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Peptide Characterization and Application Protocols pp 125–166Cite as

Application of Topologically Constrained Mini-Proteins as Ligands, Substrates, and Inhibitors

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 386))

Summary

Protein–protein interactions are governed by a variety of structural features. The sequence specificities of such interactions are usually easier to establish than the “topological specificities,” whereby interactions may be classified based on recognition of distinct three-dimensional structural motifs. Approaches to explore topological specificities have been based primarily on assembly of mini-proteins with well defined secondary, tertiary, and/or quarternary structures. The present chapter focuses on three approaches for constructing topologically well defined mini-proteins: template-assembled synthetic proteins (TASPs), disulfide-stabilized structures, and peptide-amphiphiles (PAs). Specific examples are given for applying each approach to explore topologically-dependent protein–protein interactions. TASPs are utilized to identify a metastatic melanoma receptor that binds to the α1(IV)1263–1277 region of basement membrane (type IV) collagen. A disulfide-stabilized structure incorporating a sarafotoxin (SRT) 6b model was examined as a matrix metalloproteinase (MMP)-3 inhibitor. PAs were developed as (a) fluorogenic triple-helical or polyPro II substrates for MMPs and aggrecanase members of the a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) family and (b) glycosylated and nonglycosylated ligands for metastatic melanoma cells. Topologically constrained mini-proteins have proved to be quite versatile, helping to define critical primary, secondary, and tertiary structural elements that modulate enzyme and receptor functions.

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References

  1. Sakakibara, S., Kishida, Y., Kikuchi, Y., Sakai, R., and Kakiuchi, K. (1968) Synthesis of poly-(L-prolyl-L-prolylglycyl) of defined molecular weights. Bull. Chem. Soc. Jpn. 41, 1273.

    CAS  Google Scholar 

  2. DeGrado, W. F. (1980) Design of peptides and proteins. Adv. Protein Chem. 39, 51–124.

    Google Scholar 

  3. Mayo, K. H. and Fields, G. B. (1997) Peptides as models for understanding protein folding, in Protein Structural Biology in Bio-Medical Research (Allewell, N., and Woodward, C., eds.) JAI Press, Inc., Greenwich, CT: pp. 567–612.

    Google Scholar 

  4. Lieberman, M. and Sasaki, T. (1991) Iron(II) organizes a synthetic peptide into three-helix bundles. J. Am. Chem. Soc. 113, 1470–1471.

    CAS  Google Scholar 

  5. Mutter, M., Tuchscherer, G. G., Miller, C., et al. (1992) Template-assembled synthetic proteins with four-helix-bundle topology. J. Am. Chem. Soc. 114, 1463–1470.

    CAS  Google Scholar 

  6. Ghadiri, M. R., Soares, C., and Choi, C. (1992) A convergent approach to protein design: metal ion-assisted spontaneous self-assembly of a polypeptide into a triple-helix bundle protein. J. Am. Chem. Soc. 114, 825–831.

    CAS  Google Scholar 

  7. Ghadiri, M. R., Soares, C., and Choi, C. (1992) Design of an artificial four-helix bundle metalloprotein via a novel ruthenium(II)-assisted self-assembly process. J. Am. Chem. Soc. 114, 4000–4002.

    CAS  Google Scholar 

  8. Dawson, P. E. and Kent, S. B. H. (1993) Convenient total synthesis of a 4-helix TASP molecule by chemoselective ligation. J. Am. Chem. Soc. 115, 7263–7266.

    CAS  Google Scholar 

  9. Fields, C. G., Mickelson, D. J., Drake, S. L., McCarthy, J. B., and Fields, G. B. (1993) Melanoma cell adhesion and spreading activities of a synthetic 124-residue triple-helical “mini-collagen”. J. Biol. Chem. 268, 14,153–14,160.

    CAS  Google Scholar 

  10. Fields, C. G., Lovdahl, C. M., Miles, A. J., Matthias-Hagen, V. L., and Fields, G. B. (1993) Solid-phase synthesis and stability of triple-helical peptides incorporating native collagen sequences. Biopolymers 33, 1695–1707.

    PubMed  CAS  Google Scholar 

  11. Vuilleumer, S. and Mutter, M. (1993) Synthetic peptide and template-assembled synthetic protein models of the hen egg white lysozyme 87–97 helix. Biopolymers 33, 389–400.

    Google Scholar 

  12. Tuchscherer, G., Grell, D., Mathieu, M., and Mutter, M. (1999) Extending the concept of template-assembled synthetic proteins, J. Peptide Res. 54, 185–194.

    CAS  Google Scholar 

  13. Dai, Q., Prorok, M., and Castellino, F. J. (2004) A new mechanism for metal ion-assisted interchain helix assembly in a naturally occurring peptide mediated by optimally spaced Γ-carboxyglutamic acid residues. J. Mol. Biol. 336, 731–744.

    PubMed  CAS  Google Scholar 

  14. Becker, C. F. W., Oblatt-Montal, M., Kochendoerfer, G. G., and Montal, M. (2004) 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, 17,483–17,489.

    CAS  Google Scholar 

  15. Miles, A. J., Skubitz, A. P. N., Furcht, L. T., and Fields, G. B. (1994) Promotion of cell adhesion by single-stranded and triple-helical peptide models of basement membrane collagen α1(IV)531-543: evidence for conformationally dependent and corformationally independent type IV collagen cell adhesion sites. J. Biol. Chem. 269, 30,939–30,945.

