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Thermodynamic contribution to the regulation of electron transfer in the Na(+)-pumping NADH:quinone oxidoreductase from Vibrio cholerae.
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...
Motifs Q and I are required for ATP hydrolysis but not for ATP binding in SWI2/SNF2 proteins.
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...
Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I.
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...
Mitochondrial ATP synthase catalytic mechanism: a novel visual comparative structural approach emphasizes pivotal roles for mg(2+) and p-loo...
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...
Characterization of early stage intermediates in the nucleation phase of Aβ aggregation.
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....
Active site substitution A82W improves the regioselectivity of steroid hydroxylation by cytochrome P450 BM3 mutants as rationalized by spin ...
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...
Hydrophobicity and conformational change as mechanistic determinants for nonspecific modulators of amyloid β self-assembly.
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...
The structural basis for control of eukaryotic protein kinases.
Eukaryotic protein kinases are key regulators of cell processes. Comparison of the structures of protein kinase domains, both alone and in complexes, allows generalizations to be made about the mechanisms that regulate protein kinase activation. Protein kinases in the active state ad...
Control of substrate specificity by a single active site residue of the KsgA methyltransferase.
We demonstrate that part of the discrimination between mono- and dimethyltransferase activity lies in a single residue in the active site, L114; this residue is part of a conserved motif, known as motif IV, which is common to a large group of S-adenosyl-L-methionine dependent methyltransferases. Mut...
²H solid-state nuclear magnetic resonance investigation of whole Escherichia coli interacting with antimicrobial peptide MSI-78.
We have designed a procedure to incorporate high levels of 2H-NMR labels specifically into the cell membrane of E. coli and used this approach to study the interactions between the AMP MSI-78 and the membranes of intact bacteria. The 2H NMR spectra of these membrane-deuterated bacteria a...