoptosis, which is a validated strategy for cancer chemotherapy and the treatment of other disorders. HDAC6 inhibitors generally consist of a Zn-binding group such as a hydroxamate, a linker, and a capping group; the capping group is a critical determinant of isozyme selectivity. Read More

    Selective Removal of B800 Bacteriochlorophyll a from Light-Harvesting Complex 2 of the Purple Photosynthetic Bacterium Phaeospirillum molischianum.
    Biochemistry 2018 May 17. Epub 2018 May 17.
    Department of Applied Chemistry , The University of Tokyo , Bunkyo-ku, Tokyo 113-8654 , Japan.
    The selective removal of B800 bacteriochlorophyll (BChl) a from light-harvesting complex 2 (LH2) in purple photosynthetic bacteria is a clue about elucidation of the mechanism for the transfer of energy from these pigments to B850 BChl a and their roles in the LH2 protein structure. We demonstrated that the kinetics of the removal of B800 BChl a from two representative LH2 proteins derived from Phaeospirillum molischianum and Rhodoblastus acidophilus differed significantly, in contrast to the calculated binding enthalpy. These results may be interpreted as changes in the local structure near B800 BChl a with respect to the geometries of the original crystal structures upon removal of B800 BChl a. Read More

    Comparison of Kinetics, Toxicity, Oligomer Formation, and Membrane Binding Capacity of α-Synuclein Familial Mutations at the A53 Site, Including the Newly Discovered A53V Mutation.
    Biochemistry 2018 May 21. Epub 2018 May 21.
    Department of Biosciences and Bioengineering , IIT Bombay , Powai, Mumbai , India 400076.
    The involvement of α-synuclein (α-Syn) amyloid formation in Parkinson's disease (PD) pathogenesis is supported by the discovery of α-Syn gene (SNCA) mutations linked with familial PD, which are known to modulate the oligomerization and aggregation of α-Syn. Recently, the A53V mutation has been discovered, which leads to late-onset PD. In this study, we characterized for the first time the biophysical properties of A53V, including the aggregation propensities, toxicity of aggregated species, and membrane binding capability, along with those of all familial mutations at the A53 position. Read More

    New Techniques for the Generation and Analysis of Tailored Microbial Systems on Surfaces.
    Biochemistry 2018 May 17. Epub 2018 May 17.
    Department of Chemistry , University of California, Berkeley , Berkeley , California 94720-1460 , United States.
    The interactions between microbes and surfaces provide critically important cues that control the behavior and growth of the cells. As our understanding of complex microbial communities improves, there is a growing need for experimental tools that can establish and control the spatial arrangements of these cells in a range of contexts. Recent improvements in methods to attach bacteria and yeast to nonbiological substrates, combined with an expanding set of techniques available to study these cells, position this field for many new discoveries. Read More

    Crystal Structures of the Mango-II RNA Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness.
    Biochemistry 2018 May 24. Epub 2018 May 24.
    Biochemistry and Biophysics Center , National Heart, Lung and Blood Institute , 50 South Drive, MSC 8012 , Bethesda , Maryland 20892-8012 , United States.
    Several RNA aptamers that bind small molecules and enhance their fluorescence have been successfully used to tag and track RNAs in vivo, but these genetically encodable tags have not yet achieved single-fluorophore resolution. Recently, Mango-II, an RNA that binds TO1-Biotin with ∼1 nM affinity and enhances its fluorescence by >1500-fold, was isolated by fluorescence selection from the pool that yielded the original RNA Mango. We determined the crystal structures of Mango-II in complex with two fluorophores, TO1-Biotin and TO3-Biotin, and found that despite their high affinity, the ligands adopt multiple distinct conformations, indicative of a binding pocket with modest stereoselectivity. Read More

