Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration

J Mol Biol. 2005 Sep 9;352(1):202-11. doi: 10.1016/j.jmb.2005.06.062.

Abstract

Domain swapping has been shown to be an important mechanism controlling multiprotein assembly and has been suggested recently as a possible mechanism underlying protein aggregation. Understanding oligomerization via domain swapping is therefore of theoretical and practical importance. By using a symmetrized structure-based (Gō) model, we demonstrate that in the free-energy landscape of domain swapping, a large free-energy barrier separates monomeric and domain-swapped dimeric configurations. We investigate the effect of finite monomer concentration, by implementing a new semi-analytical method, which involves computing the second virial coefficient, a thermodynamic indicator of inter-molecular interactions. This method, together with the symmetrized structure-based (Gō) model, minimizes the need for expensive many-protein simulations, providing a convenient framework to investigate concentration effect. Finally, we perform direct simulations of domain-swapped trimer formation, showing that this modeling approach can be used for higher-order oligomers.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Dimerization
  • Mathematics
  • Models, Molecular
  • Models, Theoretical
  • Protein Conformation*
  • Proteins / chemistry*
  • Proteins / metabolism*
  • Thermodynamics

Substances

  • Proteins