Novel forms of chemical protein diversity - In nature and in the laboratory

Current Opinion in Biotechnology

Volumn 15, Issue 6, 2004, Pages 607-614

  Kent, Stephen ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC METHODS; MICROPROTEINS; MOLECULAR DEVICES; NEOGLUCOPROTEINS;

AMINO ACIDS; BIOSENSORS; BIOTECHNOLOGY; CELLS; MOLECULAR STRUCTURE; POLYPEPTIDES; SYNTHESIS (CHEMICAL);

PROTEINS;

AMINO ACID; CATENANE; CONOTOXIN; FLUORESCENT DYE; NEOGLYCOPROTEIN; PROTEIN DERIVATIVE;

AMINO ACID ANALYSIS; AMINO TERMINAL SEQUENCE; CARBOXY TERMINAL SEQUENCE; DRUG ACTIVITY; DRUG POTENCY; GLYCOSYLATION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; REVIEW; SIGNAL TRANSDUCTION; X RAY CRYSTALLOGRAPHY;

CYCLOTIDES; GLYCOPROTEINS; PROTEIN ENGINEERING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS;

EID: 9244220098     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2004.10.003     Document Type: Review

References (60)

1. M. Schnölzer, and S.B.H. Kent Constructing proteins by dovetailing unprotected synthetic peptides: backbone engineered HIV protease Science 256 1992 221 225
2. P.E. Dawson, T.W. Muir, I. Clark-Lewis, and S.B.H. Kent Synthesis of proteins by native chemical ligation Science 266 1994 776 779
3. J.W. Chin, T.A. Cropp, J.C. Anderson, M. Mukherji, Z. Zhang, and P.G. Schultz An expanded eukaryotic genetic code Science 301 2003 964 967
4. H. Terlau, and B.M. Olivera Conus venoms: a rich source of novel ion channel-targeted peptides Physiol Rev 84 2004 41 68
5. M.L. Loughnan, A. Nicke, A. Jones, D.J. Adams, P.F. Alewood, and R.J. Lewis Chemical and functional identification and characterization of novel sulfated α-conotoxins from the cone snail Conus anemone J Med Chem 47 2004 1234 1241
6. M. Trabi, and D.J. Craik Circular proteins - no end in sight Trends Biochem Sci 27 2002 132 138
7. K.J. Rosengren, N.L. Daly, M.R. Plan, C. Waine, and D.J. Craik Twists, knots, and rings in proteins. Structural definition of the cyclotide framework J Biol Chem 278 2003 8606 8616 Cyclotide proteins of two distinct structural classes were isolated from plants and their structures determined at physiological pH by multidimensional NMR spectroscopy. This exceptionally thorough set of studies is the definitive structural work on the cyclotides: it establishes unambiguous disulfide connectivity and confirms the 'Cys knot' motif found in these unique proteins that contain a continuous cyclic polypeptide chain. The study also identifies a backbone twist, caused by a cis-peptide bond, that defines a 'Möbius subfamily' of cyclotides.
8. I. Botos, Z. Wu, W. Lu, and A. Wlodawer Crystal structure of a cyclic form of bovine pancreatic trypsin inhibitor FEBS Lett 509 2001 90 94
9. S. Deechongkit, and J.W. Kelly The effect of backbone cyclization on the thermodynamics of β-sheet unfolding - stability optimization of the PIN WW domain J Am Chem Soc 124 2002 4980 4986
10. J.W. Blankenship, and P.E. Dawson Thermodynamics of a designed protein catenane J Mol Biol 327 2003 537 548 A new synthetic route to a redesigned protein catenane (i.e. a protein molecule with interpenetrating cyclic polypeptide chains) is described, together with measurements of the stability of the resulting dimeric protein molecule. This is a continuation of the authors' pioneering work on topologically linked proteins.
11. K. Routenberg Love, and P.H. Seeberger Automated solid-phase synthesis of protected tumor-associated antigen and blood group determinant oligosaccharides Angew Chem Int Ed Engl 43 2004 602 605
12. J.D. Warren, J.S. Miller, S.J. Keding, and S.J. Danishefsky Toward fully synthetic glycoproteins by ultimately convergent routes - a solution to a long-standing problem J Am Chem Soc 126 2004 6576 6578 Novel chemistry for the fully convergent synthesis of glycosylated polypeptides is presented. The highlight is an ingenious thioester synthon, compatible with the organic synthetic manipulations involved in making glycopeptides, that enables subsequent direct use of the glycopeptides in native chemical ligation reactions.