    Single-Molecule Imaging Reveals Conformational Manipulation of Holliday Junction DNA by the Junction Processing Protein RuvA.
    Biochemistry 2018 May 24. Epub 2018 May 24.
    Department of Chemistry , Virginia Commonwealth University , 1001 West Main Street , Richmond , Virginia 23284 , United States.
    Interactions between DNA and motor proteins regulate nearly all biological functions of DNA such as gene expression, DNA replication and repair, and transcription. During the late stages of homologous recombination (HR), the Escherichia coli recombination machinery, RuvABC, resolves the four-way DNA motifs called Holliday junctions (HJs) that are formed during exchange of nucleotide sequences between two homologous duplex DNA. Although the formation of the RuvA-HJ complex is known to be the first critical step in the RuvABC pathway, the mechanism for the binding interaction between RuvA and HJ has remained elusive. Read More

    Comparison of Alicyclobacillus acidocaldarius OSBS to its promiscuous NSAR/OSBS relatives.
    Biochemistry 2018 May 16. Epub 2018 May 16.
    Studying the evolution of catalytically promiscuous enzymes like those from the N-succinylamino acid racemase/ o-succinylbenzoate synthase (NSAR/OSBS) subfamily can reveal mechanisms by which new functions evolve. Some enzymes in this subfamily only have OSBS activity, while others catalyze OSBS and NSAR reactions. We characterized several NSAR/OSBS subfamily enzymes as a step toward determining the structural basis for evolving NSAR activity. Read More

    Characterization and structural analysis of a novel exo-type enzyme acting on β-1,2-glucooligosaccharides from Parabacteroides distasonis.
    Biochemistry 2018 May 15. Epub 2018 May 15.
    β-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-β-1,2-glucanase from Chitinophaga pinensis ( CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homolog from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known β-1,2-glucan-degrading enzymes. Read More

    Cooperative assembly of Hsp70 subdomain clusters.
    Biochemistry 2018 May 15. Epub 2018 May 15.
    Many molecular chaperones exist as oligomeric complexes in their functional states, yet the physical determinants underlying such self-assembly behaviour, as well as the role of oligomerisation in the activity of molecular chaperones in inhibiting protein aggregation, have proved difficult to define. Here, we demonstrate direct measurements under native conditions of the changes in the average oligomer populations of a chaperone system as a function of concentration and time, and thus determine the thermodynamic and kinetic parameters governing the self-assembly process. We access this self-assembly behaviour in real time under native-like conditions through monitoring the changes in the micron-scale diffusion of the different complexes in time and space using a microfluidic platform. Read More

    Glycosylation Fosters Interactions between Model Sea Urchin Spicule Matrix Proteins. Implications for Embryonic Spiculogenesis and Biomineralization.
    Biochemistry 2018 May 17. Epub 2018 May 17.
    Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology , New York University , 345 East 24th Street , New York , New York 10010 , United States.
    The formation of embryonic mineralized skeletal elements (spicules) in the sea urchin requires the participation of proteins, many of which may interact with one another and assist in the creation of an extracellular matrix wherein mineral formation takes place. To probe this, we created a sea urchin spicule recombinant model protein pair system wherein we tested the interactions between two major spicule proteins, SpSM50 and the glycoprotein, SpSM30B/C. Both proteins are strong hydrogelators that manipulate early and later events in mineral formation. Read More

    An Efficient Method for the Expression and Purification of Aβ(M1-42).
    Biochemistry 2018 May 24. Epub 2018 May 24.
    Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States.
    Advances in amyloid research rely on improved access to the β-amyloid peptide, Aβ. N-Terminal methionine-extended Aβ, Aβ(M1-42), is a readily expressed and widely used form of Aβ with properties comparable to those of the natural Aβ(1-42) peptide. Expression of Aβ(M1-42) is simple to execute and avoids an expensive and often difficult enzymatic cleavage step associated with expression and isolation of Aβ(1-42). Read More

    Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase Define its Mutase and Lyase Activities.
    Biochemistry 2018 May 14. Epub 2018 May 14.
    Site-directed mutations and substrate analogs were used to gain insights into the branch-point reaction catalyzed by the 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO)-tyrosine aminomutase from Oryza sativa ( OsTAM). Exchanging the active residues of ( OsTAM) (Y125C/N446K) for those in a phenylalanine aminomutase TcPAM altered its substrate specificity from tyrosine to phenylalanine. The aminomutase mechanism of ( OsTAM) surprisingly changed nearly exclusively to that of an ammonia lyase making cinnamic acid (>95%) over β-phenylalanine [Biochemistry 55, 3497-3503 (2016)]. Read More

    Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis.
    Biochemistry 2018 May 23. Epub 2018 May 23.
    Department of Molecular and Cellular Biology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada.
    S-(+)-1-Amino-2-propanol dehydrogenase (APDH) is a short-chain dehydrogenase/reductase associated with the incompletely characterized Rhodococcus and Mycobacterium bacterial microcompartment (RMM). We enzymatically characterized the APDH from M. smegmatis and showed it is highly selective, with a low micromolar K for S-(+)-1-amino-2-propanol and specificity for NADP(H). Read More

    Steric Control of the Rate-Limiting Step of UDP-Galactopyranose Mutase.
    Biochemistry 2018 May 18. Epub 2018 May 18.
    Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States.
    Galactose is an abundant monosaccharide found exclusively in mammals as galactopyranose (Gal p), the six-membered ring form of this sugar. In contrast, galactose appears in many pathogenic microorganisms as the five-membered ring form, galactofuranose (Gal f). Gal f biosynthesis begins with the conversion of UDP-Gal p to UDP-Gal f catalyzed by the flavoenzyme UDP-galactopyranose mutase (UGM). Read More

    Dimerization through the RING-Finger Domain Attenuates Excision Activity of the piggyBac Transposase.
    Biochemistry 2018 May 11;57(20):2913-2922. Epub 2018 May 11.
    Regional Centre for Biotechnology , NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway , Faridabad 121001 , Haryana , India.
    The movement of the piggyBac transposon is mediated through its cognate transposase. The piggyBac transposase binds to the terminal repeats present at the ends of the transposon. This is followed by excision of the transposon and release of the nucleoprotein complex. Read More

    Pathways of Metabolite-Related Damage to a Synthetic p53 Gene Exon 7 Oligonucleotide Using Magnetic Enzyme Bioreactor Beads and LC-MS/MS Sequencing.
    Biochemistry 2018 May 23. Epub 2018 May 23.
    Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States.
    Reactive metabolites of environmental chemicals and drugs can cause site specific damage to the p53 tumor suppressor gene in a major pathway for genotoxicity. We report here a high-throughput, cell-free, 96-well plate magnetic bead-enzyme system interfaced with LC-MS/MS sequencing for bioactivating test chemicals and identifying resulting adduction sites on genes. Bioactivated aflatoxin B1 was reacted with a 32 bp exon 7 fragment of the p53 gene using eight microsomal cytochrome (cyt) P450 enzymes from different organs coated on magnetic beads. Read More

    Chimeric Guides Probe and Enhance Cas9 Biochemical Activity.
    Biochemistry 2018 May 14. Epub 2018 May 14.
    Department of Chemistry and Biochemistry , Southern Illinois University , Carbondale , Illinois 62901 , United States.
    DNA substitutions in RNA can probe the importance of A-form structure, 2'-hydroxyl contacts, and conformational constraints within RNA-guided enzymes. Using this approach, we found that Cas9 biochemical activity tolerated significant substitution with DNA nucleotides in the clustered regularly interspaced short palindromic repeat RNA (crRNA). Only minimal RNA content was needed in or near the seed region. Read More

    Identification and characterization of smallest pore-forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109.
    BMC Biochem 2018 May 9;19(1). Epub 2018 May 9.
    Department of Life Sciences and Chemistry, Jacobs-University Bremen, Campusring 1, D-28759, Bremen, Germany.
    Background: Corynebacterium urealyticum, a pathogenic, multidrug resistant member of the mycolata, is known as causative agent of urinary tract infections although it is a bacterium of the skin flora. This pathogenic bacterium shares with the mycolata the property of having an unusual cell envelope composition and architecture, typical for the genus Corynebacterium. The cell wall of members of the mycolata contains channel-forming proteins for the uptake of solutes. Read More

    Co-Translational Folding Trajectory of the HemK Helical Domain.
    Biochemistry 2018 May 14. Epub 2018 May 14.
    Department of Physical Biochemistry , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , D-37077 Goettingen , Germany.
    Protein folding begins co-translationally within the restricted space of the peptide exit tunnel of the ribosome. We have already shown that the N-terminal α-helical domain of the universally conserved N-glutamine methyltransferase HemK is compacted within the exit tunnel and rearranges into the native fold upon emerging from the ribosome. However, the exact folding pathway of the domain remained unclear. Read More

