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RESEARCH | REPORT

        S16B). As in the case of the C2 design, the C4  and diverse oligomeric states—are substantial  23. X. Feng, P. Barth, Nat. Chem. Biol. 12, 167–173 (2016).
        symmetry axis of the design coincides with  steps toward the complexity of natural trans-  24. A. D. Meruelo, S. K. Han, S. Kim, J. U. Bowie, Protein Sci. 21,
                                                                                  1746–1753 (2012).
        the crystallographic axes of the crystal lattice  membrane proteins with multiple membrane-  25. Y. Shi, Cell 159, 995–1014 (2014).
        (fig. S16C). The four tetramer structures on the  spanning regions and extra-membrane domains  26. R. Fernandez-Leiro, S. H. W. Scheres, Nature 537, 339–346
        crystal C4 axes have overall structures very  that play important roles in ligand/substrate  (2016).
        similar to each other and to the design model  recognition and structure stabilization, such
        (Fig. 4, F and G, and fig. S16A); the tetrameric  as in the adenosine 5′-triphosphate–binding cas-  ACKNOWLEDGMENTS
        transmembrane domain, HR domain, and over-  sette transporters, ion channels, ryanodine re-  We thank J. Sumida for AUC support; A. Kang for crystallization
                                                                                support; D. Ma and Z. Wang for crystallography support; and
        all tetramer structure have Ca RMSDs to the de-  ceptor, and g-secretase (25, 26). The capability to  the staff at the Advanced Light Source and P. Huang, Y. Hsia,
        sign model of 1.3 to 1.5 Å, 3.3 to 3.8 Å, and 3.3 to  accurately design complex multipass transmem-  A. Ford, L. Stewart, C. Xu, and many other members of the Baker
        3.8 Å, respectively (Fig. 4H and fig. S16D, left).  brane proteins that can be expressed in cells opens  laboratory for helpful discussions. This work was facilitated by
        The deviation in the HR domain may result  the door to the design of a new generation of multi-  the Hyak supercomputer at the University of Washington. Funding:
                                                                                This work was supported by the Howard Hughes Medical
        from crystal packing interactions between the  pass membrane protein structures and functions.  Institute (D.B.) and the National Institutes of Health (grant
        termini; the Ca RMSDs over the first 162 resi-                          R01GM063919 to J.U.B.). P.L. was supported by the Raymond
        dues are 2.2 to 2.3 Å (fig. S16D, right). The main                      and Beverly Sackler fellowship. D.M. was supported by the Basic
        deviation from the design model is a tilting of  REFERENCES AND NOTES   Science Research Program through the National Research
        the outer helices of transmembrane hairpins from  1. P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320–327  Foundation of Korea funded by the Ministry of Education (grant
                                              (2016).                           NRF-2016R1A6A3A03007871). Author contributions: P.L. and
        theaxisby~10°(Fig. 4, Fand G).                                          D.B. designed the research, and P.L., D.M., F.D., K.Y.W., J.U.B., and
                                            2. N. H. Joh et al., Science 346, 1520–1524 (2014).
          The agreement between the crystal struc-  3. K. R. Mahendran et al., Nat. Chem. 9, 411–419 (2017).  D.B. wrote the manuscript. P.L. and D.B. carried out design
        tures of TMHC2_E and TMHC4_R with the  4. P. Whitley, I. Nilsson, G. von Heijne, Nat. Struct. Biol. 1,  calculations and developed the membrane protein design method.
