BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization

Abstract

<div><div><div><p>With a large amount of research dedicated to decoding how metallic species bind to protein, in silico methods are interesting allies for experimental procedures. To date, computational predictors mostly work by identifying the best possible sequence or structural match of the target protein with metal binding templates. These approaches are fundamentally focused on the first coordination sphere of the metal. Here, we present the BioMetAll predictor that is based on a different postulate: the formation of a potential metal-binding site is related to the geometric organization of the protein backbone. We first report the set of convenient geometric descriptors of the backbone needed for the algorithm and their parametrization from a statistical analysis. Then, the successful benchmark of BioMetAll on a set of more than 50 metal-binding X-Ray structures is presented. Because BioMetAll allows structural predictions regardless of the exact geometry of the side chains, it appears extremely valuable for systems which structures (either experimental or theoretical) are not optimal for metal binding sites. We report here its application on three different challenging cases i) the modulation of metal-binding sites during conformational transition in human serum albumin, ii) the identification of possible routes of metal migration in hemocyanins, and iii) the prediction of mutations to generate convenient metal-binding sites for de novo biocatalysts. This study shows that BioMetAll offers a versatile platform for numerous fields of research at the interface between inorganic chemistry and biology, and allows to highlight the role of the preorganization of the protein backbone as a marker for metal binding.</p></div></div></div>

Rationalizing the Decavanadate(V) and Oxidovanadium(IV) Binding to G-Actin and the Competition with Decaniobate(V) and ATP

“…The catalytic pocket was first probed for zones displaying at least two donor-containing residues with a sufficient backbone preorganization to bind V IV O 2+ . 29a , 48 A docking assay was performed, and two couples of amino acids emerged as potential donors, (His73; His161) and (His161; Asp154), both of them displaying the ability to coordinate V IV O 2+ in a square pyramidal arrangement ( Table 2 ).…”

“…Dockings of V IV O 2+ moiety were performed through GOLD 5.8 47 on the regions selected in the preliminary analysis by BioMetAll, 48 instructed to find latent binding motifs with a minimum of two coordinating residues considering His, Asp, and Glu as potential donors. G-actin was docked with V IV O 2+ , V IV O(H 2 O) 2+ , and V IV O(H 2 O) 2 2+ moieties, obtained from the optimization of the oxidovanadium(IV) aquaion, [V IV O(H 2 O) 4 ] 2+ .…”

“…Dockings of V IV O 2+ moiety were performed through GOLD 5.8 47 on the regions selected in the preliminary analysis by BioMetAll, 48 instructed to find latent binding motifs with a minimum of two coordinating residues considering His, Asp, and Glu as potential donors. G-actin was docked with 2+ .…”

Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes

“…Additional efforts in the context of (metal ion)-protein binding are represented by the coordination gene implemented in GaudiMM 91,92 and the recent backbone preorganization hypothesis developed within the software BioMetAll. 93…”

“…c The value of 16-17 units marks the transition from a rigid limit to a slow-tumbling spectrum. In the light of these results, it was possible to characterize the binding sites at the molecular level: (i) a preliminary MD of HSA was carried out to collect a series of sampled conformations, particularly for the highly flexible N-terminus; (ii) using the software BioMetAll, 93 each conformation was probed for regions containing the motif (His; His; Asp/Glu) with the correct degree of preorganization to bind V IV O 2+ ; (iii) for each selected snapshot, docking simulations were performed, obtaining the first 3D structures; (iv) these structures were then relaxed by further MDs and optimized by the full DFT cluster method proposed by Siegbahn and Himo; 132 and (v) in the last step, the ΔE bind and spin Hamiltonian parameters at the BHandHLYP/6-311+g(d) level of theory were computed and compared to the experimental results, allowing the final 3D structure of the primary and secondary adducts to be obtained.…”