    Structural Basis for the Catalytic Mechanism of Ethylenediamine- N, N'-disuccinic Acid Lyase, a Carbon-Nitrogen Bond-Forming Enzyme with a Broad Substrate Scope.
    Biochemistry 2018 May 18. Epub 2018 May 18.
    Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands.
    The natural aminocarboxylic acid product ethylenediamine- N, N'-disuccinic acid [( S, S)-EDDS] is able to form a stable complex with metal ions, making it an attractive biodegradable alternative for the synthetic metal chelator ethylenediaminetetraacetic acid (EDTA), which is currently used on a large scale in numerous applications. Previous studies have demonstrated that biodegradation of ( S, S)-EDDS may be initiated by an EDDS lyase, converting ( S, S)-EDDS via the intermediate N-(2-aminoethyl)aspartic acid (AEAA) into ethylenediamine and two molecules of fumarate. However, current knowledge of this enzyme is limited because of the absence of structural data. Read More

    Downregulation of LINC00894-002 Contributes to Tamoxifen Resistance by Enhancing the TGF-β Signaling Pathway.
    Biochemistry (Mosc) 2018 May;83(5):603-611
    Department of Cell and Developmental Biology, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.
    Tamoxifen is a widely used personalized medicine for estrogen receptor (ER)-positive breast cancer, but approximately 30% of patients receiving the treatment relapse due to tamoxifen resistance (TamR). Recently, several reports have linked lncRNAs to cancer drug resistance. However, the role of lncRNAs in TamR is unclear. Read More

    Cytochrome P450 1A1 (CYP1A1) Catalyzes Lipid Peroxidation of Oleic Acid-Induced HepG2 Cells.
    Biochemistry (Mosc) 2018 May;83(5):595-602
    Key Laboratory of Antiinflammatory and Immune Medicines, Ministry of Education, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.
    Nonalcoholic fatty liver disease (NAFLD) is a chronic hepatic disease associated with excessive accumulation of lipids in hepatocytes. As the disease progresses, oxidative stress plays a pivotal role in the development of hepatic lipid peroxidation. Cytochrome P450 1A1 (CYP1A1), a subtype of the cytochrome P450 family, has been shown to be a vital modulator in production of reactive oxygen species. Read More

    An Inducible DamID System for Profiling Interactions of Nuclear Lamina Protein Component Lamin B1 with Chromosomes in Mouse Cells.
    Biochemistry (Mosc) 2018 May;83(5):586-594
    Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
    At the level of DNA organization into chromatin, there are mechanisms that define gene expression profiles in specialized cell types. Genes within chromatin regions that are located at the nuclear periphery are generally expressed at lower levels; however, the nature of this phenomenon remains unclear. These parts of chromatin interact with nuclear lamina proteins like Lamin B1 and, therefore, can be identified in a given cell type by chromatin profiling of these proteins. Read More

    Agonistic and Antagonistic Effects of Progesterone Derivatives on the Transcriptional Activity of Nuclear Progesterone Receptor B in Yeast Model System.
    Biochemistry (Mosc) 2018 May;83(5):574-585
    Lomonosov Moscow State University, Faculty of Biology, Moscow, 119899, Russia.
    Identification of progesterone selective agonists and antagonists that act through one of the nuclear progesterone receptor isoforms is of particular importance for the development of tissue-specific drugs in gynecology and anticancer therapy. Fourteen pregna-D'- and pregna-D'-pentarane progesterone derivatives with 16α,17α-cycloalkane groups and two progesterone 3-deoxyderivatives were examined for their ability to regulate transcriptional activity of human nuclear progesterone receptor isoform B (nPR-B) expressed in Saccharomyces cerevisiae yeast. Transcriptional activity of nPR-B was measured from the expression of the β-galactosidase reporter gene with a hormone-responsible element in the promoter. Read More

