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Theoretical Study of β ‐Peptide Models: Intrinsic Preferences of Helical Structures
Author(s) -
Wu YunDong,
Lin JinQiu,
Zhao YiLei
Publication year - 2002
Publication title -
helvetica chimica acta
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.74
H-Index - 82
eISSN - 1522-2675
pISSN - 0018-019X
DOI - 10.1002/1522-2675(200210)85:10<3144::aid-hlca3144>3.0.co;2-p
Subject(s) - chemistry , helix (gastropod) , residue (chemistry) , crystallography , ribbon , alpha helix , polyproline helix , peptide , electrostatics , stereochemistry , circular dichroism , organic chemistry , materials science , biochemistry , biology , ecology , snail , composite material
β ‐Peptides form various secondary structures, such as 14 ‐helix, 12 ‐helix, 10 / 12 ‐helix, 10 ‐helix, 2 8 ‐ribbon, C6 ‐ribbon, and pleated‐sheet. Thus, it is useful to understand the intrinsic backbone conformational preferences of these basic structures. By using a simple repeating‐unit method, we have calculated the preferences of C6 ‐ribbon, β ‐strand, 10 / 12 ‐helix, 14 ‐helix, 12 ‐helix, 10 ‐helix, and 2 8 ‐ribbon of a series of poly‐ β ‐alanine models, Ac‐( β ‐Ala) n ‐NH 2 , with n =1–9. Interactions among single amino acids result in cooperative residue energies. This is not found for the formations of β ‐strands, 2 8 ‐ribbons, and C6 ‐ribbons, which possess constant residue energies. In contrast, the 12 ‐helix, 10 ‐helix, and 14 ‐helix are characterized by increasing residue energies as the peptide elongates. Therefore, there is a considerable positive cooperative impetus in the gas phase for their formation. The residue energy of the 10 / 12 ‐helix increases significantly for n =2 and 3 , and then displays a zigzag pattern. Meanwhile, there is a good correlation between calculated residue energies and residue dipole moments, indicating the importance of long‐range electrostatic interactions to the cooperative residue energy. Efforts have been made to separate the electrostatic and torsional interactions between residues. Thereby, the 12 ‐, 10 ‐, and 10 / 12 ‐helices all benefit from electrostatic interactions, while the 14‐helix has the most intrinsic preference in terms of torsional interaction. The effect of MeOH on the secondary structures has also been evaluated by SCIPCM solvent model calculations.