Cytoplasmic Side Research Articles

T‐PEP Related Presentation: Alzheimer’s disease pathogenic protein SORLA forms homodimer potentially required for its function

AbstractBackgroundSo far, many genetic and molecular studies have indicated that the single‐pass transmembrane receptor SORLA can cause Alzheimer’s disease (AD) when mutated, but the detailed mechanism of how SORLA is involved in the pathogenesis of AD is still unknown. SORLA has a unique domain architecture including a huge, multidomain extracellular region with a Vps10p domain and 6 tandem repeats of fibronectin‐type‐III (3Fn) domains plus a short cytoplasmic tail. Although this unique composition must be essential for its potential function as a guiding molecule for protein sorting inside cells, there has been limited information about its overall molecular architecture. We are focusing on the function of SORLA in guiding trafficking along with the retromer complex, and recently found SORLA seems to form homodimers on the cell surface, which correlates with its function.MethodWe employed a highly efficient recombinant expression system for extracellular proteins using mammalian cells that enables detailed biochemical analysis. Using this technique, we produced recombinant secreted protein samples of the whole ectodomain and some fragments derived from human SORLA, and investigated its dimerization property by pull‐down assay followed by SDS PAGE and native PAGE. To investigate the three‐dimensional architecture, we ran a structural prediction using the amino acid sequence of SORLA’s ectodomain only without its signal sequence, propeptide, transmembrane region, and cytoplasmic region, using the program AlphaFold2.ResultOur biochemical experiments showed that human SORLA has homodimer forming property through its Vps10p domain and 3Fn domains. For theVps10p domain especially, it is indicated that the major fraction forms a homodimer in solution. Based on current structural information, we successfully created a mutant that forms covalent bound homodimer with an artificially introduced intermolecular disulfide bond. Interestingly, the predicted model of the ectodomain shows a folded compact structure, indicating that SORLA’s ectodomain forms a large globular shape on the surface of cells.ConclusionOur biochemical experiments showed that SORLA has two putative, opposite‐facing dimeric interfaces. Along with the computational molecular prediction, we propose that SORLA forms polymeric fibril‐like high dimensional structure inside the tubular endosomal membrane, supported by the retromer oligomer from the cytoplasmic side.

KATP channel activity and slow oscillations in pancreatic beta cells are regulated by mitochondrial ATP production.

Pancreatic beta cells secrete insulin in response to plasma glucose. The ATP-sensitive potassium channel (KATP ) links glucose metabolism to islet electrical activity in these cells by responding to increased cytosolic [ATP]/[ADP]. It was recently proposed that pyruvate kinase (PK) in close proximity to beta cell KATP locally produces the ATP that inhibits KATP activity. This proposal was largely based on the observation that applying phosphoenolpyruvate (PEP) and ADP to the cytoplasmic side of excised inside-out patches inhibited KATP . To test the relative contributions of local vs. mitochondrial ATP production, we recorded KATP activity using mouse beta cells and INS-1 832/13 cells. In contrast to prior reports, we could not replicate inhibition of KATP activity by PEP+ADP. However, when the pH of the PEP solutions was not corrected for the addition of PEP, strong channel inhibition was observed as a result of the well-known action of protons to inhibit KATP . In cell-attached recordings, perifusing either a PK activator or an inhibitor had little or no effect on KATP channel closure by glucose, further suggesting that PK is not an important regulator of KATP . In contrast, addition of mitochondrial inhibitors robustly increased KATP activity. Finally, by measuring the [ATP]/[ADP] responses to imposed calcium oscillations in mouse beta cells, we found that oxidative phosphorylation could raise [ATP]/[ADP] even when ADP was at its nadir during the burst silent phase, in agreement with our mathematical model. These results indicate that ATP produced by mitochondrial oxidative phosphorylation is the primary controller of KATP in pancreatic beta cells. KEY POINTS: Phosphoenolpyruvate (PEP) plus adenosine diphosphate does not inhibit KATP activity in excised patches. PEP solutions only inhibit KATP activity if the pH is unbalanced. Modulating pyruvate kinase has minimal effects on KATP activity. Mitochondrial inhibition, in contrast, robustly potentiates KATP activity in cell-attached patches. Although the ADP level falls during the silent phase of calcium oscillations, mitochondria can still produce enough ATP via oxidative phosphorylation to close KATP . Mitochondrial oxidative phosphorylation is therefore the main source of the ATP that inhibits the KATP activity of pancreatic beta cells.

