MP
Cryo-EM structure of the dopamine transporter with a novel atypical non-competitive inhibitor bound to the orthosteric site.
Pedersen CN, Yang F, Ita S, Xu Y, Akunuri R, Trampari S, Neumann CMT, Desdorf LM, Schiøtt B, Salvino JM, Mortensen OV, Nissen P, Shahsavar A.
J Neurochem. 2024 Sep;168(9):2043-2055.
doi: 10.1111/jnc.16179. Epub 2024 Jul 15.
PMID: 39010681.
The dopamine transporter (DAT) regulates dopamine removal from the synaptic cleft, a process disrupted by psychostimulants like cocaine and amphetamine, which block dopamine uptake and amplify signaling.
Atypical DAT inhibitors, which lack the rewarding effects of cocaine, are promising for treating drug use disorders.
Here: structure of the Drosophila DAT bound to an atypical inhibitor, showing how it locks the transporter in an outward-open conformation => insights into non-competitive inhibition and strategies to design more effective inhibitors.
Dynamic basis of lipopolysaccharide export by LptB2FGC.
Dajka M, Rath T, Morgner N, Joseph B.
Elife. 2024 Oct 7;13:RP99338.
doi: 10.7554/eLife.99338.
PMID: 39374147.
Study of the conformational changes in LptB2FG during LPS transport => shows how ATP binding and hydrolysis drive structural shifts that regulate the LPS entry gate. The LptC protein modulates the flexibility of this gate, while the LptF β-jellyroll domain undergoes ATP-dependent allosteric changes to facilitate unidirectional LPS transport across the periplasm.
Native β-barrel substrates pass through two shared intermediates during folding on the BAM complex.
Dos Santos TMA, Thomson BD, Marquez MD, Pan L, Monfared TH, Kahne DE.
Proc Natl Acad Sci U S A. 2024 Oct 15;121(42):e2409672121.
doi: 10.1073/pnas.2409672121. Epub 2024 Oct 8.
PMID: 39378083.
The BAM complex facilitates the folding of diverse β-barrel proteins into membranes in E. coli.
Disulfide crosslinking method => folding process of different β-barrel substrates within the BamA lumen + identification of stable folding intermediates that occur at similar stages for different substrates.
This suggests that BAM addresses common folding barriers, enabling it to efficiently fold a wide range of β-barrel proteins despite their structural diversity.
Kinetic analysis of fluorescent ligand binding to cell surface receptors: Insights into conformational changes and allosterism in living cells.
Hill SJ, Kilpatrick LE.
Br J Pharmacol. 2024 Nov;181(21):4091-4102.
doi: 10.1111/bph.16185. Epub 2023 Jul 19.
PMID: 37386806.
Equilibrium binding assays are commonly used in drug discovery to assess drug-receptor interactions, but it is very important to also understand the kinetics of interactions (how long a drug stays bound and how quickly it associates with the receptor).
Here: review highlighting the use of fluorescent ligand technologies to study ligand-receptor kinetics in living cells => insights into the conformational changes induced by drugs targeting various receptors, including GPCRs, RTKs, and cytokine receptors.
On the function of TRAP substrate-binding proteins: conformational variation of the sialic acid binding protein SiaP.
King-Hudson TJ, Davies JS, Quan S, Currie MJ, Tillett ZD, Copping J, Panjikar S, Friemann R, Allison JR, North RA, Dobson RCJ.
J Biol Chem. 2024 Sep 30:107851.
doi: 10.1016/j.jbc.2024.107851. Epub ahead of print.
PMID: 39357825.
Tripartite ATP-independent periplasmic (TRAP) transporters, like ABC transporters, use a substrate-binding protein to capture metabolites and deliver them to membrane components for import.
Here: structure of the TRAP substrate-binding protein AaSiaP from Aggregatibacter actinomycetemcomitans in open, closed, and intermediate conformations.
MD and SAXS => the unliganded AaSiaP samples multiple conformations, highlighting the role of water molecules in stabilizing the closed state and leaving the mechanism of substrate release for import unresolved.
Structural basis of thiamine transport and drug recognition by SLC19A3.
Gabriel F, Spriestersbach L, Fuhrmann A, Jungnickel KEJ, Mostafavi S, Pardon E, Steyaert J, Löw C.
