Dimerization of the p53 oligomerization domain: Identification of a folding nucleus by molecular dynamics simulations

  • Chong L
  • Snow C
  • Rhee Y
 et al. 
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Dimerization of the p53 oligomerization domain involves coupled folding and binding of monomers. To examine the dimerization, we have performed molecular dynamics (MD) simulations of dimer folding from the rate-limiting transition state ensemble (TSE). Among 799 putative transition state structures that were selected from a large ensemble of high-temperature unfolding trajectories, 129 were identified as members of the TSE via calculation of a 50% transmission coefficient from at least 20 room-temperature simulations. This study is the first to examine the refolding of a protein dimer using MD simulations in explicit water, revealing a folding nucleus for dimerization. Our atomistic simulations are consistent with experiment and offer insight that was previously unobtainable. © 2004 Elsevier Ltd. All rights reserved.

Author-supplied keywords

  • molecular dynamics simulation
  • oligomerization
  • protein folding
  • protein interactions
  • tumor suppressor p53

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  • Lillian T. Chong

  • Christopher D. Snow

  • Young Min Rhee

  • Vijay S. Pande

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