MP
Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity
Mariya Lazarova, Thomas Eicher, Clara Börnsen, Hui Zeng, Mohd Athar, Ui Okada, Eiki Yamashita, Inga M. Spannaus, Max Borgosch, Hi-jea Cha, Attilio V. Vargiu, Satoshi Murakami, Kay Diederichs, Achilleas S. Frangakis, Klaas M. Pos
bioRxiv 2024.11.22.624703;
doi: https://doi.org/10.1101/2024.11.22.624703
Identification of 2 RND protein clusters with distinct binding pocket residues
=> altering a single conserved residue between them changes drug resistance profiles and transport dynamics (differences in binding pocket architecture and initial substrate binding mechanisms may be phylogenetically conserved).
Membrane transporters modulating the toxicity of arsenic, cadmium, and mercury in human cells.
Ferdigg A, Hopp AK, Wolf G, Superti-Furga G.
Life Sci Alliance. 2024 Nov 22;8(2):e202402866.
doi: 10.26508/lsa.202402866.
PMID: 39578074.
Non-essential metals (e.g cadmium, mercury, and arsenic) are highly toxic: severe health risks but their regulation within human cells remains poorly understood.
Here: specific membrane transporters ( MRP1/ABCC1) protect against arsenic and mercury toxicity, while other increase sensitivity to cadmium (SLC39A14 and SLC30A1).
Additionally, SLC30A1 was shown to modulate cadmium toxicity by regulating intracellular zinc levels => complex roles of transporters in heavy metal toxicity.
Features of membrane protein sequence direct post-translational insertion.
Kalinin IA, Peled-Zehavi H, Barshap ABD, Tamari SA, Weiss Y, Nevo R, Fluman N.
Nat Commun. 2024 Nov 25;15(1):10198.
doi: 10.1038/s41467-024-54575-6.
PMID: 39587101.
Many C-terminal TMs bypass Sec translocon and require a specialized posttranslational insertion mechanism, facilitated by YidC in E. coli.
Fine-tuning of the hydrophilicity and length of C-terminal tails support this process, with mutations in these regions disrupting insertion (=> protein malfunction and diseases in both bacteria and humans).
Mutation-based mechanism and evolution of the potent multidrug efflux pump RE-CmeABC in Campylobacter.
Dai L, Wu Z, Sahin O, Zhao S, Yu EW, Zhang Q.
Proc Natl Acad Sci U S A. 2024 Dec 17;121(51):e2415823121.
doi: 10.1073/pnas.2415823121. Epub 2024 Nov 27.
PMID: 39602248.
CmeABC efflux system = RND-type transporter in Campylobacter jejuni.
RE-CmeABC (= a potent variant) has recently emerged, enhancing resistance to multiple drugs.
The functional gain of RE-CmeABC is linked to specific mutations in CmeB and in the efflux operon promoter (but RE-CmeA and RE-CmeC remain unchanged).
Evolutionary analysis => RE-CmeB originated from Campylobacter coli and spread within C. jejuni due to antibiotic selection pressure, with evidence of a selective sweep favoring its fixation.
Clinical relevance and role of horizontal gene transfer in its dissemination.
The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors.
Malmsheimer S, Grin I, Bohn E, Franz-Wachtel M, Macek B, Sahr T, Smollich F, Chetrit D, Meir A, Roy C, Buchrieser C, Wagner S.
PLoS Pathog. 2024 Nov 15;20(11):e1012118.
doi: 10.1371/journal.ppat.1012118.
PMID: 39546547.
Legionella use a T4bSS to translocate numerous effector proteins, including hydrophobic TMD-effectors, into eukaryotic host cells. TMD-effectors = initially targeted and inserted into the bacterial IM independently of T4bSS but require T4bSS chaperones, along with a C-terminal secretion signal, for translocation.
Here: description of a two-step secretion process for TMD-effectors, involving inner membrane intermediates extracted to the cytoplasmic side before being secreted into host cells <=> adaptability of the T4bSS.
Membrane
Molecular architecture of synaptic vesicles.
Kravčenko U, Ruwolt M, Kroll J, Yushkevich A, Zenkner M, Ruta J, Lotfy R, Wanker EE, Rosenmund C, Liu F, Kudryashev M.
Proc Natl Acad Sci U S A. 2024 Dec 3;121(49):e2407375121.
doi: 10.1073/pnas.2407375121. Epub 2024 Nov 27.