Nat Commun. 2024 Oct 2;15(1):8542.
doi: 10.1038/s41467-024-52872-8.
PMID: 39358356.
Thiamine (vitamin B1) is a vital coenzyme that humans must obtain through their diet, with its uptake into cells primarily mediated by the transporters SLC19A2 and SLC19A3.
Loss of function mutations => serious metabolic disorders.
Here: 7 cryo-EM structures of SLC19A3 in different transport cycle states, providing insights into thiamine recognition and transport, while also identifying seven new drug interactions and detailing its inhibition by fedratinib, amprolium, and hydroxychloroquine.
Membranes
Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
Mia L Abramsson, Robin A Corey, Jan L Skerle, Louise J Persson, Olivia Anden, Abraham O Oluwole, Rebecca J Howard, Erik Lindahl, Carol V Robinson, Kvido Strisovsky, Erik G Marklund, David Drew, Phillip J Stansfeld, and Michael Landreh
bioRxiv posted 8 October 2024
doi:10.1101/2024.05.27.592301
Study showing how CL stabilizes MPs and their complexes using a model protein (TMHC4_R) as a scaffold, combining MD and native mass spec.
Arrangement of positively charged residues and conformational flexibility are key factors in stabilizing CL interactions
Identification of a CL-stabilizing site in the E. coli protease GlpG, highlighting its regulatory role in enzyme substrate preference.
The application of nanodiscs in membrane protein drug discovery & development and drug delivery.
Dong Y, Tang H, Dai H, Zhao H, Wang J.
Front Chem. 2024 Sep 18;12:1444801.
doi: 10.3389/fchem.2024.1444801.
PMID: 39359422.
NDs offer significant advantages in studying MP structures, biochemical and physiological functions, as well as in drug discovery, development, and delivery.
Here: review highlighting the structural characteristics, benefits, and classifications of nanodiscs, with a particular emphasis on their growing importance in pharmaceutical industries for membrane protein-based drug research and drug delivery.
Lipopeptide antibiotics disrupt interactions of undecaprenyl phosphate with UptA.
Oluwole AO, Kalmankar NV, Guida M, Bennett JL, Poce G, Bolla JR, Robinson CV.
Proc Natl Acad Sci U S A. 2024 Oct 8;121(41):e2408315121.
doi: 10.1073/pnas.2408315121. Epub 2024 Oct 3.
PMID: 39361645.
PG pathway is a key antibacterial target, with the final step involving the translocation of the carrier lipid undecaprenyl phosphate (C55-P) across the membrane, facilitated by DedA and DUF368 domain-containing proteins.
Here: investigation of the interaction of UptA, a DedA family protein from Bacillus subtilis, with C55-P, PLs, and ATBs, using native mass spec.
UptA was found to bind C55-P in a pH-dependent manner and to be inhibited by antibiotics like amphomycin and aspartocin D, which compete for the same binding site.
Role of palmitoylation on the neuronal glycine transporter GlyT2.
Felipe R, Sarmiento-Jiménez J, Camafeita E, Vázquez J, López-Corcuera B.
J Neurochem. 2024 Sep;168(9):2056-2072.
doi: 10.1111/jnc.16181. Epub 2024 Jul 20.
PMID: 39032066.
The glycine transporter GlyT2 actively removes glycine from the synaptic cleft and helps maintain neurotransmitter levels in presynaptic vesicles, playing a crucial role in glycinergic signaling. Mutations in the GlyT2 gene (SLC6A5) cause hyperekplexia, a condition characterized by exaggerated startle responses and potentially life-threatening apnea in neonates.
Here: authors show that reversible palmitoylation of GlyT2 cysteine residues influences its inclusion in lipid rafts, as a mutant lacking these cysteines or treated with a palmitoylation inhibitor showed reduced lipid raft association, highlighting the role of post-translational modifications in GlyT2’s function.
A molecular mechanism for how pressure induces interdigitation of phospholipid bilayer membranes.
Goto M, Yoshida S, Habara S, Wilk-Kohlbrecher A, Kohlbrecher J, Tamai N, Matsuki H.
