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The importance of prolines, glycines, and combinations of these residues in transmembrane α-helices from membrane proteins has been highlighted in recent studies in which possible functional roles have been identified. In this study we build on such work by systematically pursuing the relationship between sequence and conformational properties via molecular dynamics simulation. We simulate 24 different sequence motifs involving proline and glycine pairings in a "host" polyalanine helix embedded in a solvated octane slab as a membrane mimetic. The flexibility and conformational dynamics are compared between the different motifs. We find that a proline is necessary to introduce pronounced bend/kink-swivel motions in the peptide, acting as an effective "molecular hinge" that decouples the pre- and post-proline portions of the helix. Although moderate flexibility is found in even a polyalanine helix and is pronounced slightly by glycine residues, proline produces the greatest perturbation from canonical behavior and introduces anisostropy into the kink-swivel space of the peptide. The dependence of this behavior on the given motif may be important both in interpreting existing data and in predicting the flexibility of a given sequence and suggesting possible functional roles.

Original publication

DOI

10.1021/jp026686u

Type

Journal article

Journal

Journal of Physical Chemistry B

Publication Date

16/01/2003

Volume

107

Pages

627 - 636