Characterization of a beta-glycosidase dimer interface

• Grant number: 21/03967-6
• Support Opportunities: Regular Research Grants
• Start date: February 01, 2022
• End date: January 31, 2024
• Field of knowledge: Biological Sciences - Biochemistry - Chemistry of Macromolecules
• Principal Investigator: Sandro Roberto Marana
• Grantee: Sandro Roberto Marana
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

Protein-protein interactions are central to the assembly of molecular machines and cellular processes as signalling pathways, DNA duplication and transcription, metabolism and so on. Indeed, it is an essential aspect to the comprehension of the cell functioning. Actually a deep comprehension of this topic goes beyond the identification of protein partners, depending on the determination of the forces stabilizing the protein complexes and the rate and equilibrium constants of their assembly mechanism.b-glycosidases are not traditional models to study the protein-protein interactions, however these enzymes present characteristics that make them an interesting experimental model to produce broad application concepts in this topic: a) they form oligomers, specially homodimers (58% of the oligomers); their activity is modulated by the dimerization; c) their activity is easily to detect and many synthetic substrates are available; d) high number of crystallographic structures is known.The dimer interface of the b-glycosidase GH1 termed Sfbgly (AF052729; PDB 5CG0) covers 5% of the surface area of each monomer and contains 30 residues, 63% of them can form interactions guided by the hydrophobic effect and 4 are involved in hydrogen bonds. Such features suggest that the "hydrophobic effect", an entropy increase resulting from the binding of apolar surfaces and consequent release of water molecules from that interface, would be an important component of the dimer stabilization. In addition, differences in the surface area removed from the solvent of each interface residue indicate that they present diverse contributions to the monomer interaction. Finally, the four hydrogen bonds observed in the dimer interface should be not ignored, hence setting an interesting discussion about the relative relevance of these bonds and the "hydrophobic effect" in the dimer stabilization. In short, non-covalent interactions of different type and intensity are heterogeneously distributed over the interface surface. In addition, the Sfbgly dimerization occurs through a conformer selection mechanism and the dimers are more active, suggesting that the dimerization stabilizes the more active conformation of the monomer.Based on that, it would be interesting to determine the relative importance of the interface residues and interactions to the Sfbgly dimerization, to evaluate their contribution to the stabilization of the monomers in the more active conformation and finally to trace the contact pathway, i.e., the set of interacting residues, that propagates the dimerization effect from the interface to the enzyme active site.In conclusion, this project aims at to understand how the residue interactions in the dimerization interface stabilizes the dimer and modulate the Sfbgly activity, which would be a relevant contribution to the b-glycosidases GH1 and protein-protein interaction fields. (AU)