Biochemistry (Washington)

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  1. Correction to Metal Binding Properties of Escherichia coli YjiA, a Member of the Metal Homeostasis-Associated COG0523 Family of GTPases

    Biochemistry (Washington) 52(23):4105 (2013) PMCID PMC3680914

  2. Correction to NMR of CCCC RNA Reveals a Right-Handed Helix and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics

    Biochemistry (Washington) 52(19):3390 (2013) PMCID PMC3656770

  3. A selenocysteine variant of the human copper chaperone for superoxide dismutase. A Se-XAS probe of cluster composition at the domain 3-domain 3 dimer interface.

    Biochemistry (Washington) 47(17):4916 (2008) PMID 18393442

    We report the semisynthesis of a selenocysteine (Sec) derivative of the human copper chaperone for superoxide dismutase, substituted with Sec at the C-terminal C246 residue. Measurements of hCCS-induced SOD1 activation were used to show that the C-terminal CXC sequence is both necessary and suff...
  4. Domain stabilities in protein kinase R (PKR): evidence for weak interdomain interactions.

    Biochemistry (Washington) 47(17):4887 (2008) PMID 18393532 PMCID PMC2729556

    PKR (protein kinase R) is induced by interferon and is a key component of the innate immunity antiviral pathway. Upon binding dsRNA, PKR undergoes autophosphorylation reactions that activate the kinase, leading it to phosphorylate eIF2alpha, thus inhibiting protein synthesis in virally infected ...
  5. Cu(II) binding to monomeric, oligomeric, and fibrillar forms of the Alzheimer's disease amyloid-beta peptide.

    Biochemistry (Washington) 47(17):5006 (2008) PMID 18393444

    Copper has been proposed to play a role in Alzheimer's disease through interactions with the amyoid-beta (Abeta) peptide. The coordination environment of bound copper as a function of Cu:Abeta stoichiometry and Abeta oligomerization state are particularly contentious. Using low-temperature elect...
  6. Biochemical origins of lactaldehyde and hydroxyacetone in Methanocaldococcus jannaschii.

    Biochemistry (Washington) 47(17):5037 (2008) PMID 18363381

    The biochemical routes for the metabolism of methylglyoxal and the formation of lactaldehyde and hydroxyacetone in Methanocaldococcus jannaschii have been established. The addition of methylglyoxal and NADH, NADPH, F 420H 2, or DTT to a M. jannaschii cell extract stimulated the production of bot...
  7. Volume and free energy of folding for troponin C C-domain: linkage to ion binding and N-domain interaction.

    Biochemistry (Washington) 47(17):5047 (2008) PMID 18393534

    Troponin C (TnC) is an 18-kDa acidic protein of the EF-hand family that serves as the trigger for muscle contraction. In this study, we investigated the thermodynamic stability of the C-domain of TnC in all its occupancy states (apo, Mg (2+)-, and Ca (2+)-bound states) using a fluorescent mutant...
  8. Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolases. 2. The role of helix 18 stability.

    Biochemistry (Washington) 47(17):4983 (2008) PMID 18393535

    The S-adenosyl- l-homocysteine (AdoHcy) hydrolases (SAHH) from Homo sapiens (Hs-SAHH) and from the parasite Trypanosoma cruzi (Tc-SAHH) are very similar in structure and catalytic properties but differ in the kinetics and thermodynamics of association and dissociation of the cofactor NAD (+). Th...
  9. Effector-induced structural fluctuation regulates the ligand affinity of an allosteric protein: binding of inositol hexaphosphate has distinct dynamic consequences for the T and R states of hemoglobin.

    Biochemistry (Washington) 47(17):4907 (2008) PMID 18376851 PMCID PMC2493540

    The present study reports distinct dynamic consequences for the T- and R-states of human normal adult hemoglobin (Hb A) due to the binding of a heterotropic allosteric effector, inositol hexaphosphate (IHP). A nuclear magnetic resonance (NMR) technique based on modified transverse relaxation opt...
  10. Glucose modulation of glucokinase activation by small molecules.

    Biochemistry (Washington) 47(17):5028 (2008) PMID 18370405

    Small molecule activators of glucokinase (GK) were used in kinetic and equilibrium binding studies to probe the biochemical basis for their allosteric effects. These small molecules decreased the glucose K 0.5 ( approximately 1 mM vs approximately 8 mM) and the glucose cooperativity (Hill coeffi...
  11. Structural basis of the iron storage function of frataxin from single-particle reconstruction of the iron-loaded oligomer.