Biochim Biophys Acta Biomembr. 2024 Sep 28;1866(8):184385.
doi: 10.1016/j.bbamem.2024.184385. Epub ahead of print.
PMID: 39349289.
Study of the phase transition ofPC bilayers with two saturated long-chain fatty acids under high pressure, focusing on the transition from a ripple gel phase to an interdigitated gel phase using techniques like pressure-scanning microscopy, fluorometry, and DLS.
Suggestion that pressure-induced interdigitation is driven by increased repulsive interactions among the polar head groups as they reorient from a parallel to a perpendicular alignment with respect to the bilayer surface.
Molecules
Development of Putative Bivalent Dicovalent Ligands for the Adenosine A1 Receptor.
Payne CM, Baltos JA, Langiu M, Sinh Lu C, Tyndall JDA, Gregory KJ, May LT, Vernall AJ.
Chembiochem. 2024 Oct 1;25(19):e202400242.
doi: 10.1002/cbic.202400242. Epub 2024 Jul 12.
PMID: 38777792.
Recent studies indicate that GPCRs can function as homodimers and heterodimers, yet there is a lack of chemical tools to investigate these dimeric forms.
Here: synthesis and pharmacological evaluation of a novel class of bivalent GPCR ligands, each featuring a sulfonyl fluoride warhead designed to covalently bind to both A1Rs in a homodimer.
Authors show that these bivalent compounds act as competitive antagonists, exhibit covalent binding, and show increased selectivity for A1R over the adenosine A3 receptor compared to their monovalent counterparts, suggesting that dual occupation can enhance subtype selectivity.
Acylhydrazone-based reversibly photoswitchable ion pair transporter with OFF-ON cotransport activity.
Chattopadhayay S, Wanjari P, Talukdar P.
Chem Sci. 2024 Aug 30.
doi: 10.1039/d4sc02474e. Epub ahead of print.
PMID: 39355225.
Developing an artificial cation-anion symporter with stimulus-responsive capabilities is challenging.
Here: novel photoswitchable acylhydrazone-based transporter that exhibits unique OFF-ON cation-anion co-transport abilities, demonstrating enhanced ion transport efficiency through structural modifications.
Photoswitchable detergents for light-controlled liposome lysis and channel gating.
Max L, Repp D, Beka F, Wieneke R.
Chembiochem. 2024 Oct 2:e202400517.
doi: 10.1002/cbic.202400517. Epub ahead of print.
PMID: 39356116.
The use of photoswitchable lipids to modulate membrane properties has garnered interest due to their precise spatiotemporal control.
Here: concept expanded by introducing photoswitchable detergents.
Three classes of visible light-sensitive surfactants with varying azobenzene tail chain lengths were synthesized, exhibiting water solubility, micellization, and reversible isomerization under blue and green light.
Light-induced structural changes can cause vesicle rupture for controlled cargo release and facilitate the optical activation of mechanosensitive channels in mammalian cells, enabling the rapid uptake of membrane-impermeable molecules.
Methods
How to isolate channel-forming membrane proteins using the E. coli expression system.
Piselli C.
Nat Protoc. 2024 Oct 4.
doi: 10.1038/s41596-024-01055-2. Epub ahead of print.
PMID: 39367089.
Systematic approach for the recombinant expression, isolation, and characterization of pore-forming proteins to investigate the permeability properties of biological membranes. It focuses on optimizing protein production in E. coli strain BL21Gold(de3)ΔABCF.
The protocol also allows for the insertion of purified porins into outer membrane vesicles for copurification, and it can be adapted for various membrane-active proteins from different organisms, making it a versatile tool for studying channel-forming proteins.
Recent Advances in Expression Screening and Sample Evaluation for Structural Studies of Membrane Proteins.
Huang Y, Zhang Z, Hattori M.
J Mol Biol. 2024 Oct 1;436(22):168809.
doi: 10.1016/j.jmb.2024.168809. Epub ahead of print.
PMID: 39362625.
The advent of FSEC has transformed the evaluation of MP constructs, allowing for rapid assessment of expression and behavior on a small scale without the need for extensive purification.
The review highlights the latest advances and diverse applications of FSEC in MP research.
MiLoPYP: self-supervised molecular pattern mining and particle localization in situ.