    CAS  Google Scholar 

  16. Barnes, M. J., Knight, C. G., and Farndale, R. W. (1996) The use of collagen-based model peptides to investigate platelet-reactive sequences in collagen. Biopolymers (Peptide Sci.) 40, 383–397.

    CAS  Google Scholar 

  17. Knight, C. G., Morton, L. F., Onley, D. J., et al. (1998) Identification in collagen type I of an integrin α2β1-binding site containing an essential GER sequence. J. Biol. Chem. 273, 33,287–33,294.

    CAS  Google Scholar 

  18. Emsley, J., Knight, C. G., Farndale, R. W., Barnes, M. J., and Liddington, R. C. (2000) Structural basis of collagen recognition by integrin α2β1. Cell 101, 47–56.

    PubMed  CAS  Google Scholar 

  19. Roth, W., and Heidemann, E. (1980) Triple helix-coil transition of covalently bridged collagen-like peptides. Biopolymers 19, 1909–1917.

    CAS  Google Scholar 

  20. Mutter, M., Hersperger, R., Gubernator, K., and Muller, K. (1989) The construction of new proteins: a template-assembled synthetic protein (TASP) containing both a 4-helix bundle and β-barrel-like structure. Proteins 5, 13–21.

    PubMed  CAS  Google Scholar 

  21. Tuchscherer, G., Domer, B., Sila, U., Kamber, B., and Mutter, M. (1993) The TASP concept: mimetics of peptide ligands, protein surfaces and folding units. Tetrahedron 49, 3559–3575.

    CAS  Google Scholar 

  22. Tuchscherer, G. (1993) Template assembled synthetic proteins: condensation of a multifunctional peptide to a topological template via chemoselective ligation. Tetrahedron Lett. 34, 8419–8422.

    CAS  Google Scholar 

  23. Dumy, P., Eggleston, I. M., Cervigni, S., Sila, U., Sun, X., and Mutter, M. (1995) A convenient synthesis of cyclic peptides as regioselectively addressable functionalized templates (RAFT). Tetrahedron Lett. 36, 1255–1258.

    CAS  Google Scholar 

  24. Peluso, S., Dumy, P., Eggleston, I. M., Garrouste, P., and Mutter, M. (1997) Protein mimetics (TASP) by sequential condensation of peptide loops to an immobilised topological template. Tetrahedron 53, 7231–7236.

    CAS  Google Scholar 

  25. Goodman, M., Feng, Y., Melacini, G., and Taulane, J. P. (1996) A template-induced incipient collagen-like triple-helical structure. J. Am. Chem. Soc. 118, 5156–5157.

    CAS  Google Scholar 

  26. Goodman, M., Melacini, G., and Feng, Y. (1996) Collagen-like triple helices incorporating peptoid residues. J. Am. Chem. Soc. 118, 10,928–10,929.

    CAS  Google Scholar 

  27. Feng, Y., Melacini, G., Taulane, J. P., and Goodman, M. (1996) Acetyl-terminated and template-assembled collagen-based polypeptides composed of Gly-Pro-Hyp sequences. 2. Synthesis and conformational analysis by circular dichroism, ultraviolet absorbance, and optical rotation. J. Am. Chem. Soc. 118, 10,351–10,358.

    CAS  Google Scholar 

  28. Feng, Y., Melacini, G., Taulane, J. P., and Goodman, M. (1996) Collagen-based structures containing the peptoid tesidue N-isobutylglycine (Nleu): synthesis and biophysical studies of Gly-Pro-Nleu sequences by circular dichroism, ultraviolet absorbance, and optical rotation. Biopolymers 39, 859–872.

    PubMed  CAS  Google Scholar 

  29. Melacini, G., Feng, Y., and Goodman, M. (1996) Collagen-based structures containing the peptoid residue N-isobutylglycine (Nleu). 6. Conformational analysis of Gly-Pro-Nleu sequences by 1H NMR, CD, and molecular modeling. J. Am. Chem. Soc. 118, 10,725–10,732.

    CAS  Google Scholar 

  30. Melacini, G., Feng, Y., and Goodman, M. (1997) Collagen-based structures containing the peptoid residue N-isobutylene (Nleu): conformational analysis of Gly-Nleu-Pro sequences by 1H-NMR and molecular modeling. Biochemistry 36, 8725–8732.

    PubMed  CAS  Google Scholar 

  31. Feng, Y., Melacini, G., and Goodman, M. (1997) Collagen-based structures containing the peptoid residue N-isobutylglycine (Nleu): synthesis and biophysical studies of Gly-Nleu-Pro sequences by circular dichroism and optical rotation, Biochemistry 36, 8716–8724.

    PubMed  CAS  Google Scholar 

  32. Kwak, J., De Capua, A., Locardi, E., and Goodman, M. (2002) TREN (Tris(2-aminoethyl)amine): an effective scaffold for the assembly of triple helical collagen mimetic structures. J. Am. Chem. Soc. 124, 14,085–14,091.

    CAS  Google Scholar 

  33. Oh, J., Takahashi, R., Kondo, S., et al. (2001) The membrane-anchored MMP inhibitor RECK is a key regulator of extracellular matrix integrity and angiogenesis. Cell 107, 789–800.

    PubMed  CAS  Google Scholar 

  34. Kinberger, G. A., Cai, W., and Goodman, M. (2002) Collagen mimetic dendrimers. J. Am. Chem. Soc. 124, 15,162–15,163.

    CAS  Google Scholar 

  35. Rump, E. T., Rijkers, D. T. S., Hilbers, H. W., de Groot, P. G., and Liskamp, R. M. J. (2002) Cyclotriveratrylene (CTV) as a new chiral triacid scaffold capable of inducing triple helix formation of collagen peptides containing either a native sequence or Pro-Hyp-Gly repeats. Chem. Eur. J. 8, 4613–4621.

