Molecular dynamics simulations of individual alpha-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. II. Interaction energy analysis

Biophysical Journal
T B Woolf

Abstract

The concepts of hydrophobicity and hydrophobic moments have been applied in attempts to predict membrane protein secondary and tertiary structure. The current paper uses molecular dynamics computer calculations of individual bacteriorhodopsin helices in explicit dimyristoylphosphatidylcholine bilayers to examine the atomic basis of these approaches. The results suggest that the types of interactions between a particular amino acid and the surrounding bilayer depend on the position and type of the amino acid. In particular, aromatic residues are seen to interact favorably at the interface region. Analysis of the trajectories in terms of hydrophobic moments suggests the presence of a particular face that prefers lipid. The results of these simulations may be used to improve secondary structure prediction methods and to provide further insights into the two-stage model of protein folding.

References

Apr 1, 1978·Proceedings of the National Academy of Sciences of the United States of America·J C OwickiH M McConnell
Apr 1, 1992·Protein Engineering·M SchifferF J Stevens
May 1, 1990·Biochemistry·J L Popot, D M Engelman
Jun 20, 1990·Journal of Molecular Biology·R HendersonK H Downing
Apr 29, 1987·Biochemical and Biophysical Research Communications·T NishiyaA Maeda
Feb 1, 1973·Proceedings of the National Academy of Sciences of the United States of America·P C JostG Vanderkooi
Aug 25, 1974·Journal of Molecular Biology·J P Segrest, R J Feldmann
Sep 1, 1983·Archives of Biochemistry and Biophysics·J F Post, C Dijkema
Jan 1, 1984·Annual Review of Biochemistry·D Eisenberg
Oct 15, 1984·Journal of Molecular Biology·D EisenbergR Wall
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
May 15, 1981·European Journal of Biochemistry·G von Heijne
Apr 1, 1995·Biophysical Journal·M S SansomJ Breed
May 1, 1994·Quarterly Reviews of Biophysics·M A Lemmon, D M Engelman
Mar 1, 1994·Protein Engineering·J AqvistJ E Samuelsson
Jan 1, 1993·Protein Engineering·P CronetG Vriend
Feb 5, 1993·Journal of Molecular Biology·C Landolt-MarticorenaR A Reithmeier
Apr 1, 1996·Biophysical Journal·N Ben-TalB Honig
Oct 1, 1996·Nature Structural Biology·W C Wimley, S H White
Sep 1, 1996·Biophysical Journal·F Jähnig
Aug 1, 1997·Current Opinion in Structural Biology·K M Merz

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Citations

Dec 4, 2003·Biophysical Journal·Ana Caballero-Herrera, Lennart Nilsson
Apr 8, 2000·Current Opinion in Structural Biology·L R Forrest, M S Sansom
Feb 27, 1999·Current Opinion in Structural Biology·P J Booth, A R Curran
Jul 4, 2006·Biophysical Journal·Kristen E Norman, Hugh Nymeyer
Feb 2, 1999·The Journal of General Physiology·C Townsend, R Horn
Jan 5, 2000·Biophysical Journal·I H ShrivastavaM S Sansom
Jul 25, 2006·Biophysical Journal·Hyunbum JangRuth Nussinov
Mar 3, 2010·Journal of Molecular Modeling·Siti Azma JusohVolkhard Helms
Mar 13, 1999·Biophysical Chemistry·P C Biggin, M S Sansom
Oct 7, 2004·Biophysical Journal·Sundeep S DeolMark S P Sansom
Jul 21, 2006·The Journal of Physical Chemistry. B·Themis LazaridisYong Chen
Sep 28, 2021·Journal of Biomolecular Structure & Dynamics·Gokul GovindPadmesh Anjukandi

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