title: Correlation between evolutionary structural development and protein folding.
abstract: Evolution should have played important roles in determining folding mechanisms and structures of proteins. In this article we discuss how the folding mechanisms had been affected by the early stage of evolution through which the uniqueness of structure had developed. Although the process of such early-time evolution has remained a mystery, a plausible scenario is that the evolution of proteins toward the ordered structures was guided by functional selection pressure as demonstrated in vitro and in silico. We examine the in silico functional selection of sequences and show that there is a significant correlation between two different processes toward the unique 3D structure, the evolutionary development of structure through sequence selection, and the folding process of the resultant sequence. This finding could be rephrased as protein folding recapitulates the emergence of topology in the molecular evolution. The correlation suggests a guideline for engineering foldable proteins.
authors.affiliation: Department of Complex Systems Science, Graduate School of Information Science, and Institute for Advanced Research, Nagoya University, Nagoya 464-8601, Japan.
authors.forename: Chioko
authors.initials: C
authors.lastname: Nagao
authors.forename: Tomoki P
authors.initials: TP
authors.lastname: Terada
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Yomo
authors.forename: Masaki
authors.initials: M
authors.lastname: Sasai
mesh_terms: D001665:Binding Sites; D005075:Biological Evolution; D019295:Computational Biology; D003198:Computer Simulation; D030562:Databases, Protein; D019143:Evolution, Molecular; D007700:Kinetics; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D012984:Software; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D010455:Peptides; D011506:Proteins