SAXS study of Escherichia coli Dihydrolipoamide Dehydrogenase: structural characteristics and molecular docking
- Dr. Eleonora SHTYKOVA
- Ms. Liubov DADINOVA (1.Shubnikov Institute of Crystallography, FSRC “Crystallography and Photonics” RAS, Moscow, 119333 Russia; 2. Moscow State University, Moscow, 119992 Russia)
- T.I. NAZAROVA (Moscow State University, Moscow, 119992 Russia)
- Dr. Eleonora SHTYKOVA (1. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, 119333 Russia; 2. Moscow State University, Moscow, 119992 Russia)
- Dr. E.V. RODINA (Moscow State University, Moscow, 119992 Russia)
- Dr. N.N. VOROBYEVA (Moscow State University, Moscow, 119992 Russia)
- Dr. S.A. KURILOVA (Moscow State University, Moscow, 119992 Russia)
Dihydrolipoamide dehydrogenase from Escherichia coli (LpD) is a bacterial enzyme that is involved in three different multi-enzyme complexes that catalyze similar decarboxylation reactions of 2-oxoacids. All of these complexes comprise three enzymes known as Е1, Е2, and Е3, where LpD is the Е3 component and the E2 subunit is used by LpD as the lipoamide-containing protein substrate. The Е1 and Е2 subunits have different structures in different complexes, whereas the Е3 protein is essentially the same in all of the complexes [1–4]. The pyruvate dehydrogenase complex from Gram-negative bacteria (for example, from E. coli) is composed of 24 E1 subunits and 24 E2 subunits, whereas the multiplicity of E3 remains unknown. According to different estimates, there are 12 or 24 E3 subunits; i.e., E3 may consist of six dimers or six tetramers. It was shown that E. coli LpD exists as a dimer in the crystalline state . However, the solution structure of this protein was unknown. The aim of the present study is to investigate the behavior of LpD in solution, i.e., under near-physiological conditions, by small-angle X-ray scattering (SAXS) and complementary methods. Using modern techniques for the interpretation of SAXS data and analytical ultracentrifugation we determined that in solution LpD exists as an equilibrium mixture of a dimer and a tetramer. The tetramer structure was determined by modeling SAXS data and molecular docking. The results obtained by these two methods correlate well with each other. It was shown that there is the relationship between the oligomerization of the protein in solution and its functional properties. In particular, the possible flexibility of the tetramer follows from the stoichiometric and functional demands of the multienzyme complexes containing LpD as a component.
This work was supported in part by Russian Foundation for Basic Researches (projects 15-54-74002 EMBL_а , 15-04-01406, 15-04-00563).
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