Surveying a local fitness landscape of a protein with epistatic sites for the study of directed evolution.
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.
Aita
Takuyo
T
Tsukuba Research Institute, Novartis Pharma K. K., Ohkubo 8, Tsukuba 300-2611, Japan.
Hamamatsu
Norio
N
Nomiya
Yukiko
Y
Uchiyama
Hidefumi
H
Shibanaka
Yasuhiko
Y
Husimi
Yuzuru
Y
D019020:Directed Molecular Evolution; D006207:Half-Life; D008958:Models, Molecular; D009154:Mutation; D000085822:Prolyl Oligopeptidases; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
D012697:Serine Endopeptidases; D000085822:Prolyl Oligopeptidases