Protein bağlanması ve proteinlerde mod bağlanması

In order to understand the the change in thermodynamic properties upon binding and determine the binding sides, two hexa-peptides and their bound complex structures were analyzed. In order to extract the thermodynamic properties and determine the binding side, a harmonic model was applied.The harmonic formulation is extended to large ? uctuations of residues in order to account for effects of anharmonicity. The ? uctuation probability function is constructed for this purpose as a tensorial Hermite series expansion with higher order moments of ? uctuations as coef ? cients.Mode coupling and anharmonicity in a native fluctuating protein is investigated in modal space. Molecular dynamics trajectories of Crambin are generated and used to evaluate the terms of the polynomials and to obtain the modal energies. Slowest modes have energies that are below that of the harmonic energy, kT/2 per mode, and a few fast modes have energies significantly larger than the harmonic which is a result of coupling. Detailed analysis of the lowest order two mode coupling terms is presented.It is was shown that mode coupling and anharmonicity are important for modeling the multidimensional energy landscape of Crambin. The effect of them on the fluctuational entropy is on the order of a few percent.The fluctuations and unbinding free energy profiles of two very similar proteins, HLA-B51 and HLA-B52, were investigated. HLA-B51 is related to the Behçet?s disease whereas HLA-B52 is not. Change in the dynamics of 1 helix were analyzed. Unbinding from HLA-B52 resulted in greater free energy differences than for HLA-B51.