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Harsh Dutta

@hrshdtt.bsky.social

PhD candidate @ Basak Lab, cryoEM of Drosophila membrane proteins, NTU Sg sbasaklab.com

304 Followers  |  542 Following  |  17 Posts  |  Joined: 09.11.2024  |  1.7269

Latest posts by hrshdtt.bsky.social on Bluesky

OpenAI doesn't report a single number for its climate impacts - not anywhere, in any way, shape or form.

It sounds kind of obvious but the fact that a company with such incredible electricity hunger isn't disclosing basic information about its energy consumption and associated emissions is v bad..

28.12.2024 07:58 โ€” ๐Ÿ‘ 5908    ๐Ÿ” 1555    ๐Ÿ’ฌ 93    ๐Ÿ“Œ 63
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Years after the idea and preliminary experiments, Claire Coupland's amazing structure of the endogenous vacuolar- or vesicular-ATPase in its NATIVE vesicle is now in bioRxiv "High resolution cryo-EM of V-ATPase in native synaptic vesicles"
www.biorxiv.org/content/10.1...

02.04.2024 17:11 โ€” ๐Ÿ‘ 120    ๐Ÿ” 39    ๐Ÿ’ฌ 6    ๐Ÿ“Œ 4

For folks just arriving in #AcademicBsky or #ScienceBsky, here are a couple of Biophysics starter packs. Biophysicists, pls tag yourself and others and I will add you to the new starter packs. go.bsky.app/4AUjqVz

07.11.2024 13:02 โ€” ๐Ÿ‘ 159    ๐Ÿ” 79    ๐Ÿ’ฌ 90    ๐Ÿ“Œ 6

im on every app. im in your city, in your neighborhood. the sales associate who handed you a large when you asked for a medium? that was me. i am now behind you.

20.11.2024 07:00 โ€” ๐Ÿ‘ 34959    ๐Ÿ” 2763    ๐Ÿ’ฌ 576    ๐Ÿ“Œ 273

yes, thanks for the discussion!

20.11.2024 08:00 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

this is also correctly predicted

20.11.2024 07:55 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

yep correct, the small protein is the green box in bottom right. This is a large membrane protein. The interacting region of the first protein can be verified by homology modelling. All the high confidence regions predicted by AF3 can be verified by homology, and inter domain packing is also good.

20.11.2024 07:54 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
PAE plot from AF3

PAE plot from AF3

PAE looks like this. The iPTM score is also 0.74, so these helices are really unreliable, and they take up a considerable amount of amino acids in the total sequence.

20.11.2024 07:32 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

ah I see, thanks

20.11.2024 07:12 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

thanks, yeah I figured because manual inspection of the sequence and IDR prediction server also spit out similar disordered behaviour for these regions. Most of these are just poly-Ns, some need to be checked more carefully.

20.11.2024 06:45 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 2    ๐Ÿ“Œ 0

ohh that low confidence in the middle of the curl..yikes.

20.11.2024 06:33 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

ohh do you have a visual example of 'curled' models?

20.11.2024 05:21 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
A 500 kDa protein model generated by AlphaFold 3

A 500 kDa protein model generated by AlphaFold 3

AF3 model of the protein with the binding partner

AF3 model of the protein with the binding partner

AF3 predictions for a 500 kDa protein without (left) and with (right) a known 40 kDa binding partner. Apparently disordered regions collapsing into low confidence cytosolic helices. Is AF hallucinating these helices?

19.11.2024 13:43 โ€” ๐Ÿ‘ 15    ๐Ÿ” 2    ๐Ÿ’ฌ 6    ๐Ÿ“Œ 1

thanks!

17.11.2024 12:07 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

๐Ÿ™Œ๐Ÿ™Œ

17.11.2024 12:04 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

haha it is art as long as it provokes a human emotion, pain in this case

15.11.2024 12:20 โ€” ๐Ÿ‘ 2    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

yep, it was apparently a fabrication issue because we didn't notice anything strange while handling and preparing this grid, it was only clear at the screening stage

15.11.2024 12:19 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
bad cryoEM grid imaged at low mag

bad cryoEM grid imaged at low mag

bad cryoEM grid imaged at high mag

bad cryoEM grid imaged at high mag

pain, just literal pain

15.11.2024 11:34 โ€” ๐Ÿ‘ 6    ๐Ÿ” 0    ๐Ÿ’ฌ 4    ๐Ÿ“Œ 0
Preview
FEBS Press Clinical multidrug resistance is caused by a group of integral membrane proteins that transport hydrophobic drugs and lipids across the cell membrane. One class of these permeases, known as multidrug...

ABC transporters contributing to drug resistance in bacteria: doi.org/10.1016/S001...

13.11.2024 15:04 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

trying to fix the student numbers right here ๐Ÿ˜ฌ hopefully my friends pop in too

13.11.2024 14:31 โ€” ๐Ÿ‘ 2    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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Been thinking about creating a collection of good protein structure figures, as inspiration for my own work.

#1 www.nature.com/articles/s41...

03.03.2024 08:37 โ€” ๐Ÿ‘ 155    ๐Ÿ” 51    ๐Ÿ’ฌ 5    ๐Ÿ“Œ 9

Hello world! Decided to give up on Xitter ig.

10.11.2024 15:55 โ€” ๐Ÿ‘ 4    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

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