PMID: 39602275.
Synaptic vesicles (SVs) store and release neurotransmitters => recycling.
Primary role of the Tol-Pal complex in bacterial outer membrane lipid homeostasis
Wee Boon Tan, Shu-Sin Chng
bioRxiv 2024.05.08.593160;
doi: https://doi.org/10.1101/2024.05.08.593160
Tol-Pal complex = key role in maintaining bacterial OM lipid homeostasis.
Here: uncoupling of Tol-Pal’s role in lipid balance from its division-associated functions.
=> Tol-Pal’s primary function is independent of cell division.
Monoamine transporter ubiquitination and inward-open conformation synergistically maximize transporter endocytosis.
Sorkina T, Bagalkot T, Cheng MH, Guthrie DA, Newman AH, Watkins SC, Sorkin A.
Sci Adv. 2024 Nov 22;10(47):eadq9793.
doi: 10.1126/sciadv.adq9793. Epub 2024 Nov 22.
PMID: 39576869.
Monoamine transporters, such as the dopamine transporter (DAT), regulate extracellular neurotransmitter levels.
Here: substrates like dopamine and amphetamine synergize with PKC-dependent ubiquitination to enhance clathrin-mediated endocytosis of DAT, driven by a transition from outward-open to inward-open conformations.
=> The process facilitates transporter movement from negatively curved membrane protrusions to positively invaginated clathrin-coated membranes, promoting endocytosis.
= “shape-transition” model.
Modulating Liposome Surface Charge for Maximized ATP Regeneration in Synthetic Nanovesicles.
Deutschmann S, Täuber ST, Rimle L, Biner O, Schori M, Stanic AM, von Ballmoos C.
ACS Synth Biol. 2024 Nov 26.
doi: 10.1021/acssynbio.4c00487. Epub ahead of print.
PMID: 39592139.
E. coli cytochrome bo3 oxidase + ATP synthase = lipo reconstructed minimal respiratory to generate ATP via a proton motive force (pmf).
Here: extension of the system by using natural long-chain ubiquinones and NADH or succinate as electron donors.
1) negatively charged lipids are essential for NDH-2 activity but reduce overall pmf and ATP synthesis rates.
2) The bo3 oxidase orientation in membranes depends on electrostatic interactions, with positively charged lipids supporting proper orientation but hindering quinone reduction by NDH-2.
3) pH-sensitive ionizable lipids => optimization of the membrane charge and enzyme orientation: up to 3x higher ATP synthesis rates with natural quinones compared to synthetic systems.
Adsorption Modes of Na+, Li+, and Mg2+ to a Model Zwitterionic Lipid Bilayer.
Saunders M, Adekoya-Olowofela A, Downing S, Pandit SA.
Langmuir. 2024 Nov 26.
doi: 10.1021/acs.langmuir.4c03213. Epub ahead of print.
PMID: 39591394.
ions adsorbtion to soft-porous interfaces => 3 adsorption modes based on ion dehydration (steric adsorption, imperfect adsorption and perfect adsorption).
Here: using a model system with POPC, authors find that:
- anions like Cl- always adsorb sterically,
- Mg2+ adsorbs sterically due to its lack of dehydration,
- Na+ and Li+ show different degrees of dehydration and adsorption.
=> the adsorption mode of a cation is determined by the electric field strength at the ion’s hydration shell distance.
Crystallographic insights into lipid-membrane protein interactions in microbial rhodopsins.
Bukhdruker S, Melnikov I, Baeken C, Balandin T, Gordeliy V.
Front Mol Biosci. 2024 Nov 7;11:1503709.
doi: 10.3389/fmolb.2024.1503709.
PMID: 39606035.
Understanding the direct molecular interactions between lipids and the hydrophobic surfaces of MPs, distinct from the well-known hydrophobic mismatch.
Using Xtallo of microbial rhodopsins, authors hypothesize that the first layer of lipids surrounding MPs plays a crucial role in their structure and function.
They also explore how exogenous hydrophobic molecules can compete with lipids for interaction with MPs.
Biomimetic Materials to Fabricate Artificial Cells.
Peng H, Zhao M, Liu X, Tong T, Zhang W, Gong C, Chowdhury R, Wang Q.