    CAS  Google Scholar 

  36. Brask, J. and Jensen, K. J. (2001) Carboproteins: a 4-α-helix bundle protein model assembled on a D-galactopyranoside template. Bioorg. Med. Chem. Lett. 11, 697–700.

    PubMed  CAS  Google Scholar 

  37. Thulstrup, P. W., Brask, J., Jensen, K. J., and Larsen, E. (2005) Synchroton radiation circular dichroism spectroscopy applied to metmyoglobin and a 4-α-helix bundle carboprotein. Biopolymers 78, 46–52.

    PubMed  CAS  Google Scholar 

  38. Diekmann, G. R., McRorie, D. K., Lear, J. D., Sharp, K. A., DeGrado, W. F., and Pecoraro, V. L. (1998) The role of protonation and metal chelation preferences in defining the properties of mercury-binding coiled coils. J. Mol. Biol. 280, 897–912.

    Google Scholar 

  39. Kohn, W. D., Kay, C. M., Sykes, B. D., and Hodges, R. S. (1998) Metal ion induced folding of a de novo designed coiled-coil peptide. J. Am. Chem. Soc. 120, 1124–1132.

    CAS  Google Scholar 

  40. Li, X., Suzuki, K., Kanaori, K., Tajima, K., Kashiwada, A., and Hiroaki, H. (2000) Soft metal ions, Cd(II) and Hg(II), induce triple-stranded alpha-helical assembly and folding of a de novo designed peptide in their trigonal geometries. Protein Sci. 9, 1327–1333.

    PubMed  CAS  Google Scholar 

  41. Cai, W., Kwok, S. W., Taulane, J. P., and Goodman, M. (2004) Metal-assisted assembly and stabilization of collagen-like triple helices. J. Am. Chem. Soc. 126, 15,030–15,031.

    CAS  Google Scholar 

  42. Fields, C. G., Grab, B., Lauer, J. L., Miles, A. J., Yu, Y.-C., and Fields, G. B. (1996) Solid-phase synthesis of triple-helical collagen-model peptides. Lett. Peptide Sci. 3, 3–16.

    CAS  Google Scholar 

  43. Barthe, P., Rochette, S., Vita, C., and Roumestand, C. (2000) Synthesis and NMR solution structure of an α-helical hairpin stapled with two disulfide bridges. Protein Sci. 9, 942–955.

    PubMed  CAS  Google Scholar 

  44. Blandl, T., Cochran, A. G., and Skelton, N. J. (2003) Turn stability in β-hairpin peptides: investigation of peptides containing 3:5 type I G1 bulge turns. Protein Sci. 12, 237–247.

    PubMed  CAS  Google Scholar 

  45. Weston, C. J., Cureton, C. H., Calvert, M. J., Smart, O. S., and Allemann, R. K. (2004) A stabile miniature protein with oxaloacetate decarboxylase activity. ChemBioChem 5, 1075–1080.

    PubMed  CAS  Google Scholar 

  46. Heitz, A., Le-Nguyen, D., and Chiche, L. (1999) Min-21 and Min-23, the smallest peptides that fold like a cystine-stabilized β-sheet motif: design, solution structure, and thermal stability. Biochemistry 38, 10,615–10,625.

    CAS  Google Scholar 

  47. Craik, D. J., Daly, N. L., and Waine, C. (2001) The cystine knot motif in toxins and implications for drug design. Toxicon 39, 43–60.

    PubMed  CAS  Google Scholar 

  48. Aumelas, A., Chiche, L., Kubo, S., Chino, N., Watanabe, T. X., and Kobayashi, Y. (1999) The chimeric peptide [Lys(-2)-Arg(-1)]-sarafotoxin-S6b, composed of the endothelin pro-sequence and sarafotoxin, retains the salt-bridge staple between Arg(-1) and Asp8 previously observed in [Lys(-2)-Arg(-1)]-endothelin. Implications of this salt-bridge in the contractile activity and the oxidative folding reaction. Eur. J. Biochem. 266, 977–985.

    PubMed  CAS  Google Scholar 

  49. Nielsen, J. S., Buczek, P., and Bulaj, G. (2004) Cosolvent-assisted oxidative folding of a bicyclic α-conotoxin ImI. J. Peptide Sci. 10, 249–256.

    CAS  Google Scholar 

  50. Tam, J. P., Dong, X., and Wu, C.-R. (1993) Solvent chaperone in protein folding: selective enhancement of disulfide isomers of endothelin, in Peptide Chemistry 1992: Proceedings of the 2nd Japan Symposium on Peptide Chemistry (Yanaihara, N., ed.). Escom, Leiden, The Netherlands: pp. 24–26.

    Google Scholar 

  51. Kumaran, S. and Roy, R. P. (1999) Helix-enhancing propensity of fluoro and alkyl alcohols: influence of pH, temperature and cosolvent concentration on the helical conformation of peptides. J. Peptide Res. 53, 284–293.

    CAS  Google Scholar 

  52. Mills, R. G., Atkins, A. R., Harvey, T., Junius, F. K., Smith, R., and King, G. F. (1991) Conformation of sarafotoxin-6b in aqueous solution determined by NMR spectroscopy and distance geometry. FEBS Lett. 282, 247–252.

