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Title

Μελέτη της θερμοκρασίας εξάρτησης της κυτοχρωμικής c οξειδάσης με μοριακή δυναμική

Alternative Title

Studies of Temperature dependence of cytochrome c oxidase with Molecular Dynamics

Author

Καμπαναράκης, Αλέξανδρος

Thesis advisor

Φαράντος, Σταύρος

Abstract

Cytochrome c oxidase (CcO) is the the membrane bound terminal enzyme in the respiratory chain. Molecular oxygen is reduced to water in its heme Fe/Cu_B active site. The O-O bond cleavage produces the ferryl-oxo (Fe^iv=O) intermediate. In this research, Molecular Dynamics calculations are employed to probe the frequencies of vibrational modes which involve the stretching of Fe-O during the change of dielectric constant and the change of temperature. The role of protein frame for the spectroscopic properties of the ferryl intermediate is proved to be significant, as the frequencies and the intensities of the oxygen sensitive bands is controlled by dielectric constant changes. In addition the Cytochrome c oxidase is proved to be stable in a large width of temperatures.
Concretely our research led to the following conclusions:

• H vibration Fe^iv=O of CcO is not influenced for values of dielectric constant smaller the 1.5. For values bigger the 1,5 we have a localized vibration Fe^iv=O.

• The electrostatic potential of active site of protein is an important factor of influence in vibration ν(FeO). The marginal point of this influence appears to be the value of dielectric constant 1.5.

• In our study five peaks were presented which are attributed to the vibrations of the active site.

• The study of active site of CcO is a good approach of studying the protein.

• The protein frame is stable with respect to temperature increases.

• Since the electrostatic potential appears to influence the vibration Fe^iv=O, the two peaks in 790/804 cm^-1 could be attributed in two different configurations corresponding to incidents of protonation/deprotonation of amino-acids. The value 1.5 of dielectric constant, appears to be the verge between the two configurations.

Language

Greek

Subject

Cytochrome c Oxidase

dielectric dependence

dynamic protein frame

ferryl intermediate

molecular dynamic

temperature dependence

Κυτοχρωμική c οξειδάση

διηλεκτρική εξάρτηση

θερμοκρασιακή εξάρτηση