by Maxim Stolyarchuk† [OrcID] , Julie Ledoux†, Elodie Maignant, Alain Trouvé and Luba Tchertanov*

Centre Borelli, CNRS, ENS Paris-Saclay, Université Paris-Saclay, 4 av. des Sciences, F-91190 Gif-sur-Yvette, France
*Author to whom correspondence should be addressed.
†The first two authors contributed equally.

Academic Editor: Ron Orbach
Int. J. Mol. Sci. 2021, 22(2), 802; https://doi.org/10.3390/ijms22020802
Received: 6 December 2020 / Revised: 28 December 2020 / Accepted: 11 January 2021 / Published: 14 January 2021
(This article belongs to the Special Issue Molecular Recognition in Biological and Bioengineered Systems)

Abstract
Redox (reduction–oxidation) reactions control many important biological processes in all organisms, both prokaryotes and eukaryotes. This reaction is usually accomplished by canonical disulphide-based pathways involving a donor enzyme that reduces the oxidised cysteine residues of a target protein, resulting in the cleavage of its disulphide bonds. Focusing on human vitamin K epoxide reductase (hVKORC1) as a target and on four redoxins (protein disulphide isomerase (PDI), endoplasmic reticulum oxidoreductase (ERp18), thioredoxin-related transmembrane protein 1 (Tmx1) and thioredoxin-related transmembrane protein 4 (Tmx4)) as the most probable reducers of VKORC1, a comparative in-silico analysis that concentrates on the similarity and divergence of redoxins in their sequence, secondary and tertiary structure, dynamics, intraprotein interactions and composition of the surface exposed to the target is provided. Similarly, hVKORC1 is analysed in its native state, where two pairs of cysteine residues are covalently linked, forming two disulphide bridges, as a target for Trx-fold proteins. Such analysis is used to derive the putative recognition/binding sites on each isolated protein, and PDI is suggested as the most probable hVKORC1 partner. By probing the alternative orientation of PDI with respect to hVKORC1, the functionally related noncovalent complex formed by hVKORC1 and PDI was found, which is proposed to be a first precursor to probe thiol–disulphide exchange reactions between PDI and hVKORC1.

Keywords: hVKORC1; Trx-fold proteins; protein folding; dynamics; molecular recognition; thiol–disulphide exchange; protein–protein interactions; PDI–hVKORC1 complex; 3D modelling; molecular dynamics simulation