Insights into the Solution Structure and Oligomeric State of Fructose-1,6-bisphosphate Aldolase and Pyruvate Kinase from Nakaseomyces glabratus by Small-Angle X‑ray Scattering (SAXS) and AlphaFold Prediction

Abstract

Nakaseomyces glabratus is an opportunistic pathogen of humans, causing invasive candidiasis (IC). Among the risk factors that favor IC are various host-specific factors. Although drugs are available to treat candidiasis, their clinical application remains limited. Therefore, it is necessary to identify therapeutic targets that will enable the development of new antifungals. In this regard, our research group has identified enzymes as potential therapeutic targets in N. glabratus, including fructose-1,6-bisphosphate aldolase (Fba1) and pyruvate kinase (Pk). Enzyme activity studies on these two enzymes have shown that they are important therapeutic targets against this pathogen. However, their three-dimensional structure has not yet been elucidated, an essential requirement for designating an enzyme as a therapeutic target. To propose Fba1 and Pk of N. glabratus as potential therapeutic targets, we investigated the solution structure and oligomeric state of N. glabratus Fba1 and Pk for the first time by combining Small-Angle X-ray Scattering (SAXS) with AlphaFold3 modeling. SAXS data were collected on the B21 beamline at Diamond Light Source (Didcot, UK), providing solution-scattering profiles, molecular-weight estimates, and low-resolution molecular envelopes. These data indicate that Pk is monomeric and Fba1 homodimeric in solution were used to evaluate and refine the corresponding AlphaFold3 atomic models by molecular dynamics. These structural findings for Fba1 and Pk from N. glabratus open the door to understanding these enzymes as potential therapeutic targets against this pathogen and, at the same time, a basis for future comparative studies.