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#structuralbiology

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Public
Dave nλ=2dsinθ

New Presidential executive order on proteins:

All amino acids now to be right w̶i̶n̶g̶ handed.

Leftist amino acids to be outlawed.

(Also, Z-DNA is deemed to be Communist, and is prohibited.)

Trans- and cis- peptide bonds to be banned.

Non-binary amino acid Glycine to be banned.

Proline is not a real amino acid and will be banned immediately.

Phenylalanine looks and sounds a bit like Fentanyl, banned immediately.

@strucbio #StructuralBiology #PDB

Public
michael

26-Mar-2025
Remember #ebola?
Zooming in on the #structure of the still lethal #virus

eurekalert.org/news-releases/1 #science #structuralBiology #protein #capsid

EurekAlert!Remember ebola?Kyoto, Japan -- Six years before the start of the COVID-19 pandemic, an Ebola outbreak in West Africa had people fearing the possibility of a global outbreak. This was the first time many had ever heard of the virus, but since it was first identified in 1976, there have actually been more than 20 serious Ebola incidents. Thankfully, none of them had the global reach of the coronavirus. Ebola has not been eradicated, however. This deadly virus, which causes severe hemorrhagic fever in humans and has a fatality rate of about 50%, is still at large and could thus still cause a major outbreak, unless further research finds an effective solution. A major challenge lies in the virus' structure and regulatory mechanisms, which have remained largely unclear. In particular, scientists have long struggled to fully understand its nucleocapsid, the protein shell that plays an important role in genome replication and transcription.
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Victoria Stuart 🇨🇦 🏳️‍⚧️

Molecular animations reveal DNA's unzipping mechanism: Implications for viral and cancer treatments
sciencedaily.com/releases/2025
le.ac.uk/news/2025/march/dna-h

* scientists captured 1st detailed 'molecular movie' showing DNA being unzipped at atomic level
* reveals how cells begin crucial process of copying their genetic material

Structural dynamics of DNA unwinding by a replicative helicase
nature.com/articles/s41586-025

ScienceDailyBreakthrough molecular movie reveals DNA's unzipping mechanism with implications for viral and cancer treatmentsScientists have captured the first detailed 'molecular movie' showing DNA being unzipped at the atomic level -- revealing how cells begin the crucial process of copying their genetic material.
#cancer#MolecularGenetics#StructuralBiology
Public
CSBJ

This study investigates the surprising limitations of AlphaFold 2 (AF2) in predicting protein structures—specifically its tendency to confidently predict β-solenoid folds for repeat proteins, even when the structures are unrealistic or unstable.

🔗 AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins. DOI: doi.org/10.1016/j.csbj.2025.01

📚 CSBJ: csbj.org/

AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins.
ALT
#AlphaFold#ProteinScience#StructuralBiology
Public
Miguel Correa

Our new preprint on the impact of protein phosphorylation on structures is now out!

Protein phosphorylation is a key regulator of cellular processes.It's ubiquitous, yet the function and relevance of most phosphosites is unknown. Understanding phosphosite function requires elucidating the structural mechanisms through which it acts. (1)

biorxiv.org/content/10.1101/20

@bioinformatics @strucbio #bioinformatics #protein #StructuralBiology

bioRxiv · Global comparative structural analysis of responses to protein phosphorylationPost-translational modifications (PTMs), particularly protein phosphorylation, are key regulators of cellular processes, impacting numerous aspects of protein activity. Despite widespread phosphorylation of eukaryotic proteomes, the function of most phosphosites remains unknown. Elucidating the structural mechanisms underlying phosphorylation is crucial for understanding its regulatory roles. Here, we conducted a comparative structural analysis of phosphorylated and non-phosphorylated proteins taken from the Protein Data Bank (PDB). Our study systematically evaluates how phosphorylation affects backbone conformation, protein dynamics, and mechanical strain. We found that phosphorylation commonly induces small, stabilizing conformational changes through conformational selection and frequently modulates local residue fluctuations, influencing overall protein motion. Notably, a small but significant subset of phosphosites shows mechanical coupling with functional sites, aligning with the domino model of allosteric signal transduction. This work provides a foundation for studying phosphorylation and other PTMs in their structural context, which will guide the rational design of synthetic phosphosites and enable the engineering of PTM-driven regulatory circuits in synthetic biology. ### Competing Interest Statement The authors have declared no competing interest.
Public
Matt Hodgkinson

Juan Mateos-Garcia of Google DeepMind wants equitable use of their tools like AlphaFold. They solved protein structure prediction in 2020 and this is helpful for drug discovery, but researchers in LMIC have barriers to adoption.

Used OpenAlex & PDB to study 20.6K papers citing AlphaFold. LMIC researchers are underrepresented, but study of diseases affecting LMICs is overrepresented - esp. work on natural products.

Equitable adoption There is evidence of an adoption gap LMICs and LMLICs seem underrepresented in AlphaFold vs. baseline Also visible when we focus on PDB research
ALT
Equitable impact AF disease research more focused on LMIC diseases 20% AF papers focus on diseases (vs. 34% in baseline) Share of AF in diseases with big LMIC impact 36% higher than baseline
ALT
User interviews We interviewed 10 LMIC AlphaFold users in India, Pakistan, South Africa, Tunisia, Ghana and Brazil. They focus on diseases with big LMIC impacts including Malaria, infectious diseases, Antimicrobial Resistance. AlphaFold impacts: Lowers barriers to entry Accelerates research Attracts talent to structural biology Barriers to adoption: Accessibility (IT infrastructure and skills) Lack of information about AF/its relevance Weak research ecosystem "So it reduces reliance on costly experiments too. Often in a laboratory setting, there's a lot of troubleshooting, a lot of experiments that fail. And using an online capability such as AlphaFold for this deep understanding would definitely be beneficial in reducing the reliance on costly experiments" "Indian Universities are not teaching AlphaFold because it's a very new concept and they spend the whole curriculum on teaching the basics." "I think one important factor is to make sure that people understand that AlphaFold can be like used like a database, which was not clear for a lot of people"
ALT
#ICSSI#ScienceofScience#AItools
Public
Vicomte Folmer af Helvede

#Introduction #Introduktion

I've spent a lot of my life doing #StructuralBiology and playing #Music #ClassicalMusic.

I like to #read #books, mostly #fantasy but also #clifi and #scifi.
A fan of both #StarTrek and #StarWars, each has its merits. (Yes TNG is the best, but only because I grew up with it).

Currently I'm interested in #biosustainability #sustainability, #enzymology and #ProteinEngineering. I think those technologies are important for our future together.

Danish 🇩🇰

Public
HistoPol (#HP) 🏴 🇺🇸 🏴

@nellgreenfieldboyce

This should not have happened in #Europe in 2023.

Not a a good day for #StructuralBiology and not a good day for #science.

Also, the age gap b/w the laureates and the audience is striking.

mastodon.social/@nellgreenfiel

MastodonNell Greenfieldboyce (@nellgreenfieldboyce@mastodon.social)At a meeting in Germany that attracts dozens of Nobel prize winners, one of them objected to its focus on diversity, saying “as a male scientist, I have a feeling of discrimination when I am here, in the climate that this meeting is being held.” Science magazine reports that a visibly nervous early-career researcher stood up to respond…. https://www.science.org/content/article/nobel-laureate-claimed-antimale-discrimination-early-career-researcher-called-it-out Link to video, her response is at 46:39 https://www.mediatheque.lindau-nobel.org/recordings/41064 #stem #science #Nobels #womeninstem #womeninscience #lindaunobel
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