    PubMed  CAS  Google Scholar 

  53. Kubo, S., Chino, N., Nakajima, K., et al. (1997) Improvement in the oxidative folding of endothelin-1 by a Lys-Arg extension at the amino terminus: implication of a salt bridge between Arg-1 and Asp8. Lett. Peptide Sci. 4, 185–192.

    CAS  Google Scholar 

  54. Woessner, J. F. and Nagase, H. (2000) Matrix Metalloproteinases and TIMPs. Oxford University Press, Oxford.

    Google Scholar 

  55. Birkedal-Hansen, H., Moore, W. G. I., Bodden, M. K., et al. (1993) Matrix metalloproteinases: a review. Crit. Rev. Oral Biol. Med. 4, 197–250.

    PubMed  CAS  Google Scholar 

  56. Berndt, P., Fields, G. B., and Tirrell, M. (1995) Synthetic lipidation of peptides and amino acids: monolayer structure and properties. J. Am. Chem. Soc. 117, 9515–9522.

    CAS  Google Scholar 

  57. Pakalns, T., Haverstick, K. L., Fields, G. B., McCarthy, J. B., Mooradian, D. L., and Tirrell, M. (1999) Cellular recognition of synthetic peptide amphiphiles in self-assembled monolayer films. Biomaterials 20, 2265–2279.

    PubMed  CAS  Google Scholar 

  58. Dillow, A. K., Ochsenhirt, S. E., McCarthy, J. B., Fields, G. B., and Tirrell, M. (2001) Adhesion of α5β1 receptors to biomimetic substrates constructed from peptide amphiphiles. Biomaterials 22, 1493–1505.

    CAS  Google Scholar 

  59. Rosler, A., Klok, H. A., Hamlye, I. W., Castelletto, V., and Mykhaylyk, O. O. (2003) Nanoscale structure of poly(ethylene glycol( hybrid block copolymers containing amphiphilic β-strand peptide sequences. Biomacromolecules 4, 859–863.

    PubMed  Google Scholar 

  60. Vandermeulen, G. W. M., and Klok, H. A. (2004) Peptide/protein hybrid materials: enhanced control of structure and improved performance through conjugation of biological and synthetic polymers. Macromol. Biosci. 4, 383–398.

    PubMed  CAS  Google Scholar 

  61. Yu, Y.-C., Berndt, P., Tirrell, M., and Fields, G. B. (1996) Self-assembling amphiphiles for construction of protein molecular architecture. J. Am. Chem. Soc. 118, 12,515–12,520.

    CAS  Google Scholar 

  62. Yu, Y.-C., Tirrell, M., and Fields, G. B. (1998) Minimal lipidation stabilizes protein-like molecular architecture. J. Am. Chem. Soc. 120, 9979–9987.

    CAS  Google Scholar 

  63. Yu, Y.-C., Roontga, V., Daragan, V. A., Mayo, K. H., Tirrell, M., and Fields, G. B. (1999) Structure and dynamics of peptide-amphiphiles incorporating triple-helical proteinlike molecular architecture. Biochemistry 38, 1659–1668.

    PubMed  CAS  Google Scholar 

  64. Malkar, N. B., Lauer-Fields, J. L., Borgia, J. A., and Fields, G. B. (2002) Modulation of triple-helical stability and subsequent melanoma cellular responses by single-site substitution of fluoroproline derivatives. Biochemistry 41, 6054–6064.

    PubMed  CAS  Google Scholar 

  65. Lauer-Fields, J. L., Malkar, N. B., Richet, G., Drauz, K., and Fields, G. B. (2003) Melanoma cell CD44 interaction with the α1(IV)1263-1277 region from basement membrane collagen is modulated by ligand glycoslyation. J. Biol. Chem. 278, 14,321–14,330.

    CAS  Google Scholar 

  66. Mardilovich, A. and Kokkoli, E. (2004) Biomimetic peptide-amphiphiles for functional biomaterials: the role of GRGDSP and PHSRN. Biomacromolecules 5, 950–957.

    PubMed  CAS  Google Scholar 

  67. Kokkoli, E., Ochsenhirt, S. E., and Tirrell, M. (2004) Collective and single-molecule interactions of α5β1 integrins. Langmuir 20, 2397–2404.

    PubMed  CAS  Google Scholar 

  68. Silva, G. A., Czeisler, C., Niece, K. L., et al. (2004) Selective differentiation of neural progenitor cells by high-epitope density nanofibers. Science 303, 1352–1355.

    PubMed  CAS  Google Scholar 

  69. Forns, P., Lauer-Fields, J. L., Gao, S., and Fields, G. B. (2000) Induction of protein-like molecular architecture by monoalkyl hydrocarbon chains. Biopolymers 54, 531–546.

    PubMed  CAS  Google Scholar 

  70. Hartgerink, J. D., Beniash, E., and Stupp, S. I. (2001) Self-assembly and mineralization of peptide-amphiphile nanofibers. Science 297, 1684–1688.

    Google Scholar 

  71. Malkar, N. B., Lauer-Fields, J. L., Juska, D., and Fields, G. B. (2003) Characterization of peptide-amphiphiles possessing cellular activation sequences. Biomacromolecules 4, 518–528.

    PubMed  CAS  Google Scholar 

  72. Yu, Y.-C., Pakalns, T., Dori, Y., McCarthy, J. B., Tirrell, M., and Fields, G. B. (1997) Construction of biologically active protein molecular architecture using self-assembling peptide-amphiphiles. Meth. Enzymol. 289, 571–587.

