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Biochemistry (Washington)

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  1. Structure and regulatory interactions of the cytoplasmic terminal domains of serotonin transporter.

    Biochemistry (Washington) 53(33):5444 (2014) PMID 25093911

    We combined molecular modeling, biochemical, and biophysical approaches in an iterative manner to investigate the structure of the 82-residue N-terminal and 30-residue C-terminal domains of human serotonin transporter (SERT). Several secondary structures were predicted in these domains, and structur...
  2. 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...
  3. 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...
  4. Combining experimental evidence and molecular dynamic simulations to understand the mechanism of action of the antimicrobial octapeptide jel...

    Biochemistry (Washington) 53(29):4857 (2014) PMID 24971729

    We demonstrated that the lytic, pore-forming activity of Jelleine-I is similar to that of other cationic antimicrobial peptides, which exhibit stronger activity on anionic bilayers. Results from molecular dynamics simulations suggested that the presence of a proline residue at the first position is...
  5. Evidence for a catalytically and kinetically competent enzyme-substrate cross-linked intermediate in catalysis by lipoyl synthase.

    Biochemistry (Washington) 53(28):4557 (2014) PMID 24901788

    We provide evidence for the formation of a covalent cross-link between LS and an LCP or synthetic peptide substrate in reactions in which insertion of the second sulfur atom is slowed significantly by deuterium substitution at C8 or by inclusion of limiting concentrations of SAM. The observation tha...
  6. Heterogeneous photodynamics of the pfr state in the cyanobacterial phytochrome cph1.

    Biochemistry (Washington) 53(28):4601 (2014) PMID 24940993

    Femtosecond photodynamics of the Pfr form of the red/far-red phytochrome N-terminal PAS-GAF-PHY photosensory core module of the cyanobacterial phytochrome Cph1 (termed Cph1Δ) from Synechocystis were resolved with visible broadband transient absorption spectroscopy. Multiphasic generation dynamics vi...
  7. 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...
  8. 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...
  9. 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...
  10. 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...