I have a peptide but couldn't find any existed scramble control for it in papers. I found Mimotopes website which can generate scrambled control peptide by entering my peptide sequence (25 amino acids). I think it works by randomizing completely the sequence.
How can I make sure whether the control peptide that the website generated won't interact? Will the control peptide be more robust if only scramble key part of the original sequence rather than the whole sequence? But I'm not sure how to identify the key parts. Thanks.
We generally interchange the positions of the amino acids maintaining the amphipathicity of the molecule by looking at the helical wheel of the peptide sequence.
Hope this works for you.
Good Luck!
I know the principles that interchange amino acids' positions of the targted peptides as scrambled control. However, I my project, I found several tubulin binding peptides bind to tubulin C-terminal mainly by electrostatic interaction rather than specific induced fit (shape) interactions. In this case, how should I design their scrambled peptides as negative control? Thanks
Well in that case , I think mutation of the amino acids will serve as negative controls.
Hope this works for you.
Thanks
Anshika Tandon Hello, would you be able to provide me some basic literature about helical wheels and principles of making scrambles peptides? I am just starting out in this field and feeling a bit overwhelmed.
Thanks!