title: Free-energy landscape of protein oligomerization from atomistic simulations.
abstract: In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage.
authors.affiliation: Laboratoire de Biophysique Statistique, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Barducci
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Bonomi
authors.forename: Meher K
authors.initials: MK
authors.lastname: Prakash
authors.forename: Michele
authors.initials: M
authors.lastname: Parrinello
mesh_terms: D001703:Biophysics; D019143:Evolution, Molecular; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D058105:Polymerization; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins
keywords: conformational selection; enhanced sampling; fly-casting mechanism; molecular dynamics