A conformation-locking inhibitor of SLC15A4 with TASL proteostatic anti-inflammatory activity

Dysregulation of pathogen-recognition pathways of the innate immune system is associated with multiple autoimmune disorders. Due to the intricacies of the molecular network involved, the identification of pathway- and disease-specific therapeutics has been challenging. Using a phenotypic assay monitoring the degradation of the immune adapter TASL, we identify feeblin, a chemical entity which inhibits the nucleic acid-sensing TLR7/8 pathway activating IRF5 by disrupting the SLC15A4-TASL adapter module. A high-resolution cryo-EM structure of feeblin with SLC15A4 reveals that the inhibitor binds a lysosomal outward-open conformation incompatible with TASL binding on the cytoplasmic side, leading to degradation of TASL. This mechanism of action exploits a conformational switch and converts a target-binding event into proteostatic regulation of the effector protein TASL, interrupting the TLR7/8-IRF5 signaling pathway and preventing downstream proinflammatory responses. Considering that all components involved have been genetically associated with systemic lupus erythematosus and that feeblin blocks responses in disease-relevant human immune cells from patients, the study represents a proof-of-concept for the development of therapeutics against this disease.

Allosteric inhibition of the T cell receptor by a designed membrane ligand.

The T cell receptor (TCR) is a complex molecular machine that directs the activation of T cells, allowing the immune system to fight pathogens and cancer cells. Despite decades of investigation, the molecular mechanism of TCR activation is still controversial. One of the leading activation hypotheses is the allosteric model. This model posits that binding of pMHC at the extracellular domain triggers a dynamic change in the transmembrane (TM) domain of the TCR subunits, which leads to signaling at the cytoplasmic side. We sought to test this hypothesis by creating a TM ligand for TCR. Previously we described a method to create a soluble peptide capable of inserting into membranes and binding to the TM domain of the receptor tyrosine kinase EphA2 (Alves et al., eLife, 2018). Here, we show that the approach is generalizable to complex membrane receptors, by designing a TM ligand for TCR. We observed that the designed peptide caused a reduction of Lck phosphorylation of TCR at the CD3ζ subunit in T cells. As a result, in the presence of this peptide inhibitor of TCR (PITCR), the proximal signaling cascade downstream of TCR activation was significantly dampened. Co-localization and co-immunoprecipitation in diisobutylene maleic acid (DIBMA) native nanodiscs confirmed that PITCR was able to bind to the TCR. AlphaFold-Multimer predicted that PITCR binds to the TM region of TCR, where it interacts with the two CD3ζ subunits. Our results additionally indicate that PITCR disrupts the allosteric changes in the compactness of the TM bundle that occur upon TCR activation, lending support to the allosteric TCR activation model. The TCR inhibition achieved by PITCR might be useful to treat inflammatory and autoimmune diseases and to prevent organ transplant rejection, as in these conditions aberrant activation of TCR contributes to disease.

Proton Release Reactions in the Inward H+ Pump NsXeR.

Directional ion transport across biological membranes plays a central role in many cellular processes. Elucidating the molecular determinants for vectorial ion transport is key to understanding the functional mechanism of membrane-bound ion pumps. The extensive investigation of the light-driven proton pump bacteriorhodopsin from Halobacterium salinarum(HsBR) enabled a detailed description of outward proton transport. Although the structure of inward-directed proton pumping rhodopsins is very similar to HsBR, little is known about their protonation pathway, and hence, the molecular reasons for the vectoriality of proton translocation remain unclear. Here, we employ a combined experimental and theoretical approach to tracking protonation steps in the light-driven inward proton pump xenorhodopsin from Nanosalina sp. (NsXeR). Time-resolved infrared spectroscopy reveals the transient deprotonation of D220 concomitantly with deprotonation of the retinal Schiff base. Our molecular dynamics simulations support a proton release pathway from the retinal Schiff base via a hydrogen-bonded water wire leading to D220 that could provide a putative gating point for the proton release and with allosteric interactions to the retinal Schiff base. Our findings support the key role of D220 in mediating proton release to the cytoplasmic side and provide evidence that this residue is not the primary proton acceptor of the proton transiently released by the retinal Schiff base.