    Recombinant Production, Reconstruction in Lipid-Protein Nanodiscs, and Electron Microscopy of Full-Length α-Subunit of Human Potassium Channel Kv7.1.
    Biochemistry (Mosc) 2018 May;83(5):562-573
    Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
    Voltage-gated potassium channel Kv7.1 plays an important role in the excitability of cardiac muscle. The α-subunit of Kv7. Read More

    New Data on Effects of SkQ1 and SkQT1 on Rat Liver Mitochondria and Yeast Cells.
    Biochemistry (Mosc) 2018 May;83(5):552-561
    Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, Moscow, 119071, Russia.
    Mitochondria are involved in many processes in eukaryotic cells. They play a central role in energy conservation and participate in cell metabolism and signaling pathways. Mitochondria are the main source of reactive oxygen species, excessive generation of which provokes numerous pathologies and cell death. Read More

    Regulated Gene Expression as a Tool for Analysis of Heterochromatin Position Effect in Drosophila.
    Biochemistry (Mosc) 2018 May;83(5):542-551
    Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
    Position effect variegation (PEV) is a perturbation of genes expression resulting from the changes in their chromatin organization due to the abnormal juxtaposition with heterochromatin. The exact molecular mechanisms of PEV remain enigmatic in spite of the long history of PEV studies. Here, we developed a genetic model consisting of PEV-inducing chromosome rearrangement and a reporter gene under control of the UAS regulatory element. Read More

    O-Antigens of Escherichia coli Strains O81 and HS3-104 Are Structurally and Genetically Related, Except O-Antigen Glucosylation in E. coli HS3-104.
    Biochemistry (Mosc) 2018 May;83(5):534-541
    Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia.
    Glycerophosphate-containing O-specific polysaccharides (OPSs) were obtained by mild acidic degradation of lipopolysaccharides isolated from Escherichia coli type strain O81 and E. coli strain HS3-104 from horse feces. The structures of both OPSs and of the oligosaccharide derived from the strain O81 OPS by treatment with 48% HF were studied by monosaccharide analysis and one- and two-dimensional 1H- and 13C-NMR spectroscopy. Read More

    The Effect of Experimental Hyperthyroidism on Characteristics of Actin-Myosin Interaction in Fast and Slow Skeletal Muscles.
    Biochemistry (Mosc) 2018 May;83(5):527-533
    Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, 620049, Russia.
    The molecular mechanism of the failure of contractile function of skeletal muscles caused by oxidative damage to myosin in hyperthyroidism is not fully understood. Using an in vitro motility assay, we studied the effect of myosin damage caused by oxidative stress in experimental hyperthyroidism on the actin-myosin interaction and its regulation by calcium. We found that hyperthyroidism-induced oxidation of myosin is accompanied by a decrease in the sliding velocity of the regulated thin filaments in the in vitro motility assay, and this effect is increased with the duration of the pathological process. Read More

    Blood-Derived RNA- and microRNA-Hydrolyzing IgG Antibodies in Schizophrenia Patients.
    Biochemistry (Mosc) 2018 May;83(5):507-526
    Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
    Abzymes with various catalytic activities are the earliest statistically significant markers of existing and developing autoimmune diseases (AIDs). Currently, schizophrenia (SCZD) is not considered to be a typical AID. It was demonstrated recently that antibodies from SCZD patients efficiently hydrolyze DNA and myelin basic protein. Read More

    Interleukin-4 Restores Insulin Sensitivity in Lipid-Induced Insulin-Resistant Adipocytes.
    Biochemistry (Mosc) 2018 May;83(5):498-506
    Institute of Experimental Cardiology, National Medical Research Center for Cardiology, Moscow, 121552, Russia.
    Obesity and latent inflammation in adipose tissue significantly contribute to the development of insulin resistance (IR) and type 2 diabetes. Here we studied whether the antiinflammatory interleukin-4 (IL-4) can restore insulin sensitivity in cultured 3T3-L1 adipocytes. The activity of key components of the insulin signaling cascade was assessed by immunoblotting using phospho-specific antibodies to insulin receptor substrate IRS1 (Tyr612), Akt (Thr308 and Ser473), and AS160 (Ser318) protein that regulates translocation of the GLUT4 glucose transporter to the plasma membrane. Read More

