Membrane’s digest

MP

Bitter taste receptor activation by cholesterol and an intracellular tastant.

Kim Y, Gumpper RH, Liu Y, Kocak DD, Xiong Y, Cao C, Deng Z, Krumm BE, Jain MK, Zhang S, Jin J, Roth BL.

Nature. 2024 Apr;628(8008):664-671.

doi: 10.1038/s41586-024-07253-y. Epub 2024 Apr 10.

PMID: 38600377.

CryoEM structures of the type 2 taste receptor TAS2R14 in complex with Ggust and Gi1 identify cholesterol as an orthosteric agonist and the bitter tastant cmpd28.1 as a positive allosteric modulator and agonist.

associated News and Views:

A bitter taste receptor activated in a surprising way.

Di Pizio A.

Nature. 2024 Apr;628(8008):506-507.

doi: 10.1038/d41586-024-00712-6.

PMID: 38600187.

The sensing of bitter taste results from the complex interplay of many chemical cues and a range of receptors. It emerges that this complexity might be built-in even at the level of individual receptors.

Structure and assembly of a bacterial gasdermin pore.

Johnson AG, Mayer ML, Schaefer SL, McNamara-Bordewick NK, Hummer G, Kranzusch PJ.

Nature. 2024 Apr;628(8008):657-663.

doi: 10.1038/s41586-024-07216-3. Epub 2024 Mar 20.

PMID: 38509367.

CryoEM and MS studies of a Vitiosangium gasdermin pore reveal insights into the assembly of gasdermin = large and diverse family of membrane pore-forming proteins.

Probing the stability and interdomain interactions in the ABC transporter OpuA using single-molecule optical tweezers.

van der Sleen L, Stevens JA, Marrink SJ, Poolman B, Tych K.

Cell Rep. 2024 Apr 11;43(4):114110.

doi: 10.1016/j.celrep.2024.114110. Epub ahead of print.

PMID: 38607912.

Innovative approach to measure the dynamics and stability of interdomain interactions of MPs using optical tweezers (focusing on the osmoregulatory ATP-binding cassette transporter OpuA from Lactococcus lactis in ND).

The potassium transporter TaNHX2 interacts with TaGAD1 to promote drought tolerance via modulating stomatal aperture in wheat.

Li J, Liu X, Chang S, Chu W, Lin J, Zhou H, Hu Z, Zhang M, Xin M, Yao Y, Guo W, Xie X, Peng H, Ni Z, Sun Q, Long Y, Hu Z.

Sci Adv. 2024 Apr 12;10(15):eadk4027.

doi: 10.1126/sciadv.adk4027. Epub 2024 Apr 12.

PMID: 38608020.

Role of the potassium/proton exchanger TaNHX2 in enhancing drought resistance in wheat by facilitating cross-talk between stomatal aperture regulation and GABA.

Mutants lacking TaNHX2 => reduced drought tolerance.

Overexpression of TaNHX2 => improved yield under water deficit conditions.

Structural basis of selective TRPM7 inhibition by the anticancer agent CCT128930.

Nadezhdin KD, Correia L, Shalygin A, Aktolun M, Neuberger A, Gudermann T, Kurnikova MG, Chubanov V, Sobolevsky AI.

Cell Rep. 2024 Apr 12;43(4):114108.

doi: 10.1016/j.celrep.2024.114108. Epub ahead of print.

PMID: 38615321.

Molecular mechanism underlying inhibition of TRPM7 by the anticancer agent CCT128930 (CCT) using cryo-EM, functional analysis, and MD simulations.

=> central role of the vanilloid-like site for the selective interaction of TRPM7 with small molecules that can be explored in future drug design.

Uemura S, Mochizuki T, Kato Y, Mioka T, Watanabe R, Fuchita M, Yamada M, Noda Y, Moriguchi T, Abe F.

Mtc6/Ehg2 is a novel endoplasmic reticulum-resident glycoprotein essential for high-pressure tolerance.

J Biochem. 2024 Apr 15:mvae035.

doi: 10.1093/jb/mvae035. Epub ahead of print.

PMID: 38621657.

Study showing the protective role of Mtc6 in S. cerevisiae survival under hydrostatic pressure stress by preserving the integrity of nutrient permeases.

Deletion of MTC6 => increased degradation of the leucine permease Bap2 under hydrostatic pressure, suggesting that Mtc6 aids in proper folding of nutrient permeases in the ER during stress conditions => novel model of molecular function for Mtc6.

New insights into the structure and dynamics of the TOM complex in mitochondria.

Nussberger S, Ghosh R, Wang S.

Biochem Soc Trans. 2024 Apr 17:BST20231236.

doi: 10.1042/BST20231236. Epub ahead of print.

PMID: 38629718.

