Folding of the Protein Domain hbSBD

The folding of the alpha-helice domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKD) complex is studied by the circular dichroism technique in absence of urea. Thermal denaturation is used to evaluate various thermodynamic parameters defining the equilibrium unfolding, which is well described by the two-state model with the folding temperature T_f = 317.8 K and the enthalpy change Delta H_g = 19.67 kcal/mol. The folding is also studied numerically using the off-lattice coarse-grained Go model and the Langevin dynamics. The obtained results, including the population of the native basin, the free energy landscape as a function of the number of native contacts and the folding kinetics, also suggest that the hbSBD domain is a two-state folder. These results are consistent with the biological function of hbSBD in BCKD.Comment: 25 pages, 7 figures, 1 table, published in Biophysical Journa

Sayat-Nova’s Oeuvre in the Light of Interpretation and Translation by V. Bryusov

Each national literature is a part of national history. It presents the features of the national culture and the people who live and develop in specific cultural and traditional conditions. Each nation has its unique genius that sings the national beauty. Armenian ashug Sayat’-Nova’s creativity has had a significant influence on Armenian literature. Sayat’-Nova, as a national poet, had created poetry with its genre subdivisions. We can consider such categories as spiritual, patriotic poetry, glamorous social poetry, and folk-gusan songs. The present research has been carried out along the lines of Sayat’-Nova’s verbal creativity through the interpretive prism of theorists and literary critics with special reference to Valeri Brusov, who highlighted the exclusive richness of Sayat’-Nova’s artistic devices, the peculiar features of his literary genre, style, and language. The article focused on the relevance of Russian-Armenian literary relations, which became particularly crucial with the publication of Valeri Brusov’s anthology “Poetry of Armenia” in 1916. The outstanding Russian writer, critic, and translator has highly appreciated the exceptional richness of Armenian literature and interpreted each piece of verbal creativity with great accuracy. His opinion is that Sayat’-Nova name deserves to be a part of world literature. Armenian ashug has to stand next to the honored names and glorified works of Western literature

Universal geometrical factor of protein conformations as a consequence of energy minimization

The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein conformation as a consequence of energy minimization in protein folding. Folding simulations of 10 polypeptides with chain length ranging from 183 to 548 residues manifest that the dimensionless ratio (V/(A)) of the van der Waals volume V to the surface area A and average atomic radius of the folded structures, calculated with atomic radii setting used in SMMP [Eisenmenger F., et. al., Comput. Phys. Commun., 138 (2001) 192], approach 0.49 quickly during the course of energy minimization. A large scale analysis of protein structures show that the ratio for real and well-designed proteins is universal and equal to 0.491\pm0.005. The fractional composition of hydrophobic and hydrophilic residues does not affect the ratio substantially. The ratio also holds for intrinsically disordered proteins, while it ceases to be universal for polypeptides with bad folding properties.Comment: 6 pages, 1 table, 4 figure

Multicanonical parallel simulations of proteins with continuous potentials

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