Chris LB Graham
@chrislbgraham.bsky.social
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Research Fellow at University of Warwick. Open Science, Proteins and Lipids.
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Chris LB Graham
Phill Stansfeld
19 days ago
Super collaboration with
@raffaeleieva.bsky.social
and
@fronzeslab.bsky.social
on the LptDEMY complex.
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Lori L. Burrows
2 months ago
New paper alert! We used our fav technique, genetic suppression, to understand how FimX controls function of the T4P PilB motor ATPase in Pseudomonas aeruginosa. Great collab with the Ellison lab at U Georgia who helped with some fancy microscopy to capture pilus dynamics!
doi.org/10.1371/jour...
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Twitching motility suppressors reveal a role for FimX in type IV pilus extension dynamics
Author summary Type IV pili enable Pseudomonas aeruginosa to attach to surfaces, move (twitch), and form biofilms. Pilus extension is powered by the motor protein PilB, which is regulated by other fac...
https://doi.org/10.1371/journal.pgen.1011802
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Chris LB Graham
Nature Methods
2 months ago
CaCoFold-R3D: a probabilistic model that predicts RNA 3D motifs and secondary structure using evolutionary information.
www.nature.com/articles/s41...
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All-at-once RNA folding with 3D motif prediction framed by evolutionary information - Nature Methods
CaCoFold-R3D is a probabilistic model that simultaneously predicts the RNA 3D motifs jointly with the secondary structure in a structural RNA using evolutionary information.
https://www.nature.com/articles/s41592-025-02833-w
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Nature Methods
3 months ago
GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek.
@martinsteinegger.bsky.social
@milot.bsky.social
@machine.learning.bio
www.nature.com/articles/s41...
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GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
https://www.nature.com/articles/s41592-025-02819-8
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Syma Khalid
3 months ago
Bit under the weather today, so stayed at home to write a paperā¦..instead Iāve made an image of a Lego bacterial outer membrane.
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Michael Deghelt
5 months ago
#microsky
We challenge the long-standing view that peptidoglycan alone protects cells from bursting. Our study shows that the periplasm ā enclosed by OMāPG connections ā acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria. š
www.nature.com/articles/s41...
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Peptidoglycanāouter membrane attachment generates periplasmic pressure to prevent lysis in Gram-negative bacteria - Nature Microbiology
Outer membrane attachment to peptidoglycan enables periplasmic pressure to build up and counter cytoplasmic turgor pressure, preventing lysis during osmotic challenges in Escherichia coli.
https://www.nature.com/articles/s41564-025-02058-9
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We have updated ConservFold. Now it can plot conservation onto whole protein complexes and can set the cutoffs youād like! Thought it might be useful for people.
colab.research.google.com/drive/1Lv-ak...
@crodrigueslab.bsky.social
6 months ago
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Chris LB Graham
7 months ago
Beta-lactams covalently bind to Penicillin Binding Proteins and have been the mainstay of antimicrobial chemotherapy for decades. In this new paper with colleagues @Bicycle_tx we show a new way to hit old targets:
rdcu.be/eoaRI
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Discovery and chemical optimisation of a potent, Bi-cyclic antimicrobial inhibitor of Escherichia coli PBP3
Communications Biology - Discovery of a bicyclic peptide inhibitor of cell wall biosynthesis in the Enterobacterales demonstrates applicability of a modified phage display platform to antibiotic...
https://rdcu.be/eoaRI
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Chris LB Graham
Slow Food
7 months ago
"Revolutionary"? More like reclaiming wisdom! š French farmers & scientists prove nature-based farming (no
#pesticides
, no synthetics), the way humans farmed for centuries, still delivers steady yields, stable incomes & boosts biodiversity after 30 years.
#ClimateAction
f24.my/BCO5.BS
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Down to Earth - Chemical-free farming brings life back to rural France
Faced with widespread chemical pollution and a dramatic collapse in biodiversity, farmers and scientists in western France have been testing a revolutionary farming model for over 30 years. No pestici...
https://f24.my/BCO5.BS
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Chris LB Graham
Pedro J. Cabello-Yeves
7 months ago
Another great collaboration where we studied the type IV SS of CPRs, which certainly opens new avenues for the study of these enigmatic (mostly epibiotic) organisms!