    PubMed  CAS  Google Scholar 

  73. Lauer-Fields, J. L., Broder, T., Sritharan, T., Nagase, H., and Fields, G. B. (2001) Kinetic analysis of matrix metalloproteinase triple-helicase activity using fluorogenic substrates. Biochemistry 40, 5795–5803.

    PubMed  CAS  Google Scholar 

  74. Lauer-Fields, J. L. and Fields, G. B. (2002) Triple-helical peptide analysis of collagenolytic protease activity. Biol. Chem. 383, 1095–1105.

    PubMed  CAS  Google Scholar 

  75. Lauer-Fields, J. L., Sritharan, T., Stack, M. S., Nagase, H., and Fields, G. B. (2003) Selective hydrolysis of triple-helical substrates by matrix metalloproteinase-2 and -9. J. Biol. Chem. 278, 18,140–18,145.

    CAS  Google Scholar 

  76. Lauer-Fields, J. L., Kele, P., Sui, G., Nagase, H., Leblanc, R. M., and Fields, G. B. (2003) Analysis of matrix metalloproteinase activity using triple-helical substrates incorporating fluorogenic L- or D-amino acids. Anal. Biochem. 321, 105–115.

    PubMed  CAS  Google Scholar 

  77. Minond, D., Lauer-Fields, J. L., Nagase, H., and Fields, G. B. (2004) Matrix metalloproteinase triple-helical peptidase activities are differentially regulated by substrate stability. Biochemistry 43, 11,474–11,481.

    CAS  Google Scholar 

  78. Tu, R., Mohanty, K., and Tirrell, M. (2004) Liposomal targeting through peptide-amphiphile functionalization. Am. Pharm. Rev. 7(2), 36–41.

    Google Scholar 

  79. Baronas-Lowell, D., Lauer-Fields, J. L., and Fields, G. B. (2004) Induction of endothelial cell activation by a triple-helical α2β1 integrin ligand derived from type I collagen α1(I)496-507. J. Biol. Chem. 279, 952–962.

    PubMed  CAS  Google Scholar 

  80. Baronas-Lowell, D., Lauer-Fields, J. L., Borgia, J. A., et al. (2004) Differential modulation of human melanoma cell metalloproteinase expression by α2β1 integrin and CD44 triple-helical ligands derived from type IV collagen. J. Biol. Chem. 279, 43,503–43,513.

    CAS  Google Scholar 

  81. Lockwood, N. A., Haseman, J. R., Tirrell, M. V., and Mayo, K. H. (2004) Acylation of SC dodecapeptide increases bactericidal potency against Gram-positive bacteria, including drug-resistant strains. Biochem. J. 378, 93–103.

    PubMed  CAS  Google Scholar 

  82. Chu-Kung, A. F., Bozzelli, K. N., Lockwood, N. A., Haseman, J. R., Mayo, K. H., and Tirrell, M. V. (2004) Promotion of peptide antimicrobial activity by fatty acid conjugation. Bioconjugate Chem. 15, 530–535.

    CAS  Google Scholar 

  83. Chhabra, S. R., Hothi, B., Evans, D. J., White, P. D., Bycroft, B. W., and Chan, W. C. (1998) An appraisal of new variants of Dde amine protecting group for solid phase peptide synthesis. Tetrahedron Lett. 39, 1603–1606.

    CAS  Google Scholar 

  84. Rohwedder, B., Mutti, Y., Dumy, P., and Mutter, M. (1998) Hydrazinolysis of Dde: complete orthogonality with Aloc protecting groups. Tetrahedron Lett. 39, 1175–1178.

    CAS  Google Scholar 

  85. Kates, S. A., Daniels, S. B., and Albericio, F. (1993) Automated allyl cleavage for continuous-flow synthesis of cyclic and branched peptides. Anal. Biochem. 212, 303–310.

    PubMed  CAS  Google Scholar 

  86. King, D. S., Fields, C. G., and Fields, G. B. (1990) A cleavage method which minimizes side reactions following Fmoc solid phase peptide synthesis. Int. J. Peptide Protein Res. 36, 255–266.

    CAS  Google Scholar 

  87. Fields, C. G. and Fields, G. B. (1993) Minimization of tryptophan alkylation following 9-fluorenylmethoxycarbonyl solid-phase peptide synthesis. Tetrahedron Lett. 34, 6661–6664.

    CAS  Google Scholar 

  88. Henkel, W., Vogl, T., Echner, H., et al. (1999) Synthesis and folding of native collagen III model peptides. Biochemistry 38, 13,610–13,622.

    CAS  Google Scholar 

  89. Lauer-Fields, J. L., Nagase, H., and Fields, G. B. (2000) Use of Edman degradation sequence analysis and matrix-assisted laser desorption/ionization mass spectrometry in designing substrates for matrix metalloproteinases. J. Chromatogr. A. 890, 117–125.

    PubMed  CAS  Google Scholar 

  90. Knutson, J. R., Iida, J., Fields, G. B., and McCarthy, J. B. (1996) CD44/chondroitin sulfate proteoglycan and α2β1 integrin mediate human melanoma cell migration on type IV collagen and invasion of basement membranes. Mol. Biol. Cell 7, 383–396.

    PubMed  CAS  Google Scholar 

  91. Takahashi, K., Eto, H., and Tanabe, K. K. (1999) Involvement of CD44 in matrix metalloproteinase-2 regulation in human melanoma cells. Int. J. Cancer 80, 387–395.

    PubMed  CAS  Google Scholar 

  92. Kimura, S., Kasuya, Y., Sawamura, T., et al. (1988) Structure-activity relationships of endothelin: importance of the C-terminal moiety. Biochem. Biophys. Res. Commun. 156, 1182–1186.

