MP
Biochemical, biophysical, and structural investigations of two mutants (C154Y and R312H) of the human Kir2.1 channel involved in the Andersen-Tawil syndrome.
Zuniga D, Zoumpoulakis A, Veloso RF, Peverini L, Shi S, Pozza A, Kugler V, Bonneté F, Bouceba T, Wagner R, Corringer PJ, Fernandes CAH, Vénien-Bryan C.
FASEB J. 2024 Nov 15;38(21):e70146.
doi: 10.1096/fj.202401567R.
PMID: 39520289.
Kir channels = crucial role in maintaining the membrane potential, and mutations Kir2.1-R312H and Kir2.1-C154Y are linked to Andersen-Tawil syndrome (ATS) in humans.
Here: authors show that R312H dysfunction can be rescued by wild-type (WT) subunits, whereas the dominant-negative C154Y mutation impairs the function of the entire channel complex.
MD => C154Y reduces the structural flexibility of the selectivity filter.
cryo-EM => R312H provided detailed structural insights.
Inhibition mechanism of potential antituberculosis compound lansoprazole sulfide.
Kovalova T, Król S, Gamiz-Hernandez AP, Sjöstrand D, Kaila VRI, Brzezinski P, Högbom M.
Proc Natl Acad Sci U S A. 2024 Nov 19;121(47):e2412780121.
doi: 10.1073/pnas.2412780121. Epub 2024 Nov 12.
PMID: 39531492.
Lansoprazole sulfide (LPZS), a metabolite of an acid reflux drug, inhibits M. tuberculosis through an unknown mechanism, which involves a respiratory enzyme complex.
Here: structure of III2IV2 supercomplex of M. smegmatis with bound LPZS in the Qo active site + computer simulations and functional assays.
=> deciphering of the inhibitory mechanism.
Proton-coupled electron transfer dynamics in the alternative oxidase.
Saura P, Kim H, Beghiah A, Young L, Moore AL, Kaila VRI.
Chem Sci. 2024 Oct 11;15(44):18572–80.
doi: 10.1039/d4sc05060f. Epub ahead of print.
PMID: 39444558.
Alternative oxidase (AOX) = membrane-bound iron enzyme that catalyzes O2-driven quinol oxidation in the respiratory chains.
Here: multi-scale quantum and classical molecular simulations + bioch to address the proton-coupled electron transfer (PCET) reactions responsible for catalysis in AOX from Trypanosoma brucei, the causative agent of sleeping sickness.
=> key mechanistic understanding of the catalytic machinery of AOX + molecular basis for rational DD.
Mechanism of negative μ-opioid receptor modulation by sodium ions.
Thomson NJ, Zachariae U.
Structure. 2024 Nov 11:S0969-2126(24)00458-1.
doi: 10.1016/j.str.2024.10.023. Epub ahead of print.
PMID: 39536757.
Negative allosteric modulation of GPCRs by Na+ ions was first described in the 1970s for opioid receptors and has subsequently been detected for most class A GPCRs.
Here: mutual-information based analysis to μs-timescale biomolecular simulations of the μ-opioid receptor.
=> Na+ ions exert strong effects on the conformation of the μ-opioid receptor
=> Both protein matrix and protein-internal water molecules are affected
=> Mutual-information analysis shows the effects propagate to agonist and effector sites
=> Explains why Na+ lowers agonist affinity, deactivates receptors, and reduces basal signaling.
Generating Multistate Conformations of P-type ATPases with a Conditional Diffusion Model.
Xu J, Wang Y.
J Chem Inf Model. 2024 Oct 31.
doi: 10.1021/acs.jcim.4c01519. Epub ahead of print.
PMID: 39480276.
Novel computational approach (using a conditional diffusion model combined with state classifiers and graph neural networks) to generate biologically relevant conformations, demonstrated on P-type ATPases.
AI dissection of SERCA’s Post-Albers cycle … rings so much bells !
Membrane
Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion.
Versini R, Baaden M, Cavellini L, Cohen MM, Taly A, Fuchs PFJ.
Structure. 2024 Nov 7;32(11):1997-2012.e7.
doi: 10.1016/j.str.2024.08.017. Epub 2024 Sep 18.
PMID: 39299234.
Mitofusins mediate outer mitochondrial membrane fusion but the molecular mechanism remains elusive.
Here: extensive multiscale MD to predict a model of the TM domain of the yeast mitofusin Fzo1.
=> the stability of the TM1-TM2 domain interface is regulated by the charge state of Lys716, a residue crucial for mitochondrial fusion. OK with AF2 predictions of the Fzo1-Ugo1 complex and show that a charged Lys716 destabilizes the membrane, aiding fusion initiation. Yeast experiments confirm this functional role.
