References

Anderson III, R. D., J. Zhou and S. M. Hecht. 2002. "Fluorescence resonance energy transfer between unnatural amino acids in a structurally modified dihydrofolate reductase." J Am Chem Soc 124: 9674-75. Bain, J. D., C. G. Glabe, T. A. Dix, A. R. Chamberlin and E. S. Diala. 1989. "Biosynthetic site-specific incorporation of a non-natural amino acid into a polypeptide." J Am Chem Soc 111: 8013-14.

Beatty, K. E., J. C. Liu, F. Xie, D. C. Dieterich, E. M. Schuman, et al. 2006. "Fluorescence visualization of newly synthesized proteins in mammalian cells." Angew Chem Int Ed Engl 45: 7364-7.

Beene, D. L., G. S. Brandt, W. Zhong, N. M. Zacharias, H. A. Lester, et al. 2002. "Cation-n interactions in ligand recognition by serotonergic (5-HT3A) and nicotinic acetyl-choline receptors: The anomalous binding properties of nicotine." Biochemistry 41: 10262-9.

Beene, D. L., D. A. Dougherty and H. A. Lester. 2003. "Unnatural amino acid mutagenesis in mapping ion channel function." Curr Opin Neurobiol 13: 264-70. Bilgi§er, B., A. Fichera and K. Kumar. 2001. 'A coiled coil with a fluorous core." J Am Chem Soc 123: 4393-9.

Bilgi§er, B. and K. Kumar. 2002. "Synthesis and thermodynamic characterization of self-

sorting coiled coils." Tetrahedron 58: 4105-12. Bilgi§er, B. and K. Kumar. 2004. "De novo design of defined helical bundles in membrane environments." Proc Natl Acad Sci U S A 101: 15324-9. Bretscher, L. E., C. L. Jenkins, K. M. Taylor, M. L. DeRider and R. T. Raines. 2001. "Conformational stability of collagen relies on a stereoelectronic effect [23]." J Am Chem Soc 123: 777-778. Chin, J. W. and P. G. Schultz. 2002. "In vivo photocrosslinking with unnatural amino acid mutagenesis." ChemBioChem 3: 1135-7. Cohen, B. E., T. B. McAnaney, E. S. Park, Y. N. Jan, S. G. Boxer, et al. 2002. "Probing protein electrostatics with a synthetic fluorescent amino acid." Science 296: 1700-03. Cook, S. N., W. E. Jack, X. Xiong, L. E. Danley, J. A. Ellman, et al. 1995. "Photochemically initiated protein splicing." Angew Chem Int Ed Engl 34: 1629-30. Cornish, V. W., K. M. Hahn and P. G. Schultz. 1996. "Site-specific protein modification using a ketone handle." J Am Chem Soc 118: 8150-1.

Dawson, P. E., T. W. Muir, I. Clark-Lewis and S. B. H. Kent. 1994. "Synthesis of proteins by native chemical ligation." Science 266: 776-9.

Deechongkit, S., P. E. Dawson and J. W. Kelly. 2004a. "Toward assessing the position-dependent contributions of backbone hydrogen bonding to ^-sheet folding thermodynamics employing amide-to-ester perturbations." J Am Chem Soc 126: 16762-71.

Deechongkit, S., H. Nguyen, M. Jager, E. T. Powers, M. Gruebele, et al. 2006. "^-sheet folding mechanisms from perturbation energetics." Curr Opin Struct Biol 16: 94-101.

Deechongkit, S., H. Nguyen, E. T. Powers, P. E. Dawson, M. Gruebele, et al. 2004b. "Context-dependent contributions of backbone hydrogen bonding to ^-sheet folding energetics." Nature 430: 101-05.

DeSantis, G. and J. B. Jones. 1999. "Chemical modification of enzymes for enhanced functionality." Current Opinion in Biotechnology 10: 324-30.

Dougherty, D. A. 1996. "Cation-n interactions in chemistry and biology: A new view of benzene, Phe, Tyr, and Trp." Science 271: 163-8.

Engel, J., H. T. Chen, D. J. Prockop and H. Klump. 1977. "The triple helix in equilibrium with coil conversion of collagen-like polytripeptides in aqueous and nonaqueous solvents. Comparison of the thermodynamic parameters and the binding of water to (L-Pro-L-Pro-Gly)n and (L-Pro-L-Hyp-Gly)n." Biopolymers 16: 601-22.

England, P. M., Y. Zhang, D. A. Dougherty and H. A. Lester. 1999. "Backbone mutations in transmembrane domains of a ligand-gated ion channel: Implications for the mechanism of gating." Cell 96: 89-98.

Evans Jr., T. C., J. Benner and M. Q. Xu. 1998. "Semisynthesis of cytotoxic proteins using a modified protein splicing element." Prot Sci 7: 2256-64.

Fu, Y., J. Gao, J. Bieschke, M. A. Dendle and J. W. Kelly. 2006. "Amide-to-E-olefin versus amide-to-ester backbone H-bond perturbations: Evaluating the O-O repulsion for extracting H-bond energies." J Am Chem Soc 128: 15948-9.