Review focusing on the recently determined cryo-EM structures and current knowledge of the dynamics of the mitochondrial TOM core complex. Of particular interest are recent discoveries showing that the TOM core complex can act as a mechanosensor, where the pores close as a result of interaction with membrane-proximal structures.

Type 1 secretion necessitates a tight interplay between all domains of the ABC transporter.

Anlauf MT, Bilsing FL, Reiners J, Spitz O, Hachani E, Smits SHJ, Schmitt L.

Sci Rep. 2024 Apr 18;14(1):8994.

doi: 10.1038/s41598-024-59759-0.

PMID: 38637678.

In type I secretion systems HlyB = N-terminal C39 peptidase-like domain (CLD), transmembrane domain (TMD) and a C-terminal nucleotide binding domain (NBD).

Here: chimeric transporters and domain swapping experiments => critical role of the CLD in secretion, highlighting a hierarchical mode of substrate recognition for ABC transporters (CLD is the most critical secretion determinant, while TMD and NBD might possess additional recognition or interaction sites).

Membrane

NINJ1 mediates plasma membrane rupture by cutting and releasing membrane disks.

David L, Borges JP, Hollingsworth LR, Volchuk A, Jansen I, Garlick E, Steinberg BE, Wu H.

Cell. 2024 Apr 2:S0092-8674(24)00300-3.

doi: 10.1016/j.cell.2024.03.008. Epub ahead of print.

PMID: 38614101.

NINJ1 mediates plasma membrane rupture in pyroptosis and other lytic cell death pathways.

Here: cryo-EM structure of a NINJ1 oligomer segmented from NINJ1 rings.

=> NINJ1 can form membrane disks, consistent with membrane fragmentation by recombinant NINJ1.

Live-cell and super-resolution imaging => ring-like (lipid-containing) structures on the plasma membrane that are released into the culture supernatant.

Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors.

Manrique PD, Leus IV, López CA, Mehla J, Malloci G, Gervasoni S, Vargiu AV, Kinthada RK, Herndon L, Hengartner NW, Walker JK, Rybenkov VV, Ruggerone P, Zgurskaya HI, Gnanakaran S.

Commun Chem. 2024 Apr 12;7(1):84.

doi: 10.1038/s42004-024-01161-y.

PMID: 38609430.

Evaluation of 174 molecular descriptors in 1260 antimicrobial compounds and study of their correlations with antibacterial activity in P. aeruginosa.

=> Definition of consistent rules across most data highlighting the role of the interaction between the compounds and the OM. This provides new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa.

Lipid scrambling is a general feature of protein insertases.

Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S.

Proc Natl Acad Sci U S A. 2024 Apr 23;121(17):e2319476121.

doi: 10.1073/pnas.2319476121. Epub 2024 Apr 15.

PMID: 38621120.

Study investigating the mechanism of lipid equilibration between bilayer leaflets facilitated by scramblases. Through biochemical reconstitution and MD simulations, authors show that protein insertases (responsible for inserting polypeptide chains into membranes) also possess lipid scrambling activity.

Protein-Mediated Changes in Membrane Fluidity and Ordering: Insights into the Molecular Mechanism and Implications for Cellular Function.

Gunwant V, Gahtori P, Varanasi SR, Pandey R.

J Phys Chem Lett. 2024 Apr 16:4408-4415.

doi: 10.1021/acs.jpclett.3c03627. Epub ahead of print.

PMID: 38625684.

Study of the interaction between Human Serum Albumin (HSA) and two different lipids, dDPPG and dDPPC, using Vibrational Sum Frequency Generation spectroscopy at varying membrane fluidity levels.

Liquid-expanded lipid state: HSA deeply intercalates lipid chains through electrostatic and hydrophobic interactions.

Liquid-condensed state: protein intercalation decreases due to tighter lipid packing, with HSA showing a relatively weaker interaction with dDPPC compared to dDPPG.

Electron videography of a lipid-protein tango.

Smith JW, Carnevale LN, Das A, Chen Q.

Sci Adv. 2024 Apr 19;10(16):eadk0217.

doi: 10.1126/sciadv.adk0217. Epub 2024 Apr 17.

PMID: 38630809.

New approach for “electron videography”= combination of liquid phase electron microscopy with molecular modeling.

=> film of the nanoscale structural fluctuations of individual, suspended, and unlabeled membrane protein nanodiscs in liquid.

Suggestion that lipid-protein interactions delineate dynamically modified membrane domains across unexpectedly long ranges + contributing to the molecular mechanics of the ND as a whole in a manner specific to the protein within.

Lysophosphatidylserine: A Signaling Lipid with Implications in Human Diseases.

Chakraborty A, Kamat SS.

Chem Rev. 2024 Apr 12.

doi: 10.1021/acs.chemrev.3c00701. Epub ahead of print.

PMID: 38607675.

