Conformational structure of peptides containing dehydroalanine: Formation of β-bend ribbon structure

✍ Scribed by Fateh S. Nandel; Nandita Malik; Balvinder Singh; D. V. S. Jain

• Publisher: John Wiley and Sons
• Year: 1999
• Tongue: English
• Weight: 212 KB
• Volume: 72
• Category: Article
• ISSN: 0020-7608
• DOI: 10.1002/(sici)1097-461x(1999)72:1<15::aid-qua2>3.0.co;2-2

✦ Synopsis

␣,␤-Unsaturated amino acids dehydroamino acids have been found in naturally occurring antibiotics of microbial origin and in some proteins. Due to the presence of the C C double bond, the dehydroamino acids influence the main-chain ␣ ␤ and the side-chain conformations. The lowest-energy conformational state of the model Ž . tripeptides, Ac᎐X᎐⌬Ala᎐NHMe, X s Ala, Val, Leu, Abu, or Phe corresponds to s 1 y30Њ, s 120Њ and s s 30Њ. This structure is stabilized by the hydrogen bond 1 2 2

between C O of the acetyl group and the NH of the amide group, resulting in the formation of a 10-membered ring. In the model heptapeptide containing ⌬ Ala at alternate position with Ala, Abu, and Leu, the lowest-energy conformation corresponds to s y30Њ and s 120Њ for all the Ala, Abu, and Leu residues and s s 30Њ for all ⌬ Ala residues. A graphical view of the molecule in this conformation reveals the formation of three hydrogen bonds involving the C O moiety of the ith residue and the NH moiety of the i q 3th residue, resulting in a 10-membered ring formation. In this structure, only alternate peptide bonds are involved in the intramolecular hydrogen-bond formation unlike the helices and it has been named the ␤-bend ribbon structure. The helical structures were predicted to be the most stable structures in the heptapeptide Ž . Ac᎐ Aib᎐⌬Ala ᎐NHMe with s "30Њ, s "60Њ for Aib residues and s s "30Њ 3 for ⌬ Ala residues. The computational results reveal that the ⌬ Ala residue does not induce an inverse ␥-turn in the preceding residue. It is the competitive interaction of small solvent molecules with the hydrogen-bonding sites of the peptide which gives rise Ž . to the formation of an inverse ␥-turn s y54Њ, s 82Њ; s 44Њ, s 3Њ in the 1 1 2 2 preceding residue to ⌬ Ala. The computational studies for the positional preference of ⌬ Ala in the peptide containing one ⌬ Ala and nine Ala residues reveals the formation of