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20240527_membrane digest

Membrane’s digest


The S-component fold: a link between bacterial transporters and receptors.

Partipilo M, Jan Slotboom D.

Commun Biol. 2024 May 21;7(1):610.

doi: 10.1038/s42003-024-06295-2.

PMID: 38773269.

Study identifying a structural link between microbial transporters and receptors using AI-based structure prediction tools.

=> Energy-Coupling Factor (ECF) transporters and sensor histidine kinases share a common fold, suggesting evolutionary connections and introducing the concept of “transceptors” in prokaryotes.


Dual role of the peptide-loading complex as proofreader and limiter of MHC-I presentation.

Brunnberg J, Barends M, Frühschulz S, Winter C, Battin C, de Wet B, Cole DK, Steinberger P, Tampé R.

Proc Natl Acad Sci U S A. 2024 May 28;121(22):e2321600121.

doi: 10.1073/pnas.2321600121. Epub 2024 May 21.

PMID: 38771881.

Role of individual components of the peptide-loading complex (PLC) in the presentation of MHC-I molecules.

Engineered T cell receptors and antibody-nanobody complexes => specific PLC components influence the surface composition and quality of MHC-I complexes

=> dual role in peptide proofreading and limiting peptide abundance.


Role of the Escherichia coli FocA and FocB formate channels in controlling proton/potassium fluxes and hydrogen production during osmotic stress in energy-limited, stationary phase fermenting cells.

Babayan A, Vassilian A, Poladyan A, Trchounian K.

Biochimie. 2024 Jun;221:91-98.

doi: 10.1016/j.biochi.2024.01.017. Epub 2024 Feb 1.

PMID: 38307245.

Role of E. coli FocA and FocB formate channels in regulating proton and potassium fluxes under pH and osmotic stress

=> these channels are crucial for maintaining ion gradients and H2 production, particularly under varying pH conditions.

=> study suggests that formate channels contribute to osmoregulation and energy production in stationary-phase cells.


Impact of secretin receptor homo-dimerization on natural ligand binding.

Harikumar KG, Piper SJ, Christopoulos A, Wootten D, Sexton PM, Miller LJ.

Nat Commun. 2024 May 23;15(1):4390.

doi: 10.1038/s41467-024-48853-6.

PMID: 38782989.

Study of the binding mechanisms of the secretin receptor (SecR), a class B GPCR, focusing on its dimeric and monomeric forms.

=> the ability of SecR to dimerize enhances the conformational dynamics of the receptor, facilitating more efficient G protein recruitment and activation: explains the higher functional potency of secretin at dimeric SecR.


The patatin-like protein PlpD forms structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane.

Hanson SE, Dowdy T, Larion M, Doyle MT, Bernstein HD.

Nat Commun. 2024 May 23;15(1):4389.

doi: 10.1038/s41467-024-48756-6.

PMID: 38782915.

Study revealing that the P. aeruginosa PlpD protein (part of the Omp85 superfamily) contains a periplasmic patatin-like (PL) domain that makes transient strand swap with a neighboring β-barrel domain.

By contrast to other Omp85 proteins, PlpD forms a homodimer, indicating a greater structural diversity within the Omp85 superfamily than previously thought.

This discovery suggests that the Omp85 scaffold has evolved to perform novel functions beyond its roles in OM protein assembly and translocation.


Cryo-EM structure of I domain-containing integrin αEβ7.

Akasaka H, Sato D, Shihoya W, Nureki O, Kise Y.

Biochem Biophys Res Commun. 2024 May 14;721:150121.

doi: 10.1016/j.bbrc.2024.150121. Epub ahead of print.

PMID: 38781659.

Integrin αEβ7 = significant for immune responses + drug target for inflammatory bowel disease (IBD).

Cryo-EM structure of the full-length integrin αEβ7, revealing its intermediate half-bent conformation => unique spatial arrangement where the α-I domain covers the headpiece domain.



Supported Biomembrane Systems Incorporating Multiarm Polymers and Bioorthogonal Tethering.

Martin JA, Li YM, Gilchrist ML.

Langmuir. 2024 May 20.

doi: 10.1021/acs.langmuir.4c00176. Epub ahead of print.

PMID: 38767862.

Development of supported biomembranes that mimic native lipid environments using multiarm PEG = tethering system that maintains membrane protein function and minimizes nonspecific binding.


Uniaxial Symmetry Breaking in Bacteriorhodopsin at the Thermal Phase Transition of Lipids of Purple Membranes.

Mostafa HIA.

J Phys Chem B. 2024 May 22.

doi: 10.1021/acs.jpcb.4c01517. Epub ahead of print.

PMID: 38776161.

Correlation between symmetry breaking and phase transitions in BR within the purple membrane (PM).

=> the thermal phase transitions in PM lipids affect the axial symmetry of BR, suggesting that lipid-protein interactions play a role in this process.

Symmetry-breaking properties of BR could have technical applications, especially considering its ability to influence the symmetry of helical light.


Optimizing properties of translocation-enhancing transmembrane proteins.

