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Biochemistry (Washington)

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  1. 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...
  2. 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...
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I.

    Biochemistry (Washington) 51(12):2569 (2012) PMID 22397306

    We have used energy decomposition (EDA), electrostatic free energy response (EFER), and non-covalent interaction analysis (NCI) analyses to identify residues involved in this putative checking site. We have used structures for DNA polymerase I from two different organisms, the Klenow fragment from E...
  9. Mitochondrial ATP synthase catalytic mechanism: a novel visual comparative structural approach emphasizes pivotal roles for mg(2+) and p-loo...

    Biochemistry (Washington) 51(7):1532 (2012) PMID 22243519

    We used the photosensitive phosphate analogue vanadate (V(i)) to study the enzyme's mechanism in the transition state. Significantly, these studies showed that Mg(2+) plays an important role in transition state formation during ATP synthesis. Additionally, in both MgADP·V(i)-F(1) and MgV(i)-F(1) co...
  10. Characterization of early stage intermediates in the nucleation phase of Aβ aggregation.

    Biochemistry (Washington) 51(6):1070 (2012) PMID 22283417

    These results are the first reported measurements of the real-time changes in Aβ molecular structure during the early stages of amyloid formation at the nanometer level....