Proline (Pro, P)
Proline is a cyclic amino acid whose side chain loops back to the backbone nitrogen. It rigidly constrains peptide conformation, breaks helices, forms polyproline helices and undergoes cis/trans isomerisation.
Structure and properties
Proline's side chain forms a five-membered ring with its own backbone nitrogen, making it a secondary amine and fixing one backbone angle. This rigidity lowers flexibility, and the lack of an amide hydrogen means proline cannot donate a backbone hydrogen bond. Proline therefore disrupts alpha helices and beta sheets except at their ends, and is common at turns. Runs of proline adopt the polyproline II helix, an extended left-handed structure important in protein recognition. Bonds preceding proline isomerise between cis and trans forms much more readily than other peptide bonds, which slows folding and creates conformational heterogeneity.
Role in peptides
Proline is common in short bioactive peptides because it fixes shape and resists many proteases. BPC-157 contains a run of three prolines. The Pro-Gly-Pro tail of Semax and Selank was added to slow degradation. KPV has proline at its centre. Dipeptidyl peptidase-4 cleaves after proline or alanine at the second position, which shaped the design of GLP-1 analogues. Proline-rich antimicrobial peptides act on intracellular targets rather than primarily disrupting membranes.
Stability and analysis
Cis/trans isomerisation of X-Pro bonds can produce broad or split HPLC peaks and extra NMR signals that are conformers, not impurities; raising column temperature often merges them. Asp-Pro bonds are unusually acid-labile. In synthesis, proline at the second or third position from the resin promotes diketopiperazine formation and chain loss, and couplings onto proline's secondary amine are slower. Proline itself does not oxidise or racemise readily.
In PeptideWiki compounds
Compounds whose sequence contains proline, with the number of occurrences.
- IGF-1 LR3 (7)
- BPC-157 (4)
- Exenatide (4)
- Pramlintide (3)
- Selank (3)
- Thymosin β4 (3)
- Calcitonin (salmon) (2)
- Humanin (2)
- Semax (2)
- Afamelanotide (1)
- Gonadorelin (1)
- KPV (1)
- LL-37 (1)
- Larazotide (1)
- MOTS-c (1)
- Oxytocin (1)
- Triptorelin (1)
Frequently asked questions
Why does proline give split HPLC peaks?
The bond before a proline can sit in either the cis or trans form, and interconversion can be slow on the timescale of an HPLC run. If the two forms separate partly on the column, the result is a broad, shouldered or doubled peak. These are conformers of the same molecule rather than impurities. Running the column warmer speeds interconversion and usually merges them, which is a useful diagnostic.
Is proline technically an amino acid?
Strictly, proline is an imino acid in older terminology, because its nitrogen is a secondary amine bonded to the side-chain ring. In modern usage it is counted among the twenty standard amino acids and is incorporated into proteins in the normal way. The ring is what gives proline its distinctive conformational effects, including helix breaking and cis/trans isomerisation of the preceding peptide bond.
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