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To complement the ion mobility mass spectrometry data from the gas-phase experiments on polymers and proteins we have investigated conformations of helical polypeptides by molecular dynamic simulations. Due to strong residue attraction and hydrogen bonding, not mitigated by solvent molecules, a large content of helices, turns and bends was found to persist in long alanine polypeptides (Ala)n even...
The conformational structure of unsolvated polyalanine molecules (Ala) n is explored in a wide range of chain lengths n by MD simulations using the Amber force fields. Remarkably, on cooling long Ala peptides to 303K the straight α-helix is fragmented into shorter pieces that organize into helical bundles. The straight α-helix becomes unstable in polypeptides of the length over n∼55. Several...
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