Boltz-1 H5N1 HA mutations

This paper by Lin et al. from the Dec. 5 2024 issue of Science showed how a single mutation, a glutamine to leucine change (Q226L) in the H5N1 HA amino acid sequence could change HA binding specificity from avian to human binding. The specificity was enhanced when combined with an asparagine to lysine (N224K) change at a nearby position. Since I have been playing around with Boltz-1, I thought it would be interesting to see what Boltz-1 would show about the protein structure with these changes.

I could not find the unmodified amino acids at the positions listed. Rather than using sequential site numbering for positions (initial Met would be position 1), the authors use reference site numbering, called H3 numbering. This scheme puts sites into alignment with the ectodomain structure of the H3 subtype of HA. Figure 1 from the Lin et al. paper shows the subsequence "SQVNGQRG" where the target amino acids are found. I located this subsequence in the HA sequence.

>>> from Bio import SeqIO
>>> rec = SeqIO.read("HA_reference.fasta", "fasta")
>>> rec.seq
Seq('MENIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHN...ICI')
>>> rec.seq.find("SQVNGQRG")
232
>>> rec.seq[232:240]
Seq('SQVNGQRG')
>>> rec.seq[235:238]  # target positions 236-238 index 1 positions
Seq('NGQ')
>>>

Glutamine is at BioPython position 237 (238 1-indexed) and asparagine at position 235 (236 1-indexed).

Using these positions, the sequence can be modified.

>>> from Bio.SeqRecord import SeqRecord
>>> from Bio.Seq import Seq

>>> seq_list = list(rec.seq)
>>> seq_list[237] = "L"
>>> seq_list[235] = "K"


>>> mut_rec = SeqRecord(seq = Seq(''.join(seq_list)), id = rec.id)
>>> SeqIO.write(mut_rec, "HA_mut.fasta", "fasta")

We use Boltz-1 to predict a new structure.

$ time boltz predict H5N1/data/HA_mut.fasta --use_msa_server  --num_workers 12 --output_format pdb

Matlab's molviewer is used to plot the new structure. 

Here is the Boltz-1 prediction of the wild type.

From the pictures, it's a bit hard to see, but the structure is elngared and trwisted.