13. J.S. Miller, V.Y. Dudkin, G.J. Lyon, T.W. Muir, and S.J. Danishefsky Toward fully synthetic N-linked glycoproteins Angew Chem Int Ed Engl 42 2003 431 434
14. L.A. Marcaurelle, and C.R. Bertozzi Recent advances in the chemical synthesis of mucin-like glycoproteins Glycobiology 12 2002 69R 77R
15. F. Peri, and F. Nicotra Chemoselective ligation in glycochemistry Chem Commun 2004 623 627
16. M.R. Pratt, and C.R. Bertozzi Chemoselective ligation applied to the synthesis of a biantennary N-linked glycoform of CD52 J Am Chem Soc 125 2003 6149 6159 Imaginative use of chemoselective ligation in the synthesis of N-linked glycopeptide analogs that "replace the glycosidic linkages extending from the core pentasaccharide with thioethers. The key building block, a pentasaccharide-Asn analog containing two thiol moieties, was incorporated into CD52 by peptide synthesis. An undecasaccharide mimetic was then readily generated by alkylation of this glycopeptide with an N-bromoacetamido trisaccharide. The product contains unnatural linkages at C-2 of the R-mannose residues but retains the structure of the conserved pentasaccharide core."
17. D. Macmillan, and C.R. Bertozzi Modular assembly of glycoproteins - toward the synthesis of GlyCAM-1 by using expressed protein ligation Angew Chem Int Ed Engl 42 2004 1355 1359
18. G.G. Kochendoerfer, S.-Y. Chen, F. Mao, S. Cressman, S. Traviglia, H. Shao, C. Hunter, D. Low, N. Cagle, and M. Carnevali Design and chemical synthesis of a homogeneous polymer-modified erythropoiesis protein Science 299 2003 884 887
19. S. Dalal, S. Balasubramanian, and L. Regan Protein alchemy - changing β-sheet into α-helix Nat Struct Biol 4 1997 548 552
20. W.F. Degrado Computational biology - biosensor design Nature 423 2003 132 133
21. A.M. Slovic, H. Kono, J.D. Lear, J.G. Saven, and W.F. DeGrado Computational design of water-soluble analogues of the potassium channel KcsA Proc Natl Acad Sci USA 101 2004 1828 1833
22. A. Tramontano A brighter future for protein design Angew Chem Int Ed Engl 43 2004 3222 3223
23. R. Chu, J. Takei, J.R. Knowlton, M. Andrykovitch, W. Pei, A.V. Kajava, P.J. Steinbach, X. Ji, and Y. Bai Redesign of a four-helix bundle protein by phage display coupled with proteolysis and structural characterization by NMR and X-ray crystallography J Mol Biol 323 2002 253 262
24. B. Kuhlman, G. Dantas, G.C. Ireton, G. Varani, B.L. Stoddard, and D. Baker Design of a novel globular protein fold with atomic-level accuracy Science 302 2003 1364 1368 De novo design, to a minimum free energy end point only, was used to create a 93-residue α/β protein with an arbitrary target fold not present in the Protein Structure Database (PDB). The predicted sequence was expressed in Escherichia coli and gave a soluble, monomeric, folded (by NMR dispersion and circular dichroism), very stable molecule - that is, a typical, tightly folded globular protein. The crystal structure was determined to 2.5 Å, by molecular replacement using the model's coordinates; the experimental structure was similar (near congruent in many regions) to the designed model. The potential significance of this work cannot be overstated: it "shows that globular protein folds not yet observed in nature... are physically possible (and) can be extremely stable." This extraordinary achievement does indeed "open the door to the exploration and use of a vast new world of protein structures and architectures."
25. M.A. Dwyer, L.L. Looger, and H.W. Hellinga Computational design of a biologically active enzyme Science 304 2004 1967 1971
26. D. Jantz, and J.M. Berg Expanding the DNA-recognition repertoire for zinc finger proteins beyond 20 amino acids J Am Chem Soc 125 2003 4960 4961
27. H.K. Binz, P. Amstutz, A. Kohl, M.T. Stumpp, C. Briand, P. Forrer, M.G. Grutter, and A. Plückthun High-affinity binders selected from designed ankyrin repeat protein libraries Nat Biotechnol 22 2004 575 582