                                                                                P.L. purified and characterized the designed proteins. D.M. and
        design models demonstrates that transmem-  858–862 (1994).              J.U.B. designed, performed, and analyzed single-molecule forced
                                            5. C. Choma, H. Gratkowski, J. D. Lear, W. F. DeGrado,
        brane homo-oligomers containing multiple                                unfolding experiments. K.Y.W. and M.D.V. performed mammalian
                                              Nat. Struct. Biol. 7, 161–166 (2000).
        membrane-spanning regions and extensive ex-  6. F. X. Zhou, M. J. Cocco, W. P. Russ, A. T. Brunger,  cell localization experiment. P.L. crystallized the designed proteins.
        tracellular domains can now be accurately de-  D. M. Engelman, Nat. Struct. Biol. 7, 154–160 (2000).  P.L. collected and analyzed crystallographic data with help from
                                                                                W.X.; F.D. solved structures with help from P.L.; and S.E.B., C.Z.,
        signed. For future work, the general approach  7. C. D. Tatko, V. Nanda, J. D. Lear, W. F. Degrado, J. Am.  J.A.F., G.U., and W.S. contributed the soluble scaffolds. V.K.M. wrote  Downloaded from
                                              Chem. Soc. 128, 4170–4171 (2006).
        of first designing and characterizing hydro-  8. S. E. Boyken et al., Science 352, 680–687 (2016).  the amino acid composition–based energy term. All authors
        gen bond network–containing soluble versions  9. P.-S. Huang et al., Science 346, 481–485 (2014).  discussed results and commented on the manuscript. Competing
        of the desired transmembrane structures, and  10. C. A. Rohl, C. E. M. Strauss, K. M. S. Misura, D. Baker, in  interests: D.B., P.L., S.E.B., C.Z., J.A.F., G.U., and W.S. are
                                                                                inventors on a U.S. provisional patent application submitted by the
        then converting to integral membrane proteins  Methods in Enzymology (2004), pp. 66–93.  University of Washington that covers computational design of
        by redesigning the membrane-exposed residues,  11. G. von Heijne, Nat. Rev. Mol. Cell Biol. 7, 909–918 (2006).  multipass transmembrane proteins described in this paper. Data
                                            12. A. Oberai, N. H. Joh, F. K. Pettit, J. U. Bowie, Proc. Natl. Acad.
        could be quite robust. Single-molecule forced  Sci. U.S.A. 106, 17747–17750 (2009).  and materials availability: Coordinates and structure files have
        unfolding and thermal denaturation exper-  13. A. Elazar et al., eLife 5, e12125 (2016).  been deposited to PDB with accession codes 6B87 (TMHC2_E)
                                                                                and 6B85 (TMHC4_R). All other data needed to evaluate the
        iments show that the designed proteins are  14. D. Min, R. E. Jefferson, J. U. Bowie, T.-Y. Yoon, Nat. Chem. Biol.  conclusions in the paper are present in the paper or the
        highly stable. Although the designs lack the  11, 981–987 (2015).       supplementary materials.            http://science.sciencemag.org/
        classic small residue packing in the core that  15. D. Min, M. A. Arbing, R. E. Jefferson, J. U. Bowie, Protein Sci.
                                              25, 1535–1544 (2016).
        is thought to be an important driver of mem-  16. G. I. Bell, Science 200, 618–627 (1978).  SUPPLEMENTARY MATERIALS
        brane protein folding (21–24), like natural mem-  17. R. Guo et al., Nat. Chem. Biol. 12, 353–360 (2016).  www.sciencemag.org/content/359/6379/1042/suppl/DC1
        brane proteins they bury more surface area  18. Y.-C. Chang, J. U. Bowie, Proc. Natl. Acad. Sci. U.S.A. 111,  Materials and Methods
        than do typical soluble proteins, maximizing  219–224 (2014).           Figs. S1 to S16
                                                                                Table S1
        van der Waals packing contributions (12). The  19. J. A. Fallas et al., Nat. Chem. 9, 353–360 (2017).  References (27–39)
                                            20. P.-S. Huang et al., PLOS ONE 6, e24109 (2011).
        range of the design features—variable trans-  21. S.-Q. Zhang et al., Structure 23, 527–541 (2015).
        membrane and extracellular helix lengths and  22. R. F. S. Walters, W. F. DeGrado, Proc. Natl. Acad. Sci. U.S.A.  10 October 2017; accepted 11 January 2018  on March 1, 2018
        superhelical twists, extensive soluble domains,  103, 13658–13663 (2006).  10.1126/science.aaq1739

























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