20240112_membrane digest – Membrane Protein Biochemistry Lab

Membrane’s digest

Zinke M, Lejeune M, Mechaly A, Bardiaux B, Boneca IG, Delepelaire P, Izadi-Pruneyre N.

Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake.

Nat Commun. 2024 Jan 6;15(1):331.

doi: 10.1038/s41467-023-44606-z.

Active nutrient uptake via multi-protein Ton system to transport essential nutrients like metals and vitamins.

Here: study of the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system.

=> this domain is a dynamic dimer switching between two conformations representing the proton channel’s open and closed states. The conformational switch is essential for the nutrient uptake by bacteria (in vivo experiments); the open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. An anchoring role of the PG layer is also proposed.

Eria-Oliveira AS, Folacci M, Chassot AA, Fedou S, Thézé N, Zabelskii D, Alekseev A, Bamberg E, Gordeliy V, Sandoz G, Vivaudou M.

Hijacking of internal calcium dynamics by intracellularly residing viral rhodopsins.

Nat Commun. 2024 Jan 2;15(1):65.

doi: 10.1038/s41467-023-44548-6.

Rhodopsins are widely distributed: they are also coded in the genomes of giant viruses infecting phytoplankton where their function is not settled.

Here: properties of viral rhodopsins demonstrate that they induce calcium release from intracellular IP3-dependent stores upon illumination. In vivo, this light-induced calcium release is sufficient to remote control muscle contraction in rhodopsin-expressing tadpoles.

Peter MF, Ruland JA, Kim Y, Hendricks P, Schneberger N, Siebrasse JP, Thomas GH, Kubitscheck U, Hagelueken G.

Conformational coupling of the sialic acid TRAP transporter HiSiaQM with its substrate binding protein HiSiaP.

Nat Commun. 2024 Jan 8;15(1):217.

doi: 10.1038/s41467-023-44327-3.

The tripartite ATP-independent periplasmic (TRAP) transporters use a cytoplasmic substrate binding protein (SBP) to transport a wide variety of substrates in bacteria and archaea. The two TM domains of TRAP form a monomeric elevator whose function is strictly dependent on the presence of a sodium ion gradient.

Here: disulfide engineering approach to lock the TRAP transporter HiSiaPQM from Haemophilus influenzae in different conformational states. The SBP, HiSiaP, is locked in its substrate-bound form and the transmembrane elevator, HiSiaQM, is locked in either its assumed inward- or outward-facing states.

=> characterization of the disulfide-locked constructs and use sm-TIRF microscopy to study their interactions.

=> the SBP and the transmembrane elevator are indeed conformationally coupled (open and closed state of the SBP recognize specific conformational states of the transporter and vice versa).

Membranes

Dalal V, Arcario MJ, Petroff JT 2nd, Tan BK, Dietzen NM, Rau MJ, Fitzpatrick JAJ, Brannigan G, Cheng WWL.

Lipid nanodisc scaffold and size alter the structure of a pentameric ligand-gated ion channel.

Nat Commun. 2024 Jan 2;15(1):25.

doi: 10.1038/s41467-023-44366-w.

Reconstituting pLGIC in different NDs produces distinct structures by cryo-EM. The effect extends to the extracellular domain and agonist binding site. MD indicate that ND of different size impact ELIC structure and that the ND scaffold directly interacts with ELIC.

Reconstitution of ion channels in larger nanodiscs may better approximate a lipid membrane environment.

Mu Q, Deng H, An X, Liu G, Liu C.

Designing nanodiscs as versatile platforms for on-demand therapy.

Nanoscale. 2024 Jan 9.

doi: 10.1039/d3nr05457h.

NDs have emerged as a novel platform technology in biomedical research and drug discovery. Their unique properties have made them highly desirable for diverse applications, including cancer immunotherapy, vaccine development, antibacterial and antiviral therapy, and treating Alzheimer’s disease (AD) and diabetes-related conditions. This review discusses the classifications, advantages, and applications of NDs in disease therapy.

Golla VK, Boyd KJ, May ER.

Curvature sensing lipid dynamics in a mitochondrial inner membrane model.

Commun Biol. 2024 Jan 5;7(1):29.

doi: 10.1038/s42003-023-05657-6.

Cardiolipin is the signature lipid of mitochondrial membranes and is essential for maintaining the highly curved shapes of the inner mitochondrial membrane (IMM) and the spatial arrangement of MPs.

Here: investigation of the partitioning behavior of various lipids present in the IMM using coarse-grained MD simulations: curved bilayer containing PC, PE and CL.

=> CL has a stronger preference for accumulating in regions of negative curvature than PE, in agreement with previous results. Furthermore, they find that lipid partitioning propensity is dominated by sensitivity to mean curvature, while there is a weaker correlation with Gaussian curvature.

Adrien V, Taulier N, Verchère A, Monlezun L, Picard M, Ducruix A, Broutin I, Pincet F, Urbach W.

Kinetic study of membrane protein interactions: from three to two dimensions.

Sci Rep. 2024 Jan 9;14(1):882.

doi: 10.1038/s41598-023-50827-5.

Study of interactions among membrane proteins across various dimensionalities (in solution or in membrane) by quantifying their binding rates through fluorescence recovery experiments.