    PubMed  CAS  Google Scholar 

  93. Ellman, G. L. (1959) Tissue sulfhydryl groups. Arch. Biochem. Biophys. 82, 70–77.

    PubMed  CAS  Google Scholar 

  94. Knight, C. G., Willenbrock, F., and Murphy, G. (1992) A novel coumarin-labelled peptide for sensitive continuous assays of the matrix metalloproteinases. FEBS Lett. 296, 263–266.

    PubMed  CAS  Google Scholar 

  95. Nagase, H., Fields, C. G., and Fields, G. B. (1994) Design and characterization of a fluorogenic substrate selectively hydrolyzed by stromelysin 1 (matrix metalloproteinase-3). J. Biol. Chem. 269, 20,952–20,957.

    CAS  Google Scholar 

  96. Fields, C. G., Grab, B., Lauer, J. L., and Fields, G. B. (1995) Purification and analysis of synthetic, triple-helical “minicollagens” by reversed-phase high-performance liquid chromatography. Anal. Biochem. 231, 57–64.

    PubMed  CAS  Google Scholar 

  97. Grab, B., Miles, A. J., Furcht, L. T., and Fields, G. B. (1996) Promotion of fibroblast adhesion by triple-helical peptide models of type I collagen-derived sequences. J. Biol. Chem. 271, 12,234–12,240.

    CAS  Google Scholar 

  98. Lauer-Fields, J. L., Tuzinski, K. A., Shimokawa, K., Nagase, H., and Fields, G. B. (2000) Hydrolysis of triple-helical collagen peptide models by matrix metalloproteinases. J. Biol. Chem. 275, 13,282–13,290.

    CAS  Google Scholar 

  99. Knight, C. G. (1991) A quenched fluorescent substrate for thimet peptidase containing a new fluorescent amino acid, DL-2-amino-3-(7-methoxy-4-coumaryl)propionic acid. Biochem. J. 274, 45–48.

    PubMed  CAS  Google Scholar 

  100. Anastasi, A., Knight, C. G., and Barrett, A. J. (1993) Characterization of the bacterial metalloendopeptidase pitrilysin by use of a continuous fluorescence assay. Biochem. J. 290, 601–607.

    PubMed  CAS  Google Scholar 

  101. Lauer-Fields, J. L., Juska, D., and Fields, G. B. (2002) Matrix metalloproteinases and collagen catabolism. Biopolymers (Peptide Sci.) 66, 19–32.

    CAS  Google Scholar 

  102. Malkar, N. B. and Fields, G. B. (2001) Synthesis of Nα-(fluoren-9-ylmethoxycarbonyl)-Nε-[(7-methoxycoumarin-4-yl)acetyl]-L-lysine for use in solid-phase synthesis of fluorogenic substrates. Lett. Peptide Sci. 7, 263–267.

    Google Scholar 

  103. Hurst, D. R., Schwartz, M. A., Ghaffari, M. A., et al. (2004) Catalytic- and ecto-domains of membrane type 1-matrix metalloproteinase have similar inhibition profiles but distinct endopeptidase activities. Biochem. J. 377, 775–779.

    PubMed  CAS  Google Scholar 

  104. Nagase, H. and Fields, G. B. (1996) Human matrix metalloproteinase specificity studies using collagen sequence-based synthetic peptides. Biopolymers 40, 399–416.

    PubMed  CAS  Google Scholar 

  105. Fields, G. B. (1991) A model for interstitial collagen catabolism by mammalian collagenases. J. Theor. Biol. 153, 585–602.

    PubMed  CAS  Google Scholar 

  106. Mucha, A., Cuniasse, P., Kannan, R., et al. (1998) Membrane type-1 matrix metalloproteinase and stromelysin-3 cleave more efficiently synthetic substrates containing unusual amino acids in their P ′1 positions. J. Biol. Chem. 273, 2763–2768.

    PubMed  CAS  Google Scholar 

  107. Ohuchi, E., Imai, K., Fujii, Y., Sato, H., Seiki, M., and Okada, Y. (1997) Membrane type I matrix metalloproteinase digests intersitial collagens and other extracellular matrix macromolecules. J. Biol. Chem. 272, 2446–2451.

    PubMed  CAS  Google Scholar 

  108. Miller, E. J., Finch, J. E., Jr., Chung, E., Butler, W. T., and Robertson, P. B. (1976) Specific cleavage of the native type III collagen molecule with trypsin. Arch. Biochem. Biophys. 173, 631–637.

    PubMed  CAS  Google Scholar 

  109. Birkedal-Hansen, H., Taylor, R. E., Bhown, A. S., Katz, J., Lin, H.-Y., and Wells, B. R. (1985) Cleavage of bovine skin type III collagen by proteolytic enzymes. J. Biol. Chem. 260, 16,411–16,417.

    CAS  Google Scholar 

  110. Bächinger, H. P., Bruckner, P., Timpl, R., Prockop, D. J., and Engel, J. (1980) Folding mechanism of the triple helix in type-III collagen and type-III pN-collagen. Eur. J. Biochem. 106, 619–632.

    PubMed  Google Scholar 

  111. Bruckner, P. and Prockop, D. J. (1981) Proteolytic enzymes as probes for the triple-helical conformation of procollagen. Anal. Biochem. 110, 360–368.

    PubMed  CAS  Google Scholar 

  112. Ryhänen, L., Zaragoza, E. J., and Uitto, J. (1983) Conformational stability of type I collagen triple helix: evidence for temporary and local relaxation of the protein conformation using a proteolytic probe. Arch. Biochem. Biophys. 223, 562–571.

