Discover and read the best of Twitter Threads about #biophysics
Most recents (6)
🚀 We are live! Here is the correct streaming link for all of today's discussions and performances, starting with a panel on complex time with David Krakauer, James Gleick, Ted Chiang, and David Wolpert in a few moments (measured linearly...):
#IPFest
#IPFest
"One of the ideas we had with #InterPlanetary was, 'What would it take to make science hedonistic? And instead of telling people to do it, you'd have to tell people to STOP doing it?"
- SFI President David Krakauer sets the tone for this weekend's celebrations
#IPFest
- SFI President David Krakauer sets the tone for this weekend's celebrations
#IPFest
David Krakauer: "Do you have a favorite model or metaphor for #time?"
@JamesGleick: "You've already mentioned a river; that's everybody's favorite. Borges said time is a tiger. People talk about it as a thread. We ONLY talk about time in metaphors."
@JamesGleick: "You've already mentioned a river; that's everybody's favorite. Borges said time is a tiger. People talk about it as a thread. We ONLY talk about time in metaphors."
1/ After a year of work, our paper on mRNA Degradation is finally out!
paper: arxiv.org/abs/2110.07531
code: github.com/eternagame/Kag…
paper: arxiv.org/abs/2110.07531
code: github.com/eternagame/Kag…
2/ A year ago I was approached with a unique and exciting opportunity: I was asked to help out with setting a Kaggle Open Vaccine competition, where the goal would be to come up with a Machine Learning model for the stability of RNA molecules.
3/ This is of a pressing importance for the development of the mRNA vaccines. The task seemed a bit daunting, since I have had no prior experience with RNA or Biophysics, but wanted to help out any way I could.
tinyurl.com/yw6sk5uz
1/9 Could graphene coverslips improve your single-molecule fluorescence and superresolution experiments? In our article in @AdvancedAms we combine #DNAorigami with #graphene to perform #singlemolecule #biophysics, #biosensing & #superresolution microscopy.
1/9 Could graphene coverslips improve your single-molecule fluorescence and superresolution experiments? In our article in @AdvancedAms we combine #DNAorigami with #graphene to perform #singlemolecule #biophysics, #biosensing & #superresolution microscopy.
2/9 Graphene is almost transparent and quenches fluorescence in a range of ~40 nm. Fluorescence intensity or fluorescence lifetime of single molecules directly tell you the distance of a molecule to the surface. Differences in the z-direction as small as 2.9 nm are resolved.
3/9 Dynamics with graphene energy transfer (GET). We use GET to visualize motion on top of a graphene surface and determine the timescale of fluctuations via autocorrelation analysis.
The story about mitochondria being ~10° hotter than the rest of the cell, published @PLOSBiology a couple years ago (journals.plos.org/plosbiology/ar…) got some cool, albeit indirect, support recently @naturemethods… #Biophysics #CellBiology
The original paper, which was mainly based on the temperature-dependent fluorescence of a mitochondria-targeting probe, was accompanied by a “Primer” (journals.plos.org/plosbiology/ar…) highlighting potential flaws and implications, a special sort-of-peer-review step by PLOS Biology.
This new awesome resource @naturemethods - nature.com/articles/s4159… - offers some intriguing orthogonal validation. This is a proteome-wide study of protein thermal stability across 13 organisms, conducted using a mass-spec-based approach.
Super neat story on how cellular quality control impacts the mutational landscape of proteins - beneficial mutations in DHFR during deep mutational scanning are totally altered dependent on cellular QC #Biophysics #Evolution biorxiv.org/content/10.110… Way to go! @KortemmeLab
In an initial DMS experiment on DHFR, there were a large number (25% of all sequences!) of advantageous mutations spread across the whole protein. Reintroduction of QC protein Lon reduced the number of advantageous mutants and lowered average benefit of those mutations
Changes in selection coefficient (the “advantageous-ness”) were most striking at hydrophobic/aromatic residues and buried residues - and these correlate with Tm changes of variants. So Lon seems to be imposing higher standards on DHFR, particularly for destabilizing core mutants
Protein evolvability is coupled with stability! A cool illustration of this principle in practice for engineering of amino-acid tRNA syntheses for incorporation of non-canonical amino acids in eukaryotes #Evolution #Biophysics #SynBio biorxiv.org/content/10.110… @AChemSynBio
Differences in engineerability for ncAA incorporation between two different synthases can be pinned down to different stability - mutations (particularly those that narrow / specify function) tend to decrease stability, so starting from a higher Tm gives “room for evolution”
Lack of engineerability in the less-stable synthase can be overcome by making chimeras with the more stable, less active one - the intermediate phenotypes on both activity + stability are enough to engineer ncAA incorporation at suitable levels in eukaryotic cells.