Measuring the bending rigidity of microbial glucolipid (biosurfactant) bioamphiphile self-assembled structures by neutron spin-echo (NSE): Interdigitated vesicles, lamellae and fibers.
Baccile N, Chaleix V, Hoffmann I.
Biochim Biophys Acta Biomembr. 2023 Oct 27:184243.
doi: 10.1016/j.bbamem.2023.184243. Epub ahead of print.
PMID: 39491124.
Bending rigidity = key parameter to understand the nanoscale mechanical properties of lipid membranes.
Here: bending rigidity is used to study self-assembled structures formed by a novel biobased glucolipid bioamphiphile by using neutron spin-echospectroscopy (vesicle suspensions, lamellar gels, and fiber gels).
=> unusually low values for vesicles and high values for the gels compared to typical phospholipid membranes.
Bacterial flotillins as destabilizers of phospholipid membranes.
Álvarez-Mena A, Morvan E, Martinez D, Berbon M, Savietto A, Grélard A, Turpin S, Dufourc EJ, Bramkamp M, Habenstein B.
Biochim Biophys Acta Biomembr. 2024 Nov 7:184399.
doi: 10.1016/j.bbamem.2024.184399. Epub ahead of print.
PMID: 39521105.
Flotillins = scaffolding proteins with nandomain-segregating activity. They form basket-like oligomeric architectures on the membrane, based on a membrane-targeting region, an SPFH domain and a coiled-coil “flotillin” domain. In B. subtilis, FloT and FloA localize in distinct nanodomains.
Here: deuterium and phosphorus ssNMR => effect of the different flotillins FloT and FloA and their structural components on model membranes.
=> clear disordering effect of FloT and FloA on the membranes reaching the carbon positions in the centre of the membrane, imposed by: the hydrophobic region + SPFH domain + membrane-distant flotillin domain (surprisingly).
Mapping membrane biophysical nano-environments.
Panconi L, Euchner J, Tashev SA, Makarova M, Herten DP, Owen DM, Nieves DJ.
Nat Commun. 2024 Nov 7;15(1):9641.
doi: 10.1038/s41467-024-53883-1.
PMID: 39511199.
Combination of the solvatochromic probe di-4-ANEPPDHQ with spectrally resolved single-molecule localisation microscopy => nanometre-precision localisation coordinates + generalised polarisation value.
Here: introduction of quantification algorithms to detect and map nano-domains in this marked data, demonstrating their effectiveness in both artificial membranes and live cells.
=> nm-scale mapping of MPs and assess changes in response to external perturbation with methyl-β-cyclodextrin.
Advances in methods and concepts provide new insight into antibiotic fluxes across the bacterial membrane.
Vergalli J, Réfrégiers M, Ruggerone P, Winterhalter M, Pagès JM.
Commun Biol. 2024 Nov 14;7(1):1508.
doi: 10.1038/s42003-024-07168-4.
PMID: 39543341.
Discussion on the passive influx versus active efflux of antibiotics in G- bacteria. Methodology breakthroughs provide fruitful tools to precisely dissect drug transport, identify key steps in drug resistance associated with membrane impermeability and efflux, and highlight key parameters to generate more effective drugs.
Molecules
Stable and Minimum Size Solubilization of Membrane Proteins with Cocktails of Phospholipid Analogues.
Takagi M, Nagatani A, Kawano K, Hata A, Yokoyama A, Hayashida K, Hoshi H, Sakurai M, Oyama T, Kuroda Y, Yamaoka Y, Fujiwara T, Miyanoiri Y, Hoshino M, Yano Y, Takasu K, Matsuzaki K.
ACS Appl Mater Interfaces. 2024 Nov 7.
doi: 10.1021/acsami.4c15697. Epub ahead of print.
PMID: 39509591.
New method combining two phospholipid analogues to solubilize MPs, achieving high thermal stability and preserving native states with minimal size increase, suitable for NMR and ligand screening applications.
Successfully applied to stabilize bacteriorhodopsin, neuropeptide Y2 receptor, and influenza A M2 protein.
Advances in utilizing reverse micelles to investigate membrane proteins.
Walters SH, Birchfield AS, Fuglestad B.
Biochem Soc Trans. 2024 Nov 7:BST20240830.
doi: 10.1042/BST20240830. Epub ahead of print.
PMID: 39508380.
Reverse micelles (nanoscale water cores surrounded by surfactant in a non-polar solvent) = unique and versatile membrane models for studying membrane-associated proteins.
Here: review on advances in RM formulations => better biological accuracy => enabling the encapsulation of complex protein types and improving their utility in high-resolution studies of protein-membrane interactions.
