Journal of Biological Chemistry最新文献

Rhomboid proteases are ubiquitous intramembrane serine proteases that can cleave transmembrane substrates within lipid bilayers. They exhibit many and diverse functions, such as but not limited to, growth factor signaling, immune and inflammatory response, protein quality control, and parasitic invasion. Human rhomboid protease RHBDL4 has been demonstrated to play a critical role in removing misfolded proteins from the Endoplasmic Reticulum and is implicated in severe diseases such as various cancers and Alzheimer's disease. Therefore, RHBDL4 is expected to constitute an important therapeutic target for such devastating diseases. Despite its critical role in many biological processes, the enzymatic properties of RHBDL4 remain largely unknown. To enable a comprehensive characterization of RHBDL4's kinetics, catalytic parameters, substrate specificity, and binding modality we expressed and purified recombinant RHBDL4, and employed it in a Förster Resonance Energy Transfer-based cleavage assay. Until now, kinetic studies have been limited mostly to bacterial rhomboid proteases. Our in vitro platform offers a new method for studying RHBDL4's enzymatic function and substrate preferences. Furthermore, we developed and tested potential inhibitors using our assay and successfully identified peptidyl α-ketoamide inhibitors of RHBDL4 that are highly effective against recombinant RHBDL4. We utilize ensemble docking and molecular dynamics (MD) simulations to explore the binding modality of substrate-derived peptides bound to RHBDL4. Our analysis focused on key interactions and dynamic movements within RHBDL4's active site that contributed to binding stability, offering valuable insights for optimizing the non-prime side of RHBDL4 ketoamide inhibitors. In summary, our study offers fundamental insights into RHBDL4's catalytic activities and substrate preferences, laying the foundation for downstream applications such as drug inhibitor screenings and structure-function studies, which will enable the identification of lead drug compounds for RHBDL4.

Photosystem II (PSII) is the water-splitting enzyme of oxygenic photosynthesis. Using light energy, PSII catalytically oxidizes two water molecules to fuel downstream metabolism, forming an O-O bond and releasing O₂ as a byproduct. The reaction mechanism requires the strategic removal of four protons via conserved hydrogen-bonding networks, but these pathways remain poorly understood. Site-directed mutagenesis has been used to study these pathways and the role of specific side chains, such as Lys317 of the D2 subunit. Previous studies showed that the D2-Lys317Ala substitution, which abolishes the flexible hydrogen-bonding -NH₃⁺ group, resulted in delayed O₂ release kinetics and diminished catalytic turnover, suggesting Lys317 has a crucial role in facilitating proton egress. Here, we investigated this proton egress pathway by determining the cryo-EM structure of PSII containing the D2-Lys317Ala substitution at a resolution of 1.97 Å. We observed that four new water molecules fill the space previously occupied by Lys317, but these waters lack specific water-protein interactions, leading to heterogeneity and suboptimal hydrogen bonding. We hypothesize that these waters negatively contribute to the existing hydrogen-bonding network and increase the entropic barrier for proton transfer. Additionally, we observed that a conserved chloride ion (Cl1), which is associated with Lys317, is unexpectedly maintained in D2-Lys317Ala PSII. However, unlike in wild-type, Cl1 has no measured effect on oxygen-evolution rates in D2-Lys317Ala PSII. This suggests that the role of Cl1 is dependent on the Lys317 amino group. These findings provide new insight into proton egress through the Cl1 hydrogen-bonding channel.

Every cell in the body is exposed to a certain level of CO₂ and O₂. Hypercapnia and hypoxia elicit stress signals to influence cellular metabolism and function. Both conditions exert profound yet distinct effects on metabolic pathways and mitochondrial dynamics, highlighting the need for cells to adapt to changes in the gaseous microenvironment. The interplay between hypercapnia and hypoxia signalling is key for dictating cellular homeostasis as microenvironmental CO₂ and O₂ levels are inextricably linked. Hypercapnia, characterized by elevated pCO₂, introduces metabolic adaptations within the aerobic metabolism pathways, affecting TCA cycle flux, lipid, and amino acid metabolism, OXPHOS and the ETC. Hypoxia, defined by reduced oxygen availability, necessitates a shift from OXPHOS to anaerobic glycolysis to sustain ATP production, a process orchestrated by the stabilisation of HIF-1α. Given that hypoxia and hypercapnia are present in both physiological and cancerous microenvironments, how might the coexistence of hypercapnia and hypoxia influence metabolic pathways and cellular function in physiological niches and the tumor microenvironment?

