Membrane’s digest
MP
Structural determinants for activity of the antidepressant vortioxetine at human and rodent 5-HT3 receptors.
López-Sánchez U, Munro LJ, Ladefoged LK, Pedersen AJ, Brun CC, Lyngby SM, Baud D, Juillan-Binard C, Pedersen MG, Lummis SCR, Bang-Andersen B, Schiøtt B, Chipot C, Schoehn G, Neyton J, Dehez F, Nury H, Kristensen AS.
Nat Struct Mol Biol. 2024 May 2.
doi: 10.1038/s41594-024-01282-x. Epub ahead of print.
PMID: 38698207.
Vortioxetine = an antidepressant targeting serotonin receptors, operates differently on rodent and human 5-HT3R. It stabilizes a resting inhibited state in mice and an agonist-bound-like state in humans, suppressing subsequent responses to agonists.
Here: cryo-EM, electrophysiology, voltage-clamp fluorometry and MD => drug’s mechanism, including its impact on receptor structures.
β-barrel membrane proteins fold via hybrid-barrel intermediate states.
Hartojo A, Doyle MT.
Curr Opin Struct Biol. 2024 May 9;87:102830.
doi: 10.1016/j.sbi.2024.102830. Epub ahead of print.
PMID: 38728831.
Review on recent studies using cryoEM that gave new insights into the folding process of β-barrel proteins in Gram-negative bacteria and eukaryotic organelles of bacterial origin: formation of “hybrid-barrel” intermediate states during interaction with folding machinery.
CryoEM structures reveal how the bacterial flagellum rotates and switches direction.
Singh PK, Sharma P, Afanzar O, Goldfarb MH, Maklashina E, Eisenbach M, Cecchini G, Iverson TM.
Nat Microbiol. 2024 May;9(5):1271-1281.
doi: 10.1038/s41564-024-01674-1. Epub 2024 Apr 17.
PMID: 38632342.
CryoEM structures of Salmonella enterica serovar typhimurium’s flagellar motor components: in a counterclockwise pose (4.0 Å resolution) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å).
The mechanism of bidirectional flagellar rotation in bacterial chemotaxis is described, revealing conformational changes in the C-ring and its interaction with a regulator that facilitate reversal of rotation and transmission of torque to the flagellum.
Ligand efficacy modulates conformational dynamics of the µ-opioid receptor.
Zhao J, Elgeti M, O’Brien ES, Sár CP, Ei Daibani A, Heng J, Sun X, White E, Che T, Hubbell WL, Kobilka BK, Chen C.
Nature. 2024 May;629(8011):474-480.
doi: 10.1038/s41586-024-07295-2. Epub 2024 Apr 10.
PMID: 38600384.
Understanding the molecular mechanisms of drug action on the µ-opioid receptor (µOR) is crucial for developing better pain management therapeutics.
DEER and smFRET => ligand-specific conformational changes in µOR that lead to various intrinsic efficacies at the transducer level.
Multiple conformations are identified, including pre-activated and fully activated states with distinct interactions with G-proteins and β-arrestin-1.
Promiscuous G-protein activation by the calcium-sensing receptor.
Zuo H, Park J, Frangaj A, Ye J, Lu G, Manning JJ, Asher WB, Lu Z, Hu GB, Wang L, Mendez J, Eng E, Zhang Z, Lin X, Grassucci R, Hendrickson WA, Clarke OB, Javitch JA, Conigrave AD, Fan QR.
Nature. 2024 May;629(8011):481-488.
doi: 10.1038/s41586-024-07331-1. Epub 2024 Apr 17.
PMID: 38632411.
Human calcium-sensing receptor (CaSR) = role in detecting extracellular calcium fluctuations and maintaining calcium homeostasis.
Here: structural study revealing that CaSR interacts with different G-protein subtypes (Gq, Gi, and Gs) through a common mode of coupling, involving specific regions of the receptor and G-protein subunits.
=> This expands the receptor dimer interface and facilitates G-protein activation, with the flexibility of a specific receptor region allowing for promiscuous coupling with various G-protein subtypes.
Membrane
Structural basis of TRPV1 modulation by endogenous bioactive lipids.
Arnold WR, Mancino A, Moss FR 3rd, Frost A, Julius D, Cheng Y.
Nat Struct Mol Biol. 2024 May 2.
doi: 10.1038/s41594-024-01299-2. Epub ahead of print.
PMID: 38698206.
