Chris LB Graham
chrislbgraham.bsky.social
Chris LB Graham
@chrislbgraham.bsky.social
Research Fellow at University of Warwick.
Open Science, Proteins and Lipids.
Reposted by Chris LB Graham
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...
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...
doi.org
October 13, 2025 at 8:18 PM
Reposted by Chris LB Graham
CaCoFold-R3D: a probabilistic model that predicts RNA 3D motifs and secondary structure using evolutionary information.

www.nature.com/articles/s41...
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.
www.nature.com
October 3, 2025 at 1:25 PM
Reposted by Chris LB Graham
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...
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...
www.nature.com
September 18, 2025 at 8:09 PM
Reposted by Chris LB Graham
Bit under the weather today, so stayed at home to write a paper…..instead I’ve made an image of a Lego bacterial outer membrane.
September 3, 2025 at 11:12 AM
Reposted by Chris LB Graham
#microsky
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.

Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.

📄 www.nature.com/articles/s41...
Peptidoglycan–outer 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.
www.nature.com
July 29, 2025 at 1:23 PM
We have updated ConservFold. Now it can plot conservation onto whole protein complexes and can set the cutoffs you’d like! Thought it might be useful for people. colab.research.google.com/drive/1Lv-ak... @crodrigueslab.bsky.social
June 3, 2025 at 10:03 AM
Reposted by Chris LB Graham
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
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...
rdcu.be
May 28, 2025 at 10:30 AM
Reposted by Chris LB Graham
"Revolutionary"? More like reclaiming wisdom!

👏 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
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...
f24.my
May 27, 2025 at 8:03 AM
Reposted by Chris LB Graham
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...
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 ‘omics’ technologies. Their limited bios...
www.microbiologyresearch.org
May 26, 2025 at 5:12 PM
Reposted by Chris LB Graham
AlphaFold’s 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 👇 Feedback is welcome!
Predicting macromolecular ensembles is incredibly promising. However, as no single experimental method can map a conformational ensemble’s full atomistic landscape, there are foundational questions: What exactly are we trying to predict, and how will we know when we have succeeded?
From Possibility to Precision in Macromolecular Ensemble Prediction
Proteins and other macromolecules do not exist in a single state but as dynamic ensembles of interconverting conformations, which are essential for functions such as catalysis, allosteric regulation, ...
arxiv.org
May 7, 2025 at 4:49 AM
Reposted by 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
May 3, 2025 at 7:00 AM
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
May 3, 2025 at 7:00 AM
Reposted by Chris LB Graham
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...
May 1, 2025 at 12:35 AM
Reposted by Chris LB Graham
Nature research paper: The distribution of subsurface microplastics in the ocean

https://go.nature.com/4iHBBKS
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.
go.nature.com
April 30, 2025 at 6:25 PM
Reposted by Chris LB Graham
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/...
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
academic.oup.com
April 22, 2025 at 5:00 AM
Reposted by Chris LB Graham
Introducing SAVEMONEY, AKA ‘Simple Algorithm for Very Efficient Multiplexing of Oxford Nanopore Experiments for You’

A new tool offering a faster, cheaper computational approach to democratise whole-plasmid sequencing.
buff.ly/ov7YumB
April 14, 2025 at 10:02 AM
Reposted by Chris LB Graham
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.
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 ...
www.biorxiv.org
April 7, 2025 at 2:38 PM
Reposted by Chris LB Graham
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...
March 25, 2025 at 6:19 PM
Reposted by Chris LB Graham
Two esteemed colleagues both declared to me to eat more fries and more wine if we need to live longer. It’s gonna be a great Tuesday! I also hope the cafeteria adds more fried foods to the menu www.nature.com/articles/s41...
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 aging—encompassing cognitive, physical and mental health—were studied, identifying ...
www.nature.com
March 25, 2025 at 7:21 AM
London April 11th and 12th, I’m doing a tiny workshop (I’ll 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...
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
www.eventbrite.co.uk
March 21, 2025 at 10:18 PM
Reposted by Chris LB Graham
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!
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.
pubs.acs.org
March 18, 2025 at 1:23 PM
Reposted by Chris LB Graham
Come to the opening of the Warwick Integrated Structural Biology Symposium! @uni-of-warwick.bsky.social @warwicklifesci.bsky.social
March 5, 2025 at 9:19 AM
Reposted by Chris LB Graham
A really nice tool, like others that Artyom has produced. Highly recommend.
February 25, 2025 at 9:23 AM
Reposted by Chris LB Graham
Join us at the next Science on the Hill event on Tuesday 25 February. We’ll 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
Science on the Hill - Host Defence on the Offensive! — 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...
bit.ly
February 21, 2025 at 1:00 PM