Mutations in retinal membrane guanylyl cyclase 1 (RetGC1) and its calcium-sensor protein (GCAP1) cause congenital dominant retinopathies by elevation of cGMP synthesis in photoreceptors in the dark. We explored counteracting the elevated cGMP synthesis causing photoreceptor degeneration using ectopic expression of a non-photoreceptor cGMP phosphodiesterase (PDE) isozyme PDE5. PDE5 primary structure was modified to direct the delivery of the recombinant PDE5 (PDE5r) to rod outer segments (ROS), by placing a C-terminal fragment derived from a cone-specific alpha-subunit of PDE6C at the C-terminus of the PDE5, which allowed PDE5r expressed under control of mouse rod opsin promoter to accumulate in ROS. Expression of PDE5r did not affect calcium-sensitivity of RetGC regulation in PDE5r^Tg transgenic retinas, but increased cGMP hydrolysis in the dark, which partially desensitized PDR5r^Tg rods in the dark via an 'equivalent light' effect, analogous to exposure to a constant dim light of ∼20-40 photons μm^-2 sec^-1. The calcium-sensitivity of RetGC regulation remained drastically shifted outside the normal physiological range in hybrid R838S^TgPDE5r^Tg rods expressing both PDE5r and R838S RetGC1, the mutant causing GUCY2D dominant retinopathy, but the hybrid rods demonstrated a dramatic rescue from degeneration caused by the R838S RetGC1. In a similar fashion, PDE5r expression rescued degeneration of rods harboring Y99C GCAP1, one of the GCAP1 mutants most frequently causing GUCA1A dominant retinopathy. Our results open a possibility that ectopic expression of PDE5 can be used as an approach to rescue presently incurable dominant GUCY2D and GUCA1A retinopathies at the expense of a moderate reduction in rod light-sensitivity.

The MIA40 relay system mediates the import of small cysteine-rich proteins into the intermembrane mitochondrial space (IMS). MIA40 substrates are synthesized in the cytosol and assumed to be disordered in their reduced state in this compartment. As they cross the outer mitochondrial membrane, MIA40 promotes the oxidation of critical native disulfides to facilitate folding, trapping functional species in the IMS. Here, we study the redox-controlled folding of TRIAP1, a small cysteine-rich protein with moonlighting function: regulating phospholipid trafficking between mitochondrial membranes in the IMS and preventing apoptosis in the cytosol. TRIAP1 dysregulation is connected to oncogenesis. Although TRIAP1 contains a canonical twin CX9C motif, its sequence characteristics and folding pathway deviate from typical MIA40 substrates. In its reduced state, TRIAP1 rapidly populates a hydrophobic collapsed, alpha-helical, and marginally stable molten globule. This intermediate, biases oxidative folding towards a non-native Cys37-Cys47 kinetic trap, slowing the reaction. MIA40 accelerates TRIAP1 folding rate by 30-fold, bypassing the formation of this folding trap. MIA40 drives the oxidation of the inner disulfide bond Cys18-Cys37, and subsequently, it can catalyze the formation of the outer disulfide bond Cys8-Cys47 to attain the native two-disulfide-bridged structure. We demonstrate that, unlike most MIA40 substrates, TRIAP1's folding pathway is strongly constrained by the structural requirements for its function in phospholipid traffic at the IMS. The obligatory population of a reduced, alpha-helical, metastable molten globule in the cytoplasm may explain TRIAP1's connection to the p53-dependent cell survival pathway, constituting a remarkable example of a functional molten globule state.

Parkinson's disease (PD) is a devastating neurodegenerative disease resulting from the death of dopaminergic neurons in the substantia nigra pars compacta of the midbrain. Familial and sporadic forms of the disease have been linked to mitochondrial dysfunction. Pathology has been identified with mutations in the PARK6 gene encoding PTEN-induced kinase 1 (PINK1), a quality control protein in the mitochondria. Disease-associated mutations at the transmembrane region of PINK1 protein were predicted to disrupt the cleavage of the transmembrane region by the PARL protease at the inner mitochondrial membrane. Here, using microscopy, kinetic analysis and molecular dynamic simulations, we analyzed 3 PD associated TM mutations; PINK1-C92F, PINK1-R98W and PINK1-I111S, and found that mitochondrial localization and cleavage by the PARL protease were not significantly impaired. However, clearance of hydrolyzed PINK1-R98W appears to be compromised due to altered positioning of the protein in the outer mitochondrial membrane, preventing association with TOM complexes and slowing cleavage by PARL. This single amino acid change slows degradation of proteolyzed PINK1, increasing its accumulation at the outer mitochondrial membrane and resulting in increased mitophagy and decreased mitochondrial content among these cells.