@frvalera.bsky.social
www.microbiologyresearch.org/content/jour...
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The type IV secretion system of Patescibacteria is homologous to the bacterial monoderm conjugation machinery
The Candidate Phyla Radiation, also known as Patescibacteria, represents a vast and diverse division of bacteria that has come to light via culture-independent āomicsā technologies. Their limited bios...
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001409?TRACK=RSS
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Max Bonomi
7 months ago
AlphaFoldās success builds on decades of tech advances, massive efforts to collect, curate, and share structural data, and rigorous benchmarking. What will it take to see a similar leap in structural ensemble prediction?
@stephanieaw.bsky.social
and I share some thoughts here š Feedback is welcome!
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Chris LB Graham
Just released a pre-print:
www.biorxiv.org/content/10.1...
We simulate lipid membrane toroids of bacteria, representing the point where one cell splits into two. We see they are stable and then look at how a key protein might behave at them
@crodrigueslab.bsky.social
@pstansfeld.bsky.social
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7 months ago
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Just released a pre-print:
www.biorxiv.org/content/10.1...
We simulate lipid membrane toroids of bacteria, representing the point where one cell splits into two. We see they are stable and then look at how a key protein might behave at them
@crodrigueslab.bsky.social
@pstansfeld.bsky.social
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7 months ago
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Chris LB Graham
ChimeraX
8 months ago
ChimeraX daily builds can predict small complexes of proteins, nucleic acids and small molecules using Boltz on your Mac, Windows or Linux computer without Nvidia graphics.
www.rbvi.ucsf.edu/chimerax/dat...
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Chris LB Graham
Nature
8 months ago
Nature research paper: The distribution of subsurface microplastics in the ocean
https://go.nature.com/4iHBBKS
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The distribution of subsurface microplastics in the ocean - Nature
Global data collected between 2014 and 2024 provide insights into the distribution and potential transport mechanisms of subsurface microplastics throughout the oceanic water column.
https://go.nature.com/4jUzlRv
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Chris LB Graham
Taylor priest
8 months ago
A huge, new resource for plasmid research - PlasmidScope is a database of 852,000
#plasmid
sequences with a rich set of annotations, automated online analysis and interactive visualisation
academic.oup.com/nar/article/...
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PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools
Abstract. Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They co
https://academic.oup.com/nar/article/53/D1/D179/7832352?login=false
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Chris LB Graham
eLife
8 months ago
Introducing SAVEMONEY, AKA āSimple Algorithm for Very Efficient Multiplexing of Oxford Nanopore Experiments for Youā A new tool offering a faster, cheaper computational approach to democratise whole-plasmid sequencing.
buff.ly/ov7YumB
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Chris LB Graham
Raffaele Ieva
8 months ago
Here our new preprint on the LPS holo-translocon
doi.org/10.1101/2025...
, collaboration with Yves Quentin @JulieMarcoux
@fronzeslab.bsky.social
@pstansfeld.bsky.social
-
@cbitoulouse.bsky.social
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Structural Basis of Lipopolysaccharide Assembly by the Outer Membrane Translocon Holo-Complex
Lipopolysaccharide (LPS) assembly at the surfaces-exposed leaflet of the bacterial outer membrane (OM) is mediated by the OM LPS translocon. An essential transmembrane beta-barrel protein, LptD, and a...
https://doi.org/10.1101/2025.04.10.648201
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Chris LB Graham
Allister Crow
8 months ago
New preprint! FtsEX-EnvC is a Type VII ABC transporter that activates the periplasmic enzymes needed to break the peptidoglycan layer during cell division. We tested the importance of structural features underpinning activation and the auto-inhibition mechanism that keeps it all in check.
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Probing the mechanism of peptidoglycan amidase activation by FtsEX-EnvC
The FtsEX-EnvC-AmiA/B system is a key component of the E. coli cell division machinery that directs breakage of the peptidoglycan layer during separation of daughter cells. Structural and mechanistic ...
https://www.biorxiv.org/content/10.1101/2025.04.02.646785v1
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PNAS Nexus
9 months ago
Enzymes found in landfills around the world may be able to break down plastic waste. By using metagenomics and machine learning, a global collection of plastic biocatalytic enzymes has been identified. Plastics may not be forever, anymore. In PNAS Nexus:
academic.oup.com/pnasnexus/ar...