    Argonaute Proteins and Mechanisms of RNA Interference in Eukaryotes and Prokaryotes.
    Biochemistry (Mosc) 2018 May;83(5):483-497
    Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
    Noncoding RNAs play essential roles in genetic regulation in all organisms. In eukaryotic cells, many small noncoding RNAs act in complex with Argonaute proteins and regulate gene expression by recognizing complementary RNA targets. The complexes of Argonaute proteins with small RNAs also play a key role in silencing of mobile genetic elements and, in some cases, viruses. Read More

    Spatial Structure of Glycogen Molecules in Cells.
    Biochemistry (Mosc) 2018 May;83(5):467-482
    Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
    Glycogen is a strongly branched polymer of α-D-glucose, with glucose residues in the linear chains linked by 1→4-bonds (~93% of the total number of bonds) and with branching after every 4-8 residues formed by 1→6-glycosidic bonds (~7% of the total number of bonds). It is thought currently that a fully formed glycogen molecule (β-particle) with the self-glycosylating protein glycogenin in the center has a spherical shape with diameter of ~42 nm and contains ~ 55,000 glucose residues. The glycogen molecule also includes numerous proteins involved in its synthesis and degradation, as well as proteins performing a carcass function. Read More

    Characterization of a Sulfated Anti-HIV Antibody Using an Expanded Genetic Code.
    Biochemistry 2018 May 10;57(20):2903-2907. Epub 2018 May 10.
    Department of Biomedical Engineering , University of California , Irvine , California 92617 , United States.
    Tyrosine sulfation is a crucial post-translational modification for certain antibodies that neutralize HIV. One of the most neutralizing sulfated anti-HIV antibodies, E51, contains a region in its VCDR3 loop with five tyrosine (Tyr) residues, which are hypothesized to be partially or fully sulfated to bind to HIV's gp120 coat protein. However, the gp120-binding contribution of each sulfate or more complex sulfation patterns is unknown. Read More

    Tyr51: Key Determinant of the Low Thermostability of the Colwellia psychrerythraea Cold-Shock Protein.
    Biochemistry 2018 May 18. Epub 2018 May 18.
    Department of Bioscience and Biotechnology , Konkuk University , Seoul 05029 , Republic of Korea.
    Cold-shock proteins (Csps) are expressed at lower-than-optimum temperatures, and they function as RNA chaperones; however, no structural studies on psychrophilic Csps have been reported. Here, we aimed to investigate the structure and dynamics of the Csp of psychrophile Colwellia psychrerythraea 34H, ( Cp-Csp). Although Cp-Csp shares sequence homology, common folding patterns, and motifs, including a five β-stranded barrel, with its thermophilic counterparts, its thermostability (37 °C) was markedly lower than those of other Csps. Read More

    Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase.
    Biochemistry 2018 May 21. Epub 2018 May 21.
    Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.
    The C-terminal domain of cobalamin-dependent methionine synthase (MetH) has an essential role in catalyzing the reactivation of the enzyme following the oxidation of its cobalamin cofactor. This reactivation occurs through reductive methylation of the cobalamin using S-adenosylmethionine (AdoMet) as the methyl donor. Herein, we examine the molecular recognition of AdoMet by the MetH reactivation domain utilizing structural, biochemical, and computational approaches. Read More

    Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.
    Biochemistry 2018 May 17. Epub 2018 May 17.
    Department of Biochemistry and Molecular Biology and Department of Chemistry , University of Chicago , 929 East 57th Street , Chicago , Illinois 60637 , United States.
    Steric constraints imposed by the active sites of protein and RNA enzymes pose major challenges to the investigation of structure-function relationships within these systems. As a strategy to circumvent such constraints in the HDV ribozyme, we have synthesized phosphoramidites from propanediol derivatives and incorporated them at the 5'-termini of RNA and DNA oligonucleotides to generate a series of novel substrates with nucleophiles perturbed electronically through geminal fluorination. In nonenzymatic, hydroxide-catalyzed intramolecular transphosphorylation of the DNA substrates, pH-rate profiles revealed that fluorine substitution reduces the maximal rate and the kinetic p K, consistent with the expected electron-withdrawing effect. Read More

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