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Trapping a transition state in a computationally designed protein bottle

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Science  20 Feb 2015:
Vol. 347, Issue 6224, pp. 863-867
DOI: 10.1126/science.aaa2424
  • Fig. 1 Strategy to capture a transition state.

    (A) The orientations and relative changes in energy (ΔGrel) between the ground (Φ = ~45°) and transition states (Φ = 0° and 90°) of rotation around the central bond of biphenyl are shown. (B) An overview of the computational design process used to generate candidate designs is shown.

  • Fig. 2 X-ray crystallographic analysis of BIF_1.

    (A) The x-ray crystal structure of BIF_1 is shown in yellow; BiPhe and surrounding residues are shown in sticks. Rings A and B are those closest to and farthest from the protein backbone, respectively. Electron density around the BiPhe side chain is shown as a 2FoFc map contoured to 2σ. (B) A comparison of the design model (gray) to the structure (yellow) of BIF_1 is shown; BiPhe, Trp42, and Trp81 are shown in sticks. A loop corresponding to residues 81 to 89 of the parent scaffold is shown in red. Missing density in the structure corresponding to residues 83 to 86 of BIF_1 is shown as a dashed red line. (C) A comparison of the structure of BIF_1 (yellow) to the design model (gray) is shown. BiPhe, Trp42, and Trp81 are shown in sticks. An arrow indicates rotation about χ2 in the structure relative to the design.

  • Fig. 3 A comparison of the crystal structures of BIF_1.1 to BIF_1.4.

    (A to D) Crystal structures of second-round mutants BIF_1.1 to BIF_1.4 are shown. The side chains of BiPhe, and those at positions 79 and 123, are shown in sticks. Electron density from a 2FoFc map contoured to 1.5σ [(A to C)] and 2.0σ (D) is shown for the aforementioned residues. The measured dihedral angle between the two biphenyl rings is shown beneath the biphenyl side chain in each case.

  • Fig. 4 X-ray crystal structure of BIF_0.

    (A) The crystal structure of BIF_0 is shown in blue, and BIF_1.3 is shown in gray. The BiPhe side chain and surrounding residues are shown in sticks. (B) Packing interactions between the designed protein BIF_0 and the BiPhe side are highlighted with space-filling representations of the interacting residues. (C and D) The structure of BIF_0 is shown, highlighting the BiPhe side chain; views from the front and side are shown. The BiPhe side chain and surrounding residues are shown in sticks, and 2FoFc maps are contoured to 2σ in each case.

  • Table 1 First-round computational designs.

    Designed protein names, parent scaffolds, and mutations made are listed. Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.

    Designed
    protein
    Parent scaffold
    (PDB ID)
    Computationally designed
    mutations
    BIF_11y2qS8A, I11BiPhe, F42W, Y79A, F81W, K121I, F123Y
    BIF_21anuV20G, F22I, C33W, F35BiPhe, F37W, F96G
    BIF_32h2hF48L, F60BiPhe, Y61W, F63W, A64M, I68G, P157G, I159A
    BIF_41ve0I21T, V25BiPhe, S26A, V39G, C46A, I48V
  • Table 2 Second- and third-round crystallographic analysis.

    Second-round mutant identities, biphenylalanine dihedral angle, and x-ray crystal structure resolution are listed. Dihedrals listed are averages of those measured on each side of the biphenyl ring.

    ScaffoldF42Y79F123BIF Φ (deg.)Resolution (Å)
    BIF_1WAY261.95
    BIF_1.1FSV352.10
    BIF_1.2FVV212.50
    BIF_1.3FSA152.36
    BIF_1.4FVA202.10
    BIF_0FIA02.05

Supplementary Materials

  • Trapping a transition state in a computationally designed protein bottle

    Aaron D. Pearson, Jeremy H. Mills, Yifan Song, Fariborz Nasertorabi, Gye Won Han, David Baker, Raymond C. Stevens, Peter G. Schultz

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

    Download Supplement
    • Materials and Methods
    • Figs. S1 and S2
    • Tables S1 and S2
    • References

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