| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
Biophys J, April 1999, p. 1929-1938, Vol. 76, No. 4
and
*National Center for Supercomputing Applications,
#Department of Molecular and Integrative Physiology,
§Department of Biochemistry, ¶Center for
Biophysics and Computational Biology, and Beckman Center
for Advanced Science and Technology, University of Illinois,
Urbana, Illinois 61801 USA
This paper reports on a simulation of a gramicidin
channel inserted into a fluid phase DMPC bilayer with 100 lipid
molecules. Two lipid molecules per leaflet were removed to insert the
gramicidin, so the resulting preparation had 96 lipid molecules and
3209 water molecules. Constant surface tension boundary conditions were
employed. Like previous simulations with a lower lipid/gramicidin ratio (Woolf, T. B., and B. Roux. 1996. Proteins: Struct.,
Funct., Genet. 24:92-114), it is found that tryptophan-water
hydrogen bonds are more common than tryptophan-phospholipid hydrogen
bonds. However, one of the tryptophan NH groups entered into an
unusually long-lived hydrogen bonding pattern with two glycerol oxygens
of one of the phospholipid molecules. Comparisons were made between the
behavior of the lipids adjacent to the channel with those farther away. It was found that hydrocarbon chains of lipids adjacent to the channel
had higher-order parameters than those farther away. The thickness of
the lipid bilayer immediately adjacent to the channel was greater than
it was farther away. In general, the lipids adjacent to the membrane
had similar orientations to those seen by Woolf and Roux, while those
farther away had similar orientations to those pertaining before the
insertion of the gramicidin. A corollary to this observation is that
the thickness of the hydrocarbon region adjacent to the gramicidin was
much thicker than what other studies have identified as the
"hydrophobic length" of the gramicidin channel.
Biophys J, April 1999, p. 1929-1938, Vol. 76, No. 4
© 1999 by the Biophysical Society 0006-3495/99/04/1929/10 $2.00
This article has been cited by other articles:
 |
|
 |
|
  R. J. Mashl and E. Jakobsson End-Point Targeted Molecular Dynamics: Large-Scale Conformational Changes in Potassium Channels Biophys. J., June 1, 2008; 94(11): 4307 - 4319. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. N. R. Petersen, M. O. Jensen, and C. H. Nielsen Interfacial Tryptophan Residues: A Role for the Cation-{pi} Effect? Biophys. J., December 1, 2005; 89(6): 3985 - 3996. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Venturoli, B. Smit, and M. M. Sperotto Simulation Studies of Protein-Induced Bilayer Deformations, and Lipid-Induced Protein Tilting, on a Mesoscopic Model for Lipid Bilayers with Embedded Proteins Biophys. J., March 1, 2005; 88(3): 1778 - 1798. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. B. Jordan, P. L. Easton, and J. F. Hinton Effects of Phenylalanine Substitutions in Gramicidin A on the Kinetics of Channel Formation in Vesicles and Channel Structure in SDS Micelles Biophys. J., January 1, 2005; 88(1): 224 - 234. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. G. Dzikovski, P. P. Borbat, and J. H. Freed Spin-Labeled Gramicidin A: Channel Formation and Dissociation Biophys. J., November 1, 2004; 87(5): 3504 - 3517. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Yuan, R. J. O'Connell, P. L. Feinberg-Zadek, L. J. Johnston, and S. N. Treistman Bilayer Thickness Modulates the Conductance of the BK Channel in Model Membranes Biophys. J., June 1, 2004; 86(6): 3620 - 3633. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. D. Faraldo-Gomez, G. R. Smith, and M. S. P. Sansom Molecular Dynamics Simulations of the Bacterial Outer Membrane Protein FhuA: A Comparative Study of the Ferrichrome-Free and Bound States Biophys. J., September 1, 2003; 85(3): 1406 - 1420. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. W. Allen, T. Bastug, S. Kuyucak, and S.-H. Chung Gramicidin A Channel as a Test Ground for Molecular Dynamics Force Fields Biophys. J., April 1, 2003; 84(4): 2159 - 2168. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Tang and Y. Xu From the Cover: Large-scale molecular dynamics simulations of general anesthetic effects on the ion channel in the fully hydrated membrane: The implication of molecular mechanisms of general anesthesia PNAS, December 10, 2002; 99(25): 16035 - 16040. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Edwards, B. Corry, S. Kuyucak, and S.-H. Chung Continuum Electrostatics Fails to Describe Ion Permeation in the Gramicidin Channel Biophys. J., September 1, 2002; 83(3): 1348 - 1360. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. L. de Groot, D. P. Tieleman, P. Pohl, and H. Grubmuller Water Permeation through Gramicidin A: Desformylation and the Double Helix: A Molecular Dynamics Study Biophys. J., June 1, 2002; 82(6): 2934 - 2942. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Diociaiuti, F. Bordi, A. Motta, A. Carosi, A. Molinari, G. Arancia, and C. Coluzza Aggregation of Gramicidin A in Phospholipid Langmuir-Blodgett Monolayers Biophys. J., June 1, 2002; 82(6): 3198 - 3206. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