Bartoš L, Drabinová M, Vácha R.

Biophys J. 2024 May 21;123(10):1240-1252.

doi: 10.1016/j.bpj.2024.04.009. Epub 2024 Apr 13.

PMID: 38615194.

Identification of the specific properties of TM proteins/peptides that enhance the membrane permeation of amphiphilic peptides.

Key parameters = continuous hydrophilic patch and charged residues within the membrane.

MD and experimental validation => guidelines for designing translocation-enhancing proteins/peptides.


Demixing is a default process for biological condensates formed via phase separation.

Zhu S, Shen Z, Wu X, Han W, Jia B, Lu W, Zhang M.

Science. 2024 May 24;384(6698):920-928.

doi: 10.1126/science.adj7066. Epub 2024 May 23.

PMID: 38781377.

Demonstration that excitatory and inhibitory postsynaptic densities in neurons segregate into distinct molecular assemblies through phase separation. This demixing occurs spontaneously and is not driven by diffusion.

=> role of phase separation in creating compartmentalization specificities in cellular subcompartments, which can impact synaptic function and organization.



Development of Putative Bivalent Dicovalent Ligands for the Adenosine A1 Receptor.

Payne CM, Baltos JA, Langiu M, Lu CS, Tyndall JDA, Gregory KJ, May LT, Vernall AJ.

Chembiochem. 2024 May 22:e202400242.

doi: 10.1002/cbic.202400242. Epub ahead of print.

PMID: 38777792.

New tools for investigating GPCR dimerization = bivalent GPCR ligands designed to target adenosine A1 receptor (A1R) homodimers. These compounds exhibit covalent binding and enhanced selectivity for A1R vs adenosine A3 receptor, demonstrating the potential for dual-occupation ligands to achieve receptor subtype selectivity.



Bizarre bacteria defy textbooks by writing new genes.

Callaway E.

Nature. 2024 May 22.

doi: 10.1038/d41586-024-01477-8. Epub ahead of print.

PMID: 38778202.

Discovery of bacteria with an enzyme that can read RNA templates to create new genes, reversing the typical DNA-to-RNA flow of genetic information. This enzyme produces protective proteins when the bacterium is infected by a virus, representing a significant shift in understanding bacterial genome dynamics. The findings suggest a new paradigm in genome research and potential applications in biotechnology and medicine.


Why some songs make us feel like dancing

The most dance-inducing rhythms are neither too predictable nor too surprising. An intermediate amount of syncopations — rhythmic patterns that occur when unexpected beats are emphasized — was the sweet spot for making 60 study participants want to dance. Brain activity measurements suggest that this groove experienceis triggered by the dorsal auditory pathway, which connects the auditory-information-processing region with movement areas. 

Zalta A, Large EW, Schön D, Morillon B. Neural dynamics of predictive timing and motor engagement in music listening.

Sci Adv. 2024 Mar 8;10(10):eadi2525.

doi: 10.1126/sciadv.adi2525. Epub 2024 Mar 6.

PMID: 38446888.


The body odours that attract mosquitos

Kate Golembiewski


A field trial in Zambia revealed that mosquitoes are more attracted to people emitting higher levels of carboxylic acids and other compounds produced by skin bacteria. The findings could lead to the development of more effective repellents and strategies to lure mosquitoes into traps for population control. This research enhances understanding of mosquito behavior and offers potential improvements in malaria prevention.


Laser-powered bullets reveal surprising metal hardness.

Fox D.

Nature. 2024 May 22.

doi: 10.1038/d41586-024-01514-6. Epub ahead of print.

PMID: 38778194.

Metals heated and impacted by laser-powered micro-bullets exhibit increased strength compared to less heated metals. This counterintuitive behavior under extreme conditions could inform new strategies for designing resilient materials, particularly in aerospace engineering. The study challenges traditional views on the thermal softening of metals.


Who will make AlphaFold3 open source? Scientists race to crack AI model.

Callaway E.

Nature. 2024 May 23.

doi: 10.1038/d41586-024-01555-x. Epub ahead of print.

PMID: 38783131.

Researchers are racing to create their own versions of DeepMinds revolutionary protein-structure-prediction AI AlphaFold3 which was released without its code to the frustration of many scientists. It would be bad if capabilities that are just so fundamental to our ability to do drug discovery… end up getting locked up” says computational biologist Mohammed AlQuraishi whose team hopes to complete an OpenFold3this year. Computational biophysicist David Bakers team is adapting a version of their open-fold algorithm RoseTTAFold and independent software engineer Phil Wang has begun a crowdsourced replica of AlphaFold3. Responding to the backlash DeepMind has promised to release the code by years end.


AlphaFold3 – why did Nature publish it without its code?

Nature. 2024 May;629(8013):728.

doi: 10.1038/d41586-024-01463-0.

PMID: 38778239.

Criticism of decision to publish AlphaFold3 raises important questions. Nature welcomes readersviews.

This editorial explains that Nature will update the paper with the code when DeepMind releases it.