Get access
Advertisement

Prediction, refinement, and persistency of transmembrane helix dimers in lipid bilayers using implicit and explicit solvent/lipid representations: Microsecond molecular dynamics simulations of ErbB1/B2 and EphA1

Authors

  • Liqun Zhang,

    1. Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
    Search for more papers by this author
  • Alexander J. Sodt,

    1. Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-9314
    Search for more papers by this author
  • Richard M. Venable,

    1. Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-9314
    Search for more papers by this author
  • Richard W. Pastor,

    1. Laboratory of Computational Biology, National Heart Lung Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-9314
    Search for more papers by this author
  • Matthias Buck

    Corresponding author
    1. Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
    2. Department of Neuroscience, Case Western Reserve University, Cleveland, Ohio 44106
    3. Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
    4. Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106
    • Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106
    Search for more papers by this author

Abstract

All-atom simulations are carried out on ErbB1/B2 and EphA1 transmembrane helix dimers in lipid bilayers starting from their solution/DMPC bicelle NMR structures. Over the course of microsecond trajectories, the structures remain in close proximity to the initial configuration and satisfy the majority of experimental tertiary contact restraints. These results further validate CHARMM protein/lipid force fields and simulation protocols on Anton. Separately, dimer conformations are generated using replica exchange in conjunction with an implicit solvent and lipid representation. The implicit model requires further improvement, and this study investigates whether lengthy all-atom molecular dynamics simulations can alleviate the shortcomings of the initial conditions. The simulations correct many of the deficiencies. For example, excessive helix twisting is eliminated over a period of hundreds of nanoseconds. The helix tilt, crossing angles, and dimer contacts approximate those of the NMR-derived structure, although the detailed contact surface remains off-set for one of two helices in both systems. Hence, even microsecond simulations are not long enough for extensive helix rotations. The alternate structures can be rationalized with reference to interaction motifs and may represent still sought after receptor states that are important in ErbB1/B2 and EphA1 signaling. Proteins 2013. © 2012 Wiley Periodicals, Inc.

Get access to the full text of this article

Ancillary