28. J.W. Neidigh, R.M. Fesinmeyer, and N.H. Andersen Designing a 20-residue protein Nat Struct Biol 9 2002 425 430 The protein in question is only 20 amino acids in length, but folds rapidly to give a globular fold with a tightly packed hydrophobic core. This "scrupulously optimized protein may also provide new insight into the relationship of tertiary structure to folding dynamics."
29. S.K. Sia, and P.S. Kim A designed protein with packing between left-handed and right-handed helices Biochemistry 40 2001 8981 8989 Extension of four-helix bundle protein design to the packing of left-handed and right-handed helices made from d- and l-amino acids, respectively, to give a stable d/l tetrameric protein containing two of each type of helix. A chemist's approach to the design of a novel type of metabolically stable protein with potential pharmaceutical applications.
30. J. Hauert, J. Fernandez-Carneado, O. Michielin, S. Mathieu, D. Grell, M. Schapira, O. Spertini, M. Mütter, G. Tuchscherer, and T. Kovacsovics A template-assembled synthetic protein surface mimetic of the von Willebrand factor A1 domain inhibits botrocetin-induced platelet aggregation ChemBioChem 5 2004 856 864
31. G.G. Kochendoerfer, J.M. Tack, and S. Cressman Total chemical synthesis of a 27 kDa TASP protein derived from the MscL ion channel of M. tuberculosis by ketoxime-forming ligation Bioconjug Chem 13 2002 474 480
32. C.F.W. Becker, M. Oblatt-Montal, G.G. Kochendoerfer, and M. Montal Chemical synthesis and single channel properties of tetrameric and pentameric TASPs (Template-assembled Synthetic Proteins) derived from the transmembrane domain of HIV virus protein u (Vpu) J Biol Chem 279 2004 17483 17489
33. H.D. Arndt, K.E. Hauschild, D.P. Sullivan, K. Lake, P.B. Dervan, and A.Z. Ansari Toward artificial developmental regulators J Am Chem Soc 125 2003 13322 13323
34. T.S. Burkoth, E. Beausoleil, S. Kaur, D. Tang, F.E. Cohen, and R.N. Zuckermann Toward the synthesis of artificial proteins: the discovery of an amphiphilic helical peptoid assembly Chem Biol 9 2002 647 654
35. S. Deechongkit, H. Nguyen, E.T. Powers, P.E. Dawson, M. Gruebele, and J.W. Kelly Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics Nature 430 2004 101 105
36. M. Lovrinovic, R. Seidel, R. Wacker, H. Schroeder, O. Seitz, M. Engelhard, R.S. Goody, and C.M. Niemeyer Synthesis of protein-nucleic acid conjugates by expressed protein ligation Chem Commun 2003 822 823
37. B. Bilgiçer, and K. Kumar Protein design using unnatural amino acids J Chem Educ 80 2003 1275 1281
38. P. Dawson, and S.B.H. Kent Synthesis of native proteins by chemical ligation Annu Rev Biochem 69 2000 925 962
39. T.W. Muir Semisynthesis of proteins by expressed protein ligation Annu Rev Biochem 72 2003 249 289
40. L. Alfonta, Z. Zhang, S. Uryu, J.A. Loo, and P.G. Schultz Site-specific incorporation of a redox-active amino acid into proteins J Am Chem Soc 125 2003 14662 14663
41. D. Datta, P. Wang, I.S. Carrico, S.L. Mayo, and D.A. Tirrell A designed phenylalanyl-tRNA synthetase variant allows efficient in vivo incorporation of aryl ketone functionality into proteins J Am Chem Soc 124 2002 5652 5653
42. K.L. Kiick, E. Saxon, D.A. Tirrell, and C.R. Bertozzi Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation Proc Natl Acad Sci USA 99 2002 19 24
43. A. Kienhofer, P. Kast, and D. Hilvert Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor J Am Chem Soc 125 2003 3206 3207
44. S.M. Berry, M. Ralle, D.W. Low, N.J. Blackburn, and Y. Lu Probing the role of axial methionine in the blue copper center of azurin with unnatural amino acids J Am Chem Soc 125 2003 8760 8768
45. U. Arnold, M.P. Hinderaker, B.L. Nilsson, B.R. Huck, S.H. Gellman, and R.T. Raines Protein prosthesis: a semisynthetic enzyme with a β-peptide reverse turn J Am Chem Soc 124 2002 8522 8523
46. B.G. Davis Mimicking posttranslational modifications of proteins Science 303 2004 480 482
