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1817: Coronavirus ORF6 Prediction

Closed since about 6 years ago

Intermediate Overall Prediction

Summary

Created
March 26, 2020
Expires
Max points
100
Description

Refold this coronavirus protein! This protein is encoded in the viral genome of SARS-CoV-2, in a region called ORF6, but the protein's structure is still unknown. Evidence suggests this protein inhibits the natural immune response, helping the virus survive and replicate. If we knew how this protein folds, we might be able to figure out exactly how it inhibits the immune system. The puzzle's starting structure shows SS predictions from PSIPRED, and hints which parts of the protein might fold into helices or sheets. Refold this protein to find high-scoring solutions, which will tell us how this protein is most likely to fold!



Sequence:


MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKYSQLDEEQPMEID

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Comments

beta_helix Staff Lv 1

I ran it on a few transmembrane prediction servers and indeed this looks to be the case:

Residues MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNL were predicted to be a Transmembrane Helix by PSIPRED's Membrane Helix Prediction.

(I wanted to attach a figure, but drupal is garbage)

jeff101 Lv 1

Does this mean that after this puzzle ends, you will
post a new version of it scored like a transmembrane
protein would be scored? If you let us load our
solutions from this puzzle into the reposted version,
we could watch them restructure in their new
environment, which would be interesting.

dfonda Lv 1

@Serca @bkoep @S0ckrates @Susume2
Please correct any errors you see as I'm pretty new to this.

Theorizing: ORF6 suppresses imuno so maybe it's either a friendly key or honeypot for white blood/T-cells?
e.g. either white/T/regular cells see the external part (residues 46-61) as a friendly (key) or immune cells grab it and think "oh we know this one already" (honeypot)

The Helix could be straight if it's bound to other stuff in the membrane not shown in this puzzle
the bottom 4 loops could be the connector to ORF7a/7b which might be perepherial membrane proteins?
residues 46-61 could be the key/honeypot that suppress immune function binding to something?

So I made a transmembrane helix similar to this idea
https://drive.google.com/open?id=1Qp7FkbRTFfRTuRLKJYXCigIc3qiUpPVB
my crummy try at it
https://drive.google.com/open?id=1DeoDZDvWTmLy24esRfv4dnpOGTlPyKOT

reference:
Dark Proteome of Newly Emerged SARS-CoV-2 in Comparison with Human and Bat Coronaviruses
Rajanish Giri1*, Taniya Bhardwaj1, Meenakshi Shegane1, Bhuvaneshwari R. Gehi1, Prateek Kumar1, Kundlik Gadhave1

https://drive.google.com/open?id=1kAkU7mC9NNGakBbxkrYWIRrMwSj8TRYt

dfonda Lv 1

SARS-CoV-2: MFHLVDFQVTIAEIL L IIMRTF KVS IWNLD Y II NLIIKN LSKSL TENKY SQLD EEQP MEID
SARS-CoV : MFHLVDFQVTIAEIL I IIMRTF RIA IWNLD V II SSIVRQ LFKPL TKKNY SELDD EEP MELD YP

I didn't space all the diffs as some seemed like group variants like TENKY vs TKKNY