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CrollTristan's profile
Tristan Croll
Tristan Croll
Tristan Croll
@CrollTristan

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Tristan Croll

@CrollTristan

Research associate at CIMR (he/him). Finding ways to make data-based macromolecular modelling faster, more accurate and a bit more fun. http://ko-fi.com/tristancroll 

Cambridge, England
isolde.cimr.cam.ac.uk
Joined January 2019

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    1. Tristan Croll‏ @CrollTristan 2 Aug 2021

      Sorry to go all AlphaFold-fanboy, but I have yet another example for you. This one requires a bit of back-story, so buckle in... I happen to be talking in the ACA meeting tomorrow, in Jane Richardson's session entitled "What Can & Can't We See Reliably at Resolution X?" (1/16)

      9 replies 50 retweets 306 likes
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    2. Tristan Croll‏ @CrollTristan 2 Aug 2021

      Given the subject matter, I thought this would be a good forum to talk about an approach I've had a few successes with in the past: using physics-based modelling in ISOLDE to assign sequence to "mystery" proteins in cryo-EM maps in the mid-2 to low-3 angstrom range. (2/16)

      1 reply 0 retweets 8 likes
      Show this thread
    3. Tristan Croll‏ @CrollTristan 2 Aug 2021

      (Side note: I think this is something everyone should do at least once. Not only is it really eye-opening in terms of what is and isn't possible, but it happens to make for a really engaging puzzle). (3/16)

      1 reply 0 retweets 9 likes
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    4. Tristan Croll‏ @CrollTristan 2 Aug 2021

      Anyway, the problem was that all the examples I had were from new structures that have yet to be published, so I needed something already public-domain... which led me to 6ly5, an enormous photosynthetic supercomplex from the diatom Chaetoceros gracilis. (4/16)

      1 reply 1 retweet 7 likes
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    5. Tristan Croll‏ @CrollTristan 2 Aug 2021

      Chain g of this complex was traced through strong density, but unidentified (modelled as 134 UNK residues). Headline resolution 2.38A - exactly what I was looking for. (5/16)pic.twitter.com/xBBc7cZAhu

      1 reply 0 retweets 11 likes
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    6. Tristan Croll‏ @CrollTristan 2 Aug 2021

      So I set to work - and to start with, everything seemed fine. Guess a sidechain based on density and surrounds, settle, move on. Half of the chain is a long coil threading through surrounding chains - I started there. (6/16)pic.twitter.com/BNbQQywNPW

      1 reply 0 retweets 5 likes
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    7. Tristan Croll‏ @CrollTristan 2 Aug 2021

      First sign of trouble was when I hit a site that would only sit comfortably by modelling a non-proline cis peptide... second was when I BLASTed my first 30-residue guess against the Chaetoceros gracilis genome and came up blank. But I still hadn't picked the real problem. (7/16)

      1 reply 0 retweets 6 likes
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    8. Tristan Croll‏ @CrollTristan 2 Aug 2021

      That didn't happen until I made my way back to the N-terminal alpha-helical bundle, and realised that all the sidechains were fighting me to point "down" rather than "up". Finally it dawned: could the chain have been traced backwards (a fairly common autobuilding error)? (8/16)pic.twitter.com/PSIo4GkAhm

      1 reply 0 retweets 12 likes
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    9. Tristan Croll‏ @CrollTristan 2 Aug 2021

      OK, I thought: let's try that. Ran a new BLAST search of the reversed sequence against the Chaetoceros gracilis... Still blank. Hmm... On a hunch, I expanded the search to include all eukaryotes, and *finally* got some strong hits, with E-values around 1e-11. (9/16)

      1 reply 0 retweets 6 likes
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    10. Tristan Croll‏ @CrollTristan 2 Aug 2021

      Even more encouraging, the top hit was an uncharacterised (actually, "hypothetical") protein from Craspedostauros australis, another diatom. Took that and re-BLASTed it, yielding a grand total of 24 hits out of all the eukaryotes. Nothing in the PDB, of course. (10/16)

      1 reply 0 retweets 10 likes
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      Tristan Croll‏ @CrollTristan 2 Aug 2021

      Now, finally, here's where AlphaFold2 comes in. I took that top hit, and ran by the AlphaFold notebook on Google Colab (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb#scrollTo=UGUBLzB3C6WN …). About 15 minutes later I had a model. Here's its C-terminus, rigid-body docked into the 6ly5 density. Spookily accurate. (11/16)pic.twitter.com/78YBWbZy81

      9:49 AM - 2 Aug 2021
      • 8 Retweets
      • 48 Likes
      • Yu Huang Arne Elofsson Anne-Lie 岡村 聡 Jon Fay Jacob Ronald Anderson Norika Saigawa Jake Parker Félix Balazard
      1 reply 8 retweets 48 likes
        1. New conversation
        2. Tristan Croll‏ @CrollTristan 2 Aug 2021

          The rest was in entirely the wrong place, of course - unsurprising since its structure is completely controlled by interactions in the complex - but secondary structure (helix vs. coil) was correctly predicted. (12/16)

          1 reply 0 retweets 12 likes
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        3. Tristan Croll‏ @CrollTristan 2 Aug 2021

          About 20 minutes of refitting later... no real question that this is the right protein (allowing for a few point mutations given that it's the wrong species). (13/16)pic.twitter.com/CrL1VkKgTK

          1 reply 0 retweets 9 likes
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        4. Tristan Croll‏ @CrollTristan 2 Aug 2021

          Take-home messages: - it appears AlphaFold predictions are good enough to add a lot of confidence to sequence assignments even in the face of shallow alignments like this. (14/16)

          1 reply 3 retweets 29 likes
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        5. Tristan Croll‏ @CrollTristan 2 Aug 2021

          - it's quite spooky how easy it is when working without the benefit of a sequence to get something that looks kinda-sorta right while having the backbone backwards. (15/16)

          1 reply 3 retweets 26 likes
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        6. Tristan Croll‏ @CrollTristan 2 Aug 2021

          - *Don't* assume the genome database for your organism is complete! (Actually the second time this has come up for me - the first time the mystery chain was initially unidentified because its gene was missing from the mass spec database). (fin)

          4 replies 3 retweets 40 likes
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        7. End of conversation

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