47. S. He, D. Bauman, J.S. Davis, A. Loyola, K. Nishioka, J.L. Gronlund, D. Reinberg, F. Meng, N. Kelleher, and D.G. McCafferty Facile synthesis of site-specifically acetylated and methylated histone proteins - reagents for evaluation of the histone code hypothesis Proc Natl Acad Sci USA 100 2003 12033 12038
48. W.P. Zheng, Z.S. Zhang, S. Ganguly, J.L. Weller, D.C. Klein, and P.A. Cole Cellular stabilization of the melatonin rhythm enzyme induced by nonhydrolyzable phosphonate incorporation Nat Struct Biol 10 2003 1054 1057
49. C. Peters, M. Wagner, M. Volkert, and H. Waldmann Bridging the gap between cell biology and organic chemistry: chemical synthesis and biological application of lipidated peptides and proteins Naturwissenschaften 89 2002 381 390
50. 1-ATPase motor that contains a metal-binding site that functions as a zinc-dependent reversible on/off switch. This is an innovative concept elegantly reduced to practice. These results "demonstrate the ability to engineer chemical regulation into a biomolecular motor, and represent a critical step towards controlling integrated nanochemical devices at the single molecule level."
51. A.N. Kapanidis, and S. Weiss Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules J Chem Phys 117 2002 10953 10964
52. R.M. De Lorimier, J.J. Smith, M.A. Dwyer, L.L. Looger, K.M. Sali, C.D. Paavola, S.S. Rizk, S. Sadigov, D.W. Conrad, L. Loew, and H.W. Hellinga Construction of a fluorescent biosensor family Protein Sci 11 2002 2655 2675
53. A. Frankel, S.W. Millward, and R.W. Roberts Encodamers: unnatural peptide oligomers encoded in RNA Chem Biol 10 2003 1043 1050
54. A. Keppler, H. Pick, C. Arrivoli, H. Vogel, and K. Johnsson Labeling of fusion proteins with synthetic fluorophores in live cells Proc Natl Acad Sci USA 101 2004 9955 9959
55. J.-P. Pellois, M.E. Hahn, and T.W. Muir Simultaneous triggering of protein activity and fluorescence J Am Chem Soc 126 2004 7170 7171 Describes the use of semisynthesis and structure-based design to build a caged-[fluorophore- protein] construct that contains two phosphates, a fluorescent probe, a fluorescence quenching molecule, and a photocleavable linker. The construct was built for the express purpose of providing a molecular tool for "real-time monitoring of the location of a specific protein, spatial and temporal control of its activity, and facile differentiation between its active and inactive state." A systematic series of beautifully designed proof-of-concept experiments is described, culminating in a protein with the desired properties. This remarkable paper packs an enormous amount of creative and original science, both conceptual and experimental execution, into a short (2 page) communication.
56. Dutton JL, Renda RF, Waine C, Clark RJ, Daly NL, Jennings CV, Anderson MA, Craik DJ: Conserved structural and sequence elements implicated in the processing of gene-encoded circular proteins. J Biol Chem 2004 Aug 24 [Epub ahead of print].
57. Z. Wu, J. Alexandratos, B. Ericksen, J. Lubkowski, R.C. Gallo, and W. Lu Total chemical synthesis of N-myristoylated HIV-1 matrix protein p17: structural and mechanistic implications of p17 myristoylation Proc Natl Acad Sci USA 101 2004 11587 11592
58. A. Otaka, S. Ueda, K. Tomita, Y. Yano, H. Tamamura, K. Matsuzaki, and N. Fujii Facile synthesis of membrane-embedded peptides utilizing lipid bilayer-assisted chemical ligation Chem Commun 2004 1722 1723 This paper describes the native chemical ligation of a pair of unprotected peptide segments, each of which is embedded in the same lipid bilayer. Optimized reaction conditions are selected from the range investigated. Efficient in-membrane chemical ligation could have a profound impact on the ability to prepare integral membrane proteins by chemical means.
59. A.J. Link, M.K. Vink, and D.A. Tirrell Presentation and detection of azide functionality in bacterial cell surface proteins J Am Chem Soc 126 2004 10598 10602
60. J.A. Prescher, D.H. Dube, and C.R. Bertozzi Chemical remodelling of cell surfaces in living animals Nature 430 2004 873 877