Phosphoinositide lipids = role in modulating TRP ion channels (ex: lipid modulation of TRPV1 receptor in the context of inflammatory pain).
Structural analysis => identification of a pocket within the TRPV1 that accommodates various lipid species with specific modes of binding influencing channel activity.
+ demonstration that an empty-pocket channel lacking phosphoinositide lipids adopts an agonist-like state, indicating that the ejection of these lipids from the binding pocket is crucial for channel activation by thermal or chemical stimuli.
Structural basis of closed groove scrambling by a TMEM16 protein.
Feng Z, Alvarenga OE, Accardi A.
Nat Struct Mol Biol. 2024 Apr 29.
doi: 10.1038/s41594-024-01284-9. Epub ahead of print.
PMID: 38684930.
Activation of Ca2+-dependent TMEM16 scramblases + role in inducing phosphatidylserine externalization.
Current models: TMEM16s scramble lipids by deforming the membrane near a hydrophilic groove.
Here: cryoEM direct visualization of lipid association at the closed groove of Ca2+-bound fungal nhTMEM16 in ND.
+ Functional experiments identify critical lipid-protein interaction sites essential for closed groove scrambling.
!!! the choice of scaffold protein and lipids influences nhTMEM16 conformations and distribution, emphasizing their importance in cryo-EM structure determination !!!
Protein-membrane interactions: sensing and generating curvature.
Johnson DH, Kou OH, Bouzos N, Zeno WF.
Trends Biochem Sci. 2024 May;49(5):401-416.
doi: 10.1016/j.tibs.2024.02.005. Epub 2024 Mar 19.
PMID: 38508884.
To stabilize curved membranes, cells employ proteins that sense and generate membrane curvature.
Here: review of techniques for studying curvature sensing + examples of cellular processes requiring membrane curvature.
Giant organelle vesicles to uncover intracellular membrane mechanics and plasticity.
Santinho A, Carpentier M, Lopes Sampaio J, Omrane M, Thiam AR.
Nat Commun. 2024 May 4;15(1):3767.
doi: 10.1038/s41467-024-48086-7.
PMID: 38704407.
Method for generating giant organelle vesicles (GOVs) from cells by exposing them to a hypotonic medium followed by membrane breakage => isolation of GOVs ranging from 3 to over 10 µm.
GOVs derived from ER, endosomes, lysosomes, and mitochondria, or mix.
The study evaluates the mechanical properties of each organelle-derived GOV (e.g bending rigidities).
+ demonstration of the biochemical activity of giant endoplasmic reticulum vesicles (capacity to synthesize TG and assemble lipid droplets).
Methods
Microwave-assisted and methanol/acetic acid-free method for rapid staining of proteins in SDS-PAGE gels.
Wang J, Wang Z, Zhao W, Wang Y.
Anal Biochem. 2024 May 1;691:115553.
doi: 10.1016/j.ab.2024.115553. Epub ahead of print.
PMID: 38697592.
Microwave-assisted, methanol and acetic acid-free, inexpensive method for rapid staining of SDS-PAGE proteins (using citric acid, benzoic acid, and Coomassie blue).
Proteins visualized within 30 min of destaining, after 2 min of fixing and 12 min of staining.
Toward quantitative super-resolution methods for cryo-CLEM.
Zanetti-Domingues LC, Hirsch M, Wang L, Eastwood TA, Baker K, Mulvihill DP, Radford S, Horne J, White P, Bateman B.
Methods Cell Biol. 2024;187:249-292.
doi: 10.1016/bs.mcb.2024.02.028. Epub 2024 Mar 12.
PMID: 38705627.
Highlight of the limitations of current cryogenic ultrastructural imaging techniques, such as cryoET.
=> proposition of fluorescence imaging at cryogenic conditions as alternative but shortcomings of existing wide-field fluorescence imaging methods in providing accurate three-dimensional localization.
Here: chapter introducing the development of two super-resolution cryogenic fluorescence techniques: superSIL-STORM and astigmatism-based 3D STORM.
Advantages / limitations, potential applicability to cryo-correlative light and electron microscopy workflows are examined.
Microbio
T6SS-effector hunters uncover PIX: a novel delivery/marker domain.
Bernal P.
Trends Microbiol. 2024 Apr 27:S0966-842X(24)00094-5.
doi: 10.1016/j.tim.2024.04.009. Epub ahead of print.
PMID: 38679505.
