Membrane’s digest
MP
Cryo-EM structure of the extracellular domain of murine Thrombopoietin Receptor in complex with Thrombopoietin.
Sarson-Lawrence KTG, Hardy JM, Iaria J, Stockwell D, Behrens K, Saiyed T, Tan C, Jebeli L, Scott NE, Dite TA, Nicola NA, Leis AP, Babon JJ, Kershaw NJ.
Nat Commun. 2024 Feb 7;15(1):1135.
doi: 10.1038/s41467-024-45356-2.
Thrombopoietin (Tpo) is the primary regulator of megakaryocyte and platelet numbers and is required for haematopoetic stem cell maintenance. Tpo functions by binding its receptor (TpoR) => cell proliferation or differentiation. Here: cryoEM and biochemical characterization of the murine Tpo:TpoR.
Constitutive activation mechanism of a class C GPCR.
Shin J, Park J, Jeong J, Lam JH, Qiu X, Wu D, Kim K, Lee JY, Robinson CV, Hyun J, Katritch V, Kim KP, Cho Y.
Nat Struct Mol Biol. 2024 Feb 8. doi: 10.1038/s41594-024-01224-7.
GPR156, a class C orphan GPCR, = unique because it lacks an ECD and exhibits constitutive activity.
Here: cryoEM structures of human GPR156 in the Go-free and Go-coupled states: endogenous PL molecule is located within each TMD of the GPR156 dimer. Asymmetric binding of Gα to the PL-bound GPR156 dimer restructures the first and second ICL and the carboxy-terminal part of transmembrane 7 without altering dimer conformation.
=> GPR156 is a transducer for phospholipid signaling. Constant binding of abundant phospholipid molecules and the G-protein-induced reshaping of the cytoplasmic face provide a basis for the constitutive activation of GPR156.
Conformational ensemble of yeast ATP synthase at low pH reveals unique intermediates and plasticity in F1-Fo coupling.
Sharma S, Luo M, Patel H, Mueller DM, Liao M.
Nat Struct Mol Biol. 2024 Feb 5.
doi: 10.1038/s41594-024-01219-4.
Structural and single molecule studies mitochondrial ATP synthase are conducted mostly at neutral or basic pH. However, pH of the mitochondrial matrix is slightly acidic during hypoxia and pH-dependent conformational changes in the ATP synthase have been reported.
Here: SP cryo-EM to analyze the conformational ensemble of ATP synthase at pH 6. => identification of two unique conformations with nearly identical positions of the central rotor but different catalytic site conformations.
Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter.
Currie MJ, Davies JS, Scalise M, Gulati A, Wright JD, Newton-Vesty MC, Abeysekera GS, Subramanian R, Wahlgren WY, Friemann R, Allison JR, Mace PD, Griffin MDW, Demeler B, Wakatsuki S, Drew D, Indiveri C, Dobson RCJ, North RA.
Elife. 2024 Feb 13;12:RP92307.
doi: 10.7554/eLife.92307.
Cryo-EM structure of the Haemophilus influenzae N-acetylneuraminate TRAP transporter (HiSiaQM Tripartite ATP-independent periplasmic) at 2.99 Å resolution => improved resolution permits accurate assignment of two Na+ sites and the architecture of the substrate-binding site, consistent with mutagenic and functional data + structure is a homodimer + lipids at the dimer interface + lipid trapped within link between the SiaQ and SiaM subunits.
SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains.
Janssens, A., Nguyen, V.S., Cecil, A.J. et al.
Nature 626, 617–625 (2024).
https://doi-org.insb.bib.cnrs.fr/10.1038/s41586-023-06925-5
The study identifies SlyB as a compartmentalizing transmembrane guard protein that forms stable stress-induced complexes with the OM proteome in Gram-negative bacteria.
