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Science 21 October 2005:
Vol. 310. no. 5747, pp. 499 - 501
DOI: 10.1126/science.1115649
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Reports

The Biochemical Architecture of an Ancient Adaptive Landscape

Mark Lunzer1, Stephen P. Miller1, Roderick Felsheim1,2 and Antony M. Dean1,3*

1 BioTechnology Institute
2 Department of Entomology
3 Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA.


Fig. 1. Crystallographic structures identify amino acids determining coenzyme use. Only key residues are shown (gray, carbon; red, oxygen; blue, nitrogen; yellow phosphorus). (A) Structural alignment of E. coli IMDH (13) (brown main-chain; labels designate the amino acid followed by the site number) and Thermus thermophilus IMDH (14) (blue main-chain) showing the double H-bond (pink lines) critical to NAD use. (B) Structural alignment of E. coli IMDH and E. coli IDH (green main-chain) with NADP bound (15) showing IDH residues (following the IMDH site number) H-bonding to the 2'-phosphate (2'P) of bound NADP (H-bonds from the disordered 289Lys not shown). [View Larger Version of this Image (27K GIF file)]
 

Fig. 2. Performances (103 M–1s–1) of engineered IMDH mutants toward NAD and NADP reveal a trade-off in enzyme function. (A) Distribution of performances for the 164 engineered enzymes constructed. (B) Distribution of performances for 512 genotypic intermediates predicted on the assumption of thermodynamic additivity. Symptomatic of a trade-off in performance, the interiors of both plots are devoid of mutants. [View Larger Version of this Image (22K GIF file)]
 

Fig. 3. The phenotype-fitness map of IMDH. (A) The fitnesses (green spheres of fitness radius w = 0.5 {approx} 2 SE) of 90 engineered mutants plotted against their coenzyme performances ((103 M–1s–1)). The fitted surface is the estimated phenotype-fitness map (Eq. 4). It reveals a single broad adaptive peak on which resides the NAD-specific wild-type enzyme (red sphere). NADP use is advantageous only in mutants with very poor NAD performance (e.g., the RKYVYR mutant, white sphere). (B) Escape from the lower NADP-use plateau to the higher NAD-use plateau is possible because some single amino acid replacements (blue spheres from the RKYVYR mutant, pink spheres from the wild type; asterisks denote fitness values predicted from kinetic data) produce sufficiently large effects on performance and fitness that the maladaptive valley near the origin is bypassed. [View Larger Version of this Image (28K GIF file)]
 

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