Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants

Abstract

Highlights d The structure of the human calpain-5 protease core (CAPN5-PC) is determined d CAPN5-PC contains three elongated loops compared to its classical counterparts d One loop contains a mutation identified in a patient with NIV (p.Gly267Ser) d The p.Gly267Ser mutation causes hyperactivity in CAPN5-PC and CAPN1/5-PC hybrids

TMPRSS2 structure-phylogeny repositions Avoralstat for SARS-CoV-2 prophylaxis in mice

“…The TMPRSS2-S1P model was then analyzed by ConSurf as previously described. 31 The 600 sequences from our sequence-based phylogenetic analysis underwent MSA using MAFFT and conservation scores were calculated using the Bayesian method option in ConSurf. The TMPRSS2-S1P binding pocket was inferred by comparison to the structure of Hepsin bound to a peptidomimetic inhibitor (PDB 1Z8G) in PyMOL (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.…”

“…A structural dissimilarity matrix (SDM) was constructed using the Ca RMSD values in order to generate a phylogenetic tree as previously described. 31 To expedite the pairwise alignment process, we developed a Python-based script (named 3DPhyloFold) to perform the pairwise alignment of protein structures and generate an SDM. The phylogenetic tree was constructed using the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) method in MEGAX software as previously described.…”

“…The phylogenetic tree was constructed using the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) method in MEGAX software as previously described. 31 For comparison, the sequences from the corresponding structures were also analyzed by sequence-based phylogeny. The 75 S1-peptidase sequences were aligned with MAFFT v7 26 and analyzed in IQ-TREE-1.6.2.…”

Molecular Surgery: Proteomics of a Rare Genetic Disease Gives Insight into Common Causes of Blindness

“…Since the discovery of the first NIV-causing mutations, efforts have been taken to understand the structure, function, targets, and downstream signaling effectors of the CAPN5 protease ( Bassuk et al., 2015 ; Gakhar et al., 2016 ; Mahajan et al., 2012 ; Schaefer et al., 2016 ; Wert et al., 2014 , 2015 , 2019 ). Our group solved the structure of the CAPN5 protease core domain (termed CAPN5-PC), a finding that furthers the study of NIV disease mechanisms ( Velez et al., 2020 ). The wild-type CAPN5-PC structure revealed unique structural features compared with classical calpain cores and provided clues as to how NIV mutations would increase enzymatic activity ( Figure 2 A).…”

“…Although the function of this loop is unknown, transfer of the unique PC2L2 loop (with the hyperactivating p.G267S mutation) onto rat CAPN1 led to hyperactivity in a CAPN1/5 hybrid ( Figure 2 F). This finding suggests that the PC2L2 loop can remotely regulate calpain activity independent of its non-catalytic domains ( Velez et al., 2020 ). The p.R289W mutation is associated with the most aggressive NIV phenotype and is located on the G2 loop, which houses the critical tryptophan “wedge” residue (Trp286).…”