Showing papers by "Tamás Beke-Somfai published in 2010"
TL;DR: The structure and the kinetics of two mutant enzymes in which the aspartic acid of the catalytic triad was changed to alanine or asparagine are investigated and it is concluded that the two forms are at equilibrium and the substrates bind by the conformational selection mechanism.
38 citations
TL;DR: It is concluded that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO(3)(-) ion, and that even a relatively small change in active site conformation may effectively block the back reaction in beta(TP) and, thus, promote ATP.
Abstract: Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent high-resolution X-ray structure, we conclude that formation of the P−O bond may be achieved through a transition state (TS) with a planar PO3− ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP.
9 citations
TL;DR: In this article, quantum mechanical calculations were used for an atomic level investigation of the β-sheet unfolding mechanism aided by pioneer water molecules accessing the structural motif, and it was shown that there is a qualitatively different forced unfold mechanism for parallel and antiparallel β-sheets.
Abstract: In this study, quantum mechanical calculations were used for an atomic level investigation of the β-sheet unfolding mechanism aided by pioneer water molecules accessing the structural motif. Results indicate that there is a qualitatively different forced unfold mechanism for parallel and antiparallel β-sheets. In the case of parallel β-sheets, the presence of only a single water molecule could already be enough to stimulate rupture of consecutive backbone hydrogen bonds by stepping from one H-bond to the next one, similarly as a slider opens up a zipper. The extension curves and energetics obtained at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level of theory correlate well and may explain the hyperfine resolution of experimentally observed sawtooth patterns in single molecule studies where external pulling force was applied.
3 citations