MP
Assembly and the gating mechanism of the Pel exopolysaccharide export complex PelBC of Pseudomonas aeruginosa.
Benedens M, Rosales-Hernandez C, Straathof SAP, Loschwitz J, Berninghausen O, Maglia G, Beckmann R, Kedrov A.
Nat Commun. 2025 Jun 5;16(1):5249. doi: 10.1038/s41467-025-60605-8.
PMID: 40473691.
Cryo-EM structure of the PelBC complex (exporter of Pel exopolysaccharide in P. aeruginosa).
PelC = gated channel through which the polymer is extruded.
PelB = adapter linking the IM with OM machinery.
Functional assays and mutagenesis =>conformational changes crucial for gating.
Illuminating Rhodopsin Activation in Real Time.
Katayama K.
Biophys J. 2025 Jun 18:S0006-3495(25)00378-9.
doi: 10.1016/j.bpj.2025.06.018. Online ahead of print.
PMID: 40538033.
Advanced time-resolved spectroscopy to capture the activation of rhodopsin on sub-microsecond timescales.
=> early conformational changes following photon absorption, identifying intermediate states that bridge inactive and active conformations.
Proton transfer through a charged conduit in respiratory complex I – long range effects and conformational gating.
Luka Simsive, Oleksii Zdorevskyi, and Vivek Sharma.
bioRxiv posted 17 June 2025.
doi:10.1101/2025.06.13.659531.
Study how proton transfer in respiratory complex I is controlled by electrostatics and structural gating.
MD => a continuous charged conduit facilitates long-range proton movement, regulated by conformational shifts. Gating mechanism likely couples electron transport to proton pumping.
Integrative Structure of Norovirus NS3 Suggests a Role in RNA Transport.
Meryl Haas, Jake T. Mills, Cynthia Kelley, Arnab Das, Henrietta Hof, Coco Niemel, Tim Donselaar, Ieva Drulyte, Frank J.M. van Kuppeveld, David Dulin, Joost Snijder, Morgan R. Herod, and Daniel L. Hurdiss.
bioRxiv posted 17 June 2025.
doi:10.1101/2025.06.17.659504.
Integrative structural biology => modeling of the NS3 protein of norovirus as a scaffold potentially involved in RNA trafficking.
Cryo-EM and XL-MS => membrane-proximal structure that binds RNA.
The dynamic architecture of NS3 suggests a regulatory role in viral genome delivery or replication.
In mitochondrial disease respiratory complex III2 assembles complex I via toxic intermediate.
Maria G. Ayala-Hernandez, Anetzy Bermudez Torales, Hannah Camille Tan, Claire B Montgomery, Abhilash Padavannil, Gino Cortopassi, and James Anthony Letts.
bioRxiv posted 18 June 2025.
doi:10.1101/2025.06.17.660237.
Study showing that in mitochondrial dysfunction, the assembly of respiratory complex I can be hijacked by aberrant forms of complex III₂.
=> formation of a non-productive, possibly toxic intermediate that impairs mitochondrial respiration.
Cryo-EM structures of a pentameric ligand-gated ion channel in liposomes.
Dalal V, Tan BK, Xu H, Cheng WWL.
bioRxiv [Preprint]. 2025 Jun 2:2025.03.21.644626.
doi: 10.1101/2025.03.21.644626.
PMID: 40502198.
Cryo-EM structures of a pentameric LGIC reconstituted into liposomes, capturing multiple conformational states.
The lipid environment preserves physiological gating behavior and reveals previously unobserved states: lipids modulate channel activation and desensitization.
Correlating membrane-protein dynamics with function: Integrating bioinformatics, molecular dynamics, and single-molecule FRET.
Higinbotham HR, Arbour CA, Imperiali B.
bioRxiv [Preprint]. 2025 Jun 5:2025.06.05.658054. doi: 10.1101/2025.06.05.658054.
PMID: 40501851.
in silico + experimental techniques to link MP conformational dynamics with function.
FRET + MD + evolutionary analysis => functionally critical motion in several transporter families are mapped.
Identification of conserved dynamic “hotspots” that correlate with substrate specificity and efficiency.
De novo design of miniprotein agonists and antagonists targeting G protein-coupled receptors.
