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Do Valine Side Chains Have an Influence on the Folding Behavior of β ‐Substituted β ‐Peptides?
Author(s) -
Glättli Alice,
Seebach Dieter,
van Gunsteren Wilfred F.
Publication year - 2004
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/hlca.200490223
Subject(s) - chemistry , side chain , valine , circular dichroism , folding (dsp implementation) , molecular dynamics , branching (polymer chemistry) , protein folding , monomer , stereochemistry , crystallography , steric effects , amino acid , computational chemistry , biochemistry , organic chemistry , polymer , electrical engineering , engineering
Abstract The influence of valine side chains on the folding/unfolding equilibrium and, in particular, on the 3 14 ‐helical propensity of β 3 ‐peptides were investigated by means of molecular‐dynamics (MD) simulation. To that end, the valine side chains in two different β 3 ‐peptides were substituted by leucine side chains. The resulting four peptides, of which three have never been synthesized, were simulated for 150 to 200 ns at 298 and 340 K, starting from a fully extended conformation. The simulation trajectories obtained were compared with respect to structural preferences and folding behavior. All four peptides showed a similar folding behavior and were found to predominantly adopt 3 14 ‐helical conformations, irrespective of the presence of valine side chains. No other well‐defined conformation was observed at significant population in any of the simulations. Our results imply that β 3 ‐peptides show a structural preference for 3 14 ‐helices independent of the branching nature of the side chains, in contrast to what has been previously proposed on the basis of circular‐dichroism (CD) measurements.