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Originally published as Biophys J. BioFAST on December 30, 2005.
doi:10.1529/biophysj.105.069625
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Biophysical Journal 90:1855-1864 (2006)
© 2006 The Biophysical Society

Conformation and Environment of Channel-Forming Peptides: A Simulation Study

Jennifer M. Johnston *, Gabriel A. Cook {dagger}, John M. Tomich {dagger} and Mark S. P. Sansom *

* Department of Biochemistry, University of Oxford, Oxford, United Kingdom OX1 3QU; and {dagger} Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506

Correspondence: Address reprint requests to Mark S. P. Sansom, Tel.: 44-1865-275371; Fax: 44-1865-275273; E-mail: mark.sansom{at}bioch.ox.ac.uk.

Ion channel-forming peptides enable us to study the conformational dynamics of a transmembrane helix as a function of sequence and environment. Molecular dynamics simulations are used to study the conformation and dynamics of three 22-residue peptides derived from the second transmembrane domain of the glycine receptor (NK4-M2GlyR-p22). Simulations are performed on the peptide in four different environments: trifluoroethanol/water; SDS micelles; DPC micelles; and a DMPC bilayer. A hierarchy of {alpha}-helix stabilization between the different environments is observed such that TFE/water < micelles < bilayers. Local clustering of trifluoroethanol molecules around the peptide appears to help stabilize an {alpha}-helical conformation. Single (S22W) and double (S22W,T19R) substitutions at the C-terminus of NK4-M2GlyR-p22 help to stabilize a helical conformation in the micelle and bilayer environments. This correlates with the ability of the W22 and R19 side chains to form H-bonds with the headgroups of lipid or detergent molecules. This study provides a first atomic resolution comparison of the structure and dynamics of NK4-M2GlyR-p22 peptides in membrane and membrane-mimetic environments, paralleling NMR and functional studies of these peptides.




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