2009/02/13 by Kazuhito Itoh, Masaki Sasai
Biochemistry, Genetics and Molecular Biology · Materials Science · Physics and Astronomy · #Enzyme Structure and Function #Protein Structure and Dynamics #RNA and protein synthesis mechanisms #cond-mat.dis-nn #q-bio.BM
paper · pdf · doi:10.1063/1.3097018
to appear in J. Chem. Phys
arxiv created 2009/02/13 · openalex publication_date 2009/04/13 · arxiv updated 2009/12/01 · openalex created_date 2016/06/24 · openalex updated_date 2026/07/28
Theory of multidimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in terms of cooperativity within individual regions and interactions among multiple regions and thus obtained classification is used to analyze the folding process of several example proteins. Ribosomal protein S6, src-SH3 domain, CheY, barnase, and BBL domain are analyzed with the two-dimensional representation by using a structure-based Hamiltonian model. The extension to the higher dimensional representation leads to the finer description of the folding process. Barnase, NtrC, and an ankyrin repeat protein are examined with the three-dimensional representation. The multidimensional representation allows us to directly address questions on folding pathways, intermediates, and transition states.