Yanbo Zhang

Graduation Semester and Year

2013

Language

English

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Chemistry

Department

Chemistry and Biochemistry

First Advisor

Roshan Perera

Abstract

Heme b (protoporphyrin IX or protoheme) plays a major role in the structure and function in proteins such as myoglobin (Mb), hemoglobin (Hb), horseradish peroxidase (HRP), catalase, cytochrome P450 as well as catalase peroxidase (KatG). This highly conjugated porphyrin system forms the cradle for the iron containing prosthetic group of the hemeproteins. Although the surrounding chiral protein scaffold is important in protein reactivity and selectivity, the heme iron prosthetic group creates a focal point for the substrate reactivity.The genetic incorporation of unnatural amino acids (UAA) into proteins in vivo, using the same biosynthetic machinery used by living cells to synthesize proteins, has proven a powerful technique for investigating structure and function of proteins. An orthogonal tRNA/aminoacyl-tRNA synthetase pair allows selective and efficient incorporation of unnatural amino acids into proteins in vivo at sites specified by the amber nonsense codon, TAG. These include redox-active amino acids, metal-binding amino acids, fluorescent and infrared probes, photo- and chemically reactive amino acids and post-translationally modified amino acids. Therefore, this method potentially paves the way for the design of proteins that display enhanced or unique functionality. Furthermore, this novel biotechnological tool produces native conformation of proteins with high yields at low cost. Contrary to this, the total synthesis of proteins with UAA using solid-phase synthesis is much more complicated due to size limitations (~60-100 amino acids) as well as producing denatured proteins at a very low yield. We will be examining two important heme protein targets, KatG, Mb, and enhanced green fluorescence protein (EGFP) to uncover their structural and functional secrets using this biotechnological tool. The overall goal of this research is to establish an experimental framework that enables the site-specific incorporation of unnatural amino acids into various recognized sites in these proteins targets, to study the functional secrets in these proteins, and to construct biopolymer mimics for industrial applications. Three factors control the functional properties of these enzymes: (i) the coordination state of the iron complex; (ii) the nature of the axial ligands in the fifth and sixth coordination sites; and (iii) the protein active site heme environment including the polarity of the surroundings and the accessibility of substrates and solvents to the metal.

Disciplines

Chemistry | Physical Sciences and Mathematics

Comments

Degree granted by The University of Texas at Arlington

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