Effects of i and i+3 residue identity on cis-trans isomerism of the aromatic(i+1)-prolyl(i+2) amide bond: implications for type VI beta-turn formation

• Published in: Biopolymers 2006, Vol.84 (2), p.192-204
• Main Authors: Meng, Hai Yun, Thomas, Krista M, Lee, Aaron E, Zondlo, Neal J
• Format: Article
• Language: English
• Subjects: Amides - analysis; Amides - chemistry; Dipeptides - analysis; Dipeptides - chemistry; Dipeptides - metabolism; Isomerism; Nuclear Magnetic Resonance, Biomolecular; Peptides - analysis; Peptides - chemical synthesis; Peptides - chemistry; Peptides - metabolism; Phosphorylation; Proline - chemistry; Proline - metabolism; Protein Conformation; Protein Structure, Secondary
• ISSN: 0006-3525
• DOI: 10.1002/bip.20382

Cis-trans isomerization of amide bonds plays critical roles in protein molecular recognition, protein folding, protein misfolding, and disease. Aromatic-proline sequences are particularly prone to exhibit cis amide bonds. The roles of residues adjacent to a tyrosine-proline residue pair on cis-trans isomerism were examined. A short series of peptides XYPZ was synthesized and cis-trans isomerism was analyzed. Based on these initial studies, a series of peptides XYPN, X = all 20 canonical amino acids, was synthesized and analyzed by NMR for i residue effects on cis-trans isomerization. The following effects were observed: (a) aromatic residues immediately preceding Tyr-Pro disfavor cis amide bonds, with K(trans/cis)= 5.7-8.0, W > Y > F; (b) proline residues preceding Tyr-Pro lead to multiple species, exhibiting cis-trans isomerization of either or both X-Pro amide bonds; and (c) other residues exhibit similar values of K(trans/cis) (= 2.9-4.2), with Thr and protonated His exhibiting the highest fraction cis. beta-Branched and short polar residues were somewhat more favorable in stabilizing the cis conformation. Phosphorylation of serine at the i position modestly increases the stability of the cis conformer. In addition, the effect of the i+3 residue was examined in a limited series of peptides TYPZ. NMR data indicated that aromatic residues, Pro, Asn, Ala, and Val at the i+3 residue all favor cis amide bonds, with aromatic residues and Asn favoring more compact phi at Tyr(cis) and Ala and Pro favoring more extended phi at Tyr(cis). D-Alanine at the i+3 position particularly disfavors cis amide bonds.