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Original post on mastodon.social

`Surprisingly..extracted diffusion coefficient at the free energy barrier on the number of native contacts coordinate increases with protein length. This facilitation..in larger proteins is explained by increased cooperative native contact formation during folding, which reduces the roughness of […]

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4- year PDRA position: lnkd.in/euijUXW4 closes 1st May.

4-year PhD position: lnkd.in/eWUsRrv4 closes 1st June.

Both positions are expected to start on 1st October. Reach out for more info!

@astonaime.bsky.social @leverhulme.ac.uk #membraneproteins #proteinfolding

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synth-pdb High-Performance Protein Structure Generator for AI/ML and Education

📢 Documentation for synth-pdb is live!
Generate realistic PDB files with:
- Mixed secondary structures (α-helix, β-sheet)
- Energy minimization (OpenMM)
- NMR observables
- Interactive Jupyter tutorials
Check it out: elkins.github.io/synth-pdb
#StructuralBiology #NMR #ProteinFolding #OpenScience

J&J bets on Isomorphic for AI-powered drug hunt Isomorphic Labs has added Johnson & Johnson to the roster of pharma companies tapping into its AI-based drug discovery engine

#JnJ #Isomorphic #Alphabet #IsomorphicLabs #pharmacompanies #AIbaseddrugdiscovery #researchcollaboration #drugdevelopment #EliLilly #Novartis #smallmoleculetherapeutics #largemoleculetherapeutics #biologics #AIdrivendrugdesign #DeepMind #AlphaFold #proteinfolding
zurl.co/dBpBC

From impossible to inevitable: How DeepMind's AI predicted 200M protein structures & revolutionized drug discovery—sparking debates on science equity. #AIInnovationsUnleashed #ProteinFolding
www.aiinnovationsunleashed.com/ai-in-scienc...

Unraveling C-Peptide’s Role in MIDY: A Structural Perspective Proinsulin folding requires dynamic positioning of the C-peptide to guide A- and B-chain alignment and disulfide pairing. Mutant INS-gene-induced diabetes of youth (MIDY) arises when single-residue substitutions disrupt this process. We mapped the conformational free-energy landscapes of wild-type (WT) proinsulin and seven MIDY variants using metadynamics and molecular dynamics simulations. WT exhibits a deep free-energy minimum at compact conformations. In contrast, MIDY mutants display a continuum of destabilization: E(A4)K retains near-WT stability, Akita (C(A7)Y), V(B18)A, and R(Cpep + 2)C show moderate loss of the native basin, while H(B5)D, L(A16)P, and Y(B26)C collapse the closed–open barrier and populate misfolded open states >50% of the time. Structural analyses reveal that WT and E(A4)K preserve robust A–C docking, with the C-peptide flexibly engaging the A-chain groove. Destabilizing mutants progressively erode these native A–C contacts while forming compensatory, non-native B–C interactions. Per-residue energy decomposition highlights the loss of canonical salt bridges and emergence of aberrant electrostatic and hydrophobic hot spots, correlating with the collapse of the folding free-energy barrier. Secondary-structure analysis further shows that mutants rigidify the normally disordered C-peptide, increasing helical or strand propensity in a mutation-specific manner. Collectively, these findings establish a continuum from near-native stability to overt misfolding, mechanistically linking single-site mutations to altered folding landscapes and aggregation risk in MIDY. The results highlight the C-peptide as a dynamic linchpin of proinsulin folding and suggest that restoring its flexible docking could provide a therapeutic avenue.

New from our group: Unraveling C-Peptide’s Role in MIDY: A Structural Perspective | ACS Omega pubs.acs.org/doi/10.1021/...

Congratulations @sranga88.bsky.social and my lab folks! 🎉

#proteinfolding #proinsulin #mutations #Cpeptide #structuralbiology #computationalbiology #MDsimulations

New research identifies a regulator that helps the brain use amyloid assembly in a controlled way – with implications for cognitive aging.

longevity.technology/news/amyloid...

#longevity #brainhealth #cognitiveaging #neuroscience #amyloid #alzheimersresearch #proteinfolding #agingresearch #memory

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Buzzing about AI accelerating scientific discovery! AlphaFold, predicting protein structures, is revolutionizing biology. It's like giving scientists a superpower to unlock life's deepest secrets, paving the way for new medicines. This innovation expands the knowable! #AIforScience #ProteinFolding

🎉 Happy 5th Birthday, AlphaFold! 🧬 From Nobel Prize wins to transforming protein folding, this AI is revolutionizing biology. How do you think it will change medicine? Share your thoughts! ✨ #AI #DeepMind #ProteinFolding LINK

Five years after AlphaFold cracked protein folding, its new AI partner Gemini 2.0 joins as a co‑scientist, debating hypotheses with the PI. Curious how an agentic system reshapes discovery? Dive in. #AlphaFold #Gemini2 #ProteinFolding

🔗 aidailypost.com/news/alphafo...

Mathematical modelling of mutant glycoprotein fate in the ER Background The endoplasmic reticulum (ER) coordinates glycoprotein quality control through competing pathways: ER quality control (ERQC) and ER-associated degradation (ERAD). The fate of a glycoprotei...