Goodman, M., M. Bhumralkar, E. A. Jefferson, J. Kwak and E. Locardi. 1998. "Collagen mimetics." Biopolymers 47: 127-42.

Griffin, B. A., S. R. Adams and R. Y. Tsien. 1998. "Specific covalent labeling of recombinant protein molecules inside live cells." Science 281: 269-72.

Harbury, P. B., J. J. Plecs, B. Tidor, T. Alber and P. S. Kim. 1998. "High-resolution protein design with backbone freedom." Science 282: 1462-7.

Heckler, T. G., L. H. Chang, Y. Zama, T. Naka, M. S. Chorghade, et al. 1984. "T4 RNA ligase mediated preparation of novel "chemically misacylated" tRNAPheS." Biochemistry 23: 1468-73.

Hofmann, R. M. and T. W. Muir. 2002. "Recent advances in the application of expressed protein ligation to protein engineering." Curr Opin Biotechnol 13: 297-303.

Hohsaka, T. and M. Sisido. 2002. "Incorporation of non-natural amino acids into proteins." Curr Opin Chem Biol 6: 809-15.

Holmgren, S. K., L. E. Bretscher, K. M. Taylor and R. T. Raines. 1999. "A hyperstable collagen mimic." Chem Biol 6: 63-70.

Holmgren, S. K., K. M. Taylor, L. E. Bretscher and R. T. Raines. 1998. "Code for collagen's stability deciphered [9]." Nature 392: 666-7.

Hortin, G. and I. Boime. 1983. "Applications of amino acid analogs for studying co- and post-translational modifications of proteins." Methods Enzymol 96: 777-84.

Ibba, M., P. Kast and H. Hennecke. 1994. "Substrate specificity is determined by amino acid binding pocket size in Escherichia coli phenylalanyl-tRNA synthetase." Biochemistry 33: 7107-12.

Jenkins, C. L. and R. T. Raines. 2002. "Insights on the conformational stability of collagen." Nat Prod Rep 19: 49-59.

Köhrer, C., E. L. Sullivan and U. L. RajBhandary. 2004. "Complete set of orthogonal 21st aminoacyl-tRNA synthetase-amber, ochre and opal suppressor tRNA pairs: Concomitant suppression of three different termination codons in an mRNA in mammalian cells." Nucleic Acids Res 32: 6200-11.

Kwon, I. and D. A. Tirrell. 2007. "Site-specific incorporation of tryptophan analogues into recombinant proteins in bacterial cells." J Am Chem Soc 129: 10431-7.

Lemke, E. A., D. Summerer, B. H. Geierstanger, S. M. Brittain and P. G. Schultz. 2007. "Control of protein phosphorylation with a genetically encoded photocaged amino acid." Nat Chem Biol 3: 769-72.

Li, L., W. Zhong, N. Zacharias, C. Gibbs, H. A. Lester, et al. 2001. "The tethered agonist approach to mapping ion channel proteins—toward a structural model for the agonist binding site of the nicotinic acetylcholine receptor." Chem Biol 8: 47-58.

Link, A. J., M. L. Mock and D. A. Tirrell. 2003. "Non-canonical amino acids in protein engineering." Curr Opin Biotechnol 14: 603-09.

Liu, D. R., T. J. Magliery and P. G. Schultz. 1997. "Characterization of an 'orthogonal' suppressor tRNA derived from E. coli tRNA2(Gln)." Chem Biol 4: 685-91.

Liu, W., A. Brock, S. Chen, S. Chen and P. G. Schultz. 2007. "Genetic incorporation of unnatural amino acids into proteins in mammalian cells." Nat Methods 4: 239-44.

Lu, T., A. Y. Ting, J. Mainland, L. Y. Jan, P. G. Schultz, et al. 2001. "Probing ion permeation and gating in a K+ channel with backbone mutations in the selectivity filter." Nat Neurosci 4: 239-46.

Lummis, S. C. R., D. L. Beene, N. J. Harrison, H. A. Lester and D. A. Dougherty. 2005. "A cation-n binding interaction with a tyrosine in the binding site of the GABAC receptor." Chem Biol 12: 993-7.

Monahan, S. L., H. A. Lester and D. A. Dougherty. 2003. "Site-specific incorporation of unnatural amino acids into receptors expressed in mammalian cells." Chem Biol 10: 573-80.

Muir, T. W., D. Sondhi and P. A. Cole. 1998. "Expressed protein ligation: A general method for protein engineering." Proc Natl Acad Sci U S A 95: 6705-10.

Naarmann, N., B. Bilgi§er, H. Meng, K. Kumar and C. Steinem. 2006. "Fluorinated interfaces drive self-association of transmembrane a helices in lipid bilayers." Angew Chem Int Ed Engl 45: 2588-91.

Noren, C. J., S. J. Anthony-Cahill, M. C. Griffith and P. G. Schultz. 1989. "A general method for site-specific incorporation of unnatural amino acids into proteins." Science 244: 182-8.

Nowak, M. W., P. C. Kearney, J. R. Sampson, M. E. Saks, C. G. Labarca, et al. 1995. "Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells." Science 268: 439-42.

