Design of a minimal di-nickel hydrogenase peptide

Abstract

Ancestral metabolic processes involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13–amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism. These experimental results demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.

Structural Determinants of the Catalytic Nia-L Intermediate of [NiFe]-Hydrogenase

“…Our results not only provide novel insights into the sophisticated mechanism of H 2 activation in [NiFe]-hydrogenases but also deciphered the contribution of the protein scaffold to fine-tune proton and electron dynamics, which is of general importance for structure/function studies of (metallo)­enzymes operating with effective proton/electron transfer mechanisms. In this context, the identification of specific protein interactions required for efficient PCET (e.g., H + acceptors/donors at H-B distance from the active site) might be mimicked in artificial hydrogenases as those reported by Chakraborty and Falkowski/Nanda, , whose catalytic mechanisms are still unclear (a protonated cysteine thiolate has not yet been shown to be involved) and which lack catalytic reversibility. The impact of secondary sphere interactions has been addressed in a number of biological and synthetic systems capable of cleaving/producing H 2 . , For example, the Shafaat group has successfully equipped the active site of Ni-substituted rubredoxin with a proton relay, and the Dey/Artero labs have recently developed a bidirectional, [FeFe]-hydrogenase-mimicking electrocatalyst capable of transferring protons by means of an arene-functionalized azadithiolate bridge. , These mechanistic aspects have been also identified as crucial for certain synthetic enzymes (e.g., the cobalt-reconstituted heme systems from Lombardi/Bren), , where changes in protein folding, buffer acidity, and structure that mimic the role of the proton relay in [NiFe]–/[FeFe]-hydrogenases have been shown to increase the H 2 -evolving efficiency …”

A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism

“…Furthermore, comprising membranes their backbones can sequester metals and phosphate without reliance on the side-chain order (Zhang et al, 1993;Milner-White and Russell, 2005;Childers et al, 2009Childers et al, , 2010Maury, 2009;Greenwald and Riek, 2010;Li et al, 2010;Goodwin et al, 2012;Milner-White, 2019). Other short peptides that do involve side chains have shown similar or superior mastery over metal-ion chelation and, thereby, agency (Aithal et al, 2023;Timm et al 2023).…”

Informing the Cannabis Conjecture: From Life’s Beginnings to Mitochondria, Membranes and the Electrome—A Review

“…So, it is likely that the core metabolism and structure of modern life will reflect its beginnings, which could well be this energy gradient. For example, it is possible that one of the earliest catalytic systems involved a very simple nickel-iron hydrogenase, indeed, it is possible to design one with 13 amino acids, which can extract energy from a hydrogen gradient-today of course, these proteins are vastly more complex [33]. The key in this is that life will have evolved around the core properties of the earliest existing pre-biotic molecules.…”