🥳 New paper out! We model how misfolded glycoproteins balance folding vs degradation, estimate experimentally elusive quantities and provide a framework relevant for rare missense diseases.

#ComputationalBiology #Glycobiology #ProteinFolding #RareDisease #Bioinformatics

Lipid-regulated assembly mechanisms and functional energetics of the essential bacterial chaperone BamA BamA is a highly conserved essential outer membrane chaperone of all Gram-negative bacteria. Our understanding of the BamA machinery remains incomplete, delaying knowledge-based antibacterial design. ...

Our work is now online!

#biophysics #membraneprotein #proteinfolding #microsky

Read here: pubs.rsc.org/en/Content/A...

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#LessSocialMediaMoreLife #MisfoldedProteins #ProteinFolding #Type2Diabetes #AlzheimersDisease #MetabolicSyndrome #wellnessatwork #wellnessquotes #physicalwellbeing #Health #Science #MedicalResearch #Disease #LessSocialMediaMoreLife

RESEARCH PAPER: UPR deficiency leads to poor growth, aneuploidy, and a trade-off between ER and general proteostasis in yeast
By Bartolutti et al. and Gloria Brar
➡️ https://genesdev.cshlp.org/content/39/23-24/1434.full

#aneuploidy #unfoldedproteinresponse #UPR #proteinfolding #proteostasis #yeast

He had to call that system AlphaFold

#proteinfolding #deepmind #alphago #alphastar

Was watching The Thinking Game and realized I had zero intuition for protein folding. Tried building one from first principles with metaphors, physics, and ChatGPT 5.1 as a sounding board. Somehow that turned into a full ‘cell weather dashboard.’ Learning: 24k tokens worth.

#proteinfolding

This #STTT review provides a comprehensive overview of #ProteinFolding biology, detailing the roles of key #MolecularChaperones, the multifactorial causes of #ProteinMisfolding, and emerging therapeutic innovations targeting #Proteostasis.

#OpenAccess: doi.org/10.1038/s413...

Conformational plasticity links structural instability of NAA10F128I and NAA10F128L mutants to their catalytic deregulation. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.11.014

🔗 Conformational plasticity links structural instability of NAA10F128I and NAA10F128L mutants to their catalytic deregulation. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.cs...

📚 CSBJ: www.csbj.org

#Biophysics #Enzymology #StructuralBiology #Mutations #ProteinFolding

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#BioCompute v1.0.13 bit.ly/biocompute-sheet

Three more AF3-like models for #ProteinFolding

Pearl: arxiv.org/abs/2510.24670
ODesign: odesign1.github.io/static/pdfs/...
OpenFold (published earlier this week)

Find the full list at:
#ProteinFolding #AlphafoldandCo bit.ly/biofold

@delalamo.xyz on the perceived advantage that AF3 has over other #ProteinFolding software out there.

Navigating the landscape of protein folding and proteostasis: from molecular chaperones to therapeutic innovations - Signal Transduction and Targeted Therapy Signal Transduction and Targeted Therapy - Navigating the landscape of protein folding and proteostasis: from molecular chaperones to therapeutic innovations

This review provides a comprehensive analysis of #ProteinFolding biology, highlighting #MolecularChaperones, causes of #misfolding, disease links, and therapeutic strategies targeting #proteostasis to restore protein homeostasis. #medsky

#OpenAccess #STTT: doi.org/10.1038/s413...

Mathematicians And Physicists: Accidentally Saving Lives With Knots

Mathematicians And Physicists: Accidentally Saving Lives With Knots

#Mathematics #Physics #Knottheory #Interdisciplinary #Proteinfolding

sciencehumor.io/math-memes/mathematician...

🌟 A groundbreaking hybrid classical-quantum method is set to revolutionize protein folding predictions! 🧬 How do you think quantum computing will shape the future of healthcare? 💡 #ProteinFolding #QuantumComputing #HealthcareInnovation #Biotech #MedicalResearch LINK

SimpleFold Shows Protein Folding Can Skip Complex AI Architecture

SimpleFold shows a standard transformer can predict protein structures, with performance scaling from 100 million to 3 billion parameters, still on consumer‑grade hardware. Read more: getnews.me/simplefold-shows-protein... #simplefold #proteinfolding

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#LessSocialMediaMoreLife #MisfoldedProteins #ProteinFolding #Type2Diabetes #AlzheimersDisease #MetabolicSyndrome #wellnessatwork #wellnessquotes #physicalwellbeing #Health #Science #MedicalResearch #Disease #LessSocialMediaMoreLife

Last weekend, I found myself explaining my molecular research to an elderly person over tea and cookies. As I watched her eyes glaze over at terms like "protein folding" and "molecular ... Last weekend, I found myself explaining my molecular research to an elderly person over tea and cookies. As I watched her eyes glaze over at terms like "protein folding" and "molecular dynamics," I re...

Turning jargon into clarity: start with relatable analogies, show real-world impact, and keep it visual ✍️🧶 What strategies help you make science click? Read more → link #scicomm #communication #proteinfolding

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