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Chris LB Graham
Kelvin Lau @klausenhauser on š āāļøššŖ”
9 months ago
Two esteemed colleagues both declared to me to eat more fries and more wine if we need to live longer. Itās gonna be a great Tuesday! I also hope the cafeteria adds more fried foods to the menu
www.nature.com/articles/s41...
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Optimal dietary patterns for healthy aging - Nature Medicine
In two longitudinal cohorts followed for 30 years, the associations of eight different dietary patterns with healthy agingāencompassing cognitive, physical and mental healthāwere studied, identifying ...
https://www.nature.com/articles/s41591-025-03570-5
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London April 11th and 12th, Iām doing a tiny workshop (Iāll be there the Saturday) with my friend on how to do PCR on worms plastic poop. It could be interesting if anyone wants to teach anyone a bit of hands on science on a weekend. PCR: barcode bacterial DNA
www.eventbrite.co.uk/e/pcr-barcod...
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PCR: barcode bacterial DNA
Grow bacteria, extract their DNA and investigate like a scientist. Possibly the only serious PCR experiment open to non-student in London
https://www.eventbrite.co.uk/e/pcr-barcode-bacterial-dna-tickets-1264734377569?utm-campaign=social&utm-content=attendeeshare&utm-medium=discovery&utm-term=listing&utm-source=wsa&aff=ebdsshwebmobile
9 months ago
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Chris LB Graham
Antonia Sagona
9 months ago
pubs.acs.org/doi/10.1021/...
New paper from the lab! Thanks to Fabrizio Alberti and his lab for the great collaboration and to Michael Tadesse for all his hard work!! Thanks
@warwicklifesci.bsky.social
, MIBTP and BBSRC for funding!
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One-Two Punch: Phage-Antibiotic Synergy Observed against Staphylococcus aureus by Combining Pleurotin and Phage K
The surge in antibiotic-resistant Staphylococcus aureus infections has been deemed a major public health concern. There is an urgent need for novel antimicrobial therapies, chemical and nonantibiotic. The basidiomycota-derived, secondary metabolite pleurotin has been shown to be effective against Gram-positive bacteria, while bacteriophages could be the ultimate nonantibiotic alternative. In this study, the combination of pleurotin and phage K targeting S. aureus was examined. Pleurotin was isolated from the basidiomycota fungus Hohenbuehelia grisea. The cytotoxicity of pleurotin was assessed in two human cell lines in comparison to pleuromutilin, vancomycin, and phage K. The antibiotics were then tested independently or in combination with phage K against two S. aureus strains. Cytotoxicity of pleurotin in human cells was comparable to vancomycin and pleuromutilin. Results suggest that adding phage K has a synergistic effect and can lower the MIC for pleurotin, pleuromutilin, and vancomycin. This demonstrates that pleurotin could be a viable antistaphylococcal drug.
https://pubs.acs.org/doi/10.1021/acsomega.4c09831
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Chris LB Graham
9 months ago
Come to the opening of the Warwick Integrated Structural Biology Symposium!
@uni-of-warwick.bsky.social
@warwicklifesci.bsky.social
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Branko Rihtman
10 months ago
A really nice tool, like others that Artyom has produced. Highly recommend.
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Chris LB Graham
School of Life Sciences, University of Warwick
10 months ago
Join us at the next Science on the Hill event on Tuesday 25 February. Weāll delve into how different biological systems combat attacks from other organisms - highlighting the human and plant immune systems. Find out more and book your place
bit.ly/435PAGo
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Science on the Hill - Host Defence on the Offensive! ā Resonate Festival
Science on this Hill is back for 2025! Visit the team at Gibbet Hill to find out about how biological systems combat attacks from other organisms, discover the techniques used by human and plant immun...
https://bit.ly/435PAGo
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Chris LB Graham
10 months ago
come and join in !
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