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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 11h

This is reminiscent of the subset of bacterial toxins that hijack retrograde translocation and the ERAD machinery to get into the cytosol. Their active, translocated subunits are also lysine deserts!

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 20h

The proteasome-substrate-shuttle protein UBQLN2 contains—like other quality control system proteins—a long region devoid of lysine (a lysine desert)

Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation

doi.org/10.1101/2025...

Fig. 1 – UBQLN2 is a conserved lysine-depleted protein. (A) Sequence comparison of
UBQLN2 orthologs in the indicated species. Intrinsically disordered regions in human
UBQLN2 based on MobiDB are shown as a blue bar. The domain organization based on the
SMART database is marked. Lysine residues are marked as black squares. (B) ESM-2
predictions of all possible single amino acid substitutions of human UBQLN2 presented as a
heat map. The wild-type residues are marked in blue. ESM-2 scores close to zero (light
yellow colors) indicate that the amino acid substitution is compatible with the ESM-2
language model, whereas negative scores (dark orange colors) indicate that the variant is
incompatible with the ESM-2 model. The domain organization (based on SMART) is aligned
above the map. Note that substitutions to lysine or cysteine in general appear detrimental, in
particular downstream of the UBL domain. (C) The AlphaFold2 predicted structured of
human UBQLN2 (AF-Q9UHD9-F1) (left panel). The UBL domain is colored blue, and the
UBA domain is colored orange and the STI1 regions green. Zoom in on the UBL domain
(right panel) with the lysine residues highlighted as stick representations and colored based
on the relative accessible surface area (rASA, dark red exposed; grey, buried).

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 6d

Christopher did a great job on this cover!

Structural Biology @actacrystd.iucr.org · 6d

October issue is now available! journals.iucr.org/d/issues/202...

The cover highlights the article on categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures from the Richardson lab @duke-university.bsky.social : doi.org/10.1107/S205...

Image credit: Chistopher Williams

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 10d

I did not know that! That explains some very odd emails!

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 13d

I’ve frequently posted the version revised in response to referee comments to bioRxiv, on the assumption that anything up to and including the author accepted version is allowed, though not to Nature family. I wonder if @ritastrack.bsky.social could comment?

James Fraser @fraserlab.com · 13d

Still technically not allowed by @nature.com family journals though right?

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 16d

I checked and there are over a hundred of my papers in the list. But almost all of them, at least from recent years, are open access with the CC-BY license, so I don’t think they would need my permission. Books would be a different matter.

Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 23d

Well deserved! I’ve always been deeply impressed by David’s insights into a wide variety of areas!

Arne Elofsson @bioinfo.se · 23d

www.kva.se/en/news/rese...

Researcher offering insight into Parkinson’s awarded the Gregori Aminoff Prize - Kungl. Vetenskapsakademien

David Eisenberg has been awarded this year’s Gregori Aminoff Prize in Crystallography. He has pioneered the study of amyloid proteins’ molecular structure, providing new knowledge about neurodegenerat...

www.kva.se

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 24d

This looks really impressive!

Oli Clarke @olibclarke.bsky.social · 25d

This one is a bit of a departure from the usual and definitely a work in progress!

We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.

Read on for details... 1/x

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 29d

These are fantastic courses in an amazing location!

Pietro Roversi @pietro1968.bsky.social · 29d

crystalerice.org/2026/

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · Sep 8

Just ran into this earlier today! I had asked for alerts on our ROCKET paper (which you reviewed) but only found the PREreview link when I checked the bioRxiv home for the paper.

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Reposted by Randy Read 🇨🇦🇬🇧

Antoni Wrobel @agwrobel.bsky.social · Sep 8

Dear scientific community,

I am looking for two postdoctoral structural biologists to join my group at the Department of Biochemistry, University of Oxford.

my.corehr.com/pls/uoxrecru...

my.corehr.com/pls/uoxrecru...

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Reposted by Randy Read 🇨🇦🇬🇧

Structural Biology @actacrystd.iucr.org · Sep 3

The September issue is here! tinyurl.com/bdeby9au

The cover highlights XFBLD-Platform, a crystallographic fragment-screening platform at Shanghai Synchrotron Radiation Facility. Find out more at tinyurl.com/36rzxazr

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · Sep 2

This is well worth your time!
Alisia and Minhuan are both rising stars!

Alisia Fadini @alisiafadini.bsky.social · Sep 2

We'll cover our latest work on low resolution applications, a run-through of our codebase, and tutorials of how to run ROCKET on your own data. Join if you're interested!! 🚀

SBGrid Consortium @sbgrid.bsky.social · Sep 2

Our monthly software webinars will resume in October with @alisiafadini.bsky.social and @minhuanli.bsky.social covering AlphaFold as a Prior: Guiding Protein Structure Prediction Using Experimental Data with ROCKET.

Tuesday, October 14, 2025 at 12:00pm ET
Register here: buff.ly/uLlQGVr

#SBGrid

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Reposted by Randy Read 🇨🇦🇬🇧

Social Media Lab @socialmedialab.ca · Aug 27

"Bluesky now platform of choice for science community. It's not just you. Survey says: "Twitter sucks now and all the cool kids are moving to Bluesky" arstechnica.com/science/2025...

Bluesky now platform of choice for science community

It’s not just you. Survey says: “Twitter sucks now and all the cool kids are moving to Bluesky”…

arstechnica.com

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · Aug 15

Congratulations!

