i am doing a point mutation of tyrosine to alanine leading to 3 alanine in a row in the peptide sequence.
the structure before mutation is alpha helix, will the mutation may lead to disruption of the alpha helix?
Dear Shobhan Kuila ,
As a matter of fact, according to: Pace, C. N., & Scholtz, J. M. (1998). A helix propensity scale based on experimental studies of peptides and proteins. Biophysical journal, 75(1), 422–427. https://doi.org/10.1016/s0006-3495(98)77529-0 Alanine has the highest helix propensity. In other words your helix becomes even more stable.
An indication can be obtained by using a secondary structure prediction program like:
SOPMA https://npsa.lyon.inserm.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html
JPred4 http://www.compbio.dundee.ac.uk/jpred4/index.html
Just change the FASTA form of your sequence and see whether a drastic change is to be expected or not.
Best regards.
PS. See for an example of a little comparison between different secondary structure prediction programs: Article The role and significance of potential lipid-binding regions...
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