AlphaFold: a solution to a 50-year-old grand challenge in biology

Re:AlphaFold: a solution to a 50-year-old grand challenge in... by thamer on Monday November 30, 2020 @08:59PM (#25261433)

There's something I don't understand about protein shapes. There are tons of software solutions – on the web and offline – to visualize the shape of proteins from their sequence of amino acids. How do these work then, if we don't know how the atoms might be arranged in space?

For example, this[1] is the code for SARS-Cov-2's Spike(S) protein. From what I understand of this page it's pretty short, only ~1,757 proteins (corresponding to ~3,821 bases in RNA).

And here[2] is a visualization of it in 3D. You'll likely recognize the characteristic mushroom shape that's been portrayed in 3D models of SARS-CoV-2 in the media. How does this software work if there's no real way to tell how the protein is arranged?

[1] https://www.ncbi.nlm.nih.gov/nuccore/NC_045512 (search for spike glycoprotein on that page)

[2] https://3dmol.csb.pitt.edu/viewer.html?pdb=6X6P&style=stick&...

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Re:AlphaFold: a solution to a 50-year-old grand challenge in... by paraschopra on Monday November 30, 2020 @09:17PM (#25261540)

Al such proteins have been crystallised and we know their shape experimentally.

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Re:AlphaFold: a solution to a 50-year-old grand challenge in... by thamer on Tuesday December 01, 2020 @04:39AM (#25263826)

Thanks for the answer! That explains it. I was looking just at the amino acid sequence and missing a whole lot.

I read the protein folding and X-ray crystallography articles on Wikipedia and they had most of the answers I was looking for. I also saw a request being made by this JavaScript 3D viewer to fetch the PDB (Protein Data Bank) file for the model, which is a text file with tens of thousands of lines describing the coordinates of atoms in space as well as their bonds and other structures. It even has some metadata about the way the data was collected.

For the spike protein linked above: http://files.rcsb.org/view/6X6P.pdb

I find it fascinating that we're even able to scan the 3D structure of molecules with such precision.

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Re:AlphaFold: a solution to a 50-year-old grand challenge in... by jassany on Monday November 30, 2020 @09:14PM (#25261524)

I work suggest trying to understand how the haemoglobin protein works... The shape of it is not too confusing too look at.

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