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Biochemistry (Washington)

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  1. Decreased Amyloidogenicity Caused by Mutational Modulation of Surface Properties of the Immunoglobulin Light Chain BRE Variable Domain.

    Biochemistry (Washington) 53(31):5162 (2014) PMID 25062800

    We identified the key residues for destabilization of the native state of amyloidogenic VL in the LC of BRE by analyzing the stability of chimeric mutants of BRE and REI VL; the latter immunoglobulin is not associated with AL amyloidosis. The results suggest that the surface-exposed residues N45 and...
  2. Evidence of the Direct Involvement of the Substrate TCP Radical in Functional Switching from Oxyferrous O2 Carrier to Ferric Peroxidase in t...

    Biochemistry (Washington) 53(30):4956 (2014) PMID 24972312

    We report details of our investigations into the H2O2-mediated conversion of oxy-DHP to the ferric or ferryl ([TCP] < [H2O2]) state triggered by both biologically relevant [TCP and 4-bromophenol (4-BP)] and nonrelevant (ferrocyanide) compounds. At <50 μM H2O2, all of these conversion reactions are c...
  3. Neuraminidase substrate promiscuity permits a mutant Micromonospora viridifaciens enzyme to synthesize artificial carbohydrates.

    Biochemistry (Washington) 53(24):3982 (2014) PMID 24870444

    We identified as methyl N-acetyl-α-D-neuraminyl-(2 → 6)-α-D-galactopyranoside. The MvNA Y370G-catalyzed coupling of N-acetylneuraminic acid to these three methyl α-d-glycopyranoside acceptors is favored by factors of 18–27-fold over the competing hydrolysis reaction. These coupling efficiencies like...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. 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....
  9. Active site substitution A82W improves the regioselectivity of steroid hydroxylation by cytochrome P450 BM3 mutants as rationalized by spin ...

    Biochemistry (Washington) 51(3):750 (2012) PMID 22208729

    We present engineered drug metabolizing P450 BM3 mutants as a novel tool for regioselective hydroxylation of steroids at the 16ß-position. In particular we show that by replacing alanine at position 82 by a tryptophan in P450 BM3 mutants M01 and M11, the selectivity towards 16ß-hydroxylation for b...
  10. Hydrophobicity and conformational change as mechanistic determinants for nonspecific modulators of amyloid β self-assembly.

    Biochemistry (Washington) 51(1):126 (2012) PMID 22133042

    We describe here a detailed study of the mechanism of action of one representative compound, lacmoid, in the context of the inhibition of the aggregation of the amyloid β-peptide (Aβ) associated with Alzheimer's disease. We show that lacmoid binds Aβ(1-40) in a surfactant-like manner and countera...