I heard about the alanine scanning mutagenesis but not the other amino acid mutagenesis. Is there any specialty in alanine?
Alanine (Ala) has propensity to form alpha helices but can also occur in beta sheets and is generally equivalent to simply truncating a side chain back to the beta carbon, which is the first side chain atom. The beta carbon position depends upon the backdone dihedral angles of the polypeptide so is really part of the main chain structure of the protein. Thus, alanine is generally an accepted single residue first choice for mutational scanning because it retains the beta carbon but no other side chain chemistry. Glycine which removes the beta carbon is unusually flexible and can take on polypeptide backbone conformations generally not allowed by other amino acids, so mutation to glycine will cause flexibility and possible conformational changes convoluted with the effects of removing the side chain atoms making interpretation more complex than for Ala. Replacing side chains with larger, more constrained (such as branched beta carbon side chains of valine and Isoleucine), more polar, differently charged, or more hydrophobic atoms may all cause changes in structures and conformation along with the side chain chemistry thereby complicating analyses of results more than Ala.
Alanine (Ala) has propensity to form alpha helices but can also occur in beta sheets and is generally equivalent to simply truncating a side chain back to the beta carbon, which is the first side chain atom. The beta carbon position depends upon the backdone dihedral angles of the polypeptide so is really part of the main chain structure of the protein. Thus, alanine is generally an accepted single residue first choice for mutational scanning because it retains the beta carbon but no other side chain chemistry. Glycine which removes the beta carbon is unusually flexible and can take on polypeptide backbone conformations generally not allowed by other amino acids, so mutation to glycine will cause flexibility and possible conformational changes convoluted with the effects of removing the side chain atoms making interpretation more complex than for Ala. Replacing side chains with larger, more constrained (such as branched beta carbon side chains of valine and Isoleucine), more polar, differently charged, or more hydrophobic atoms may all cause changes in structures and conformation along with the side chain chemistry thereby complicating analyses of results more than Ala.
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