Gram-negative bacteria use the T6SS to eject effectors into prey cells, aided by delivery domains. Recently uncovered by Carobbi et al., a new delivery domain, PIX, allowed the identification of hundreds of new effectors. They are order- and function-specific and exclusively orphan effectors, raising novel questions in the field.
Staphylococcus aureus membrane vesicles: an evolving story.
Wang X, Lee JC.
Trends Microbiol. 2024 Apr 26:S0966-842X(24)00088-X.
doi: 10.1016/j.tim.2024.04.003. Epub ahead of print.
PMID: 38677977.
Research has shown that S. aureus generates extracellular membrane vesicles (MVs) that package a variety of bacterial components, many of which are virulence factors.
Here: review summarizing recent advances in understanding S. aureus extracellular membrane vesicles (MVs) : biogenesis, cargo, and potential role in the pathogenesis of staphylococcal infections.
Miscellaneous
Major AlphaFold upgrade offers boost for drug discovery.
Callaway E.
Nature. 2024 May 8.
doi: 10.1038/d41586-024-01383-z. Epub ahead of print.
PMID: 38719965.
A new version of DeepMind’s AlphaFold !
=> predict protein structures during interactions with other molecules.
=> predict the shape of proteins that contain function-altering modifications or their structure alongside those of DNA RNA and other cellular players.
Access to the AlphaFold3 server however is limited — partly to protect the advantage of DeepMind’s own drug-discovery spin-off company.
The paper:
Accurate structure prediction of biomolecular interactions with AlphaFold 3.
Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick J, Bodenstein SW, Evans DA, Hung CC, O’Neill M, Reiman D, Tunyasuvunakool K, Wu Z, Žemgulytė A, Arvaniti E, Beattie C, Bertolli O, Bridgland A, Cherepanov A, Congreve M, Cowen-Rivers AI, Cowie A, Figurnov M, Fuchs FB, Gladman H, Jain R, Khan YA, Low CMR, Perlin K, Potapenko A, Savy P, Singh S, Stecula A, Thillaisundaram A, Tong C, Yakneen S, Zhong ED, Zielinski M, Žídek A, Bapst V, Kohli P, Jaderberg M, Hassabis D, Jumper JM.
Nature. 2024 May 8.
doi: 10.1038/s41586-024-07487-w. Epub ahead of print.
PMID: 38718835.
discussed in this podcast:
Who’s making chips for AI? Chinese manufacturers lag behind US tech giants.
O’Callaghan J.
Nature. 2024 May 3.
doi: 10.1038/d41586-024-01292-1. Epub ahead of print.
PMID: 38702580.
China’s AI sector could be five to ten years behind the United States, partly because it can’t access the most advanced computer chips. In 2022, the United States imposed export controls on the fastest chips and on equipment that could be used to produce such chips => this has dramatically limited China’s progress with training AI models.
Cubic millimetre of brain mapped in spectacular detail.
Wong C.
Nature. 2024 May 9.
doi: 10.1038/d41586-024-01387-9. Epub ahead of print.
PMID: 38724661.
Researchers have created an exquisitely detailed atlas of a tiny piece of one woman’s brain which had been removed during surgery to treat her epilepsy. The sample was cut into thousands of nanometre-thick slices and each was imaged with electron microscopes. AI tools then classified different structures and cells and created a 3D reconstruction of the sample.
=> 1.4 petabytes of electron microscopy data classified and quantified cell types vessels and synapses and developed a freely available tool for analyzing these data. Their findings allowed the authors to identify previously unknown aspects of the human temporal cortex.
ref. article:
A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution.
Shapson-Coe A, Januszewski M, Berger DR, Pope A, Wu Y, Blakely T, Schalek RL, Li PH, Wang S, Maitin-Shepard J, Karlupia N, Dorkenwald S, Sjostedt E, Leavitt L, Lee D, Troidl J, Collman F, Bailey L, Fitzmaurice A, Kar R, Field B, Wu H, Wagner-Carena J, Aley D, Lau J, Lin Z, Wei D, Pfister H, Peleg A, Jain V, Lichtman JW.
Science. 2024 May 10;384(6696):eadk4858.
doi: 10.1126/science.adk4858. Epub 2024 May 10.
PMID: 38723085.
My PI yelled at me and I’m devastated. What do I do?
Forrester N.
Nature. 2024 May 2.
doi: 10.1038/d41586-024-01309-9. Epub ahead of print.
PMID: 38702581.
It can be hard when junior scientists feel unsupported. Nature asked three scientists for their advice on how to respond.