DeFrND: detergent-free reconstitution into native nanodiscs with designer membrane scaffold peptides
Qian Ren, Jing Wang, Vinay Idikuda, Shanwen Zhang, Jeehae Shin, W. Grant Ludlam, Luis M Real Hernandez, Ilya Levental, Kirill Martemyanov, Baron Chanda, Huan Bao
bioRxiv 2024.11.07.622281;
doi: https://doi.org/10.1101/2024.11.07.622281
Successful reconstitution of MPs in NDs requires prior solubilization and purification in detergents + the detergent-mediated reconstitution of NDs is unlikely to recapitulate the precise composition or asymmetry of native membranes.
Here: development of membrane-solubilizing peptides to directly extract membrane proteins from native cell membranes into nanoscale discoids.
Methods
Subtraction of liposome signals in cryo-EM structural determination of protein-liposome complexes
S. Li, M. Li, Y. Wang, and X. Li.
Chinese Physics B, 2024.
https://iopscience.iop.org/article/10.1088/1674-1056/ad4cdb/meta
Reconstituting MPs in liposomes and determining their structure is a common method for determiningMP structures using SPA cryo-EM but the strong signal of liposomes often interferes.
Here: liposome signal subtraction method based on SP 2D classification average images.
=> subtract the liposome signals from the original particle images.
Optimizing Transmembrane Protein Assemblies in Nanodiscs for Structural Studies: A Comprehensive Manual.
Vilela F, Sauvanet C, Bezault A, Volkmann N, Hanein D.
Bio Protoc. 2024 Nov 5;14(21):e5099.
doi: 10.21769/BioProtoc.5099.
PMID: 39525973.
Microbio
Physiological Effects of TolC-Dependent Multidrug Efflux Pumps in Escherichia coli: Impact on Motility and Growth Under Stress Conditions.
Di Maso AM, Ruiz C.
Microbiologyopen. 2024 Dec;13(6):e70006.
doi: 10.1002/mbo3.70006.
PMID: 39529380.
Effects on swimming motility and growth under stress conditions of E. coli mutants individually deleted for each inner TolC-dependent pumps + a mutant deleted for AcrZ + mutant simultaneously deleted for all eight pumps (ΔtolC).
Most E. coli mutants lacking individual pumps or AcrZ showed increased swimming motility and maintained or even enhanced growth under various stress conditions, except for ΔemrY and ΔacrZ mutants.
However, the mutant lacking all pumps exhibited significantly slower growth => critical role of TolC-dependent efflux for optimal growth.
=> while individual pumps are largely dispensable due to overlapping functions, the TolC system is essential for robust growth under stress.
Unveiling the impact of Leptospira TolC efflux protein on host tissue adherence, complement evasion, and diagnostic potential.
Hota S, Kumar M.
Infect Immun. 2024 Nov 12;92(11):e0041924.
doi: 10.1128/iai.00419-24. Epub 2024 Oct 11.
PMID: 39392312.
Miscellaneous
AI protein-prediction tool AlphaFold3 is now more open.
Callaway E.
Nature. 2024 Nov 11.
doi: 10.1038/d41586-024-03708-4. Epub ahead of print.
PMID: 39528695.
The code underlying AF3 is open at last => we can now download the software code and use it for non-commercial applications. The initial publication, six months ago, of AlphaFold3 without its code drew criticisms from scientists, who said the move undermined reproducibility.
see also:
CRISPR builds a big tomato that’s actually sweet.
Kozlov M.
Nature. 2024 Nov 13. doi: 10.1038/d41586-024-03722-6.
Epub ahead of print.
Editing a pair of genes in tomato plants (Solanum lycopersicum) boosts the fruit’s sugar levels by up to 30%, with no difference in size. Cultivated tomatoes today are up to 100 times larger than their wild counterparts, but the size boost comes with a sweetness sacrifice. When researchers used CRISPR-Cas9 technology to deactivate two genes that encode for a protein that degrades sugar-production enzymes, the plants bore much sweeter fruit.
A Second Academic Exodus From X?
IHE (Inside Higher Ed). November 13, 2024
A wave of academics and researchers say they have defected from the X social media platform Xm. “It has become a toxic cesspool, is owned by someone I despise, and has become a tool for disinformation,” wrote former university president Paul LeBlanc. Many are heading to upstart Twitter-lookalike Bluesky, which has reported an explosion in users in recent days. Others worry that turning away from Twitter is tantamount to a retreat from public engagement. “I think it is bad for the commons if all the academics disappear and only talk to each other,” says economist Paul Novosad.
Water-hose tool use and showering behavior by Asian elephants.
Urban L, Becker R, Ochs A, Sicks F, Brecht M, Kaufmann LV.
Curr Biol. 2024 Nov 6:S0960-9822(24)01371-X.
doi: 10.1016/j.cub.2024.10.017. Epub ahead of print.
PMID: 39520985.
This elephant learned to use a hose as a shower. Then her rival sought revenge. Behaviors reveal sophisticated tool use—and possible “pranking”—among pachyderms: