Author(s)

Fateh S. Nandel, Avneet Saini

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Aliphatic homo-polypeptoids of NAla, NVal, NIle and NLeu both in the presence and absence of protecting groups adopt helical structures without hydrogen bonds with Φ, Ψ values of ~ 0, ± 90° with trans amide bonds. These structures are stabilized by carbonyl-carbonyl interactions and characterized by ~ 3.16 residues per turn with a pitch of ~ 6.13 Å. It has been shown that like polyvaline and polyleucine peptides, poly-peptoids can also be exploited for the construction of potential surfactant like molecules by incorporating charged amino acid residues at the N terminal. A single-handed template with Φ, Ψ values of ~ 0, 90° can be attained by incorporating L-leu or L-val at the C-terminal of poly-NIle. Analysis of the simulation results in water as a function of time reveals that the opening of helical structures without hydrogen bonds takes place at sub-picosecond time scale starting from the N-terminal. This leads to the formation of collagen or inverse-collagen type structures (Φ, Ψ ~ -60, 145° and 60, -145° respectively) stabilized by interactions of water molecules with the backbone carbonyl groups.

Peptoids; Conformation; Helical Structure without Hydrogen Bonds; Collagen and Inverse-Collagen Type Structures

Nandel, F. and Saini, A. (2011) Peptoids with aliphatic sidechains as helical structures without hydrogen bonds and collagen/ inverse-collagen type structures. Journal of Biophysical Chemistry, 2, 37-48. doi: 10.4236/jbpc.2011.21006.