How do cells convert mechanical information into a molecular process? The @alushinlab.bsky.social has captured the first snapshot of a mechanical signaling complex in action, findings in @nature.com that have implications for disorders related to myosin dysfunction.
🔗: https://bit.ly/41Kshjw
Our latest work on shape-programmable tissues is out in @science.org. By positioning topological defects in cellular nematics, we encode frustrated 2D force fields that relax into predictable 3D shapes. Collaboration with Marino Arroyo’s lab, led by @pauguillamat.bsky.social at @ibecbarcelona.eu.
A 3D model of DNA. Text says RSB training, an introduction to CryoEM, Tuesday 7 July, 9:30-16:30, The University of Leicester
Are you looking for a training course that will provide you with an introduction to cryoEM and its applications in structural biology ? Then join us in July!
📆 Tues 7 Jul, 9:30-16:30, University of Leicester
Book your place: my.rsb.org.uk/item.php?eve...
#Training #CryoEM
Our paper on the proton-driven secondary active #transporter SbmA for antimicrobial peptides is finally out! We used #cryoEM, #EPR, #MD to show that it resembles and undergoes conformational changes like #ABC transporter TMDs consistent with an alternating-access transport mechanism.
Across scales from cells🦠 to atoms⚛️ – We reveal how anaerobic #bacteria break down very stable aromatic compounds found e.g. in oil spills 🛢️ #Bioremediation #TeamTomo 🧪 🧶🧬 🔬
Awesome collab with Lena, Matthias, @schullerjm.bsky.social @rnfr2d2.bsky.social @tomaspascoa.bsky.social @tamb-o.bsky.social
a simplified evolutionary tree of eukaryotes with pictures of various microbes
New #ISEPpapers #preprint by @deemteam.bsky.social: Re-evaluating the eukaryotic Tree of Life with independent phylogenomic data www.biorxiv.org/content/10.6...
#Protists #Microbes #Evolution #Eukaryotes #TreeOfLife #Phylogeny #Phylogenomics #Bioinformatics #Algae
How do “LEGO-like” electron-bifurcating modules combine to drive degradation in BTEX-contaminated ecosystems?
Check out our latest preprint, where we use cryo-EM and cryo-ET to reveal how the 1 MDa BCRII complex powers extremely endergonic aromatic ring reduction.
www.biorxiv.org/content/10.6...
One of biggest mysteries in biology: how did complex eukaryotic cells evolve from simple microbes? ~1.8 billion years ago, an archaeal cell likely merged with a bacterium to form the first eukaryotic cell, but can we ever find direct evidence of this transformative event? 🦠 🚶♂️
Now published J. Med. Chem! @zestytoast.bsky.social's structure of type II NADH dehydrogenase from mycobacteria. A promising drug target for TB & other mycobacterial infections, Yingke demonstrates how an inhibitor can block transfer of electrons from NADH to the ETC.
pubs.acs.org/doi/full/10....
In the first preprint from the lab, @sandaru-ileperuma.bsky.social demonstrates that the P. aeruginosa NQR complex supports virulence factors and identifies inhibitors of this complex. He also uncovered some interesting NQR dynamics controlled at the substrate binding site. tinyurl.com/yush599n
I am excited to share our most recent work collaborating with @centriolelab.bsky.social and @stearnslab.bsky.social to look at the ciliary base of mammalian multiciliated cells w/ cryo-ET, XL/MS, and U-ExM www.biorxiv.org/content/10.6...
April's Molecule of the Month: Insect Odorant Receptors
These protein complexes allow insects to detect a wide variety of volatile compounds, from clove oil to DEET
#Ichthyosporea are not just the 5–6 species we and others have helped establish as models. Our recent synthesis suggests that ~95% of their species-level diversity remains uncultivated. In other words, we still know only a fraction of the map! #protistsonSky @ibe-barcelona.bsky.social @prbb.org
Excited to share our new paper in @natcomms.nature.com !
Here, we present the cryo-EM structure of the Cytc₆:PSI complex from Chlamydomonas reinhardtii👇
www.nature.com/articles/s41...
Added custom menus, including one to quickly add common monomers (detergents, buffers etc):
Added a little script to chimerax-trimmings to automate the creation of panels for model-map fit figures.
