Protein Engineering, Vol. 14, No. 9, 633-638,
September 2001
© 2001 Oxford University Press
A cross-section of the fitness landscape of dihydrofolate reductase
1 Tsukuba Research Institute, Novartis Pharma KK, Ohkubo 8, Urawa Tsukuba, 300-2611, 2 Department of Functional Materials Science, Saitama University, 338-8570 and 3 National Institute of Bioscience and Human Technology, 1–1 Higahi, Tsukuba, 305-8566, Ibaraki, Japan
In vitro molecular evolution is regarded as a hill-climbing on a fitness landscape in sequence space, where the ‘fitness’ is a quantitative measure of a certain physicochemical property of a biopolymer. We analyzed a ‘cross-section’ of the enzymatic activity landscape of dihydrofolate reductase (DHFR) by using a method of analysis of a fitness landscape. We limited the sequence space of interest to the five-dimensional sequence space, where the coordinate corresponds to the 1st, 16th, 20th, 42nd and 92nd site in the DHFR sequence. Thirty six mutants mapped into the limited sequence space were taken in the analysis. As a result, the cross-section is of the rough Mt Fuji type based on the mutational additivity. The ratio of the mean slope to the roughness is 2.8 and the Z-score of the original ratio against a distribution of random references is 7.0, which indicates a large statistical significance. The existence of such a cross-section was discussed in terms of the occurrence probability of sets of five sites distantly separated from each other on the DHFR 3D structure. Our results support the effectiveness of the evolution strategy which exploits the accumulation of advantageous single point mutations in such a cross-section.
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