Huang Q, Zhou Y, Bartesaghi A.
Nat Methods. 2024 Sep 9.
doi: 10.1038/s41592-024-02403-6. Epub ahead of print.
PMID: 39251798.
Cryo-electron tomography faces challenges such as automatic protein identification and localization persist due to molecular crowding, imaging distortions, and large dataset sizes, leading to methods that often require extensive manual intervention and have limited accuracy.
Here: MiLoPYP, a two-step contrastive learning framework that enhances molecular pattern detection and localization, improving the applicability of high-resolution techniques for in situ structural analysis.
Metal fluorides-multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide.
Pellegrini E, Juyoux P, von Velsen J, Baxter NJ, Dannatt HRW, Jin Y, Cliff MJ, Waltho JP, Bowler MW.
Structure. 2024 Oct 3;32(10):1834-1846.e3.
doi: 10.1016/j.str.2024.07.007. Epub 2024 Aug 5.
PMID: 39106858.
Metal fluorides, which mimic the charge of phosphate groups, serve as multifunctional tools to study these enzymes by allowing researchers to trap them in important catalytic states and perform spectroscopic analyses.
Here: best practices for obtaining enzyme-metal fluoride complexes for structural techniques and introduces scandium tetrafluoride as a new metal fluoride with a significant anomalous signal for soft X-ray applications.
A cell-free system for functional studies of small membrane proteins.
Jiang S, Çelen G, Glatter T, Niederholtmeyer H, Yuan J.
J Biol Chem. 2024 Oct 1:107850.
doi: 10.1016/j.jbc.2024.107850. Epub ahead of print.
PMID: 39362471.
Many small hydrophobic proteins across all domains of life are predicted to localize to cell membranes and play crucial roles in various biological processes, such as cell signaling and nutrient transport; however, their functions often remain unclear due to challenges in protein production.
Here: combination of a cell-free system with lipid sponge droplets to synthesize small membrane proteins in vitro, successfully producing functionally active proteins like MgrB, SafA, and AcrZ at micromolar concentrations.
In situ surface-enhanced Raman spectroscopy for membrane protein analysis and sensing.
Xu G, Yu J, Liu S, Cai L, Han XX.
Biosens Bioelectron. 2024 Sep 30;267:116819.
doi: 10.1016/j.bios.2024.116819. Epub ahead of print.
PMID: 39362137.
Review highlighting the advantages of surface-enhanced Raman spectroscopy (SERS) for in situ, real-time characterization of MPs under physiological conditions, detailing SERS theories, strategies for assembling phospholipid biolayers, and approaches for sensing protein interactions.
Glucose Transporter-Targeting Chimeras Enabling Tumor-Selective Degradation of Secreted and Membrane Proteins.
Yun C, Li N, Zhang Y, Fang T, Ma J, Zheng Z, Zhou S, Cai X.
ACS Chem Biol. 2024 Oct 18;19(10):2254-2263.
doi: 10.1021/acschembio.4c00584. Epub 2024 Oct 7.
PMID: 39374326.
Novel strategy for tumor-selective protein degradation by utilizing facilitative glucose transporters (GLUTs), which are overexpressed in various cancers, to drive the endocytosis and lysosomal degradation of target proteins.
Authors developed GLUT-targeting chimeras (GTACs) by conjugating glucose ligands to antibodies specific for proteins like streptavidin, TNF-α, and HER2, demonstrating that GTACs enhanced internalization and degradation of these proteins while improving tumor-targeting efficiency.
Miscellaneous
Olfactory neurons selectively respond to related visual and verbal cues.
Franks K, Schaefer A.
Nature. 2024 Oct;634(8034):547-548.
doi: 10.1038/d41586-024-03056-3.
PMID: 39384914.
What is the neural basis of our perceptual experience? Simultaneous recordings from many individual neurons in humans provide surprising insights into how odours are processed in different regions of the brain.
A Versatile Magnetic Nanoplatform for Plug-and-Play Functionalization: Genetically Programmable Cargo Loading to Bacterial Magnetosomes by SpyCatcher “Click Biology”.
Mickoleit F, Beierl JJ, Markert S, Klein MA, Stäbler SY, Maier DS, Schüler D.
