[Generalized ordering parameter S2 for N-H peptide bonding as measure of the conformational flexibility of proteins: comparison of algorithms of S2 calculation from molecular dynamics simulation data].

NMR spectroscopy in combination with molecular dynamics (MD) simulation technique is a powerful tool for investigation of biomolecule conformations. In the present study we compare the two algorithms of calculation of the generalized order parameter S2 for the peptide N-H bond from MD simulation data. The program based on this algorithm has been written and the effect of an adjustible parameter on results of calculation was studied.

[Conformational changes in HIV-1 proteinase: effect of protonation of the active center on conformation of HIV-1 proteinase in water].

At weak acidic pH, where HIV-1 proteinase is most stable and active, its catalytic Asp 25/25' dyad shares one proton. At a physiological pH the dyad is deprotonated, however, 2 ns molecular dynamics simulations of the HIV-1 protease with monoprotonated and deprotonated Asp25/25' dyad is performed, in order to investigate the influence of Asp25/25' protonation state on the proteinase dynamics. For net charge neutralization the 4 Cl- ions were included.

[New species of Microsporidia from the gallbladder of deep-sea fishes].

Two new species of myxosporidians with gigantic spores are described from the gall bladder of Alepocephalus australis caught at 1500 m depth. Both species differ in gigantic sizes of spores that apparently is characteristic of myxosporidians of fishes inhabiting such great depths.