Bioinformatics and machine learning were used to validate glutamine metabolism-related genes and immunotherapy in osteoporosis patients

BackgroundOsteoporosis (OP), often referred to as the “silent disease of the twenty-first century,” poses a significant public health concern due to its severity, chronic nature, and progressive course, predominantly affecting postmenopausal women and elderly individuals. The pathogenesis and progression of this disease have been associated with dysregulation in tumor metabolic pathways. Notably, the metabolic utilization of glutamine has emerged as a critical player in cancer biology. While metabolic reprogramming has been extensively studied in various malignancies and linked to clinical outcomes, its comprehensive investigation within the context of OP remains lacking.MethodsThis study aimed to identify and validate potential glutamine metabolism genes (GlnMgs) associated with OP through comprehensive bioinformatics analysis. The identification of GlnMgs was achieved by integrating the weighted gene co-expression network analysis and a set of 28 candidate GlnMgs. Subsequently, the putative biological functions and pathways associated with GlnMgs were elucidated using gene set variation analysis. The LASSO method was employed to identify key hub genes, and the diagnostic efficacy of five selected GlnMgs in OP detection was assessed. Additionally, the relationship between hub GlnMgs and clinical characteristics was investigated. Finally, the expression levels of the five GlnMgs were validated using independent datasets (GSE2208, GSE7158, GSE56815, and GSE35956).ResultsFive GlnMgs, namely IGKC, TMEM187, RPS11, IGLL3P, and GOLGA8N, were identified in this study. To gain insights into their biological functions, particular emphasis was placed on synaptic transmission GABAergic, inward rectifier potassium channel activity, and the cytoplasmic side of the lysosomal membrane. Furthermore, the diagnostic potential of these five GlnMgs in distinguishing individuals with OP yielded promising results, indicating their efficacy as discriminative markers for OP.ConclusionsThis study discovered five GlnMgs that are linked to OP. They shed light on potential new biomarkers for OP and tracking its progression.

The Mass Spectrometry Identification, Antimicrobial Genes Detection, and Proteomics Analysis of Stutzerimonas stutzeri Strain Was Isolated from Industrial Wastewater

A large amount of organic matter, heavy metals, and even antibiotics are present in industrial wastewater, aquaculture waters, and various types of sewage, along with abundant microorganisms. To date, only a few studies involving the resistance and proteomics of Stutzerimonas stutzeri in high-salt wastewater are available. Herein, a comprehensive assessment of a newly isolated Stutzerimonas stutzeri strain, which is present in high-salt wastewater, was performed using mass spectrometry, genetic identification, and biochemical analysis to characterize the genetic and biochemical properties. Growth experiments revealed that the Stutzerimonas stutzeri strain had a moderate growth rate in nutrient broth, and the bacterial count was not high. Further analysis highlighted an apparent susceptibility of this strain to most antibiotics but some resistance to chloramphenicol and minocycline. A resistance gene assay results showed that the gene gyrB was associated with antibiotic resistance in this Stutzerimonas stutzeri strain. Proteomic analysis revealed for the first time the co-existence of two drug-resistance-related proteins (Multidrug/solvent RND membrane fusion protein and MexE) in Stutzerimonas stutzeri. Moreover, Stutzerimonas stutzeri isolated from high-salt wastewater was subjected to drug resistance gene detection, and the total protein of Stutzerimonas stutzeri was detected by protein mass spectrometry analysis. The subcellular classification shows that the 50 proteins with the highest abundance are divided into cell inner membrane, cell outer membrane, cytoplasm, cytoplasmic side, membrane, multi-pass membrane protein, and peripheral membrane protein, among which the proportion of cytoplasmic components is the highest. Overall, this study’s findings provide a new perspective for further research on the characteristics of Stutzerimonas stutzeri in high-salt wastewater.

Inhibition Mechanism of Anti-TB Drug SQ109: Allosteric Inhibition of TMM Translocation of Mycobacterium Tuberculosis MmpL3 Transporter.

