Doğal halde olmayan proteinlerin istatiksel mekaniği ve yerel dinamiği

Statistical Mechanics and Local Chain Dynamicsof Denaturated ProteinsAbstractBioinformatics is a fast growing research area and describes any use of computers tohandle biological information. One of the major research efforts is structure prediction ofproteins. The torsion angles (phi-psi) of proteins are considered as the degrees of freedomof a protein because of their control of the proteins? three dimensional structures. In thisthesis, we used rotational isomeric state model in order to calculate statistical averagesand correlations for torsional angles of denaturated proteins. For this purpose, wegrouped each consecutive three residues (triplets) starting from first and used moleculardynamics simulations on triplets. Afterwards, we constructed energy maps for the phi-psiangles of the central residue of each triplet considered. Results showed that triplets haveintrinsic propensities for some conformational preferences which favor the choice of thenative state torsional angles and they are context dependent, determined by the aminoacid sequence of the protein. Furthermore, we improved the stochastic weights with theaim of introducing the long range effects in two different approaches: Monte Carlomethod and genetic algorithm method. Besides, we calculated heat capacity as functionof temperatures by statistical mechanics for three different sets of stochastic weightswhich are obtained from molecular dynamics, Monte Carlo method and genetic algorithmmethod. Additionally, we proposed a dynamic rotational isomeric state model analogousto rotational isomeric state model and calculated transition probabilities from one state toanother. The states are chosen as alpha-helix, beta-sheets, turns and all other states.Results support the idea that during folding, secondary structures forms sequentially.