Muratspahić E, Feldman D, Kim DE, Qu X, Bratovianu AM, Rivera-Sánchez P, Dimitri F, Cao J, Cary BP, Belousoff MJ, Keov P, Chen Q, Ren Y, Fine J, Sappington I, Schlichthaerle T, Zhang JZ, Pillai A, Mihaljević L, Bauer M, Torres SV, Motmaen A, Lee GR, Tran L, Wang X, Goreshnik I, Vafeados DK, Svendsen JE, Hosseinzadeh P, Lindegaard N, Brandt M, Waltenspühl Y, Deibler K, Oostdyk L, Cao W, Anantharaman L, Stewart L, Halloran L, Spangler JB, Sexton PM, Roth BL, Krumm BE, Wootten D, Tate CG, Norn C, Baker D.
bioRxiv [Preprint]. 2025 Jun 5:2025.03.23.644666.
doi: 10.1101/2025.03.23.644666.
PMID: 40501737.
Engineering of synthetic miniproteins to either activate or block diverse GPCRs (computational design and experimental validation).
Cryo-EM and signaling assays confirm the high specificity and tunability of the binders.
Modulation of receptor function without native ligands => possibilities for therapeutic applications and GPCR mechanistic dissection.
Membranes
Functional targeting of membrane transporters and enzymes to peroxisomes.
Siu KH, Lee V, Dueber JE.
Nat Chem Biol. 2025 Jun 16.
doi: 10.1038/s41589-025-01948-7. Online ahead of print.
PMID: 40524007.
Modular strategy to redirect membrane-bound enzymes and transporters to peroxisomes in yeast.
Engineering of membrane targeting sequences + synthetic biology tools => rewiring of metabolic pathways to compartmentalize specific reactions.
Peroxisomal localization enhances flux and minimizes toxic intermediates.
A versatile toolkit for organelle engineering in metabolic design.
Coupling between membrane undulations and lipid curvature leads to transient local enrichment of cardiolipin in mitochondrial membranes.
Christopher T Lee, Kailash Venkatraman, Itay Budin, and Padmini Rangamani.
bioRxiv posted 18 June 2025.
doi:10.1101/2025.01.17.633669.
Computational modeling => fluctuations in membrane shape can drive local accumulation of CL.
Coupling between curvature and undulations enhances lipid segregation in mitochondrial membranes. Transient enrichments may support protein complex assembly or metabolic microdomains.
Dynamic interplay between membrane physics and lipid organization.
Anthracene-Bridged Detergents for Membrane Protein Studies.
Song L, Dai Y, Zhou X, Tan Y, Zhou Z, Zheng X, Zhao F, Yang M, Tao H.
Chempluschem. 2025 Jun 17:e202500320.
doi: 10.1002/cplu.202500320. Online ahead of print.
PMID: 40525229.
New class of anthracene-bridged detergents designed to stabilize MPs for structural and functional studies (rigid core => enhanced hydrophobic interactions with TMs => protein solubilization +++ and activity +++).
Biophysical assays => superior performance compared to conventional detergents.
Methods
Graphene Nanodots as Substrates for SEIRAS and SERS Studies on Membrane Proteins.
Murillo-Bello A, Ricciardulli AG, Umar AR, Gerasimova T, Friedrich T, Javahiraly N, Samorì P, Hellwig P.
Langmuir. 2025 Jun 16.
doi: 10.1021/acs.langmuir.5c01808. Online ahead of print.
PMID: 40522217.
Use of graphene nanodots as enhanced substrates for surface-enhanced infrared absorption (SEIRAS) and Raman scattering (SERS) spectroscopy.
= strong signal amplification while maintaining MP functionality in supported bilayers.
=> allows real-time structural insights into protein-lipid interactions and conformational changes.
An Optical Approach to Modulating Membrane Protein Endocytosis Using a Light-Responsive Tag for Recruiting β-Arrestin.
Kuang Q, Endo M, Dong Q, Li Y, Lee YH, Li Q, Ozawa T.
ACS Chem Biol. 2025 Jun 17. doi: 10.1021/acschembio.5c00096. Online ahead of print.
PMID: 40526401.
Photoactivatable system to control MP internalization by recruiting β-arrestin in a light-dependent manner. A synthetic light-responsive tag enables precise spatiotemporal modulation of receptor endocytosis.
Reversible and tunable => new control over cellular signaling and trafficking.
A fluorescent reporter and single-turnover kinetics reveal new insight into BAM complex function.
Bergman WN, Sousa MC.
bioRxiv [Preprint]. 2025 May 31:2025.05.30.657120.
doi: 10.1101/2025.05.30.657120.
PMID: 40502037.
Fluorescent assay to study the bacterial BAM complex under single-turnover conditions.
Kinetic analysis => previously underappreciated pause phase during OMP insertion.
TMVisDB: Annotation and 3D-visualization of Transmembrane Proteins.
Olenyi T, Marquet C, Grekova A, Houri L, Heinzinger M, Dallago C, Rost B.
J Mol Biol. 2025 Aug 1;437(15):168997.
doi: 10.1016/j.jmb.2025.168997. Epub 2025 Feb 11.
