Secondary structure analysis of peptides with relevance to iron–sulfur cluster nesting

Abstract

Peptides coordinated to iron-sulfur clusters, referred to as maquettes, represent a synthetic strategy for constructing biomimetic models of iron-sulfur metalloproteins. These maquettes have been successfully employed as building blocks of engineered heme-containing proteins with electron-transfer functionality; however, they have yet to be explored in reactivity studies. The concept of iron-sulfur nesting in peptides is a leading hypothesis in Origins-of-Life research as a plausible path to bridge the discontinuity between prebiotic chemical transformations and extant enzyme catalysis. Based on past biomimetic and biochemical research, we put forward a mechanism of maquette reconstitution that guides our development of computational tools and methodologies. In this study, we examined a key feature of the first stage of maquette formation, which is the secondary structure of aqueous peptide models using molecular dynamics simulations based on the AMBER99SB empirical force field. We compared and contrasted S…S distances, [2Fe-2S] and [4Fe-4S] nests, and peptide conformations via Ramachandran plots for dissolved Cys and Gly amino acids, the CGGCGGC 7-mer, and the GGCGGGCGGCGGW 16-mer peptide. Analytical tools were developed for following the evolution of secondary structural features related to [Fe-S] cluster nesting along 100 ns trajectories. Simulations demonstrated the omnipresence of peptide nests for preformed [2Fe-2S] clusters; however, [4Fe-4S] cluster nests were observed only for the 16-mer peptide with lifetimes of a few nanoseconds. The origin of the [4Fe-4S] nest and its stability was linked to a "kinked-ribbon" peptide conformation. Our computational approach lays the foundation for transitioning into subsequent stages of maquette reconstitution, those being the formation of iron ion/iron-sulfur coordinated peptides.

Natural selection based on coordination chemistry: computational assessment of [4Fe–4S]-maquettes with non-coded amino acids

“…3.1. Secondary structure analysis of FdM-7 peptides Previously, we have reported a detailed secondary structure analysis for the CGGCGGC (FdM-7-G-C) peptide [33], which revealed the omnipresence of [2Fe-2S] nests (25 ± 3%) along the NVT MD trajectories. The same analysis defined an upper limit of only 1.6% of the frames with peptide backbone conformation amenable to [4Fe-4S] cluster coordination.…”

“…The high [2Fe-2S] nest frequency also translates into a high percentage of favourable S(Hey) positions (orange bars, [4Fe-4S] nesting ceiling) in which the triangle formed by the S(Hey) centres is not transected by the peptide backbone. Depending on whether a stepwise cluster assembly (Scheme 1 in [33]) or ligand-exchange process takes place involving a preformed cluster [19], the former can lead to [4Fe-4S] cluster side chain rearrangement and thus cluster assembly, while the latter could take place during a single collision event that we considered here (vide infra).…”

“…In the given study, we considered short (7-mer, yIAyGAy, where y = U, C or J) and long (16-mer, GGyGGGyGGyGGyGGW, where y = U, C or J) peptide sequences in which the Cys-containing peptides have already been investigated experimentally [18,19] and computationally [33]. The initial structures with expanded conformations were generated using the PROTEIN utility in the Tinker suite of modelling programs [34][35][36][37] and optimized using the AMBER99SB [38][39][40][41] force field parameters.…”

“…The temperature and pressure control was achieved by using Berendsen thermostat and barostat [47]. The NPT and NVT MD simulations used the Nose-Hoover [48] and Beeman [49] [33]. Furthermore, short (1 ns) simulations were completed for three β-mercaptoethanol (βME) molecules, as free ligands in solution and complete [4Fe-4S]-maquettes with frozen S-CH 2groups without the presence of the iron and sulfide ions in the above-mentioned water bath.…”

“…The motivation to investigate the secondary structure of 16mer peptides containing non-coded thioGly and homoCys residues originates from our previous observations of the formation of stable [4Fe-4S] cluster nests with circa 2 ns lifetime [33] Although to a more modest degree than observed before (0.6%, [33]), only the FdM-16-G-C peptide shows an appreciable 0.1% probability for forming a [4Fe-4S] nest. As can be seen from the cumulative numbers in the last column of table 1, for a 100 ns trajectory this means that approximately 1000 nesting frames are ready for accepting a preformed [4Fe-4S] cluster via a direct ligand-exchange process, which corresponds to a rare-event, but with not zero probability.…”