Vojtech Klusák

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The formation of a hydrophobic core of globular proteins is believed to be the consequence of exterior hydrophobic forces of entropic nature. This, together with the low occurrence of hydrogen bonds in the protein core, leads to the opinion that the energy contribution of core formation to protein folding and stability is negligible. We show that(More)
An analysis of the crystal structure of [BmPBP...bombykol] complex identified nine amino acid residues involved in a variety of intermolecular interactions binding the ligand. Using simple model fragments as the representatives of the residues, the interaction energies of their complexes with bombykol were calculated using high-level ab initio methods. The(More)
Glutamate carboxypeptidase II (GCPII, EC is a zinc-dependent exopeptidase and an important therapeutic target for neurodegeneration and prostate cancer. The hydrolysis of N-acetyl-l-aspartyl-l-glutamate (N-Ac-Asp-Glu), the natural dipeptidic substrate of the GCPII, is intimately involved in cellular signaling within the mammalian nervous system,(More)
Activation and reaction energies for four model systems capturing the essential physicochemical features of the hydrolysis of the peptide bond have been calculated at various level of theory, including the presumably accurate CCSD(T) calculations. The models studied covered a part of the spectrum encountered in biological systems: the hydrolysis in the(More)
Correlated ab initio calculations on large systems, such as the popular MP2 (or RI-MP2) method, suffer from the intramolecular basis set superposition error (BSSE). This error is typically manifested in molecules with folded structures, characterized by intramolecular dispersion interactions. It can dramatically affect the energy differences between various(More)
Human glutamate carboxypeptidase II (GCPII) is a transmembrane metallopeptidase found mainly in the brain, small intestine, and prostate. In the brain, it cleaves N-acetyl-L-aspartyl-glutamate, liberating free glutamate. Inhibition of GCPII has been shown to be neuroprotective in models of stroke and other neurodegenerations. In prostate, it is known as(More)
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