Honors Theses

Date of Award

Spring 5-7-2026

Document Type

Undergraduate Thesis

Department

Chemistry and Biochemistry

First Advisor

Saumen Chakraborty

Second Advisor

Sujay Ray

Third Advisor

Jonah Jurss

Relational Format

Dissertation/Thesis

Abstract

Methane is a high energy small molecule found in large quantities in the atmosphere that can have negative impacts on human health and the climate. Methane, however, can be oxidized to methanol, a potential biofuel. The challenge is activating the high-energy C-H bond for this oxidation to occur. Methanotrophic bacteria possess enzymes that readily carry out this conversion known as particulate methane monooxygenases (pMMOs). pMMOs are large, membrane bound proteins that contain four copper binding sites where it has been established two of these cannot be used for methane oxidation. Between the other two sites, CuC and CuD, the functionality is unknown. In both cases, copper is coordinated by 2 His and a third amino acid; Asp in CuC and Arg in CuD. Because of its size and location in the membrane, isolation of pMMO is difficult and targeted study of individual binding sites is complex. Artificially designed copper proteins (ArCuPs) propose a solution for this through the mechanistic study of target proteins by designing simpler scaffolds with lower costs. Here I present the design of promising constructs that can be used as CuC and CuD binding site mimics to probe the functionality of these sites to carry out methane oxidation and to better understand the mechanics behind pMMO. Structural analysis and characterization of these constructs’ kinetics, copper affinity, and more allow for the furthering of understanding on the functionality of pMMOs’ binding sites.

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