CAPN5 Crystal Structure Solved

Palo Alto, CA —  In the article published in the January 2020 issue of Cell Reports, “Structural insights into the unique activation mechanisms of a non-classical calpain and its disease-causing variants,” lead author Gabriel Velez, an MD., Ph.D. student in the Mahajan Lab, reported the crystal structure of the calpain-5 protease core domain (CAPN5-PC). The article also detailed functional and biophysical characterization of the CAPN5 protein using in vitro activity assays, small-angle X-ray scattering (SAXS), and phylogenetic analysis. 

Hyperactivating mutations in the CAPN5 gene cause Autosomal Dominant Neovascular Inflammatory Vitreoretinopathy (ADNIV), a rare inflammatory eye disease. Until recently, the structure of CAPN5-PC had not been determined, making it difficult to design novel inhibitors to treat ADNIV. Jing Yang and Saif Khan performed the initial protein crystallization studies in collaboration with Dr. Lokesh Gakhar.

“Their efforts got us our first usable X-ray dataset that led to the final CAPN5-PC structure,” stated Principle Investigator Vinit Mahajan M.D., Ph.D.

“We wanted to identify regions in the CAPN5 structure that weren’t present in other calpains so that we could design CAPN5-specific inhibitors with reduced off-target profiles. Calpains, however, are highly divergent in their primary sequences, which can make sequence-based determination of these regions difficult,” stated Gabe. “Instead, we used a structure-based phylogenetic analysis that allowed for direct comparison of calpains structures based on their 3D shape.” 

This analysis showed that CAPN5-PC contains three elongated loops compared to classical calpains. One loop contained a hyperactivating mutation that causes ADNIV, revealing a function in this region for regulating proteolytic activity. 

“It’s possible that these loops could serve as targets for allosteric inhibitors,” stated Young Joo Sun, a co-author on the paper. 

“Structural insights into the unique activation mechanisms of a non-classical calpain and its disease-causing variants” was published in Cell Reports, January 2020. 

Authors include:  Gabriel Velez, Young Joo Sun, Saif Khan, Jing Yang, Jonathan Herrmann, Teja Chemudupati, Robert E. MacLaren, Lokesh Gakhar, Soichi Wakatsuki,  Alexander G. Bassuk, and Vinit B. Mahajan.