The mycolic acid transporter MmpL3 is driven by proton motive forces (PMF) and functions via an antiport mechanism. Although the crystal structures of the Mycobacterium smegmatis MmpL3 transporter alone and in complex with a trehalose monomycolate (TMM) substrate and an antituberculosis drug candidate SQ109 under Phase 2b-3 Clinical Trials are available, no water and no conformational change in MmpL3 were observed in these structures to explain SQ109's inhibition mechanism of proton and TMM transportation. In this study, molecular dynamics simulations of both apo form and inhibitor-bound MmpL3 in an explicit membrane were used to decipher the inhibition mechanism of SQ109. In the apo system, the close-open motion of the two TM domains, likely driven by the proton translocation, drives the close-open motion of the two PD domains, presumably allowing for TMM translocation. In contrast, in the holo system, the two PD domains are locked in a closed state, and the two TM domains are locked in an off pathway wider open state due to the binding of the inhibitor. Consistent with the close-open motion of the two PD domains, TMM entry size changes in the apo system, likely loading and moving the TMM, but does not vary much in the holo system and probably impair the movement of the TMM. Furthermore, we observed that water molecules passed through the central channel of the MmpL3 transporter to the cytoplasmic side in the apo system but not in the holo system, with a mean passing time of ∼135 ns. Because water wires play an essential role in transporting protons, our findings shed light on the importance of PMF in driving the close-open motion of the two TM domains. Interestingly, the key channel residues involved in water passage display considerable overlap with conserved residues within the MmpL protein family, supporting their critical function role.

Ligand recognition and G protein coupling of the human itch receptor MRGPRX1

MRGPRX1, a Mas-related GPCR (MRGPR), is a key receptor for itch perception and targeting MRGPRX1 may have potential to treat both chronic itch and pain. Here we report cryo-EM structures of the MRGPRX1-Gi1 and MRGPRX1-Gq trimers in complex with two peptide ligands, BAM8-22 and CNF-Tx2. These structures reveal a shallow orthosteric pocket and its conformational plasticity for sensing multiple different peptidic itch allergens. Distinct from MRGPRX2, MRGPRX1 contains a unique pocket feature at the extracellular ends of TM3 and TM4 to accommodate the peptide C-terminal “RF/RY” motif, which could serve as key mechanisms for peptidic allergen recognition. Below the ligand binding pocket, the G6.48XP6.50F6.51G6.52X(2)F/W6.55 motif is essential for the inward tilting of the upper end of TM6 to induce receptor activation. Moreover, structural features inside the ligand pocket and on the cytoplasmic side of MRGPRX1 are identified as key elements for both Gi and Gq signaling. Collectively, our studies provide structural insights into understanding itch sensation, MRGPRX1 activation, and downstream G protein signaling.

Two conformations of the Tom20 preprotein receptor in the TOM holo complex

The TOM complex is the main entry point for precursor proteins (preproteins) into mitochondria. Preproteins containing targeting sequences are recognized by the TOM complex and imported into mitochondria. We have determined the structure of the TOM core complex from Neurospora crassa by single-particle electron cryomicroscopy at 3.3 Å resolution, showing its interaction with a bound preprotein at 4 Å resolution, and of the TOM holo complex including the Tom20 receptor at 6 to 7 Å resolution. TOM is a transmembrane complex consisting of two β-barrels, three receptor subunits, and three short transmembrane subunits. Tom20 has a transmembrane helix and a receptor domain on the cytoplasmic side. We propose that Tom20 acts as a dynamic gatekeeper, guiding preproteins into the pores of the TOM complex. We analyze the interactions of Tom20 with other TOM subunits, present insights into the structure of the TOM holo complex, and suggest a translocation mechanism.

Real-Time Observation of Capsaicin-Induced Intracellular Domain Dynamics of TRPV1 Using the Diffracted X-ray Tracking Method.

The transient receptor potential vanilloid type 1 (TRPV1) is a multimodal receptor which responds to various stimuli, including capsaicin, protons, and heat. Recent advances in cryo-electron microscopy have revealed the structures of TRPV1. However, due to the large size of TRPV1 and its structural complexity, the detailed process of channel gating has not been well documented. In this study, we applied the diffracted X-ray tracking (DXT) technique to analyze the intracellular domain dynamics of the TRPV1 protein. DXT enables the capture of intramolecular motion through the analysis of trajectories of Laue spots generated from attached gold nanocrystals. Diffraction data were recorded at two different frame rates: 100 μs/frame and 12.5 ms/frame. The data from the 100 μs/frame recording were further divided into two groups based on the moving speed, using the lifetime filtering technique, and they were analyzed separately. Capsaicin increased the slope angle of the MSD curve of the C-terminus in 100 μs/frame recording, which accompanied a shifting of the rotational bias toward the counterclockwise direction, as viewed from the cytoplasmic side. This capsaicin-induced fluctuation was not observed in the 12.5 ms/frame recording, indicating that it is a high-frequency fluctuation. An intrinsiccounterclockwise twisting motion was observed in various speed components at the N-terminus, regardless of the capsaicin administration. Additionally, the competitive inhibitor AMG9810 induced a clockwise twisting motion, which is the opposite direction to capsaicin. These findings contribute to our understanding of the activation mechanisms of the TRPV1 channel.

