Graduation Year

2015

Document Type

Dissertation

Degree

Ph.D.

Degree Name

Doctor of Philosophy (Ph.D.)

Department

Chemistry

Degree Granting Department

Chemistry

Major Professor

Randy Larsen, Ph.D.

Committee Member

Maurice Edington, Ph.D.

Committee Member

Brian Space, Ph.D.

Committee Member

Ioannis Gelis, Ph.D.

Keywords

Carbon Monoxide-bound, Cytochrome-c, Nitrogen Monoxide-bound, Photo-initiation, Protein Folding

Abstract

The protein folding problem involves understanding how the tertiary structure of a protein is related to its primary structure. Hence, understanding the thermodynamics associated with the rate-limiting steps for the formation of the earliest events in folding is most crucial to understanding how proteins adopt native secondary and tertiary structures. In order to elucidate the mechanism and pattern of protein folding, an extensively studied protein, Cytochrome-c (Cc), was chosen as a folding system to obtain detailed time-resolved thermodynamic profiles for the earliest events in the protein folding process. Cytochrome-c is an ideal system for understanding the folding process for several reasons. One being that the system can unfold and refold reversibly without the loss of the covalently attached heme group. A number of studies have shown that under denaturing conditions, ferrous Cc (Fe2+Cc) heme group in the presence of carbon monoxide (CO) results in a disruption of the axial heme Methionine-80 (Met80) bond ultimately unfolding the protein. CO-photolysis of this ferrous species results in the formation of a transient unfolded protein that is poised in a non-equilibrium state with the equilibrium state being that of the native folded Fe2+Cc complex. This allows for the refolding reaction of the protein to be photo-initiated and monitor on ns - ms timescales. While CO cannot bind to the ferric form, nitrogen monoxide (NO) photo-release has been developed to photo-trigger ferric Cc (Fe3+Cc) unfolding under denaturing conditions. Photo-dissociation of NO leaves the Fe3+complex in a conformational state that favors unfolding thus allowing the early unfolding events of Fe3+Cc to be probed. Overall the results presented here involve the use of the ligands CO and NO along with photoacoustic calorimetry (PAC) to photo-trigger the folding/unfolding reaction of Cc (and modified Cc). Thus, obtaining enthalpy and molar volume changes directly associated with the initial folding/unfolding events occurring in the reaction pathways of both Fe2+ and Fe3+Cc systems that are most essential to understanding the driving forces involved in forming the tertiary native conformation. The PAC data shows that folding of proteins results from a hierarchy of events that potentially includes the formation of secondary structures, hydrophobic collapse, and/or reorganization of the tertiary complex occurring over ~ns – tens of s time ranges. In addition, the PAC kinetic fits presented in this work is the first to report Cc folding exhibiting heterogeneous kinetics (in some cases) by utilizing a stretched exponential decay function.

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