title: Surveying a local fitness landscape of a protein with epistatic sites for the study of directed evolution.
abstract: We present a method for analysis of a fitness landscape of a biopolymer with significantly epistatic sites. The analysis is based on a quasi-additive fitness model. The fitness model is constructed with additive terms conducted by "site-fitness" and epistatic terms conducted by "pair-fitness," where the site-fitness is a fitness contribution from an independent residue and the pair-fitness is a fitness contribution from a pair of epistatic residues. As a case study, we analyzed the sequence-fitness data for 45 clones of thermostable prolyl endopeptidase mutants. They were generated by a mutation scrambling method, which can accumulate advantageous mutations. The fitness contributions from 14 single-point mutations including E67Q and Q656R were identified by the analysis. As a result, we found that the fitness model with a significant epistatic term by a pair of the 67th site and 656th site was in good agreement with the experimental data and that the explored landscape in the binary 14-dimensional sequence space is still a mountainous landscape with twin peaks. The validity was supported by the analysis of mutant fitness distributions derived from another mutation scrambling experiment and by (3D) structural data.
authors.affiliation: Tsukuba Research Institute, Novartis Pharma K. K., Ohkubo 8, Tsukuba 300-2611, Japan.
authors.forename: Takuyo
authors.initials: T
authors.lastname: Aita
authors.forename: Norio
authors.initials: N
authors.lastname: Hamamatsu
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Nomiya
authors.forename: Hidefumi
authors.initials: H
authors.lastname: Uchiyama
authors.forename: Yasuhiko
authors.initials: Y
authors.lastname: Shibanaka
authors.forename: Yuzuru
authors.initials: Y
authors.lastname: Husimi
mesh_terms: D019020:Directed Molecular Evolution; D006207:Half-Life; D008958:Models, Molecular; D009154:Mutation; D000085822:Prolyl Oligopeptidases; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
chemical_list: D012697:Serine Endopeptidases; D000085822:Prolyl Oligopeptidases