SlyB = periplasmic β-sandwich domain and a glycine zipper domain forming a transmembrane α-helical hairpin, exhibits discrete phospholipid and LPS binding sites. Under conditions causing lipid asymmetry loss, SlyB oligomerizes into ring-shaped TM complexes, encapsulating β-barrel proteins into lipid nanodomains of variable size, highlighting its role in cell envelope proteostasis and integrity during stress.
Oxygen-evolving photosystem II structures during S1–S2–S3 transitions.
Li, H., Nakajima, Y., Nango, E. et al.
Nature 626, 670–677 (2024).
https://doi-org.insb.bib.cnrs.fr/10.1038/s41586-023-06987-5
Serial femtosecond crystallography reveals the structural dynamics of photosystem II during the S-state transitions that produce dioxygen, providing insight into electron transfer, water insertion, proton release and O–O bond formation on sub-microsecond timescales.
The structure of the Caenorhabditis elegans TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction.
Clark S, Jeong H, Posert R, Goehring A, Gouaux E.
Proc Natl Acad Sci U S A. 2024 Feb 20;121(8):e2314096121.
doi: 10.1073/pnas.2314096121.
Mechanotransduction = mechanical force converted into electrical signal. Transmembrane channel-like (TMC) proteins have been linked to a variety of mechanosensory processes. Caenorhabditis elegans express two TMC homologs, TMC-1 and TMC-2 = likely pore-forming subunits of mechanosensitive ion channels.
Here: SPA cryoEM of the native TMC-2 complex isolated from C. elegans: 2x pore-forming TMC-2 subunit + calcium and integrin binding protein CALM-1 + TM inner ear protein TMIE.
=> protein-lipid interactions, as well as a π-helical structural motif in the pore-forming helices.
Genetic analysis reveals a robust and hierarchical recruitment of the LolA chaperone to the LolCDE lipoprotein transporter.
Lehman KM, May KL, Marotta J, Grabowicz M.
mBio. 2024 Feb 14;15(2):e0303923.
doi: 10.1128/mbio.03039-23. Epub 2024 Jan 9.
LolCDE transporter is needed to supply the OM with lipoproteins and has been a focus of recent antibiotic discovery. In vitro evidence recently proposed a two-part interaction of LolC with LolA lipoprotein chaperone via “Hook” and “Pad” regions. Here: they show that this model does not reflect lipoprotein trafficking in vivo. Only the Hook is essential for lipoprotein trafficking and is remarkably robust to mutational changes. The Pad is non-essential for lipoprotein trafficking but plays an ancillary role, contributing to trafficking efficiency.
Structure of human phagocyte NADPH oxidase in the activated state.
Liu, X., Shi, Y., Liu, R. et al.
Nature (2024).
https://doi.org/10.1038/s41586-024-07056-1
The phagocyte NADPH oxidase complex, composed of NOX2 and p22 subunits, facilitates electron transfer from intracellular NADPH to extracellular oxygen. Activation involves membrane translocation and cytosolic factor binding, although the precise mechanism remains unclear.
Here: structure of the activated human NOX2-p22 complex, bound by fragments of p47, p67, and Rac1 cytosolic factors, reveals that the p67-Rac1 complex induces NOX2 contraction, stabilizing NADPH binding and reducing the distance between key domains. Additionally, structural rearrangements facilitate efficient electron transfer between redox centers in NOX2, leading to phagocyte NADPH oxidase activation.
Membranes
Formation of Cell-Sized Liposomes Incorporating a β-Barrel-Structured Porin through Rehydration of a Phospholipid-Membrane Protein Dried Film.
Tosaka T, Kamiya K.
ACS Omega. 2024 Jan 26;9(5):5911-5918.
doi: 10.1021/acsomega.3c09431.
Dehydration-rehydration method (proteo-GUVs formed using a dried film containing phospholipids and MPs through rehydration with an alternating current electric field and a supporting gel) makes it difficult to form proteo-GUVs under physiological salt concentration and charged PL conditions or carry the risk of gel contamination of lipid membranes.