    Biochemistry (Washington) 47(17):4948 (2008) PMID 18393441 PMCID PMC3932613

    The mitochondrial protein frataxin plays a central role in mitochondrial iron homeostasis, and frataxin deficiency is responsible for Friedreich ataxia, a neurodegenerative and cardiac disease that affects 1 in 40000 children. Here we present a single-particle reconstruction from cryoelectron mi...
  12. Platelet endothelial cell adhesion molecule 1 (PECAM-1) and its interactions with glycosaminoglycans: 1. Molecular modeling studies.

    Biochemistry (Washington) 47(17):4851 (2008) PMID 18393439

    Platelet endothelial cell adhesion molecule 1 (PECAM-1) has many functions, including its roles in leukocyte extravasation as part of the inflammatory response and in the maintenance of vascular integrity through its contribution to endothelial cell-cell adhesion. PECAM-1 has been shown to media...
  13. Monitoring aromatic picosecond to nanosecond dynamics in proteins via 13C relaxation: expanding perturbation mapping of the rigidifying core mutation, V54A, in eglin c.

    Biochemistry (Washington) 47(17):4876 (2008) PMID 18393447 PMCID PMC3062916

    Long-range effects, such as allostery, have evolved in proteins as a means of regulating function via communication between distal sites. An NMR-based perturbation mapping approach was used to more completely probe the dynamic response of the core mutation V54A in the protein eglin c by monitori...
  14. Cyanolysis and azidolysis of epoxides by haloalcohol dehalogenase: theoretical study of the reaction mechanism and origins of regioselectivity.

    Biochemistry (Washington) 47(17):4973 (2008) PMID 18393443

    Haloalcohol dehalogenase HheC catalyzes the reversible dehalogenation of vicinal haloalcohols to form epoxides and free halides. In addition, HheC is able to catalyze the irreversible and highly regioselective ring-opening of epoxides with nonhalide nucleophiles, such as CN (-) and N 3 (-). For ...
  15. Inhibitors of the molybdenum cofactor containing 4-hydroxybenzoyl-CoA reductase.

    Biochemistry (Washington) 47(17):4964 (2008) PMID 18393440

    4-Hydroxybenzoyl-CoA reductase (4-HBCR) is a member of the xanthine oxidase (XO) family of molybdenum cofactor containing enzymes and catalyzes the irreversible removal of a phenolic hydroxy group by reduction, yielding benzoyl-CoA and water. In this work the effects of various activity modulati...
  16. Human quiescin-sulfhydryl oxidase, QSOX1: probing internal redox steps by mutagenesis.

    Biochemistry (Washington) 47(17):4955 (2008) PMID 18393449 PMCID PMC3542536

    The flavoprotein quiescin-sulfhydryl oxidase (QSOX) rapidly inserts disulfide bonds into unfolded, reduced proteins with the concomitant reduction of oxygen to hydrogen peroxide. This study reports the first heterologous expression and enzymological characterization of a human QSOX1 isoform. Lik...
  17. Platelet endothelial cell adhesion molecule 1 (PECAM-1) and its interactions with glycosaminoglycans: 2. Biochemical analyses.

    Biochemistry (Washington) 47(17):4863 (2008) PMID 18327914

    Platelet endothelial cell adhesion molecule 1 (PECAM-1) (CD31), a member of the immunoglobulin (Ig) superfamily of cell adhesion molecules with six Ig-like domains, has a range of functions, notably its contributions to leukocyte extravasation during inflammation and in maintaining vascular endo...
  18. Enzyme kinetics and binding studies on inhibitors of MEK protein kinase.

    Biochemistry (Washington) 47(17):5017 (2008) PMID 18393446

    Inhibition of the protein kinase, MEK1, is a potential approach for the treatment of cancer. Inhibitors may act by prevention of activation (PoA), which involves interfering with phosphorylation of nonactivated MEK1 by the upstream kinase, B-RAF. Modulation also may occur by inhibition of cataly...
  19. Characterization of a lysine-specific histone demethylase from Arabidopsis thaliana.

    Biochemistry (Washington) 47(17):4936 (2008) PMID 18393445

    Arabidopsis thaliana has four genes with close homology to human histone H3 lysine 4 demethylase (HsLSD1), a component of various transcriptional corepressor complexes that often also contain histone deacetylases and the corepressor protein CoREST. All four Arabidopsis proteins contain a flavin ...
  20. Multidomain initiation factor 2 from Thermus thermophilus consists of the individual autonomous domains.

    Biochemistry (Washington) 47(17):4992 (2008) PMID 18393450

    The three-dimensional chalice-like crystal structure of initiation factor 2 IF2/eIF5B from Methanobacterium thermoautotrophicum represents a novel fold and domain architecture in which the N-terminal G domain and the C-terminal C domain are separated by an approximately 40 A alpha-helix. Homolog...