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Biochemistry (Washington)

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  1. Dynamics of MutS-Mismatched DNA Complexes Are Predictive of Their Repair Phenotypes.

    Biochemistry (Washington) 53(12):2043 (2014) PMID 24588663

    We present single-molecule Förster resonance energy transfer measurements of the DNA bending dynamics induced by Thermus aquaticus MutS and the E41A mutant of MutS, which is known to have error specific deficiencies in signaling repair. We compared three DNA mismatches/IDLs (T-bulge, GT, and CC) wit...
  2. Inhibition of Ligand Exchange Kinetics via Active-Site Trapping with an Antibody Fragment.

    Biochemistry (Washington) 53(12):1879 (2014) PMID 24617671

    We describe the first example of an inhibitory antibody fragment (nanobody ca1697) that binds simultaneously to an enzyme (the enzyme dihydrofolate reductase from Escherichia coli) and its bound substrate (folate). Binding of the antibody to the substrate causes a 20-fold reduction in the rate of fo...
  3. Conformational Dynamics of a Y-Family DNA Polymerase during Substrate Binding and Catalysis As Revealed by Interdomain Förster Resonance Ene...

    Biochemistry (Washington) 53(11):1768 (2014) PMID 24568554

    Numerous kinetic, structural, and theoretical studies have established that DNA polymerases adjust their domain structures to enclose nucleotides in their active sites and then rearrange critical active site residues and substrates for catalysis, with the latter conformational change acting to kinet...
  4. Formation of a Stacked Dimeric G-Quadruplex Containing Bulges by the 5'-Terminal Region of Human Telomerase RNA (hTERC).

    Biochemistry (Washington) 53(10):1595 (2014) PMID 24601523

    We investigate the structure formed by the first 18-nt of the 5'-terminal region of the human telomerase RNA (hTERC or hTR) using gel electrophoresis and UV, CD, and NMR spectroscopy. Our data suggest that this 18-nt sequence, r(GGGUUGCGGAGGGUGGGC), can form a stacked dimeric G-quadruplex in potassi...
  5. Structure-based energetics of mRNA decoding on the ribosome.

    Biochemistry (Washington) 53(10):1714 (2014) PMID 24564511

    We report extensive computer simulations that allow us to quantitatively calculate tRNA discrimination and uncover the energetics underlying accuracy in code translation. We show that the tRNA-mRNA interaction energetics varies drastically along the path from initial selection to peptide bond format...
  6. Manipulating conserved heme cavity residues of chlorite dismutase: effect on structure, redox chemistry, and reactivity.

    Biochemistry (Washington) 53(1):77 (2014) PMID 24364531 PMCID PMC3893830

    Chlorite dismutases (Clds) are heme b containing oxidoreductases that convert chlorite to chloride and molecular oxygen. In order to elucidate the role of conserved heme cavity residues in the catalysis of this reaction comprehensive mutational and biochemical analyses of Cld from "Candidatus Nitros...
  7. Interactions between cytochromes P450 2B4 (CYP2B4) and 1A2 (CYP1A2) lead to alterations in toluene disposition and P450 uncoupling.

    Biochemistry (Washington) 52(23):4003 (2013) PMID 23675771 PMCID PMC3750074

    These results suggest the major functional effects of the P450·P450 interaction are mediated by changes in the relative abilities of the P450s to receive electrons from CPR. Furthermore, CPR may play an effector role by causing a conformational change in CYP1A2 that makes its metabolism more efficie...
  8. Tranilast binds to aβ monomers and promotes aβ fibrillation.

    Biochemistry (Washington) 52(23):3995 (2013) PMID 23679559

    We used solution NMR to determine that tranilast binds to Aβ40 monomers with ∼300 μM affinity. Remarkably, tranilast increases Aβ40 fibrillation more than 20-fold in the thioflavin T assay at a 1:1 molar ratio, as well as significantly reducing the lag time. Tranilast likely promotes fibrillation by...
  9. Thermodynamic contribution to the regulation of electron transfer in the Na(+)-pumping NADH:quinone oxidoreductase from Vibrio cholerae.

    Biochemistry (Washington) 51(19):4072 (2012) PMID 22533880

    The Na+ pumping NADH:quinone oxidoreductase (Na+-NQR) is a fundamental enzyme of the oxidative phosphorylation metabolism and ionic homeostasis in several pathogenic and marine bacteria. In order to understand the mechanism that couples the electron transfer with the sodium transloca...
  10. Motifs Q and I are required for ATP hydrolysis but not for ATP binding in SWI2/SNF2 proteins.

    Biochemistry (Washington) 51(18):3711 (2012) PMID 22510062

    We have sought to define the role of motifs Q and I in ATP hydrolysis mediated by ADAAD. We show that in ADAAD both motifs Q and I are required for only ATP catalysis but not for ATP binding. In addition, the conserved glutamine present in motif Q also dictates the catalytic rate. The ability of the...