Ambient temperature structural studies of Penicillin-binding Protein 2a of Methicillin-Resistant Staphylococcus aureus with XFELs and synchrotrons

Grieco, A.; Quereda-Moraleda, I.; Botha, S.; Dorner, K.; Schmidt, C.; Han, H.; Vakili, M.; Schulz, J.; Koua, F.; de Wijn, R.; Kharitonov, K.; Round, A.; Bielecki, J.; Kupitz, C.; Lisova, S.; Schleissner, P.; Sierra, R.; Mariani, V.; Basu, S.; Orlans, J.; Rose, S.; de Sanctis, D.; Gee, L. B.; Bean, R.; Mobashery, S.; Chang, M.; Hermoso, J.; Martin-Garcia, J. M.; Martin Garcia, J. M.

doi:10.1101/2025.02.22.637770

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bioRxiv · 10.1101/2025.02.22.637770

Ambient temperature structural studies of Penicillin-binding Protein 2a of Methicillin-Resistant Staphylococcus aureus with XFELs and synchrotrons

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Abstract

Penicillin-binding protein 2a (PBP2a) is a transpeptidase responsible for the {beta}-lactam resistance in methicillin-resistant Staphylococcus aureus (MRSA), posing significant challenges to antibiotic therapy. PBP2as unique structural features, including its highly flexible active site and allosteric regulation, enable it to maintain catalytic activity even in the presence of {beta}-lactam antibiotics. Despite extensive characterization using cryogenic crystallography, key questions remain about its dynamic properties and conformational changes under near-physiological conditions. Room-temperature crystallography methods, particularly serial femtosecond X-ray crystallography (SFX) at XFELs, provide a powerful approach to capture these dynamics. Unlike cryogenic conditions that can constrain protein flexibility, SFX enables the study of conformational variability and interaction networks closer to physiological states. Here, we present the first room-temperature structures of PBP2a obtained using SFX to uncover insights into the enzymes flexibility, allosteric communication, and catalytic mechanisms. These findings are built upon optimized large-scale production and crystallization protocols for PBP2a, ensuring high-quality microcrystals suitable for SFX data collection. The room-temperature structures reveal novel interaction patterns, including unique salt bridge networks and dynamic structural elements absent in cryogenic studies. Furthermore, comparative analyses highlight how environmental conditions influence the conformational states of PBP2a, providing new perspectives on its resistance mechanisms. By integrating structural data from EuXFEL and LCLS, this study not only enhances our understanding of PBP2as functional dynamics but also underscores the value of room-temperature crystallography in studying antibiotic resistance. These insights could guide the design of next-generation {beta}-lactam antibiotics capable of overcoming PBP2a-mediated resistance.

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Grieco, A., Quereda-Moraleda, I., Botha, S., Dorner, K., Schmidt, C., Han, H., Vakili, M., Schulz, J., Koua, F., de Wijn, R., Kharitonov, K., Round, A., Bielecki, J., Kupitz, C., Lisova, S., Schleissner, P., Sierra, R., Mariani, V., Basu, S., Orlans, J., Rose, S., de Sanctis, D., Gee, L. B., Bean, R., Mobashery, S., Chang, M., Hermoso, J., Martin-Garcia, J. M., Martin Garcia, J. M.. 2025-02-23. Ambient temperature structural studies of Penicillin-binding Protein 2a of Methicillin-Resistant Staphylococcus aureus with XFELs and synchrotrons. https://doi.org/10.1101/2025.02.22.637770

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