arXiv subjects

Shura Hayryan

Publications and source records attributed to Shura Hayryan.

3 recordsLinked to original sources

arXiv2006

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.

q-bio.BM↗

arXiv2004

Helix-coil Transition in Closed Circular DNA

A simplified model for the closed circular DNA (ccDNA) is proposed to describe some specific features of the helix-coil transition in such molecule. The Hamiltonian of ccDNA is related to the one introduced earlier for the linear DNA. The basic assumption is that the reduced energy of the hydrogen bond is not constant through the transition process but depends effectively on the fraction of already broken bonds. A transformation formula is obtained which relates the temperature of ccDNA at a given degree of helicity during the transition to the temperature of the corresponding linear chain at the same degree of helicity. The formula provides a simple method to calculate the melting curve for the ccDNA from the experimental melting curve of the linear DNA with the same nucleotide sequence.

q-bio.BM↗

arXiv2003

A New Analytical Method for Computing Solvent Accessible Surface Area and its Gradients for Macromolecules

In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a new analytical method for this purpose. In the proposed algorithm, we consider the transformation which maps the spherical circles of intersection of atomic surfaces in three-dimensional space onto the circles on a two-dimensional plane and the problem of computing solvent accessible surface area is transformed into the problem of computing corresponding curve integrals on the plane. This allows to consider only integrals over the circular trajectories on the plane. The algorithm is suitable for parallelization. Testings on several small proteins have shown a high accuracy of the algorithm and a good performance.

cond-mat↗