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Computational investigation of retro‐isomer equilibrium structures: Intrinsically disordered, foldable, and cyclic peptides
Author(s) -
Zerze Gül H.,
Stillinger Frank H.,
Debenedetti Pablo G.
Publication year - 2020
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1002/1873-3468.13558
Subject(s) - peptide , cyclic peptide , chemistry , molecular dynamics , crystallography , intrinsically disordered proteins , chemical physics , computational chemistry , biochemistry
We use all‐atom modeling and advanced‐sampling molecular dynamics simulations to investigate quantitatively the effect of peptide bond directionality on the equilibrium structures of four linear (two foldable, two disordered) and two cyclic peptides. We find that the retro forms of cyclic and foldable linear peptides adopt distinctively different conformations compared to their parents. While the retro form of a linear intrinsically disordered peptide with transient secondary structure fails to reproduce a secondary structure content similar to that of its parent, the retro form of a shorter disordered linear peptide shows only minor differences compared to its parent.