Hello
I am currently searching for literature about amino acid propensities to exclusively form certain secondary structures regardless of what kind of peptide or protein do they form (e.g. membrane, cytosolic, soluble, globular protein etc). What are your thoughts on this one?
May you also recommend literature to support your answer. This would help me give a mechanistic basis of secondary structure formation from a given set of amino acid residues.
Thank you very much.
Hi Simon,
I may be able to partially help you with your question. Proline and Glycine are considered to be "helix breakers", therefore they will not likely be incorporated in this secondary structure. Proline has a specific cyclic structure, which doesnt fit into an alpha-helix structure. Glycine instead is to small for this type of secondary structure. This information can be found in standard biochemical books such as the "Stryer - Biochemistry"
There is no absolute rule, only probablistic determinations.
Biro, J. Amino acid size, charge, hydropathy indices and matrices for protein structure analysis. Theor Biol Med Model 3, 15 (2006). https://doi.org/10.1186/1742-4682-3-15
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