Characterization of metal cofactors involved in GDGT-MAS Csp3-Csp3 bond formation

Project Summary Enzyme-catalyzed Csp3-Csp3 bond formation initiated from two inert carbons has been elusive in biological systems. Until recently, no known enzyme had been described to exhibit such activity; however, it was proposed that if such activity did exist, it would need to be facilitated through two sequential radical initiations, of which the initial radical would need to be stabilized until prior is formed. Members of the radical S- adenosylmethionine (RS) enzyme superfamily are characterized by an open coordination site [4Fe-4S] cluster, which facilitates reductive cleavage of S-adenosylmethionine (SAM) to form methionine and a 5’-deoxyadenosyl radical (5’-dA•). This highly reactive 5’-dA• abstracts hydrogen (H•) from inactivated carbons on a wide range of substrates, affording diverse biological reactions. Recently, our lab identified glycerol dibiphytanyl glycerol tetraether (GDGT) - macrocyclic archaeol synthase (MAS) from Methanocaldococcus jannaschii, an RS that facilitates the Csp3-Csp3 bond formation from two inert carbons. Natively, GDGT-MAS catalyzes the formation of a membrane-spanning macrocyclic lipid, GDGT, and macrocyclic archaeol (mA), which, when present, affords the host high thermal, pH, and osmotic stability. Such features make macrocyclic tetraethers attractive drug delivery nanocontainer components. However, the proposed mechanism of Csp3-Csp3 bond formation only describes the role of two of the four total metal cofactors in the enzyme: the RS domain [4Fe-4S] ([4Fe-4S]RS) and the C-terminal [4Fe-4S] cluster ([4Fe-4S]C). In our previously published work, we provided evidence that post-radical initiation of the first terminal sp3 carbon, the radicalized phytanyl chain forms a C-S bond with the sulfur of the [4Fe-4S]C cluster. This bond formation is predicted to protect the radical intermediate while sequential radical initiations occur. However, additional evidence is needed to confirm the existence of the C-S intermediate. Additionally, it remains unknown how the remaining metal cofactors, the rubredoxin-like Fe ion and N-terminal [4Fe-4S] ([4Fe-4S]N), might influence this novel bond formation. This proposed work aims to elucidate the role of the metal cofactors in GDGT-MAS, the first documented enzyme to facilitate the formation of Csp3-Csp3 bonds from two completely inert carbons. Preliminary data shows that the Booker Lab has found conditions that generate excess C-S bond intermediate while successfully obtaining soluble metal cofactor knock-outs. This proposal outlines the spectroscopic and electrochemical characterization of GDGT-MAS and its variants (Aim 1 and 2). Furthermore, in silico experiments designed to characterize the role protein and lipid dynamics play in the metal cofactor-mediated Csp3-Csp3 formation are outlined (Aim 3). These include utilizing molecular simulations to characterize lipid translocation into the active site and identifying environmental factors that may facilitate such.