Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration.
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.
Yang
Sichun
S
Center for Theoretical Biological Physics and Department of Physics, University of California San Diego, La Jolla, CA 92093-0374, USA.
Levine
Herbert
H
Onuchic
José N
JN
D019281:Dimerization; D008433:Mathematics; D008958:Models, Molecular; D008962:Models, Theoretical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
D011506:Proteins