Chem Rev. 2024 Nov 26.
doi: 10.1021/acs.chemrev.4c00241. Epub ahead of print.
PMID: 39591535.
Review exploring artificial cell research to recreate the complexity of natural cells in vitro.
=> bottom-up strategies, discussing the construction of artificial cells using biomimetic materials: from simple scaffolds to advanced compartmental systems + functional modules simulating metabolism and communication networks.
Molecules
A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs.
Brown C, Ghosh S, McAllister R, Kumar M, Walker G, Sun E, Aman T, Panda A, Kumar S, Li W, Coleman J, Liu Y, Rothman JE, Bhattacharyya M, Gupta K.
Nat Methods. 2024 Nov 28.
doi: 10.1038/s41592-024-02517-x. Epub ahead of print.
PMID: 39609567.
Novel platform for extracting MPs directly from cellular membranes into native NDs, preserving their local membrane context.
Platform uses a library of membrane-active polymers and includes an open-access database detailing extraction efficiencies for over 2,000 mammalian MPs.
Methods
A nanobody-based microfluidic chip for fast and automated purification of protein complexes.
De Keyser P, de Waard M, Jimidar ISM, Verloy S, Janvier S, Kalichuk V, Zögg T, Wohlkönig A, Pardon E, Steyaert J, Desmet G.
Lab Chip. 2024 Nov 26.
doi: 10.1039/d4lc00728j. Epub ahead of print.
PMID: 39588652.
Novel protein purification technique called Nanobody Exchange Chromatography (NANEX), which uses Nanobodies® (Nbs) to capture target proteins and their interaction partners.
Technique miniaturized into a packed bed microfluidic chip (μNANEX) => fully automated, reproducible purifications with small sample sizes in just minutes.
Unlocking cell surface enzymes: A review of chemical strategies for detecting enzymatic activity.
Zhou Z, Chen T, Zhu Y, Chen L, Li J.
Anal Chim Acta. 2024 Dec 15;1332:343140.
doi: 10.1016/j.aca.2024.343140. Epub 2024 Aug 22.
PMID: 39580158.
A review of chemical strategies for detecting enzymatic activity on cell surfaces.
A roadmap to cysteine specific labeling of membrane proteins for single-molecule photobleaching studies.
Ernst M, Mahoney-Kruszka R, Zelt NB, Robertson JL.
Methods. 2024 Nov 23:S1046-2023(24)00251-2.
doi: 10.1016/j.ymeth.2024.10.013. Epub ahead of print.
PMID: 39586432.
Methodology for screening potential cysteine labeling sites on purified membrane proteins, crucial for quantifying oligomerization via single-molecule photobleaching analysis.
The technique relies on fluorophore conjugation to a substituted cysteine, but cysteine reactivity can be unpredictable due to factors like solvent accessibility and electrostatics (here, authors show that only about 30% of initially selected labeling sites are effective for single-molecule fluorescence studies).
Unraveling GPCRs Allosteric Modulation. Cannabinoid 1 Receptor as a Case Study.
Cruz A, Warshel A.
Proteins. 2024 Nov 25.
doi: 10.1002/prot.26762. Epub ahead of print.
PMID: 39584635.
Using a protein-dipole Langevin-dipole model combined with CG simulations, authors identified key complexes between Cannabinoid type-1 receptor (CB1R, a GPCR) and its allosteric modulators, providing insights into the receptor’s structural dynamics.
Unraveling membrane protein localization and interactions in nanodiscs.
Koh YH, Kim SJ, Roh SH.
FEBS Lett. 2024 Nov 28.
doi: 10.1002/1873-3468.15059. Epub ahead of print.
PMID: 39607859.
Behavior of MPs reconstituted in NDs using cryo-EM structures.
=> MPs prefer to localize at the edges of nanodisc shells and interact directly with MSPs, reducing protein dynamics.
Microbio
Bacterial efflux pump OMPs as vaccine candidates against multidrug-resistant Gram-negative bacteria.
Silva TO, Bulla ACS, Teixeira BA, Gomes VMS, Raposo T, Barbosa LS, da Silva ML, Moreira LO, Olsen PC.
J Leukoc Biol. 2024 Nov 27;116(6):1237-1253.
doi: 10.1093/jleuko/qiae154.
PMID: 39011942.
Review exploring the potential of targeting OM proteins of efflux pumps as vaccine candidates against multidrug-resistant Gram-negative bacteria. Importance of exploring alternative treatments to combat antimicrobial resistance.