Review examining the significance of lyso-PS as a signaling lysophospholipid in mammals and its implications in various human autoimmune and neurological disorders (lyso-PS structure, distribution, chemical synthesis, and SAR studies with synthetic analogs) + discussion of the role of aberrant lyso-PS metabolism and signaling in human diseases.

Molecules

A new preparation method of covalent annular nanodiscs based on MTGase.

Dong Y, Li M, Kang L, Wang W, Li Z, Wang Y, Wu Z, Zhu C, Zhu L, Zheng X, Qian D, Dai H, Wu B, Zhao H, Wang J.

Arch Biochem Biophys. 2024 Apr 16;756:109997.

doi: 10.1016/j.abb.2024.109997. Epub ahead of print.

PMID: 38621443.

A drawback of commonly used NDs is their limited homogeneity and stability.

Here: novel approach to construct covalent annular nanodiscs (cNDs) by leveraging microbial transglutaminase (MTGase) to catalyze isopeptide bond formation.

Findings suggest that cNDs represent a more suitable tool for investigating interactions between membrane proteins and lipids, as well as for analyzing MP structures.

Tailored Branched Polymer-Protein Bioconjugates for Tunable Sieving Performance.

Kapil K, Murata H, Szczepaniak G, Russell AJ, Matyjaszewski K.

ACS Macro Lett. 2024 Apr 16;13(4):461-467.

doi: 10.1021/acsmacrolett.4c00059. Epub 2024 Apr 4.

PMID: 38574342.

Synthesis and characterization of protein-branched polymer bioconjugates, using chymotrypsin as a model protein.

Conformational analysis confirmed controlled polymer grafting, while enzymatic assays demonstrated that densely grafted polymers prevented protein inhibitor penetration, preserving up to 90% of enzymatic activity.

Methods

Evaluating the efficacy of protein quantification methods on membrane proteins.

Löptien J, Vesting S, Dobler S, Mohammadi S.

bioRxiv [Preprint]. 2024 Apr 2:2024.04.02.587709.

doi: 10.1101/2024.04.02.587709. PMID: 38617264.

Lowry, BCA, and Coomassie Bradford assays on a candidate MP, the Na,K-ATPase + comparison to an ELISA, newly developed

=> the three conventional methods significantly underestimate the concentration of NKA compared to the ELISA.

Transmembrane proteins-Different anchoring systems.

Roterman I, Stapor K, Konieczny L.

Proteins. 2024 May;92(5):593-609.

doi: 10.1002/prot.26646. Epub 2023 Dec 7.

PMID: 38062872.

Analysis focusing on the stability and local flexibility of MPs. Different forms of anchorage were identified. The different anchoring system was found to stabilize protein molecules with possible local fluctuation.

Rapid Enrichment of a Native Multipass Transmembrane Protein via Cell Membrane Electrophoresis through Buffer pH and Ionic Strength Adjustment.

Liu TT, Huang SH, Chao L.

J Am Chem Soc. 2024 Apr 17.

doi: 10.1021/jacs.3c13579. Epub ahead of print.

PMID: 38628144.

Supported membrane electrophoresis is hindered by the slow mobility of MPs. Adjusting buffer pH and ionic strength => enrichment of a 12TM MP cell membrane electrophoresis, allowing for separation within a native-like environment in minutes.

Interpretation: distinct electric and drag forces acting on transmembrane and aqueous-exposed portions of proteins, highlighting the influence of pH and ionic strength on driving forces and electrophoretic mobility, with potential applications for concentrating and isolating MPs.

HS-AFM single-molecule structural biology uncovers basis of transporter wanderlust kinetics.

Jiang Y, Miyagi A, Wang X, Qiu B, Boudker O, Scheuring S.

Nat Struct Mol Biol. 2024 Apr 17.

doi: 10.1038/s41594-024-01260-3. Epub ahead of print.

PMID: 38632360.

HS AFM to uncover the basis of kinetic mode switching in Pyrococcus horikoshii amino acid transporter GltPh: generally applicable and possibilities for time-resolved dynamic single-molecule structural biology.

Membrane extension MP reconstitution + localization AFM + PCA and hidden Markov modeling => association of structural states to a functional timeline, allowing six structures to be solved from a single molecule.

Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies.

Zhu Y, Akkaya KC, Ruta J, Yokoyama N, Wang C, Ruwolt M, Lima DB, Lehmann M, Liu F.

Nat Commun. 2024 Apr 17;15(1):3290.

doi: 10.1038/s41467-024-47569-x.

PMID: 38632225.

Spatial proteomics methods are limited in ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes.

Here: CLASP = Cross-Link Assisted Spatial Proteomics strategy that addresses these shortcomings (using human mitochondria as a model system).

=> allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data + validation in synaptic vesicles.

Microbio

Emerging roles for ABC transporters as virulence factors in uropathogenic Escherichia coli.