Here: method for the formation of proteo-GUVs containing physiological salt concentrations and negatively charged phospholipids that do not require an electric field and a supporting gel. This method can be applied for the functional evaluation of β-barrel porin.
Exploring membrane asymmetry and its effects on membrane proteins.
Pabst G, Keller S.
Trends Biochem Sci. 2024 Feb 13:S0968-0004(24)00021-5.
doi: 10.1016/j.tibs.2024.01.007.
Free energy needed to maintain highly asymmetric, non-equilibrium distributions of lipids and proteins between their two leaflets.
In this review: recent progress in quantitative research enabled by using compositionally controlled asymmetric model membranes.
Peptide Translocation Across Asymmetric Phospholipid Membranes.
Bartoš L, Vácha R.
Biophys J. 2024 Feb 14:S0006-3495(24)00105-X.
doi: 10.1016/j.bpj.2024.02.006.
Study how two types of amphiphilic molecules translocate across both asymmetric and symmetric membranes (computer simulations with CG and atomistic force fields => free energy profiles for the passage of model amphiphilic peptides and a lipid across various membranes).
=> small differential stress between symmetric and asymmetric membranes in the region of lipid headgroups but differ around the center of the membrane.
=> using symmetric membranes falls short in providing an accurate depiction of peptide translocation across asymmetric membranes.
Molecules
A proteome-wide quantitative guide for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs
Caroline Brown, Snehasish Ghosh, Rachel McAllister, Mukesh Kumar, Gerard Walker, Eric Sun, Talat Aman, Aniruddha Panda, Shailesh Kumar, Wenxue V Li, Jeff Coleman, Yansheng Liu, James E Rothman, Moitrayee Bhattacharyya, Kallol Gupta
bioRxiv 2024.02.10.579775;
doi: https://doi.org/10.1101/2024.02.10.579775
Library of membrane-active polymers => platform for HT analysis of the membrane proteome: near-complete spatially resolved extraction of target MPs from endogenous membranes + open-access quantitative database that provides the most efficient extraction conditions of 2065 unique mammalian MPs.
MPs directly from their endogenous organellar membranes at physiological expression levels while maintaining the nanoscale local membrane environment.
Extraction from Endoplasmic reticulum, mitochondria, lysosome, Golgi, and transient organelles such as the autophagosome. Extraction and purification of target MPs from different organellar membranes with high efficiency and purity.
Further, the database (publicly available resource) can be extended to capture multiprotein complexes between overexpressed MPs.
Polymer-extracted structure of the mechanosensitive channel MscS reveals the role of protein-lipid interactions in the gating cycle.
Moller E, Britt M, Zhou F, Yang H, Anshkin A, Ernst R, Sukharev S, Matthies D.
bioRxiv [Preprint]. 2024 Feb 5:2024.01.22.576751.
doi:10.1101/2024.01.22.576751.
Removal or displacement of lipids, can result in non-native conformations or a strong preference for certain states at the exclusion of others.
As a tension sensor, MscS is very sensitive and highly adaptive; it readily opens under super-threshold tension and closes under no tension, but under lower tensions, it slowly inactivates and can only recover when tension is released.
Central question in the field = assignment of the frequently observed non-conductive conformation to either a closed or inactivated state.
Here: 3 Å MscS structure in native nanodiscs obtained with Glyco-DIBMA polymer extraction, eliminating the lipid removal step that is common to all previous structures.
=> preserved lipids in their native locations, and the functional effects of their destabilization illustrate a novel inactivation mechanism based on an uncoupling of the peripheral tension-sensing helices from the gate.
Methods
An efficient method for detecting membrane protein oligomerization and complex using 05SAR-PAGE.
Huang L, Tong Q, Chen L, Zhao W, Zhang Z, Chai Z, Yang J, Li C, Liu M, Jiang L.
Electrophoresis. 2024 Feb 8.
doi: 10.1002/elps.202300243.