The Escherichia coli TolC efflux pump protein is immunogenic and elicits protective antibodies.
Silva TO, Teixeira BA, Costa LVS, Barbosa LS, do Nascimento LC, Fanticelli JGC, Rotilho C, Branco RVC, Silva LS, Ferreira ME, Costa TL, Monteiro SV, Dos Santos Abreu J, Rajsfus BF, Bulla ACS, Carneiro J, Allonso D, Salgado DR, Echevarria-Lima J, da Silva ML, Moreira LO, Olsen PC.
J Leukoc Biol. 2024 Nov 27;116(6):1398-1411.
doi: 10.1093/jleuko/qiae201.
PMID: 39278634.
TolC emerges as a potential therapeutic target.
Here: study evaluating the immune response to TolC from E. coli, revealing that human plasma contained higher levels of anti-TolC IgG and IgA.
Study suggests that TolC immunization enhances survival in E. coli infections, reinforcing its potential as a vaccine target against antimicrobial-resistant bacteria.
Mito
Textbook oxidative phosphorylation needs to be rewritten.
Kowaltowski AJ, Abdulkader F.
Trends Biochem Sci. 2024 Nov 21:S0968-0004(24)00254-8.
doi: 10.1016/j.tibs.2024.11.002. Epub ahead of print.
PMID: 39578214.
Oxidative phosphorylation (OxPhos) is the energy-transfer process that generates most of our ATP, fueled by proton and electrical gradients across the inner mitochondrial membrane. A new surprising finding by Hernansanz-Agustín et al. demonstrates that between one-third and half of this gradient is attributable to Na+, transported in exchange for protons within complex I.
Here is the article:
A transmitochondrial sodium gradient controls membrane potential in mammalian mitochondria.
Hernansanz-Agustín P, Morales-Vidal C, Calvo E, Natale P, Martí-Mateos Y, Jaroszewicz SN, Cabrera-Alarcón JL, Acín-Pérez R, López-Montero I, Vázquez J, Enríquez JA.
Cell. 2024 Nov 14;187(23):6599-6613.e21. doi: 10.1016/j.cell.2024.08.045. Epub 2024 Sep 19. PMID: 39303716.
Eukaryotic cell function and survival rely on the use of a mitochondrial H+ electrochemical gradient (Δp) = membrane (IMM) potential (ΔΨmt) + pH gradient (ΔpH).
So far, ΔΨmt has been assumed to be composed exclusively of H+.
Here: authors discovered that a Na+ gradient equates with the H+ gradient and controls half of ΔΨmt in coupled-respiring mammalian mitochondria. This is controlled by the activity of Na+-specific Na+/H+ exchanger (mNHE).
Miscellaneous
Looking back at the timely launch of Nature Structural Biology in 1994.
Cambillau C.
Nat Struct Mol Biol. 2024 Nov 28.
doi: 10.1038/s41594-024-01436-x. Epub ahead of print.
PMID: 39609653.
‘Dark proteome’ survey reveals thousands of new human genes.
Pennisi E.
Science. 2024 Nov 29;386(6725):951-952.
doi: 10.1126/science.adu8277. Epub 2024 Nov 28.
PMID: 39607933.
Database confirms that overlooked segments of the genome code for a multitude of tiny proteins
Should I climb the career ladder as a manager, or will I regret leaving the lab bench behind?
Lizak M.
Nature. 2024 Nov 20.
doi: 10.1038/d41586-024-03237-0. Epub ahead of print.
Incorporation of photosynthetically active algal chloroplasts in cultured mammalian cells towards photosynthesis in animals.
Aoki R, Inui Y, Okabe Y, Sato M, Takeda-Kamiya N, Toyooka K, Sawada K, Morita H, Genot B, Maruyama S, Tomo T, Sonoike K, Matsunaga S.
Proc Jpn Acad Ser B Phys Biol Sci. 2024 Nov 11;100(9):524-536.
doi: 10.2183/pjab.100.035. Epub 2024 Oct 31.
PMID: 39477444.
Feasibility of incorporating functional chloroplasts into animal cells, offering a foundation for developing artificially photosynthetic animal cells.
How to thank your lab mates: eight ways to show gratitude at the end of year
Nature CAREER FEATURE 27 November 2024
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