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Simulation of an all‐β 3 ‐icosapeptide containing the 20 proteinogenic side chains: Effect of temperature, pH, counterions, solvent, and force field on helix stability
Author(s) -
Trzesniak Daniel,
Jaun Bernhard,
Mathad Raveendra I.,
van Gunsteren Wilfred F.
Publication year - 2006
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20601
Subject(s) - chemistry , counterion , side chain , solvent , helix (gastropod) , nuclear magnetic resonance spectroscopy , alpha helix , crystallography , ionic bonding , folding (dsp implementation) , amino acid , hydrogen bond , methanol , instability , computational chemistry , ion , stereochemistry , molecule , circular dichroism , organic chemistry , ecology , biochemistry , snail , electrical engineering , biology , engineering , polymer , physics , mechanics
Simulations of various β‐peptides have in the last years clarified several issues concerning peptide folding equilibria and interpretation of experimental data, especially from NMR and CD spectroscopy. These simulations involved different temperatures, pH‐values, ionic strengths, solvents, and force‐field parameters, but a variation of these factors for one β‐peptide has not yet been done. To investigate the influence of varying these factors, we analyze the helix stability of an all‐β 3 ‐icosapeptide bearing all 20 proteinogenic amino acid side chains, which is experimentally observed to fold into a 3 14 ‐helix in methanol but not in water. Structural aspects, such as hydrogen‐bonded rings and salt bridges, are discussed and a comparison with NMR primary (NOE distance bounds and 3 J‐values) and secondary (NMR derived model structures) data is made. We further investigate the reasons for the 3 14 ‐helix stability/instability in methanol/water. Of all factors studied, the presence of counterions seems to be the one inducing most significant effects in the simulations. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 636–645, 2006 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com