Protein S-palmitoylation is a reversible lipophilic posttranslational modification regulating a diverse number of signaling pathways. Within transmembrane proteins (TMPs), S-palmitoylation is implicated in conditions from inflammatory disorders to respiratory viral infections. Many small-scale experiments have observed S-palmitoylation at juxtamembrane Cys residues. However, most large-scale S-palmitoyl discovery efforts rely on trypsin-based proteomics within which hydrophobic juxtamembrane regions are likely underrepresented. Machine learning- by virtue of its freedom from experimental constraints - is particularly well suited to address this discovery gap surrounding TMP S-palmitoylation. Utilizing a UniProt-derived feature set, a gradient boosted machine learning tool (TopoPalmTree) was constructed and applied to a holdout dataset of viral S-palmitoylated proteins. Upon application to the mouse TMP proteome, 1591 putative S-palmitoyl sites (i.e. not listed in SwissPalm or UniProt) were identified. Two lung-expressed S-palmitoyl candidates (synaptobrevin Vamp5 and water channel Aquaporin-5) were experimentally assessed, as were 3 Type I transmembrane proteins (Cadm4, Chodl and Havcr2). Finally, TopoPalmTree was used for rational design of an S-palmitoyl site on KDEL-Receptor 2. This readily interpretable model aligns the innumerable small-scale experiments observing juxtamembrane S-palmitoylation into a proteomic tool for TMP S-palmitoyl discovery and design, thus facilitating future investigations of this important modification.

Deubiquitinating enzymes function to cleave ubiquitin moieties from modified proteins, serving to maintain the pool of free ubiquitin in the cell while simultaneously impacting the fate and function of a target protein. Like all eukaryotes, Plasmodium parasites rely on the dynamic addition and removal of ubiquitin for their own growth and survival. While humans possess around 100 DUBs, Plasmodium contains ∼20 putative ubiquitin hydrolases, many of which bear little to no resemblance to those of other organisms. In this study, we characterize PfUBP-1, a large ubiquitin hydrolase unique to Plasmodium spp that has been linked to endocytosis and drug resistance. We demonstrate its ubiquitin activity, linkage specificity and assess the repercussions of point mutations associated with drug resistance on catalytic activity and parasite fitness. We confirm that the deubiquitinating activity of UBP-1 is essential for parasite survival, implicating an important role for ubiquitin signaling in endocytosis.

Cell-to-cell communication is mediated by vesicles ranging from 30 to 150 nanometers, known as exosomes. These exosomes shuttle bioactive molecules such as proteins, lipids, and nucleic acids, thus playing crucial roles in both health and disease mechanisms. Exosomes form within the endocytic pathway through the process of inward budding of the endosomal membrane, facilitated by the progressive acidification of the endosomal lumen. Although endosomal pH is known to be critical for exosome production, the precise molecular mechanisms involved remain poorly defined. Maintaining optimal endosomal pH involves meticulous coordination between proton pumping and leakage mechanisms. The sodium-proton exchanger NHE9, located on the endosomal membrane, modulates endosomal pH by transporting protons out of the endosomes in exchange for sodium or potassium ions. Here, we use genetic engineering, biochemistry, and advanced microscopy to demonstrate that the sodium-proton exchanger NHE9 significantly affects exosome production by regulating endosomal pH. NHE9-mediated endosomal alkalization impairs Rab7 activation, thereby disrupting the delivery of multivesicular endosomes (MVEs) to lysosomes. Moreover, luminal alkalization promotes the recruitment of Rab27b. This enhances the targeting of MVEs to the cell periphery, their fusion with the plasma membrane, and subsequent exosome secretion. Our findings reveal the detailed molecular mechanisms through which endosomal pH regulates exosome production. Additionally, we identify NHE9 as a potential target for therapeutic strategies aimed at controlling exosome dynamics.

Transient receptor potential vanilloid 4 (TRPV4) is a Ca²⁺-permeable channel activated by diverse physical and chemical stimuli, including mechanical stress and endogenous lipid arachidonic acid (AA) and its metabolites. Phosphorylation of TRPV4 by protein kinase A (PKA) and protein kinase C (PKC) is a predominant mechanism for channel regulation, especially in the cytoplasmic domains due to their importance in protein assembly, and channelopathies. However, studies corresponding to phosphorylation sites for these kinases remain incomplete. We investigated the role of Ser-823 residue as a potential phosphorylation site in regulating TRPV4 activity and chemical agonist-induced channel activation. Using mass spectrometry, we identified a new phosphorylation site Ser-823 residue and confirmed the previously known phosphorylation site Ser-824 in the C-terminal tail. The low level of phosphorylation at Ser-823 was stimulated by PKC and to a lesser extent by PKA in human coronary artery endothelial cells (HCAECs) and human embryonic kidney 293 (HEK 293) cells. AA-induced TRPV4 activation was enhanced in the phosphomimetic S823E but was blunted in the S823A/S824A mutants, whereas the channel activation by the synthetic agonist GSK1016790A was unaffected. Further, TRPV4 activation by AA but not GSK1016790A was blunted or abolished by PKA inhibitor alone or in combination with PKC inhibitor, respectively. Using computational modeling, we refined a previously proposed structural model for TRPV4 regulation by Ser-823 and Ser-824 phosphorylation. Together, these results provide insight into how stimuli-specific TRPV4 activation is regulated by the phosphorylation of discrete residues (e.g., Ser-823 and Ser-824) in the C-terminal domains of the TRPV4 channel.