05SAR-PAGE for the identification of membrane protein oligomerization and the analysis of weak protein interactions.
0.05% (w/v) sarkosyl-polyacrylamide gel electrophoresis (05SAR-PAGE) used to identify the oligomer states of the membrane proteins CpxA, EnvZ, and Ma-Mscl with high sensitivity.
2D electrophoresis (05SAR/sodium dodecyl sulfate-PAGE) +WB + LCMS => study of CpxA/OmpA in cell lysate.
Quantifying a light-induced energetic change in bacteriorhodopsin by force spectroscopy.
Jacobson DR, Perkins TT.
Proc Natl Acad Sci U S A. 2024 Feb 13;121(7):e2313818121.
doi: 10.1073/pnas.2313818121.
Changes in intramolecular energetics that underlie BR motions have remained elusive to experimental quantification.
Here: measurement of energetics on the millisecond time scale using atomic-force-microscopy-based single-molecule force spectroscopy.
=> general single-molecule force spectroscopy approach for measuring ligand-induced energetics and lifetimes in membrane proteins.
Light Color-Controlled pH-Adjustment of Aqueous Solutions Using Engineered Proteoliposomes.
Harder D, Ritzmann N, Ucurum Z, Müller DJ, Fotiadis D.
Adv Sci (Weinh). 2024 Feb 11:e2307524.
doi: 10.1002/advs.202307524.
Controlling the pH at the microliter scale can be useful for applications in research, medicine, and industry.
Here: vesicular system translating light of different colors into specific pH changes in the surrounding solution (2 light-driven proton pumps bacteriorhodopsin and blue light-absorbing proteorhodopsin Med12, that are oriented in opposite directions in the lipid membrane).
A computer-controlled measuring device implements a feedback loop for automatic adjustment and maintenance of a selected pH value.
=> pH range spanning more than two units can be established, providing fine temporal and pH resolution.
ProteinMPNN Recovers Complex Sequence Properties of Transmembrane β-barrels.
Dolorfino M, Samanta R, Vorobieva A.
bioRxiv [Preprint]. 2024 Feb 1:2024.01.16.575764.
doi: 10.1101/2024.01.16.575764.
Deep-learning (DL) methods have to meet the challenge of de novo membrane protein (MP) and the design of complex β-sheet folds.
Here: comprehensive benchmark of one DL protein sequence design method, ProteinMPNN, using TM and water-soluble β-barrel folds as a model.
Microbio
An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance.
Kelvin J. Y. Wu et al.
Science 383, 721-726 (2024).
doi:10.1126/science.adk8013
Structural analysis of ribosomes bound to previously developed antibiotics to design a conformationally restricted molecule, dubbed cresomycin, that adopts the exact conformation necessary for binding. Computational, structural, and biochemical experiments confirmed the expected binding mode. Cresomycin potently inhibits Gram-negative and -positive bacteria, including multi-drug-resistant strains, both in vitro and in a mouse infection model.
Roles of linker region flanked by transmembrane and peptidoglycan binding region of PomB in energy conversion of the Vibrio flagellar motor.
Miyamura Y, Nishikino T, Koiwa H, Homma M, Kojima S.
Genes Cells. 2024 Feb 14.
doi: 10.1111/gtc.13102.
The flagellar components PomA and PomB in Vibrio spp. form a complex contributing to flagella rotation; PomB’s transmembrane segment is linked to the basal body T-ring while its plug region prevents ion flux. Deletion mutants of PomB (Δ61-140 and Δ71-150) exhibit impaired motility, yet some swimming cells are observed with speeds comparable to wild-type; introducing these mutants into a wild-type strain does not affect swimming ability, suggesting functional redundancy. Furthermore, plug mutations in these mutants rescue reduced motility, indicating that the linker and plug regions are dispensable for PomB’s motor function but crucial for its regulation.
