The effect of environment on the stability of an integral membrane helix: Molecular dynamics simulations of surfactant protein C in chloroform, methanol and water

The effect of environment on the stability of an integral membrane helix: Molecular dynamics... A series of three molecular dynamics simulations at 300 K in explicit solvent environments of chloroform, methanol and water has been performed on the pulmonary surfactant lipoprotein, SP-C, comprising several consecutive valine residues in order to investigate the stability of the α-helical conformation. Two additional simulations were performed on truncated SP-C with a five-residue N-terminal deletion at 300 K and 500 K in water, the high temperature run in order to increase the rate of peptide denaturation. Indications of destabilization appear in chloroform during 1 ns while the SP-C α-helix is remarkably stable during 1 ns in methanol and water. In particular the polyvalyl part comprising residues Val15 to Val21 remains intact even at elevated temperature, and the valines do no disrupt the α-helical conformation. The valyl-rotamer sampling is partly restricted. Unfolding takes place successively along the primary sequence starting from the C-terminal end. Factors affecting polypeptide stability in molecular dynamics simulations are addressed. The intrinsic helix-forming tendency of valine residues and its dependence on the sequence context, and the role of the solvent environment in stabilizing or destabilizing an α-helical fold, are discussed. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Molecular Biology Elsevier

The effect of environment on the stability of an integral membrane helix: Molecular dynamics simulations of surfactant protein C in chloroform, methanol and water

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Publisher
Elsevier
Copyright
Copyright © 1995 Academic Press Limited
ISSN
0022-2836
DOI
10.1016/S0022-2836(05)80156-1
Publisher site
See Article on Publisher Site

Abstract

A series of three molecular dynamics simulations at 300 K in explicit solvent environments of chloroform, methanol and water has been performed on the pulmonary surfactant lipoprotein, SP-C, comprising several consecutive valine residues in order to investigate the stability of the α-helical conformation. Two additional simulations were performed on truncated SP-C with a five-residue N-terminal deletion at 300 K and 500 K in water, the high temperature run in order to increase the rate of peptide denaturation. Indications of destabilization appear in chloroform during 1 ns while the SP-C α-helix is remarkably stable during 1 ns in methanol and water. In particular the polyvalyl part comprising residues Val15 to Val21 remains intact even at elevated temperature, and the valines do no disrupt the α-helical conformation. The valyl-rotamer sampling is partly restricted. Unfolding takes place successively along the primary sequence starting from the C-terminal end. Factors affecting polypeptide stability in molecular dynamics simulations are addressed. The intrinsic helix-forming tendency of valine residues and its dependence on the sequence context, and the role of the solvent environment in stabilizing or destabilizing an α-helical fold, are discussed.

Journal

Journal of Molecular BiologyElsevier

Published: Apr 7, 1995

References

  • Molecular dynamics with coupling to an external bath
    Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; Di Nola, A.; Haak, J.R.
  • Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: the effect of fluctuating internuclear distances
    Tropp, J.
  • Theory of the phase transition between helix and random coil in polypeptide chains
    Zimm, B.H.; Bragg, J.K.

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