Protection of Catalytic Cofactors by Polypeptides as a Driver for the Emergence of Primordial Enzymes

Abstract

Enzymes catalyze the chemical reactions of life. For nearly half of known enzymes, catalysis requires the binding of small molecules known as cofactors. Polypeptide-cofactor complexes likely formed at a primordial stage and became starting points for the evolution of many efficient enzymes. Yet, evolution has no foresight so the driver for the primordial complex formation is unknown. Here, we use a resurrected ancestral TIM-barrel protein to identify one potential driver. Heme binding at a flexible region of the ancestral structure yields a peroxidation catalyst with enhanced efficiency when compared to free heme. This enhancement, however, does not arise from protein-mediated promotion of catalysis. Rather, it reflects protection of bound heme from common degradation processes and a resulting longer life time and higher effective concentration for the catalyst. Protection of catalytic cofactors by polypeptides emerges as a general mechanism to enhance catalysis and may have plausibly benefited primordial polypeptide-cofactor associations.

Coenzyme-Protein Interactions since Early Life

“…The role of loops could thus be important for the flexibility and versatility of early peptide- coenzyme binding sites. It has been noted that evolutionary benefits would be presented by sequences that could adopt closed loop conformations, providing stability and protection to early coenzymes and such hubs could truly transition the peptide-coenzyme world towards primordial enzymes (Goncearenco and Berezovsky 2011, Gamiz-Arco et al, 2021; Toledo-Patiño et al, 2022; Gutierrez-Rus et al, 2023). Besides sequences without regular secondary structure elements, beta-sheets have been considered a more prevalent and significant motif during early stages of protein evolution than alpha helices.…”

Ancestral versus Modern Substrate Scope in Family-1 Glycosidases

“…Yet, low-level activities may serve as starting points for the directed laboratory evolution of enzymes that efficiently catalyze the actual chemical transformation that is of biotechnological interest. [6][7][8] More generally, enzyme promiscuity is likely linked to conformational diversity, a biophysical feature known to contribute to evolvability, i.e., to the capability to generate new functionalities. [9][10][11] Overall, promiscuity is a desirable feature in enzymes intended for biotechnological applications.…”