An amino acid chain does not stay stretched out in solution: it folds into repeating patterns. The alpha helix is a spiral in which each C=O group forms a hydrogen bond with the N–H four positions further along. The beta sheet forms when extended stretches of the chain line up side by side. In between there are turns and loops that change the direction of the chain.
In short peptides the structure is often transient and depends heavily on the environment: many peptide hormones are disordered in water and adopt a helix when they bind to their receptor or to a membrane. GLP-1 and its analogues, for example, form a helix in the region that interacts with the receptor.
Secondary structure also relates to handling problems: the tendency to form beta sheets between neighbouring molecules underlies many aggregation processes, including amyloid fibrils.
Many design modifications (helix-promoting amino acids, cyclisations, chemical staples) aim to stabilise the active conformation. Understanding secondary structure helps explain why an analogue is more potent or more stable.
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Definition for educational and scientific purposes. It is not medical advice or a recommendation for use. NeoPeptidos products are sold labelled for research use only (RUO).