Here: original approach for gauging a two-dimensional binding constant between membrane proteins embedded in two opposite membranes.

Molecules

Otrin N, Otrin L, Bednarz C, Träger TK, Hamdi F, Kastritis PL, Ivanov I, Sundmacher K.

Protein-Rich Rafts in Hybrid Polymer/Lipid Giant Unilamellar Vesicles.

Biomacromolecules. 2024 Jan 8.

doi: 10.1021/acs.biomac.3c00972.

Mixtures of PL and certain amphiphilic polymers offer an interface for proteins and mimic the segregation behavior of rafts. However, insertion of complex membrane proteins is experimentally challenging and thus far has been largely limited to natural lipids.

Here: co-reconstitution of the proton pump bo3 oxidase and ATP synthase in hybrid polymer/lipid giant unilamellar vesicles (GUVs) via fusion/electroformation. Variations of the current method allow for tailored reconstitution protocols and control of the vesicle size.

Methods

Kumar K, Arnold AA, Gauthier R, Mamone M, Paquin JF, Warschawski DE, Marcotte I.

19F solid-state NMR approaches to probe antimicrobial peptide interactions with membranes in whole cells.

Biochim Biophys Acta Biomembr. 2024 Jan 2;1866(3):184269.

doi: 10.1016/j.bbamem.2023.184269.

Antimicrobial peptides (AMPs) = promising therapeutic candidates (broad-spectrum and membrane-lytic activity). It is equally important to investigate and understand their impact on eukaryotic cells.

Here: 19F solid-state nuclear magnetic resonance (ssNMR) to examine the interaction of AMPs with whole red blood cells (RBCs).

Microbials

Vieira Da Cruz A, Jiménez-Castellanos JC, Börnsen C, Van Maele L, Compagne N, Pradel E, Müller RT, Meurillon V, Soulard D, Piveteau C, Biela A, Dumont J, Leroux F, Deprez B, Willand N, Pos KM, Frangakis AS, Hartkoorn RC, Flipo M.

Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae.

EMBO Mol Med. 2023 Dec 20.

doi: 10.1038/s44321-023-00007-9.

Medicinal chemistry development and drug-like properties of BDM91288, a pyridylpiperazine-based AcrB efflux pump inhibitor.

In vitro evaluation => BDM91288 confirmed it to potentiate the activity of a panel of antibiotics against K. pneumoniae as well as revert clinically relevant antibiotic resistance mediated by acrAB-tolC overexpression.

cryo-EM => BDM91288 binding to the transmembrane region of K. pneumoniae AcrB was confirmed, further validating the mechanism of action of this inhibitor.

Finally, PcO studies demonstrated that oral administration of BDM91288 significantly potentiated the in vivo efficacy of levofloxacin treatment in a murine model of K. pneumoniae lung infection.

Bera A, Roy RK, Joshi P, Patra N.

Machine Learning-Guided Discovery of AcrB and MexB Efflux Pump Inhibitors.

J Phys Chem B. 2024 Jan 10.

doi: 10.1021/acs.jpcb.3c05845.

Study aiming at identifying potent inhibitor-like molecules of AcrB and MexB employing supervised classification models trained upon the molecular descriptors of previously known inhibitors. Based on the MIC values of the reported inhibitors, they were classified into highly potent and less potent categories. A total of 10 different classification models were built using various molecular descriptors.

=> 8 hit molecules after the multistep filtering process. To assess their activity toward AcrB and MexB, several MD simulations of their ligand-bound structures were performed + calculation of binding free-energy values.

Miscellaneous

seminar, 18/1, with Prof. Anthony Watts about the importance of water in membrane receptor funtion and what it means for optogenetics.

1.75-billion-year-old fossils help explain how photosynthesis evolved

https://www.newscientist.com/article/2410391-1-75-billion-year-old-fossils-help-explain-how-photosynthesis-evolved/

The oldest fossil evidence of photosynthesis has been found inside tiny cyanobacteria that lived around 1.75 billion years ago, 1.2 billion years earlier than the previous record-holder. The photosynthetic structures, known as thylakoids, were found inside fossilized Navifusa majensis. Cyanobacteria are thought to have triggered the Great Oxidation Event more than 2 billion years ago, which transformed Earth’s atmosphere. “One idea is that, perhaps, they invented thylakoids at this time and this increased the quantity of oxygen on Earth,” says paleobiologist Emmanuelle Javaux, who contributed to the discovery. “Now that we’ve found very old thylakoids and that they can be preserved in very old rocks, we think that we could go further back in time and try to test this hypothesis.”

Antibiotic resistance is a growing threat — is climate change making it worse?

doi: https://doi.org/10.1038/d41586-023-04077-0

Researchers are studying how extreme weather and rising temperatures can encourage the spread of drug-resistant infections.

Climate change and antibiotic resistance are both major threats to human health, and the risks multiply when they intersect. Increased average minimum temperatures have been linked to higher rates of antibiotic resistance — maybe by making it easier for them to evolve. And extreme temperatures can force people to spend more time indoors, where infection can spread. Tackling these issues together will require global action — and recognition of inequity between richer and poorer nations. Some public health researchers argue for a new UN treaty, similar to existing climate treaties, calling for a 35% reduction in drug-resistant infections by 2035.