Miscellaneous
Glowing plant hits the US market
It will soon be able to buy glowing petunias (Petunia hybrida) in the USA. The US$29 plant, sold by biotech firm Light Bio, contains genes from a bioluminescent mushroom (Neonothopanus nambi).
https://nature.us17.list-manage.com/track/click?u=2c6057c528fdc6f73fa196d9d&id=1508aaa136&e=ecd8cb93e6
Air pollution turns moths off flowers
Air pollution makes the scent of a night-blooming plant less enticing to pollinating moths. Researchers discovered that nitrate radicals severely degrade key odour components that attract pollinating insects to the pale evening primrose (Oenothera pallida). Nitrate radicals, which can come from various sources including vehicle emissions, are particularly abundant when there’s no sunlight to break them down. Artificial flowers spiked with the pollution-degraded scent received 70% fewer visits from wild hawkmoths than fake flowers with intact odour. Because hawkmoths are some of the primrose’s main pollinators this could reduce the plant’s fruit production by almost 30%.
https://nature.us17.list-manage.com/track/click?u=2c6057c528fdc6f73fa196d9d&id=87a6798610&e=ecd8cb93e6
Designer phospholipid capping ligands for soft metal halide nanocrystals.
Morad, V., Stelmakh, A., Svyrydenko, M. et al.
Nature 626, 542–548 (2024).
https://doi-org.insb.bib.cnrs.fr/10.1038/s41586-023-06932-6
Phospholipids enhance the structural and colloidal integrity of hybrid organic–inorganic lead halide perovskites and lead-free metal halide nanocrystals, which then exhibit enhanced robustness and optical properties.
Electrically driven proton transfer promotes Brønsted acid catalysis by orders of magnitude.
Westendorff KS, Hülsey MJ, Wesley TS, Román-Leshkov Y, Surendranath Y.
Science. 2024 Feb 16;383(6684):757-763.
doi: 10.1126/science.adk4902.
Electric fields can enhance reaction rates by 100,000-fold.
Here: probing of the influence of catalyst potential and interfacial electric fields on heterogeneous Brønsted acid catalysis.
A plant mechanism of hijacking pathogen virulence factors to trigger innate immunity.
Yu Xiao et al.
Science 383, 732-739 (2024).
doi:10.1126/science.adj9529
Many plant pathogens release cell wall–degrading enzymes to facilitate access into the cell.
Here: Xiao et al. establish how a plant polygalacturonase-inhibiting protein (PGIP) interacts with a fungal polygalacturonase enzyme => alters how the fungus binds to cell wall polysaccharides and influences substrate preferences and the types of degradation products generated to increase immunity. Proteins from two different species combine to make an enzymatic complex with different behavior from either alone.
Estimating the role of air quality improvements in the decline of suicide rates in China.
Zhang, P., Carleton, T., Lin, L. et al.
Nat Sustain (2024).
https://doi-org.insb.bib.cnrs.fr/10.1038/s41893-024-01281-2
Evidence linking heavy air pollution to increased suicide risk credits air-quality improvements with preventing more than 45,000 suicides.
A Photolithographable Electrolyte for Deeply Rechargeable Zn Microbatteries in On-Chip Devices.
Z. Qu, J. Ma, Y. Huang, T. Li, H. Tang, X. Wang, S. Liu, K. Zhang, J. Lu, D. D. Karnaushenko, D. Karnaushenko, M. Zhu, O. G. Schmidt,
Adv. Mater. 2024, 2310667. https://doi-org.insb.bib.cnrs.fr/10.1002/adma.202310667
Coffee is life !!!
Zinc = promising material for rechargeable batteries but it suffers from dendrite formation and corrosion during cycling, and these issues are exacerbated as the size of the battery is reduced.
Here: Qu et al. added caffeine to the surface of a cross-linked polyacrylamide hydrogel electrolyte and found that the caffeine prevented corrosion + helped form zinc complexes that aided in reversibility during cycling.