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Reposted by Randy Read 🇨🇦🇬🇧

Structural Biology @actacrystd.iucr.org · Aug 5

The August issue is out! journals.iucr.org/d/issues/202...

On the cover: ~15% of the ligands in a high-resolution set of FABP structures had a different chemical composition to that expected from the starting materials or final synthesis product. Find out more at doi.org/10.1107/S205...

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Reposted by Randy Read 🇨🇦🇬🇧

Titia Sixma @titiasixma.bsky.social · Jul 31

Happy to see this out, great work from Niels, combining kinetic analysis, cryoEM and an unexpected gain-of-function mutant, nice work from master students Jan and Nina, from Kaustav and from Alex for the kinetics
‪@oncodeinstitute.bsky.social‬,
‪@nkinl.bsky.social‬

Niels Keijzer @nkeijzer.bsky.social · Jul 31

I'm very proud that our paper, and with that the main project of my PhD, has just been published by @natcomms.nature.com! 🎉
Here, we reveal the unique, molecular mechanism by which USP1/UAF1 cleaves ubiquitin chains on PCNA, which may direct DNA damage tolerance.

doi.org/10.1038/s414...

USP1/UAF1 targets polyubiquitinated PCNA with an exo-cleavage mechanism that can temporarily enrich for monoubiquitinated PCNA - Nature Communications

DNA damage tolerance is regulated by ubiquitination of PCNA. Here, the authors present kinetic and structural studies showing that USP1/UAF1 prefers trimming K63- and K48-ubiquitin chains down over cl...

doi.org

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · Jul 29

Years later, he got in touch and asked if I would like to have a guest in my lab to collaborate on a phasing project. This is how I ended up with the fantastic Monarin Uervirojnangkoorn in my lab for a year of her PhD!

Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · Jul 29

I have two fond memories of Rolf. In the late 1980s, when I was just becoming independent, he asked for a copy of my program, SIGMAA. I said sure, send me a mag tape, and he said no, I have a budget for this (Hoechst era) and offered several thousand dollars. Travel budget sorted for a couple years!

Structural Biology @actacrystd.iucr.org · Jul 29

Jeroen R. Mesters: Rolf Peter Hilgenfeld (1954–2025)
doi.org/10.1107/S205... #IUCr

Rolf Peter Hilgenfeld (1954–2025)

Rolf Hilgenfeld lived a life in the fast lane, devoted entirely to science, in which he absorbed a wealth of knowledge, conscientiously created new knowledge and passionately passed it on to his stude...

doi.org

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · Jul 29

Pipe stems (Dutch)

Adam Sharp @adamcsharp.bsky.social · Jul 29

Happy World Rain Day! It’s raining…

– Cats and dogs (English)
– Old ladies and sticks (Welsh)
– Like a pissing cow (French)
– As from Esteri’s ass (Finnish)
– Penguins headfirst (Uruguayan Spanish)
– Pilot whales (Faroese)
– Chair legs (Greek)
– Wheelbarrows (Czech)
– Men (hallelujah)

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Reposted by Randy Read 🇨🇦🇬🇧

Structural Biology @actacrystd.iucr.org · Jul 29

Elspeth F. Garman: Perspective on a large-scale ligand structure characterization ... ##IUCrhttps://journals.iucr.org/paper?S2059798325006631

Perspective on a large-scale ligand structure characterization

An introduction to a set of three related papers in this issue describing 216 ligand-bound fatty acid-binding protein structure determinations and the pitfalls that can arise in such a study.

journals.iucr.org

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Reposted by Randy Read 🇨🇦🇬🇧

Alexandre Bonvin @amjjbonvin.bsky.social · Jul 29

Blind structure prediction experiments like CASP and CAPRI are catalysts of new developments

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Reposted by Randy Read 🇨🇦🇬🇧

Alexandre Bonvin @amjjbonvin.bsky.social · Jul 29

A small reminder to all structural biologists around working on biomolecular complexes: please consider sharing your complexes as targets for CAPRI - AI has not solved all structure prediction problems and there are still challenges! See www.capri-docking.org/contribute/

CAPRI Docking

www.capri-docking.org

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Reposted by Randy Read 🇨🇦🇬🇧

IUCr2026 @iucr2026.bsky.social · Jul 28

The 27th Congress and General Assembly of the International Union of Crystallography will be held in magnificent Calgary in the heart of Alberta, Canada from Aug 11-18, 2026.
Interested in cutting-edge structural science?
Sign up for updates at www.iucr2026.org/

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · Jul 24

Wow, that brings back old memories from my PhD!

IUCr2026 @iucr2026.bsky.social · Jul 24

The first 3D protein structure determined in Canada, S. griseus protease B, was solved by Louis Delbaere and Michael James in 1974.
Shown is the re-refined structure of the protease complexed with the third domain of the ovomucoid inhibitor
www.rcsb.org/structu...

RCSB PDB - 3SGB: STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEASE B AND THE THIRD DOMAIN OF THE TURKEY OVOMUCOID INHIBITOR AT 1.8 ANGSTROMS RESOLUTION

STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEASE B AND THE THIRD DOMAIN OF THE TURKEY OVOMUCOID INHIBITOR AT 1.8 ANGSTROMS RESOLUTION

www.rcsb.org

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · Jul 24

In case you tried the first link, here’s one that works!

Miro Astore @miroastore.bsky.social · Jul 23

Omg thank you. Oops

www.biorxiv.org/content/10.1...

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge

Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in v...

www.biorxiv.org

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