MP
The mycobacterial ABC transporter IrtAB employs a membrane-facing crevice for siderophore-mediated iron uptake.
Gonda I, Sorrentino S, Galazzo L, Lichti NP, Arnold FM, Mehdipour AR, Bordignon E, Seeger MA.
Nat Commun. 2025 Jan 29;16(1):1133.
doi: 10.1038/s41467-024-55136-7.
PMID: 39880813
Mycobacterial ABC transporter IrtAB = importer for iron-charged mycobactin by alternating IF and outward-occluded conformations without OF state.
Mechanism of sensor kinase CitA transmembrane signaling.
Zhang XC Xue K Salvi M Schomburg B Mehrens J Giller K Stopp M Weisenburger S Böning D Sandoghdar V Unden G Becker S Andreas LB Griesinger C.
Nat Commun. 2025 Jan 2216(1):935.
doi: 10.1038/s41467-024-55671-3.
PMID: 39843904.
Histidine kinases (HKs) = bacterial sensors. TM signalling mechanism is unclear.
Here: ssNMR/crystallo/distance measurements => citrate binding to the extracytoplasmic domain triggers a helical conformational change in the linker to transmembrane helix => piston-like motion and structural rearrangement in the cytosolic domain.
The allosteric mechanism of G-protein-coupled receptors is induced fit, not conformational selection.
Kazem Asadollahi, Paul R. Gooley, Thomas R. Weikl
bioRxiv 2025.01.28.635241;
doi: https://doi.org/10.1101/2025.01.28.635241
Allosteric activation of GPCRs = shift from inactive to active conformations, with two possible kinetic mechanisms: induced fit or conformational selection.
The grapevine ABC transporter B family member 15 is a trans-resveratrol transporter out of grapevine cells
Martínez-Márquez Ascensión , Martins Viviana , Sellés-Marchart Susana, Gerós Hernâni , Corchete Purificación , Bru-Martínez Roque.
Front. Plant Sci., 20 January 2025
Sec. Plant Proteomics and Protein Structural Biology
Volume 15 – 2024 |
https://doi.org/10.3389/fpls.2024.1450638
Stilbenes, particularly trans-resveratrol, serve as crucial defense compounds in grapevines, accumulating in the extracellular medium under stress.
The juxtamembrane sequence of small ankyrin 1 mediates the binding of its cytoplasmic domain to SERCA1 and is required for inhibitory activity.
Li Y, Wright NT, Bloch RJ.
J Biol Chem. 2025 Jan 23:108216.
doi: 10.1016/j.jbc.2025.108216. Epub ahead of print.
PMID: 39863105.
SERCA1 is regulated by small ankyrin 1 (sAnk1), which inhibits its ATPase activity through direct interaction. The cytoplasmic domain of sAnk1 binds SERCA1 with a 444 nM affinity.
A historical perspective on the multifunctional outer membrane channel protein TolC in Escherichia coli.
Wright M, Kaur M, Thompson LK, Cox G.
NPJ Antimicrob Resist. 2025 Jan 25;3(1):6.
doi: 10.1038/s44259-025-00078-3.
PMID: 39863731.
Since its discovery nearly 60 years ago, TolC has been associated with various cellular functions in E. coli, including the efflux of environmental stressors and virulence factors. It also acts as a receptor for specific bacteriophages and the colicin E1 toxin.
Advances in fungal sugar transporters: unlocking the potential of second-generation bioethanol production.
Pereira LMS Taveira IC Maués DB de Paula RG Silva RN.
Appl Microbiol Biotechnol. 2025 Jan 22109(1):19.
doi: 10.1007/s00253-025-13408-2.
PMID: 39841260 Review.
Second-generation (2G) bioethanol, produced from lignocellulosic biomass, depends on fungal sugar transporters (STs) for the uptake of monosaccharides released during biomass hydrolysis.
ST structure and function in fungi reveal their roles in cellulase induction, sugar signaling, and overcoming challenges like substrate competition and limited pentose metabolism.
Membranes
Atomic scale description of the allosteric coupling between a lipid bilayer and a membrane protein
Clarisse Fourel, Yanna Gautier, Alexandre Pozza, François Giraud, Elodie Point, Christel Le Bon, Karine Moncoq, Guillaume Stirnemann, Jérôme Hénin, Ewen Lescop, Laurent J. Catoire
bioRxiv 2025.01.24.634742;
doi: https://doi.org/10.1101/2025.01.24.634742
Biological membranes rely on dynamic interactions between lipids and proteins to function effectively.
Here: high-pressure NMR and MD to show that OmpX delays lipid gelation by liquefying surrounding lipids through hydrophobic and surface-matching mechanisms (alteration of the bilayer’s mechanical properties).
=> unexpected allosteric pathway where lipid dynamics influence both the protein’s surface and core.
