title: Direct molecular dynamics observation of protein folding transition state ensemble.
abstract: The concept of the protein transition state ensemble (TSE), a collection of the conformations that have 50% probability to convert rapidly to the folded state and 50% chance to rapidly unfold, constitutes the basis of the modern interpretation of protein engineering experiments. It has been conjectured that conformations constituting the TSE in many proteins are the expanded and distorted forms of the native state built around a specific folding nucleus. This view has been supported by a number of on-lattice and off-lattice simulations. Here we report a direct observation and characterization of the TSE by molecular dynamic folding simulations of the C-Src SH3 domain, a small protein that has been extensively studied experimentally. Our analysis reveals a set of key interactions between residues, conserved by evolution, that must be formed to enter the kinetic basin of attraction of the native state.
authors.affiliation: Center for Polymer Studies, Department of Physics, Boston University, Boston, MA 02215, USA. fding@polymer.bu.edu
authors.forename: Feng
authors.initials: F
authors.lastname: Ding
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Buldyrev
authors.forename: H Eugene
authors.initials: HE
authors.lastname: Stanley
authors.forename: Eugene I
authors.initials: EI
authors.lastname: Shakhnovich
mesh_terms: D003198:Computer Simulation; D004735:Energy Transfer; D008958:Models, Molecular; D011487:Protein Conformation; D011489:Protein Denaturation; D015202:Protein Engineering / Q000379:methods; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D016392:Proto-Oncogene Proteins pp60(c-src) / Q000737:chemistry*; D013696:Temperature; D018909:src Homology Domains
chemical_list: D016392:Proto-Oncogene Proteins pp60(c-src)