It zones the map around (by default) 40aa parts of each chain (but doesn't cut in the middle of helices). Saves each as a png, metadata to csv.
Saves each view as a scene for tweaking views.
Our work with the Brun lab on the in situ architecture of the Caulobacter crescentus Tad pilus machine is published in mBio. Amazing collaborative effort led by James Iarocci @jamesiarocci.bsky.social
Excited to share our work on the structure and function of cytoplasmic lattices within mouse embryos. A collaborative effort with @niakanlab.bsky.social and work led by @kashishsingh.bsky.social and @inaharasimov.bsky.social . It is now out on BioRxiv: www.biorxiv.org/content/10.6...
Happy to share my first adventure in #TeamTomo in collaboration with the talented @inaharasimov.bsky.social. It was a fun experience experience with a lot of learning along the way.
Finally got around to porting my coot-trimmings scripts over to Coot 1... only the hotkeys are working (nothing requiring creating a custom menu or GUI dialog), but I've added a couple of new ones, e.g. copy/pasting ligands.
Check it out & let me know what you think! 😊
github.com/olibclarke/c...
Schematic overview of crista shaping components in traditional and unconventional model organisms. (A) The MICOS in yeast (left) and T. brucei (right). Conserved proteins directly involved in membrane bending are shown in green, conserved proteins with an indirect or unclear involvement in membrane bending are shown in red, T. brucei-specific proteins are shown in yellow if directly involved in membrane bending, or in purple if they have an indirect effect. Numbers refer to the respective MICOS components: MIC60, MIC19, MIC10, MIC12, MIC26 and MIC27 in yeast, and MIC24, MIC34, MIC40, MIC10-1, MIC10-2, MIC20, MIC17, MIC32 and MIC16 in T. brucei. (B) Schematic figure of ATP synthase characteristics in yeast, T. brucei, T. gondii and P. falciparum. Dimeric ATP synthase structures have been solved for yeast, T. brucei and T. gondii, revealing dimer angles of 86°, 60° and 19°, respectively. For P. falciparum, the dimer angle is unknown. The different oligomerization states observed in these organisms are associated with different cristae shapes. In yeast, dimer rows produce lamellar cristae; in T. brucei, helical arrays of dimers produce discoidal cristae; in T. gondii, hexameric oligomerization generates bulbous cristae. The oligomerization state of P. falciparum ATP synthase is unknown (indicated by the question mark) but P. falciparum has been shown to have bulbous morphology of cristae.
In their Review, Silvia Tassan-Lugrezin, Silje Debets, Laura van Niftrik, Taco Kooij & Irina Bregy compare crista across Euglenozoa, Alveolata & Opisthokonta to delineate evolutionarily conserved mechanisms underpinning a general model for crista formation.
journals.biologists.com/jcs/article/...
Nature research paper: Snapshots of the dynamic basis of NTSR1 G protein subtype promiscuity
go.nature.com/4rqJcSA
In a new Science study, researchers find that some bird species share convergent evolutionary changes in key physiological traits and metabolic genes that enable their high-sugar diets. https://scim.ag/4bgMrpy
At the center of every nuclear pore lies a mystery. Here, clumps of proteins wiggle disordered tails around like seaweed. How do they drive a molecular machine that moves so many molecules in and out of the nucleus efficiently, with little room for error? www.quantamagazine.org/disorder-dri...
The discovery adds to the Archimedes Palimpsest, an important medieval manuscript containing texts from the Greek mathematician Archimedes
For the first time, researchers have simulated nearly every chemical reaction in a living bacterial cell
go.nature.com/4lrAulM
Figure 1. Cryo-EM of abundant protein complexes in native membranes.
Figure 2. Cryo-EM of membrane proteins in vesicles.
Figure 3. 3D reconstruction of V-ATPase in native synaptic vesicle membranes.
Figure 4. Generation of membrane vesicles for structure determination of proteins in their native lipid bilayer.
I've written a review on what I think is an extremely exciting direction in cryo-EM:
Cryo-EM of endogenous membrane proteins in their native lipid bilayer
Open access in Quarterly Reviews of Biophysics:
doi.org/10.1017/S003...
Please check out our new preprint! Using single cell analysis paired with HCR to visualize transcript localization we have identified cell and tissue-specific expression of various genes encoding tubulins, kifs, and dyneins during neural crest development!
Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...