Shea AE, Forsyth VS, Stocki JA, Mitchell TJ, Frick-Cheng AE, Smith SN, Hardy SL, Mobley HLT.

Proc Natl Acad Sci U S A. 2024 Apr 16;121(16):e2310693121.

doi: 10.1073/pnas.2310693121. Epub 2024 Apr 12.

PMID: 38607934.

We lack a fundamental understanding of how uropathogens propel growth in the host to fuel pathogenesis.

Here: in silico, in vivo, and in vitro screens to better understand the role of UPEC transport mechanisms and their contributions to uropathogenesis.

ABC family of transporters = most conserved among uropathogenic bacterial species; contribute significantly to fitness and virulence in the urinary tract.

Bacterial efflux pumps excrete SYTO™ dyes and lead to false-negative staining results.

Minero GAS, Larsen PB, Hoppe ME, Meyer RL.

Analyst. 2024 Apr 15;149(8):2232-2235.

doi: 10.1039/d3an02112b.

PMID: 38445898.

Bacterial efflux pumps have affinity for a range of SYTO™ dyes that are commonly used to label bacteria

=> efflux pump activity leads to false negative results from bacterial staining.

=> SYTO™ dyes should be used with caution on live samples.

Functional promiscuity of small multidrug resistance transporters from Staphylococcus aureus, Pseudomonas aeruginosa, and Francisella tularensis.

Spreacker PJ, Wegrzynowicz AK, Porter CJ, Beeninga WF, Demas S, Powers EN, Henzler-Wildman KA.

Mol Microbiol. 2024 Apr;121(4):798-813.

doi: 10.1111/mmi.15231. Epub 2024 Jan 29.

PMID: 38284496.

Broad screen to identify potential substrates of three SMRs: PAsmr from P. aeruginosa; FTsmr from F. tularensis; and SAsmr from S. aureus (screen of metabolic differences in E. coli expressing each transporter versus an inactive mutant).

Resistance compounds were generally charged.

Susceptibility substrates were generally uncharged and is proposed to occur via substrate-gated proton leak (addition of bicarbonate antagonizes the susceptibility phenotype).

Hydrophobicity was not correlated with phenotype.

Miscellaneous

already mentionned last 20240308 but let’s give it an additional shoutout, as it makes this week’s Science front cover :

Generalized biomolecular modeling and design with RoseTTAFold All-Atom.

Krishna R, Wang J, Ahern W, Sturmfels P, Venkatesh P, Kalvet I, Lee GR, Morey-Burrows FS, Anishchenko I, Humphreys IR, McHugh R, Vafeados D, Li X, Sutherland GA, Hitchcock A, Hunter CN, Kang A, Brackenbrough E, Bera AK, Baek M, DiMaio F, Baker D.

Science. 2024 Apr 19;384(6693):eadl2528.

doi: 10.1126/science.adl2528. Epub 2024 Apr 19.

PMID: 38452047.

A milestone map of mouse-brain connectivity reveals challenging new terrain for scientists.

Eisenstein M.

Nature. 2024 Apr;628(8008):677-679.

doi: 10.1038/d41586-024-01096-3.

PMID: 38622253.

A pioneering ‘connectomics’ collaboration has successfully reconstructed one cubic millimetre of brain tissue, but researchers are still just scratching the surface of the complexity it contains.

A step along the path towards AlphaFold – 50 years ago.

Nature. 2024 Apr;628(8008):509.

doi: 10.1038/d41586-024-01094-5.

PMID: 38627511.

Nature 19 April 1974: ”In the right conditions, many proteins spontaneously and reversibly fold into their biologically active conformation … Such observations have appropriately been interpreted as evidence that the linear sequence of amino acid residues … carries all the necessary information for directing the folding process, and it is just a short step to speculation that artificial synthesis or genetic engineering of novel sequences will lead to conformations with novel catalytic and control functions. But which sequences will lead to the desired conformation, and achieve it in reasonable time? … What does seem clear is that the final stages of folding will be the most difficult to … predict … [S]uccess will owe as much to the size and speed of future generations of computers as it does to the programs and data fed to them. But it is remarkable that one can now discuss the difficulty of predicting the final stages of folding, not the folding as a whole”.

Persistent interaction patterns across social media platforms and over time.

Avalle M, Di Marco N, Etta G, Sangiorgio E, Alipour S, Bonetti A, Alvisi L, Scala A, Baronchelli A, Cinelli M, Quattrociocchi W.

Nature. 2024 Apr;628(8008):582-589.

doi: 10.1038/s41586-024-07229-y. Epub 2024 Mar 20.

PMID: 38509370.

Long conversations online consistently exhibit higher toxicity, yet toxic language does not invariably discourage people from participating in a conversation, and toxicity does not necessarily escalate as discussions evolve.