Unnexin is a protein subunit of a large-pore channel expressed by unicellular organisms

Cells of vertebrate and invertebrate organisms express proteins specialized in membrane channel-based cell-cell communication that are absent in unicellular organisms. We recently described the prediction of some members of the large-pore channel family in kinetoplastids, consisting of proteins called unnexins, which share several structural features with innexin and pannexin proteins. Here, we demonstrated that the unnexin1 protein (Unx1) is delivered to the cell membrane, displaying a topology consisting of four transmembrane domains with C and N termini on the cytoplasmic side and form large-pore channels that are permeable to small molecules. Low extracellular Ca2+/Mg2+ levels or extracellular alkalinization, but not mechanical stretching, increases channel activity. The Unx1 channel mediates the influx of Ca2+ and does not form intercellular dye coupling between HeLa Unx1 transfected cells. Unx1 channel function was further evidenced by its ability to mediate ionic currents when expressed in Xenopus oocytes. Downregulation of Unx1 mRNA with morpholine contains Trypanosoma cruzi invasion. Phylogenetic analysis revealed the presence of Unx1 homologs in other protozoan parasites, suggesting a conserved function for these channel parasites in other protists. Our data demonstrate that Unx1 forms large-pore membrane channels, which may serve as a diffusional pathway for ions and small molecules that are likely to be metabolic substrates or waste products, and signaling autocrine and paracrine molecules that could be involved in cell invasion. As morpholinos-induced downregulation of Unx1 reduces the infectivity of trypomastigotes, the Unx1 channels might be an attractive target for developing trypanocide drugs.

Single hormone or synthetic agonist induces Gs/Gi coupling selectivity of EP receptors via distinct binding modes and propagating paths

To accomplish concerted physiological reactions, nature has diversified functions of a single hormone at at least two primary levels: 1) Different receptors recognize the same hormone, and 2) different cellular effectors couple to the same hormone-receptor pair [R.P. Xiao, Sci STKE 2001, re15 (2001); L. Hein, J. D. Altman, B.K. Kobilka, Nature 402, 181-184 (1999); Y. Daaka, L. M. Luttrell, R. J. Lefkowitz, Nature 390, 88-91 (1997)]. Not only these questions lie in the heart of hormone actions and receptor signaling but also dissecting mechanisms underlying these questions could offer therapeutic routes for refractory diseases, such as kidney injury (KI) or X-linked nephrogenic diabetes insipidus (NDI). Here, we identified that Gs-biased signaling, but not Gi activation downstream of EP4, showed beneficial effects for both KI and NDI treatments. Notably, by solving Cryo-electron microscope (cryo-EM) structures of EP3-Gi, EP4-Gs, and EP4-Gi in complex with endogenous prostaglandin E2 (PGE2)or two synthetic agonists and comparing with PGE2-EP2-Gs structures, we found that unique primary sequences of prostaglandin E2 receptor (EP) receptors and distinct conformational states of the EP4 ligand pocket govern the Gs/Gi transducer coupling selectivity through different structural propagation paths, especially via TM6 and TM7, to generate selective cytoplasmic structural features. In particular, the orientation of the PGE2 ω-chain and two distinct pockets encompassing agonist L902688 of EP4 were differentiated by their Gs/Gi coupling ability. Further, we identified common and distinct features of cytoplasmic side of EP receptors for Gs/Gi coupling and provide a structural basis for selective and biased agonist design of EP4 with therapeutic potential.