    PubMed  Google Scholar 

  113. Sieron, A. L., Fertala, A., Ala-Kokko, L., and Prockop, D. J. (1993) Deletion of a large domain in recombinant human procollagen II does not alter the thermal stability of the triple helix. J. Biol. Chem. 268, 21,232–21,237.

    CAS  Google Scholar 

  114. Fan, P., Li, M. H., Brodsky, B., and Baum, J. (1993) Backbone dynamics of (Pro-Hyp-Gly)10 and a designed collagen-like triple-helical peptide by 15N NMR relaxation and hydrogen-exchange measurements. Biochemistry 32, 13,299–13,309.

    CAS  Google Scholar 

  115. Fiori, S., Saccá, B., and Moroder, L. (2002) Structural properties of a collagenous heterotrimer that mimics the collagenase cleavage site of collagen type I. J. Mol. Biol. 319, 1235–1242.

    PubMed  CAS  Google Scholar 

  116. Stultz, C. M. (2002) Localized unfolding of collagen explains collagenase cleavage near imino-poor sites. J. Mol. Biol. 319, 997–1003.

    PubMed  CAS  Google Scholar 

  117. Niyibizi, C., Chan, R., Wu, J.-J., and Eyre, D. (1994) A 92 kDa gelatinase (MMP-9) cleavage site in native type V collagen. Biochem. Biophys. Res. Commun. 202, 328–333.

    PubMed  CAS  Google Scholar 

  118. Nagase, H. and Kashiwagi, M. (2003) Aggrecanases and cartilage matrix degradation. Arthritis Res. Ther. 5, 94–103.

    PubMed  CAS  Google Scholar 

  119. Tanzawa, K., Berger, J., and Prockop, D. J. (1985) Type I procollagen N-proteinase from whole chick embryos: cleavage of a homotrimer of pro-α1(I) chains and the requirement for procollagen with a triple-helical conformation. J. Biol. Chem. 260, 1120–1126.

    PubMed  CAS  Google Scholar 

  120. Arnold, W. V., Fertala, A., Sieron, A. L., et al. (1998) Recombinant procollagen II: deletion of D period segments identifies sequences that are required for helix stabilization and generates a temperature-sensitive N-proteinase cleavage site. J. Biol. Chem. 273, 31,822–31,828.

    CAS  Google Scholar 

  121. Miller, J. A., Liu, R.-Q., Davis, G. L., Pratta, M. A., Trzaskos, J. M., and Copeland, R. A. (2003) A microplate assay specific for the enzyme aggrecanase. Anal. Biochem. 314, 260–265.

    PubMed  CAS  Google Scholar 

  122. Lauer-Fields, J. L., Sritharan, T., Kashiwagi, M., Nagase, H., and Fields, G. B. (2007) Substrate conformation modulates aggrecanase (ADAMTS-4) affinity and sequence specificity: suggestion of a common topological specificity of functionally diverse proteases. J. Biol. Chem. 282, in press.

    Google Scholar 

  123. Dori, Y., Bianco-Peled, H., Satija, S. K., Fields, G. B., McCarthy, J. B., and Tirrell, M. (2000) Ligand accessibility as a means to control cell response to bioactive bilayer membranes. J. Biomed. Mater. Res. 50, 75–81.

    PubMed  CAS  Google Scholar 

  124. Bianco-Peled, H., Dori, Y., Schneider, J., Sung, L.-P., Satija, S., and Tirrell, M. (2001) Structural study of langmuir monolayers containing lipidated poly(ethylene glycol) and peptides. Langmuir 17, 6931–6937.

    CAS  Google Scholar 

  125. Lauer, J. L., Gendron, C. M., and Fields, G. B. (1998) Effect of ligand conformation on melanoma cell α3β1 integrin-mediated signal transduction events: implications for a collagen structural modulation mechanism of tumor cell invasion. Biochemistry 37, 5279–5287.

    PubMed  CAS  Google Scholar 

  126. Fields, G. B., Lauer, J. L., Dori, Y., Forns, P., Yu, Y.-C., and Tirrell, M. (1998) Proteinlike molecular architecture: biomaterial applications for inducing cellular receptor binding and signal transduction. Biopolymers 47, 143–151.

    PubMed  CAS  Google Scholar 

  127. McCarthy, J. B., Mickelson, D. J., Fields, C. G., and Fields, G. B. (1993) The use of collagen-model peptides to correlate collagen primary and secondary structural effects with the mechanisms of tumor cell adhesion, motility and invasion, in Peptides 1992 (Schneider, C. H., and Eberle, A. N., eds.). Escom Science Publishers, Leiden, The Netherlands: pp. 109–110.

    Google Scholar 

  128. Dennis, J., Waller, C., Timpl, R., and Schirrmacher, V. (1982) Surface sialic acid reduces attachment of metastatic tumour cells to collagen type IV and fibronectin. Nature 300, 274–276.

    PubMed  CAS  Google Scholar 

  129. Hakomori, S. (1990) Bifunctional role of glycosphingolipids: modulators for transmembrane signaling and mediators for cellular interactions. J. Biol. Chem. 265, 18,713–18,716.

    CAS  Google Scholar 

  130. Spillmann, D. and Burger, M. M. (1996) Carbohydrate-carbohydrate interactions in adhesion. J. Cell. Biochem. 61, 562–568.