ACS Nano. 2024 Oct 15;18(41):27974-27987.
doi: 10.1021/acsnano.4c05588. Epub 2024 Oct 4.
PMID: 39365667.
Bacterial magnetosomes (MAGs) are a type of magnetic iron oxide nanoparticle with significant potential for biomedical and biotechnological applications.
Here: introduction of a versatile platform for the surface functionalization of MAGs using the SpyTag-SpyCatcher (ST-SC) bioconjugate system => efficient binding of various protein cargo, including enzymes, antibodies, and fluorophores. The ST-SC system enables the generation of multifunctional MAGs with controlled properties and applications, such as selective protein pulldown, making them a flexible nanoscaffold for diverse uses in biotechnology and biomedicine.
Growing number of Earth’s ‘vital signs’ endangered by climate change
James Dinneen
A blunt and damning report on the state of the climate crisis concludes that “much of the very fabric of life on Earth is imperilled”. A selection of 35 planetary vital signs such as greenhouse gas emissions and Antarctic ice loss tell the tale: 25 of them have reached record levels this year. Most broke records last year too. “It is staggering that in a world where billions of people are already suffering from the impacts of climate change fossil fuel emissions and deforestation rates are not slowing but they are actually increasing” says ecologist and co-author Thomas Crowther.
How to keep research afloat during an administrative stint.
Wild S.
Nature. 2024 Oct 8.
doi: 10.1038/d41586-024-03228-1. Epub ahead of print.
PMID: 39379725.
“Research is not a tap that you can switch on and off” says plant geneticist Brenda Wingfield. She spent eight years as deputy dean of research at her institution a role that like any senior management job comes with administrative demands that can make it difficult to keep one foot in research. Wingfield and other scholars who have spent time in management positions gave Nature their tips on how you can keep research creativity flowing during a tenure as one of the higher-ups.
The huge toll of PhDs on mental health: data reveal stark effects.
Schwaller F.
Nature. 2024 Oct;634(8033):277-278.
doi: 10.1038/d41586-024-03136-4.
PMID: 39354137.
The longer someone continues their doctoral studies the more they need access to mental-health services and medicines such as antidepressants and sedatives. A study of more than 20000 Swedish PhD students found that by their fifth year of study PhD candidates were 40% more likely to be prescribed psychiatric medication compared with the year before they started studying. After the average length of a PhD their uptake of mental-health services by students drops again.
Your toothbrush is teeming with hundreds of types of viruses
Carissa Wong
Toothbrushes and showerheads are hotbeds of unknown viruses — but before you throw yours away they aren’t the kind that’s harmful to humans. Researchers analysed swabs from 36 toothbrushes and 96 shower heads and found DNA from more than 600 bacteriophages — viruses that infect bacteria. Most of these viruses had never been described before. “It’s amazing how much untapped biodiversity is all around us” says microbiologist and co-author Erica Hartmann. “And you don’t even have to go far to find it it’s right under our noses.”
Bacteria implanted in fungi hints at ancient relationships that helped cells evolve.
Callaway E.
Nature. 2024 Oct;634(8034):520-521.
doi: 10.1038/d41586-024-03224-5.
With a tiny hollow needle and a bicycle pump scientists have successfully kick-started an artificial endosymbiotic relationship by implanting bacteria into a fungus cell. These relationships in which a microbial partner lives harmoniously within the cells of another organism are thought to be what sparked the evolution of complex life. The systems could help researchers to understand how cell structures such as mitochondria and chloroplasts emerged more than a billion years ago. Researchers recreated a natural symbiosis by implanting the bacterium Mycetohabitans rhizoxinica into the fungi Rhizopus microsporus. When spores germinated bacteria were also present in the cells of the next generation of fungi showing that the endosymbiosis could be passed onto offspring.
How to win a Nobel prize: what kind of scientist scoops medals?
Smith K, Ryan C.
Nature. 2024 Oct 3.
doi: 10.1038/d41586-024-02897-2. Epub ahead of print.
PMID: 39363021.
What subjects have past winners studied? What age were they when they won? Where do they live? Nature crunched the data on the 346 prizes and their 646 winners to work out which characteristics can be reliably linked to medals.
A ”leisurely scroll” (sic):