Identification of the Primary Factors Determining theSpecificity of Human VKORC1 Recognition by Thioredoxin-Fold Proteins

Int J Mol Sci. 2021 Jan 14;22(2):802. doi: 10.3390/ijms22020802.

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

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Binding Sites
  • Humans
  • Membrane Glycoproteins / chemistry
  • Membrane Glycoproteins / genetics
  • Membrane Glycoproteins / metabolism
  • Membrane Proteins / chemistry
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism
  • Molecular Dynamics Simulation
  • Oxidation-Reduction
  • Protein Disulfide Reductase (Glutathione) / chemistry
  • Protein Disulfide Reductase (Glutathione) / genetics
  • Protein Disulfide Reductase (Glutathione) / metabolism
  • Protein Disulfide-Isomerases / chemistry
  • Protein Disulfide-Isomerases / genetics
  • Protein Disulfide-Isomerases / metabolism
  • Protein Domains*
  • Protein Folding*
  • Sequence Homology, Amino Acid
  • Thioredoxins / chemistry*
  • Thioredoxins / genetics
  • Thioredoxins / metabolism
  • Vitamin K Epoxide Reductases / chemistry*
  • Vitamin K Epoxide Reductases / genetics
  • Vitamin K Epoxide Reductases / metabolism

Substances

  • Membrane Glycoproteins
  • Membrane Proteins
  • TMX1 protein, human
  • Thioredoxins
  • VKORC1 protein, human
  • Vitamin K Epoxide Reductases
  • Protein Disulfide Reductase (Glutathione)
  • TMX4 protein, human
  • TXNDC12 protein, human
  • Protein Disulfide-Isomerases