Mechanism of action for small-molecule inhibitors of triacylglycerol synthesis

Inhibitors of triacylglycerol (TG) synthesis have been developed to treat metabolism-related diseases, but we know little about their mechanisms of action. Here, we report cryo-EM structures of the TG-synthesis enzyme acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1), a membrane bound O-acyltransferase (MBOAT), in complex with two different inhibitors, T863 and DGAT1IN1. Each inhibitor binds DGAT1’s fatty acyl-CoA substrate binding tunnel that opens to the cytoplasmic side of the ER. T863 blocks access to the tunnel entrance, whereas DGAT1IN1 extends further into the enzyme, with an amide group interacting with more deeply buried catalytic residues. A survey of DGAT1 inhibitors revealed that this amide group may serve as a common pharmacophore for inhibition of MBOATs. The inhibitors were minimally active against the related MBOAT acyl-CoA:cholesterol acyltransferase 1 (ACAT1), yet a single-residue mutation sensitized ACAT1 for inhibition. Collectively, our studies provide a structural foundation for developing DGAT1 and other MBOAT inhibitors.

Lipid flipping in the omega-3 fatty-acid transporter

Mfsd2a is the transporter for docosahexaenoic acid (DHA), an omega-3 fatty acid, across the blood brain barrier (BBB). Defects in Mfsd2a are linked to ailments from behavioral and motor dysfunctions to microcephaly. Mfsd2a transports long-chain unsaturated fatty-acids, including DHA and α-linolenic acid (ALA), that are attached to the zwitterionic lysophosphatidylcholine (LPC) headgroup. Even with the recently determined structures of Mfsd2a, the molecular details of how this transporter performs the energetically unfavorable task of translocating and flipping lysolipids across the lipid bilayer remains unclear. Here, we report five single-particle cryo-EM structures of Danio rerio Mfsd2a (drMfsd2a): in the inward-open conformation in the ligand-free state and displaying lipid-like densities modeled as ALA-LPC at four distinct positions. These Mfsd2a snapshots detail the flipping mechanism for lipid-LPC from outer to inner membrane leaflet and release for membrane integration on the cytoplasmic side. These results also map Mfsd2a mutants that disrupt lipid-LPC transport and are associated with disease.

Relevance of Sugar Transport across the Cell Membrane.

Sugar transport through the plasma membrane is one of the most critical events in the cellular transport of nutrients; for example, glucose has a central role in cellular metabolism and homeostasis. The way sugars enter the cell involves complex systems. Diverse protein systems participate in the membrane traffic of the sugars from the extracellular side to the cytoplasmic side. This diversity makes the phenomenon highly regulated and modulated to satisfy the different needs of each cell line. The beautiful thing about this process is how evolutionary processes have diversified a single function: to move glucose into the cell. The deregulation of these entrance systems causes some diseases. Hence, it is necessary to study them and search for a way to correct the alterations and utilize these mechanisms to promote health. This review will highlight the various mechanisms for importing the valuable sugars needed to create cellular homeostasis and survival in all kinds of cells.

Mutational analysis of a conserved positive charge in the c-ring of E. coli ATP synthase

F1Fo ATP synthase is a ubiquitous molecular motor that utilizes a rotary mechanism to synthesize adenosine triphosphate (ATP), the fundamental energy currency of life. The membrane-embedded Fo motor converts the electrochemical gradient of protons into rotation, which is then used to drive the conformational changes in the soluble F1 motor that catalyze ATP synthesis. In E. coli, the Fo motor is composed of a c10 ring (rotor) alongside subunit a (stator), which together provide two aqueous half channels that facilitate proton translocation. Previous work has suggested that Arg50 and Thr51 on the cytoplasmic side of each subunit c are involved in the proton translocation process, and positive charge is conserved in this region of subunit c. To further investigate the role of these residues and the chemical requirements for activity at these positions, we generated 13 substitution mutants and assayed their in vitro ATP synthesis, H+ pumping, and passive H+ permeability activities, as well as the ability of mutants to carry out oxidative phosphorylation in vivo. While polar and hydrophobic mutations were generally tolerated in either position, introduction of negative charge or removal of polarity caused a substantial defect. We discuss the possible effects of altered electrostatics on the interaction between the rotor and stator, water structure in the aqueous channel, and interaction of the rotor with cardiolipin.

Elucidating the pH gating mechanism of Helicobacter pyloris urea channel UreI.

