Chris LB Graham

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life.

This paper describes a ribozyme, a catalytic RNA molecule, able to do just that..

Fascinating stuff…

🧪🦠

www.science.org/doi/10.1126/...

Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)

Characterization of two novel bacteriophages infecting clinical isolates of Serratia spp. and therapeutic efficacy in a Galleria mellonella model of infection AbstractAims. This study aimed to isolate virulent bacteriophages (phages) with the capacity to lyse clinical strains belonging to the genus Serratia. Furt

🚨 New Research Alert!
Our team has discovered two new bacteriophages that target Serratia spp.—a major cause of hospital‑associated infections and a growing antibiotic‑resistance threat.
📄 Open‑access article in Journal of Applied Microbiology: doi.org/10.1093/jambio/lxag011

Excited to share our preprint that describes the mechanism of action of an historical infection remedy called Bald’s Eyesalve. In this preprint, we show that Bald’s Eyesalve has multifaceted mechanism of action against both S. aureus and A. baumannii (1/n).

Image-based bacterial phenotyping and antimicrobial drug discovery using smart high-throughput super-resolution microscopy at University of Warwick on FindAPhD.com PhD Project - Image-based bacterial phenotyping and antimicrobial drug discovery using smart high-throughput super-resolution microscopy at University of Warwick, listed on FindAPhD.com

iCASE PhD project available in my lab, combining microscopy method development with high throughput screening of bacteria. Applications to antibiotic drug discovery and screening for new cell division proteins. Collaboration with Cairn Research #microsky #bioimaging
www.findaphd.com/phds/project...

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...

A pipeline that joins GREMLIN coevolution, to mmseqs2 and input structures. Also hypothetical gene networks

Check out these tools to detect co-evolution in protein-protein interactions developed by postdoc @chrislbgraham.bsky.social

Very useful as a hypothesis generator, complementing protein interaction prediction from Alphafold.

www.biorxiv.org/content/10.6...

(Top left) CoEVFold window, MMSEQ2 alignment and a3m production based on query sequence – B subtilis FtsW-PbpB >50% sequence coverage. Red – Low coverage/conservation, Blue/Green – High coverage/conservation (Top right) Coevolution of FtsW-PbpB performed using pipeline on transformed alignment. Indicating regions of intermolecular and intramolecular coevolution Dark Blue – coevolution high, White – no observed coevolution Z score min=0, max=3 (Bottom panel) user input structure FtsW-PbpB predicted by Alphafold, inter-protein coevolution has been indicated using red dashed lines = Coevolution at user thresholds (12A, <1.5 Z score).

We finally released a little coevolution pipeline, so you can add coevolution to predicted structures. With this you can understand more how proteins may genetically interact, as heteromers, homomers or hypothetical networks (or perhaps not) www.biorxiv.org/content/10.6...

MemPrO: A Predictive Tool for Membrane Protein Orientation Membrane proteins play a vital role in numerous cellular processes, including ion transport, intercellular communication, and antibiotic resistance. Ensuring their accurate orientation within lipid bi...

🌟 New Tool Alert!

We present MemPrO – a toolkit for orienting and building membrane protein systems:

✅ Membrane protein orientation 
✅ Mixed membrane building 
✅ Double membranes & curvature 
✅ Peptidoglycan cell wall support

🔗 github.com/pstansfeld/mempro 
📖 pubs.acs.org/doi/10.1021/...

Fantastic to be part of this which was published today, Dr Nic Briggs and newly minted Dr Jack Stone from my lab did the experimental works that contributed to the paper with Christophe Grangeasse and colleagues. @warwicklifesci.bsky.social

Super collaboration with @raffaeleieva.bsky.social and @fronzeslab.bsky.social on the LptDEMY complex.

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...

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...

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.

CaCoFold-R3D: a probabilistic model that predicts RNA 3D motifs and secondary structure using evolutionary information.

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...

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...

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.

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.

#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...

@crodrigueslab.bsky.social

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

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...

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

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...

"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

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...

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...

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!

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

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

Have you got a website with quotes to share?

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...

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.

Nature research paper: The distribution of subsurface microplastics in the ocean

https://go.nature.com/4iHBBKS

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

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/...