Politz, J. C. 1999. "Use of caged fluorochromes to track macromolecular movement in living cells." Trends Cell Biol 9: 284-7.

Raines, R. T. 2007. Hyperstable collagen based on 4-fluoroproline residues. ACS Symposium Series 949: 477-86.

Rodriguez, E. A., H. A. Lester and D. A. Dougherty. 2006. "In vivo incorporation of multiple unnatural amino acids through nonsense and frameshift suppression." Proc Natl Acad Sci USA 103: 8650-5.

Sakamoto, K., A. Hayashi, A. Sakamoto, D. Kiga, H. Nakayama, et al. 2002. "Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells." Nucleic Acids Res 30: 4692-4699.

Scheike, J. A., C. Baldauf, J. Spengler, F. Albericio, M. T. Pisabarro, et al. 2007. "Amide-to-ester substitution in coiled coils: The effect of removing hydrogen bonds on protein structure." Angew Chem Int Ed Engl 46: 7766-9.

Schnarr, N. A. and A. J. Kennan. 2001. "Coiled-coil formation governed by unnatural hydrophobic core side chains [9]." J Am Chem Soc 123: 11081-2.

Schnarr, N. A. and A. J. Kennan. 2004. "Coiled-coil surface presentation: an efficient HIV gp41 binding interface mimic." J Am Chem Soc 126: 10260-1.

Short III, G. F., M. Lodder, A. L. Laikhter, T. Arslan and S. M. Hecht. 1999. "Caged HIV-1 protease: Dimerization is independent of the ionization state of the active site aspartates." J Am Chem Soc 121: 478-9.

Summerer, D., S. Chen, N. Wu, A. Deiters, J. W. Chin, et al. 2006. 'A genetically encoded fluorescent amino acid." Proc Natl Acad Sci U S A 103: 9785-9.

Tang, Y., G. Ghirlanda, N. Vaidehi, J. Kua, D. T. Mainz, et al. 2001. "Stabilization of coiled-coil peptide domains by introduction of trifluoroleucine." Biochemistry 40: 2790-6.

Turcatti, G., K. Nemeth, M. D. Edgerton, J. Knowles, H. Vogel, et al. 1997. "Fluorescent labeling of NK2 receptor at specific sites in vivo and fluorescence energy transfer analysis of NK2 ligand-receptor complexes." Receptors and Channels 5: 201-07.

Turcatti, G., K. Nemeth, M. D. Edgerton, U. Meseth, F. Talabot, et al. 1996. "Probing the structure and function of the tachykinin neurokinin-2 receptor through biosynthetic incorporation of fluorescent amino acids at specific sites." J Biolog Chem 271: 19991-8.

Van Hest, J. C. M., K. L. Kiick and D. A. Tirrell. 2000. "Efficient incorporation of unsaturated methionine analogues into proteins in vivo." J Am Chem Soc 122: 1282-8.

Vázquez, M. E., J. B. Blanco and B. Imperiali. 2005. "Photophysics and biological applications of the environment-sensitive fluorophore 6-N,N-dimethylamino-2,3-naphthalimide." J Am Chem Soc 127: 1300-06.

Walker, J. W., S. H. Gilbert, R. M. Drummond, M. Yamada, R. Sreekumar, et al. 1998. "Signaling pathways underlying eosinophil cell motility revealed by using caged pep-tides." Proc Natl Acad Sci U S A 95: 1568-73.

Wang, J., J. Xie and P. G. Schultz. 2006a. "A genetically encoded fluorescent amino acid." J Am Chem Soc 128: 8738-9.

Wang, L., J. Xie and P. G. Schultz. 2006b. "Expanding the genetic code." Annu Rev Biophys Biomol Struct 35: 225-49.

Wang, K., H. Neumann, S. Y. Peak-Chew and J. W. Chin. 2007. "Evolved orthogonal ribo-somes enhance the efficiency of synthetic genetic code expansion." Nat Biotechnol 25: 770-7.

Wang, L., A. Brock, B. Herberich and P. G. Schultz. 2001. "Expanding the genetic code of Escherichia coli." Science 292: 498-500.

Xie, J. and P. G. Schultz. 2006. "A chemical toolkit for proteins—an expanded genetic code." Nat Rev Mol Cell Biol 7: 775-82.

Zhang, J., R. E. Campbell, A. Y. Ting and R. Y. Tsien. 2002. "Creating new fluorescent probes for cell biology." Nat Rev Mol Cell Biol 3: 906-18.

Zhang, Z., B. A. C. Smith, L. Wang, A. Brock, C. Cho, et al. 2003. "A new strategy for the site-specific modification of proteins in vivo." Biochemistry 42: 6735-46.

Zhong, W., J. P. Gallivan, Y. Zhang, L. Li, H. A. Lester, et al. 1998. "From ab initio quantum mechanics to molecular neurobiology: A cation-n binding site in the nicotinic receptor." Proc Natl Acad Sci U S A 95: 12088-93.

Zoller, M. J. and M. Smith. 1987. "Oligonucleotide-directed mutagenesis: a simple method using two oligonucleotide primers and a single-stranded DNA template." Methods Enzymol 154: 329-50.

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