PMID: 40133784
TMVisDB = comprehensive platform that integrates functional annotation and 3D visualization of MPs using deep learning-based structure predictions.
The database allows users to explore protein topology, domain organization, and membrane orientation interactively. It supports large-scale analysis and comparison of structural features across protein families.
Complete computational design of high-efficiency Kemp elimination enzymes.
Listov D, Vos E, Hoffka G, Hoch SY, Berg A, Hamer-Rogotner S, Dym O, Kamerlin SCL, Fleishman SJ.
Nature. 2025 Jun 18.
doi: 10.1038/s41586-025-09136-2. Epub ahead of print.
PMID: 40533551.
Advanced computational strategies => de novo design of enzymes catalyzing Kemp elimination with efficiencies surpassing natural counterparts.
Oprimization of designed active sites through physics-based modeling and ensemble refinement.
Experimental validation => catalytic efficiencies > 100x higher than prior artificial enzymes.
Microbio
Superbug Surge-A Tale of Seven-Year Battle Against Escalating Antimicrobial Resistance in North India.
Fomda BA, Qadri U, Bashir G, Qadri SM, Nazir SS, Hakak I.
Curr Microbiol. 2025 Jun 19;82(8):340.
doi: 10.1007/s00284-025-04321-y.
PMID: 40536523.
7-year epidemiological study of AMR trends in North India.
Report of a worrying increase in MDR Klebsiella pneumoniae and Acinetobacter baumannii, especially in intensive care settings.
Inadequate stewardship, over-the-counter antibiotic access, and inconsistent infection control contributed to the crisis.
Urgent need for policy interventions and regional AMR surveillance systems.
Screening de novo designed protein binders in unpurified lysate using flow induced dispersion analysis.
Francisca Pinheiro, Jan S. Nowak, Elena Zueva, Emily C. Pheasant, Ida Kjaersgaard Grene, Vili Lampinen, and Magnus Kjaergaard
bioRxiv posted 18 June 2025.
doi:10.1101/2025.06.17.660127.
HT method to screen synthetic protein binders directly in cell lysates using flow-induced dispersion analysis (FIDA).
Bypassing of purification => rapid and quantitative assessment of binding affinity and specificity.
Compatible with diverse target classes and binder scaffolds.
Judge orders NIH to restore hundreds of grants cut under Trump.
Science.
https://www.science.org/content/article/judge-orders-nih-restore-hundreds-grants-cut-under-trump
A federal judge in Boston has ruled that the NIH must immediately restore approximately 800 grants touching on politically sensitive topics that it abruptly canceled earlier this year.
”the agency’s decision to terminate grants in areas such as racial health disparities and transgender health were arbitrary and capricious” => no legally valid process behind its reasoning.
Linking Cell Size, Vmax and Km in Phototrophs and Chemotrophs: Insights From Bayesian Inference.
Sasaki R, Seto M.
Environ Microbiol Rep. 2025 Jun;17(3):e70114.
doi: 10.1111/1758-2229.70114.
PMID: 40537143.
Bayesian modeling to explore the relationship between microbial cell size and enzymatic kinetics (Vmax and Km).
=> scaling laws differ between phototrophs and chemotrophs, reflecting adaptations to energy acquisition strategies.
Suggest that evolutionary pressures shape both cellular architecture and enzyme efficiency.
Pangolin hunting in southeast Nigeria is motivated more by local meat consumption than international demand for scales.
Emogor CA, Wasser SK, Coad L, Balmford B, Ingram DJ, Wijesinghe A, Atsu BA, Bassey F, Ogu DS, Okafor N, Balmford A.
Nat Ecol Evol. 2025 Jun 13.
doi: 10.1038/s41559-025-02734-3. Epub ahead of print.
PMID: 40514569.
Field study in southeastern Nigeria reveals that local dietary preferences, not just the illegal wildlife trade, drive pangolin hunting. Interviews and market analyses show that pangolin meat is valued as a delicacy and status symbol in local communities.
=> Conservation strategies must address domestic cultural drivers alongside international trafficking. Effective protection will require both law enforcement and locally grounded education campaigns.
Humpback Whales Blow Poloidal Vortex Bubble Rings.
Sharpe, F., Frediani, J., Hubbard, J., Perrine, D., Hilbourne, S., Reidenberg, J.S., Doyle, L.R. and McCowan, B.
Mar Mam Sci 2025 e70026.
https://doi.org/10.1111/mms.70026.
Scientists exploring how we might speak to extraterrestrials say that humpback whales might be signalling to us with bubbles.
Researchers found 12 examples of whales creating bubble rings near people, but none in various multi-year studies that observed whales remotely using drones.