A membrane-associated conveyor belt controls the rotational direction of the bacterial type 9 secretion system
Abhishek Trivedi, Jacob A. Miratsky, Emma C. Henderson, Abhishek Singharoy, Abhishek Shrivastava
bioRxiv 2024.09.23.614571; doi: https://doi.org/10.1101/2024.09.23.614571
T9SS in bacteria enables gliding motility and protein secretion, using a rotary mechanism powered by the pmf to drive an adhesin-coated conveyor belt along the outer membrane.
Here: the C-terminus of GldJ reverses the T9SS’s rotational direction in F. johnsoniae => role of the GldJ-GldK interface in directional control.
Proposed “tri-component gearset” model where the conveyor belt provides adaptive feedback to the T9SS, influencing bacterial motility.
Advancing membrane biology: single-molecule approaches meet model membrane systems.
Shin J Jeong SH Shon MJ.
BMB Rep. 2025 Jan58(1):33-40.
PMID: 39701026 Review.
Evolution of model membranes like NDs and GUVs + advancements in force spectroscopy and fluorescence microscopy on tunable lipid bilayers.
Combination of single-molecule approaches with model membranes => new insights into ion channel function, membrane fusion, and protein dynamics.
Examining the Biophysical Properties of the Inner Membrane of Gram-Negative ESKAPE Pathogens.
Gazerani G, Piercey LR, Reema S, Wilson KA.
J Chem Inf Model. 2025 Jan 28.
doi: 10.1021/acs.jcim.4c01457. Online ahead of print.
PMID: 39874531.
Martini CG MD => species-specific IM composition, particularly CL concentration, plays a critical role in determining membrane biophysical properties.
In situ NMR reveals a pH sensor motif in an outer membrane protein that drives bacterial vesicle production
Nicholas A Wood, Tata Gopinath, Kyungsoo Shin, and Francesca M Marassi
bioRxiv posted 24 January 2025
doi:10.1101/2025.01.21.634179
OMVs in diderm bacteria play key roles in processes like secretion and pathogenesis. In Salmonella enterica Typhimurium, OMV biogenesis is activated in acidic host cell vacuoles by the pH-sensitive outer membrane protein PagC.
Here: ssNMR and EM => identification of a pH-sensing motif in PagC (histidine protonation around pH 6 => structural changes and upregulates OMV production, aggregation, and biofilm formation).
Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1)
Tianle Chen, Francesca Vallese, Eva Gil-Iturbe, Kookjoo Kim, Matthias Quick, Oliver Clarke, Emad Tajkhorshid
bioRxiv 2024.10.15.616105; doi: https://doi.org/10.1101/2024.10.15.616105
Anionic lipids significantly influence the conformational transitions of the anion exchanger 1 (AE1): they modulate the energy landscape of AE1, stabilizing specific conformational states and affecting its functional dynamics.
Lipid Curvature and Fluidity Influence Lipid Incorporation Disparities in Nanodiscs.
Sarcinella MC, Jones JD, Sorensen MJ, Edgcombe SA, Ruotolo BT, Kennedy RT, Bailey RC.
Anal Chem. 2025 Jan 30.
doi: 10.1021/acs.analchem.4c05494. Online ahead of print.
PMID: 39885642.
NDs simplistic lipid compositions fail to replicate the complexity of native membranes, and lipid incorporation into NDs often deviates from expected levels.
Here: ND formation, purification, and LC-MSMS analysis => quantification of lipid incorporation and demonstration that even minor changes in lipid composition alter nanodisc size, dispersity, and biophysical properties, such as cholesterol-driven modulation of lipid fluidity.
=> Need for rigorous characterization of multilipid NDs to ensure they accurately model biological membranes.
Methods
Single-molecule tweezers decoding hidden dimerization patterns of membrane proteins within lipid bilayers
Victor W. Sadongo, Eojin Kim, Seoyoon Kim, W.C. Bhashini Wijesinghe, Tae Seung Lee, Jeong-Mo Choi, and Duyoung Min
bioRxiv posted 24 January 2025
doi:10.1101/2025.01.22.634249
Dimerization of TM proteins = essential biological process. Often simplified as a two-state transition from freely diffusing monomers to fully formed dimers is likely more complex due to intricate inter-residue interactions.
Li L, Zhang J, Huang C, Li Y, Liu Z, Xu J, Chen Y, Zhao Y, Zhang P.
Anal Chem. 2025 Jan 27. doi: 10.1021/acs.analchem.4c05510. Epub ahead of print.
PMID: 39869837.
SPR = valuable tool for studying MP binding due to label-free detection and high sensitivity but the use of biologically incompatible gold films limits its applications.
=> Development of a new surface-sensitive waveguide imaging technique with a silica surface for better cell attachment and more precise measurements (8x improvement of SPR measurement precision + in situ single-cell analysis and cell-to-cell heterogeneity).
Microbio
Moonlighting antibiotics: the extra job of modulating biofilm formation.
Cordisco E Serra DO.
Trends Microbiol. 2025 Jan 18:S0966-842X(24)00327-5.
doi: 10.1016/j.tim.2024.12.011. Online ahead of print.
PMID: 39828459 Review.
At sub-lethal concentrations, antibiotics modulate bacterial physiology and behavior. One key effect is on biofilm formation.
