Author ORCID Identifier

https://orcid.org/0000-0002-1341-6975

Date Available

11-9-2024

Year of Publication

2024

Document Type

Doctoral Dissertation

Degree Name

Doctor of Philosophy (PhD)

College

Arts and Sciences

Department/School/Program

Chemistry

Advisor

Anne-Frances Miller

Abstract

Anaerobic bacteria and archaea thrive in seemingly inhospitable environments because they are extremely energy efficient. Their capacity to fully utilize electrochemical energy is based in large part on their ability to conduct electron transfer bifurcation ('bifurcation') at strongly reducing potentials, thereby producing extremely potent reducing agents able to fix nitrogen and make molecular hydrogen. This chemistry is made possible by the use of a flavin as the site of bifurcation, supported by a specialized protein environment and mechanisms that control the flow of individual electrons.

Bifurcating electron transfer flavoproteins (Bf-ETFs) are versatile protein modules that provide the bifurcating capability associated with several metabolic functions. Bf-ETFs enable use of low-energy electron reserves such as NADH to charge the carriers ferredoxin and flavodoxin with high-energy electrons. Bf-ETFs possess two flavin adenine dinucleotide (FAD) cofactor. The bifurcating FAD (Bf-FAD) receives two electrons from NADH, subsequently distributing them through two distinct pathways. One pathway involves an exothermic electron transfer to a high-potential acceptor via the second FAD, designated the ET-FAD (electron transfer FAD). This provides the driving force needed to send the second electron to ferredoxin or flavodoxin, at lower (more reducing) potential.

Investigations centered on elucidating the crystal structure and internal dynamics of flavodoxin (Fld), a high-energy acceptor in the bifurcation process. 19F NMR was used to examine conformational heterogeneity and dynamics of Fld free in solution, to characterize the flexibility of a 20-residue stretch of Fld's peptide chain that is believed to mediate the interaction between Fld and ETF. Detailed temperature-dependent NMR studies, alongside paramagnetic relaxation investigations comparing Fld in both its oxidized and semi-reduced forms, detailed internal dynamics pivotal to Fld's interactions with diverse partner proteins.

Complementary research explored the conformational dynamics of ETF, employing small-angle neutron scattering (SANS). This approach revealed a notable divergence from previously published structures, demonstrating presence of a more extended ETF conformation in solution. Significant reduction-triggered conformational alterations were also discerned via SANS by comparing the fully oxidized and reduced states of ETF. Molecular dynamics simulations-based data modeling suggest coexistence of multiple ETF conformations, ranging from extended to compact, in solution.

Finally, conformational consequences of complex formation between ETF and a partner protein were examined. We demonstrated isolation of a complex between ETF and is high-potential acceptor Butyryl CoA dehydrogenase (BCD). Innovative application of segmental deuteration of BCD in combination with SANS, enabled comprehensive insights into the conformational shifts of ETF upon complex formation. Contrast variation SANS, utilizing 80% deuterated BCD, was used to identify the match point, paving the way for advanced analysis of the complex's structural dynamics.

This work enriches comprehension of the roles played by dynamics in bifurcation, and advances new technical approaches for future explorations of conformational changes within multidomain proteins.

Digital Object Identifier (DOI)

https://doi.org/10.13023/etd.2024.120

Funding Information

Doe Grant DE- SC0021283

Kentucky EPSCoR PON2 635 2000003148

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