Proteinlerin katlanma mekanızmasını anlamak için bir optimizasyon yaklaşımı

FormName of the Student : Şerife ŞentürkProgram of Study : Computational Science and EngineeringThesis Title : An Optimization Approach To Study the Dynamics ofCo-translational FoldingAbstractAn optimization model is implemented to obtain the possible pathways for the folding ofthe protein chain as the protein folds in the exit tunnel of the ribosome during andfollowing its synthesis. In this model, the folding problem is formulated as an optimalcontrol problem in which a particular form of energy is minimized subject to the dynamicmodel predictions and physical constraints. It is assumed that the chain grows and foldsat the same time while it is still being synthesized. The optimization models changeaccording to the length of the partial chain. The co-translational folding dynamics of afast-folding protein, chicken villin headpiece protein, is simulated. The model isimplemented using different growth rates for the protein to fold and the results for thedifferent growth rates are compared. The folding dynamics is analyzed as a processcomposed of early stage, intermediate stage and late stage according to the secondarystructure property of chicken villin protein. Also, the important role of long-range contactpairs is presented and the input variables are analyzed.Advisor: Prof. Dr. Yaman Arkun Date: 02.11.06Director: Prof. Dr. Süleyman Özekici Date: 02.11.06