help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Efremov, R. G.
Right arrow Articles by Arseniev, A. S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Efremov, R. G.
Right arrow Articles by Arseniev, A. S.

Biophys J, May 1999, p. 2460-2471, Vol. 76, No. 5

A Solvent Model for Simulations of Peptides in Bilayers. II. Membrane-Spanning alpha -Helices

Roman G. Efremov,* Dmitry E. Nolde,* Gérard Vergoten,# and Alexander S. Arseniev*

 *M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, Moscow V-437, 117871 GSP, Russia; and  #Université des Sciences et Technologies de Lille, Centre de Recherches et d'Etudes en Simulations et Modélisation Moléculaires, Bâtiment C8, 59655 Villeneuve d'Ascq Cedex, France

We describe application of the implicit solvation model (see the first paper of this series), to Monte Carlo simulations of several peptides in bilayer- and water-mimetic environments, and in vacuum. The membrane-bound peptides chosen were transmembrane segments A and B of bacteriorhodopsin, the hydrophobic segment of surfactant lipoprotein, and magainin2. Their conformations in membrane-like media are known from the experiments. Also, molecular dynamics study of surfactant lipoprotein with different explicit solvents has been reported (Kovacs, H., A. E. Mark, J. Johansson, and W. F. van Gunsteren. 1995. J. Mol. Biol. 247:808-822). The principal goal of this work is to compare the results obtained in the framework of our solvation model with available experimental and computational data. The findings could be summarized as follows: 1) structural and energetic properties of studied molecules strongly depend on the solvent; membrane-mimetic media significantly promote formation of alpha -helices capable of traversing the bilayer, whereas a polar environment destabilizes alpha -helical conformation via reduction of solvent-exposed surface area and packing; 2) the structures calculated in a membrane-like environment agree with the experimental ones; 3) noticeable differences in conformation of surfactant lipoprotein assessed via Monte Carlo simulation with implicit solvent (this work) and molecular dynamics in explicit solvent were observed; 4) in vacuo simulations do not correctly reproduce protein-membrane interactions, and hence should be avoided in modeling membrane proteins.

Biophys J, May 1999, p. 2460-2471, Vol. 76, No. 5
© 1999 by the Biophysical Society   0006-3495/99/05/2460/12  $2.00


This article has been cited by other articles:


Home page
 Biophys. JHome page
M. B. Ulmschneider, J. P. Ulmschneider, M. S. P. Sansom, and A. Di Nola
A Generalized Born Implicit-Membrane Representation Compared to Experimental Insertion Free Energies
Biophys. J., April 1, 2007; 92(7): 2338 - 2349.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
A. Kessel, D. Shental-Bechor, T. Haliloglu, and N. Ben-Tal
Interactions of Hydrophobic Peptides with Lipid Bilayers: Monte Carlo Simulations with M2{delta}
Biophys. J., December 1, 2003; 85(6): 3431 - 3444.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
R. G. Efremov, P. E. Volynsky, D. E. Nolde, P. V. Dubovskii, and A. S. Arseniev
Interaction of Cardiotoxins with Membranes: A Molecular Modeling Study
Biophys. J., July 1, 2002; 83(1): 144 - 153.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 1999 by the Biophysical Society.