Here: review exploring how natural and clinical antibiotics act as modulators of biofilm formation, offering mechanistic insights and highlighting emerging patterns that guide future research.
Infectious Diseases Chemical “Cookbooks”: Celebrating Women’s Authorship in ACS Infectious Diseases.
Zgurskaya HI.
ACS Infect Dis. 2025 Jan 29.
doi: 10.1021/acsinfecdis.4c00916. Online ahead of print.
PMID: 39878352
Along with compiling a superbe collection ”Celebrating Women’s Authorship in ACS Infectious Diseases” (here: https://pubs.acs.org/page/aidcbc/vi/women-authorship), women authors were invited to share their personal stories on choosing and becoming infectious diseases researchers and, as has been important since ancient times, to share their wisdom with younger trainees and scientists.
Miscellaneous
Who wants to be a Nobel ?
Quantifying the evolution of individual scientific impact.
R. Sinatra et al. Science 2016
doi: http://dx.doi. org/10.1126/ science.aaf5239
Spoiler: An “older” researcher is less likely to publish a great discovery because he publishes statistically less than a young researcher and does much less science. That aside, the probability of publishing something major is not related to age.
Nature’s reach: narrow work has broad impact
Gates AJ, Ke Q, Varol O, Barabási AL.
Nature. 2019 Nov;575(7781):32-34.
doi: 10.1038/d41586-019-03308-7.
PMID: 31695218.
https://www.nature.com/immersive/d41586-019-03165-4/index.html
This is the work of a network scientist (Albert-László Barabási) who has studied all Nature’s publications on the occasion of the journal’s 150th anniversary to create a huge network of publications.
– The number of publications doubles every 15 years, but the impact of publications does not change, as a result of a policy of publication pressure.
Long-Distance Interdisciplinarity Leads to Higher Scientific Impact.
V. Larivière et al. PlosOne 2015
doi: https://doi.org/10.1371/journal.pone.0122565
The publications with the greatest impact are inspired by different disciplines There’s even a cross-disciplinary matrix in the article that you can use when looking for your next collaborations.
Large teams develop and small teams disrupt science and technology.
L. Wu. Nature 2019
doi : https://doi.org/10.1038/s41586-019-0941-9
Analysis of 65 million papers.
=> Small teams, where people have been publishing together for a long time, tend to publish very new things.
=> Very large teams tend to develop existing ideas.
Scratching promotes allergic inflammation and host defense via neurogenic mast cell activation.
Liu AW, Zhang YR, Chen CS, Edwards TN, Ozyaman S, Ramcke T, McKendrick LM, Weiss ES, Gillis JE, Laughlin CR, Randhawa SK, Phelps CM, Kurihara K, Kang HM, Nguyen SN, Kim J, Sheahan TD, Ross SE, Meisel M, Sumpter TL, Kaplan DH.
Science. 2025 Jan 31;387(6733):eadn9390.
doi: 10.1126/science.adn9390. Epub 2025 Jan 31.
PMID: 39883751.
In mice, scratching activates an immune response that helps to protect the skin against harmful infections, which could also explain why humans find a good scratch satisfying. When mice scratched itchy patches on their ears, the tissue swelled, and pain-sensing neurons released a molecule that attracts immune cells called neutrophils. Mice prevented from scratching with a ‘cone of shame’ had less swollen ears with fewer immune cells in them. Those that scratched were also less likely to have the potentially dangerous bacterium Staphylococcus aureus on their ears, which suggests that scratching has anti-bacterial benefits.
China’s cheap, open AI model DeepSeek thrills scientists.
Gibney E.
Nature. 2025 Jan 30.
doi: 10.1038/d41586-025-00229-6. Epub ahead of print.
PMID: 39849139.
Like OpenAI’s industry-leading o1, DeepSeek-R1 is a ‘reasoning’ model that uses a ‘chain of thought’ method to solve complex tasks, including sometimes backtracking and evaluating its approach — making them more adept than earlier LLMs at solving scientific problems. But, unlike o1, DeepSeek has been released as ‘open-weight’, meaning that researchers can study and build on the algorithm. There are also mini ‘distilled’ versions of R1 to allow researchers with limited computing power to play with the model. And then there’s the price. Using DeepSeek’s interface, an experiment that cost more than US$300 with o1, costs less than $10 with R1, says AI scientist Mario Krenn.
Why don’t you remember all your dreams?
By Lauren Leffer
Popular Science
“It can be very valuable for people to pay attention to their dreams — not necessarily to overanalyze their meaning, but to understand how dreaming is a sign your brain is doing important emotional and cognitive work.” Cognitive neuroscientist Jing Zhang has some tips if you want to remember more of your dreams. (Popular Science | 7 min read)
Phase behavior of Cacio and Pepe sauce.
Giacomo Bartolucci, Daniel Maria Busiello, Matteo Ciarchi, Alberto Corticelli, Ivan Di Terlizzi, Fabrizio Olmeda, Davide Revignas, Vincenzo Maria Schimmenti
arXiv:2501.00536 [cond-mat.soft]