Hello
I am just wondering if you have ideas or if you can share review articles or literatures about insights/strategies/methods for structure-activity relationship study of peptides? I am only familiar with the reason and context of alanine-scanning mutagenesis because it is widely used for SAR study of peptides; but in case I want to mutate the peptide further with other amino acids, what would be my basis in choosing a residue to mutate it?
For instance, if I want to check the effect of (+) or (-) residue substitution, what should I choose between lysine/arginine/histidine, or aspartic acid/glutamic acid?
If I want to check the hydrophobic effect residue substitution, what should I choose between valine, leucine, isoleucine etc.?
If I want to check the effect of the aromatic residue substitution, what should I choose between phenylalanine, tyrosine and tryptophan?
Your insights would help me to develop a rationalized, context-based and guided amino-acid substitution for SAR study of peptides that would not "waste" chemical reagents for chemical synthesis.
Thanks.
Dear Simon Miguel Lopez ,
It all depends very much on what you’re aiming for, but using some bioinformatics might as you say minimize that you “"waste" chemical reagents for chemical synthesis”. There are methods to:
-Predict secondary structure, using for example SOPMA: https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html
-Predict hydrophobicity, net charge etc. using Heliquest: https://heliquest.ipmc.cnrs.fr/
-Predict the tendency of the peptide to form a transmembrane helix using ∆G predictor: https://dgpred.cbr.su.se/index.php?p=TMpred
-Predict possible lipid binding potential using Heliquest based Eisenberg plot: Article New User-Friendly Approach to Obtain an Eisenberg Plot and I...
For an example using Heliquest etc. see: Article Identification and in silico analysis of helical lipid bindi...
Best regards.
Can also predict QSAR properties, calculate the hydrophilicity, molecular characteristics, etc. on the sequence, better shorter sequence, changed/replaced AA. Also lookout for topless tree method.
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