Over 50% of the world population suffer from chronic gastric infection with Helicobacter pyloris which is linked to peptic ulcer disease and stomach cancer. Yet, the efficacy of the common therapy including antibiotics is decreasing. An alternative drug target could be H. pyloris pH gatedinner-membrane urea channel UreI, which is pivotal for the survival of the pathogen in the acidic environment of the human stomach. However, despite in vivo studies and high-resolution structures in the open and closed state, HpUreIs gating mechanism is still elusive. Using yeast complementation assays, we tested (i) homologues urea channels, (ii) point mutations of charged residues also on the cytoplasmic side, and (iii) variants carrying changes at the periplasmic side at the N- and C-terminus as well as in periplasmic loop 1 (PL1). The functionality and pH gating behaviour of these constructs are compared to the wild type protein in the physiological relevant pH range from 4.0 to 7.0. Our in vivo studies are guided and accompanied by an extensive sequence- and structure-based analysis of homologues urea channels. The results question the hypothesis of PL1 and PL2 constituting the main pH-sensor of HpUreI but confirm the importance of the N- and C-terminus in the pH gating mechanism. For example, additional amino acids at the C-terminus provoke a urea impermeable HpUreI, emphasizing its importance for the stability of the open state. Furthermore, the urea channels from Helicobacter hepaticus and Streptococcus salivarius, lacking such extensive periplasmic loops, show similar pH dependence as HpUreI. Overall, yeast complementation assays are an cost-effective tool for testing qualitative differences in protein variant activity for a broad range of solutes.

Discovery of novel potassium-competitive acid blockers: Protonated form of ligand-receptor complex system.

Potassium-competitive acid blockers (P-CABs) are acid-suppressing drugs targeting the gastric proton pump (H+,K+-ATPase). They are able to mediate the electro-neutral exchange of H+ and K+ coupled with ATP hydrolysis. Because the conditions of both the cytoplasmic side (pH ∼7) and extracytoplasmic side (pH ∼1) of the target H+,K+-ATPase is are quite different, putting into consideration the moderate protonated forms of both the target protein and the P-CABs is important for system modeling. The three different protonated forms of the receptor models were evaluated with experimental data using docking and molecular dynamics. Here, we utilized the in-silico approaches to discover possible inhibitors against H+,K+-ATPase. Candidate substances were screened from the ChEMBL, Enamine, and Mcule databases. The high-throughput virtual screening (HTVS) was performed to screen for potent compounds. Molecular dynamics (MD) simulations were carried out among high docking scored candidates to validate the stability and binding affinity. These findings show that the proper modeling of the target-ligand complex is important for screening potent compounds, especially in extreme environments.

Myelin protein zero - the structural foundation behind peripheral compact myelin.

Schwann cells are the myelinating glia of the peripheral nervous system (PNS). During PNS development, Schwann cell precursors differentiate into mature Schwann cells after the radial sorting of axons and form myelin around selected axonal segments. This multilayered, highly lipid-rich and insulative membrane structure significantly accelerates nerve impulse propagation, which is a pre-requisite for the efficient function of the PNS. During this differentiation process, protein zero (P0), a single-pass transmembrane protein, is expressed in high amounts. P0 is the most abundant PNS myelin protein, at up to 50% of total protein, and its accumulation in membranes eventually forms stable compact myelin. Failure to do so, like in the case of mutated or truncated protein, results in non-compacted myelin and demyelination. This subsequently causes incurable peripheral neuropathies, such as Charcot-Marie-Tooth disease (CMT) and Dejerine-Sottas syndrome (DSS), where CMT alone afflicts nearly 3 million people globally. To understand the compaction and maturation of PNS myelin, and the molecular etiology of disease, uncovering the structure-function relationships of P0 are of great importance. We demonstrate the molecular foundation of P0-mediated membrane stacking using a hybrid structural biology approach: on the extracellular side, immunoglobulin (Ig)-like domains form a zipper-like assembly of apposing protein monomers, whereas on the cytoplasmic side, the short, positively charged P0 tail (P0ct) glues membranes together. P0ct undergoes a substantial folding event during membrane binding, and we provide rationale to why membrane stacking is affected in diseases through functional in vitro mutagenesis studies. Additionally, we speculate on how post-translational modifications in P0ct help P0 locate to its target compartments, without inducing premature membrane stacking. Our results shed light on the essential role of P0 in during myelin maturation, and why other proteins fail to replace P0 when its function is compromised.