    PubMed  CAS  Google Scholar 

  131. Borsig, L., Wong, R., Feramisco, J., Nadeau, D. R., Varki, N. M., and Varki, A. (2001) Heparin and cancer revisited: mechanistic connections involving platelets, P-selectin, carcinoma mucins, and tumor metastasis. Proc. Natl. Acad. Sci. USA 98, 3352–3357.

    PubMed  CAS  Google Scholar 

  132. Naor, D., Slonov, R. V., and Ish-Shalom, D. (1997) CD44: structure, function, and association with the malignant process, in Advances in Cancer Research (Vande Woude, G. F. and Klein, G., eds.) Academic, Orlando, FL: pp. 241–319.

    Google Scholar 

  133. Babel, W. and Glanville, R. W. (1984) Structure of human-basement-membrane (type IV) collagen: complete amino-acid sequence fo a 914-residue-long pepsin fragment from the α1(IV) chain. Eur. J. Biochem. 143, 545–556.

    PubMed  CAS  Google Scholar 

  134. Miles, A. J., Knutson, J. R., Skubitz, A. P. N., Furcht, L. T., McCarthy, J. B., and Fields, G. B. (1995) A peptide model of basement membrane collagen α1(IV) 531-543 binds the α3β1 integrin. J. Biol. Chem. 270, 29,047–29,050.

    CAS  Google Scholar 

  135. Cho, S. K., Yeh, J.-C., Cho, M., and Cummings, R. D. (1996) Transcriptional regulation of α1,3-galactosyltransferase in embryonal carcinoma cells by retinoic acid. J. Biol. Chem. 271, 3238–3246.

    PubMed  CAS  Google Scholar 

  136. Iyer, S. P. and Hart, G. W. (2003) Dynamic nuclear and cytoplasmic glycosylation: enzymes of O-GlcNAc cycling. Biochemistry 42, 2493–2499.

    PubMed  CAS  Google Scholar 

  137. Haltiwanger, R. S., Kelly, W. G., Roquemore, E. P., et al. (1992) Glycosylation of nuclear and cytoplasmic proteins is ubiquitous and dynamic. Biochem. Soc. Trans. 20, 264–269.

    PubMed  CAS  Google Scholar 

  138. Wells, L., Vosseller, K., and Hart, G. W. (2001) Glycosylation of nucleoplasmic proteins: signal transduction and O-GlcNAc. Science 291, 2376–2378.

    PubMed  CAS  Google Scholar 

  139. Hamazaki, H. and Hotta, K. (1980) Enzymatic hydrolysis of disaccharide unit of collagen: isolation of 2-O-alpha-D-glucopyranosyl-O-beta-D-galactopyranosyl-hydroxylysine glucohydrolase from rat spleens. Eur. J. Biochem. 111, 587–591.

    PubMed  CAS  Google Scholar 

  140. Ishii, I., Iwase, H., Hamazaki, H., and Hotta, K. (1987) Comparative study of specific alpha-1,2-glucosidase activity toward glucosyl galactosyl hydroxylysine in various animal species. Comp. Biochem. Physiol. B 88, 313–316.

    PubMed  CAS  Google Scholar 

  141. Spiro, M. J. and Spiro, R. G. (1971) Studies on the biosynthesis of the hydroxylysine-linked disaccharide unit of basement membranes and collagens II: kidney galactosyltransferase. J. Biol. Chem. 246, 4910–4918.

    PubMed  CAS  Google Scholar 

  142. Babiarz, B. and Cullen, E. (1992) 3T3 Cell surface galactosyltransferase is a calcium-dependent adhesion molecule for collagen type IV. Exp. Cell Res. 203, 276–279.

    PubMed  CAS  Google Scholar 

  143. Privitera, S., Prody, C. A., Callahan, J. W., and Hinek, A. (1998) The 67-kDa enzymatically inactive alternatively spliced variant of β-galactosidase is identical to the elastin/laminin-binding protein. J. Biol. Chem. 273, 6319–6326.

    PubMed  CAS  Google Scholar 

  144. Nayak, B. R. and Spiro, R. G. (1991) Localization and structure of the asparagine-linked oligosaccharides of type IV collagen from glomerular basement membrane and lens capsule. J. Biol. Chem. 266, 13,978–13,987.

    CAS  Google Scholar 

  145. Andreu, D., Albericio, F., Sole, N. A., Munson, M. C., Ferrer, M., and Barany, G. (1994) Formation of disulfide bonds in synthetic peptides and proteins, in Peptide Synthesis Protocols: Methods in Molecular Biology, Vol. 35 (Pennington, M. W. and Dunn, B. M., eds.). Humana, Totowa, NJ: pp. 91–169.

    Google Scholar 

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Authors and Affiliations

  1. College of Biomedical Sciences and Department of Chemistry & Biochemistry, Florida Atlantic University, Boca Raton, FL

    Janelle L. Lauer-Fields, Keith Brew & Gregg B. Fields

  2. Department of Chemistry & Biochemistry, Florida Atlantic University, Boca Raton, FL

    Dmitriy Minond

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  1. Janelle L. Lauer-Fields
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  2. Dmitriy Minond
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  4. Gregg B. Fields
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  1. Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL

    Gregg B. Fields

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Lauer-Fields, J.L., Minond, D., Brew, K., Fields, G.B. (2007). Application of Topologically Constrained Mini-Proteins as Ligands, Substrates, and Inhibitors. In: Fields, G.B. (eds) Peptide Characterization and Application Protocols. Methods in Molecular Biology™, vol 386. Humana Press. https://doi.org/10.1007/978-1-59745-430-8_5

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  • DOI: https://doi.org/10.1007/978-1-59745-430-8_5

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