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Non-Protein Amino Acids in the Design of Secondary Structure Scaffolds

  • Protocol
Book cover Protein Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 340))

Abstract

The use of stereochemically constrained amino acids permits the design of short peptides as models for protein secondary structures. Amino acid residues that are restrained to a limited range of backbone torsion angles (ϕ-ψ) may be used as folding nuclei in the design of helices and β-hairpins. α-Amino-isobutyric acid (Aib) and related Cαα dialkylated residues are strong promoters of helix formation, as exemplified by a large body of experimentally determined structures of helical peptides. DPro-Xxx sequences strongly favor type II’ turn conformations, which serve to nucleate registered β-hairpin formation. Appropriately positioned DPro-Xxx segments may be used to nucleate the formation of multistranded antiparallel β-sheet structures. Mixed (α/β) secondary structures can be generated by linking rigid modules of helices and β-hairpins. The approach of using stereochemically constrained residues promotes folding by limiting the local structural space at specific residues. Several aspects of secondary structure design are outlined in this chapter, along with commonly used methods of spectroscopic characterization.

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References

  1. Ramachandran, G. N., Ramakrishnan, C., and Sasisekharan, V. (1963) Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95–99.

    Article  PubMed  CAS  Google Scholar 

  2. Ramachandran, G. N. and Ramakrishnan, C. (1965) Stereochemical criteria for polypeptide and protein chain conformation. II. Allowed conformations for a pair of peptide units. Biophys. J. 5, 909–933.

    Article  PubMed  Google Scholar 

  3. Ramachandran, G. N. and Sasisekharan, V. (1968) Conformation of polypeptides and proteins. Adv. Protein. Chem. 23, 283–438.

    Article  PubMed  CAS  Google Scholar 

  4. Venkatraman, J., Shankaramma, S. C., and Balaram, P. (2001) Design of folded peptides. Chem. Rev. 101, 3131–3152.

    Article  PubMed  CAS  Google Scholar 

  5. Prasad, B. V. V. and Balaram, P. (1984) The stereochemistry of peptides containing a-aminoisobutyric acid. CRC Crit. Rev. Biochem. 16, 307–384.

    Article  PubMed  CAS  Google Scholar 

  6. Kaul, R. and Balaram, P. (1999) Stereochemical control of peptide folding. Bioorg. Med. Chem. 7, 105–117.

    Article  PubMed  CAS  Google Scholar 

  7. Allen, F. H. (2002) The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr. B58, 380–388.

    CAS  Google Scholar 

  8. Aravinda, S., Shamala, N., Roy, R. S., and Balaram, P. (2003) Non-protein amino acids in peptide design. Proc. Indian Acad. Sci. (Chem. Sci.) 115, 373–400.

    Article  CAS  Google Scholar 

  9. Smith, J. A. and Pease, L. G. (1980) Reverse turns in peptides and proteins. CRC Crit. Rev. Biochem. 8, 315–399.

    Article  PubMed  CAS  Google Scholar 

  10. Rose, G. D., Gierasch, L. M., and Smith, J. A. (1985) Turns in peptides and proteins. Adv. Protein Chem. 37, 1–109.

    Article  PubMed  CAS  Google Scholar 

  11. Venkatachalam, C. M. (1968) Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 6, 1425–1436.

    Article  PubMed  CAS  Google Scholar 

  12. Wilmot, C. M. and Thornton, J. M. (1988) Analysis and prediction of the different types of β-turn in proteins. J. Mol. Biol. 203, 221–232.

    Article  PubMed  CAS  Google Scholar 

  13. Sibanda, B. L. and Thornton, J. M. (1985) β-hairpin families in globular proteins Nature 316, 170–174.

    Article  PubMed  CAS  Google Scholar 

  14. Gunasekaran, K., Ramakrishnan, C., and Balaram, P. (1997) β-hairpins in proteins revisited: lessons for de novo design. Protein Eng. 10, 1131–1141.

    Article  PubMed  CAS  Google Scholar 

  15. Richardson, J. S. and Richardson, D. C. (1989) Principles and patterns of protein conformation, in Prediction of Protein Structure and the Principles of Protein Conformation (Fasman, G. D., ed.), Plenum, New York, pp. 1–98.

    Google Scholar 

  16. Srinivasan, N., Anuradha, V. S., Ramakrishnan, C., Sowdhamini, R., and Balaram, P. (1994) Conformational characteristics of asparaginyl residues in proteins. Int. J. Peptide Protein Res. 44, 112–122.

    Article  CAS  Google Scholar 

  17. Stigers, K. D., Soth, M. J., and Nowick, J. S. (1999) Designed molecules that fold to mimic protein secondary structures. Curr. Opin. Chem. Biol. 3, 714–723.

    Article  PubMed  CAS  Google Scholar 

  18. Toniolo, C., Bonora, G. M., Bavoso, A., Benedetti, E., di Blasio, B., Pavone, V., et al. (1983) Preferred conformations of peptides containing α,α-disubstituted α-amino acids. Biopolymers 22, 205–215.

    Article  CAS  Google Scholar 

  19. Karle, I. L. and Balaram, P. (1990) Structural characteristics of a-helical peptide molecules containing Aib residues. Biochemistry 29, 6747–6756.

    Article  PubMed  CAS  Google Scholar 

  20. Karle, I. L., Flippen-Anderson, J. L., Uma, K., and Balaram, P. (1990) Apolar peptide models for conformational heterogeneity, hydration, and packing of polypeptide helices: crystal structure of hepta-and octapeptides containing α-aminoisobutyric acid. Proteins 7, 62–73.

    Article  PubMed  CAS  Google Scholar 

  21. Karle, I. L., Flippen-Anderson, J. L., Uma, K., and Balaram, P. (1993) Unfolding of an α-helix in peptide crystals by solvation: conformational fragility in a heptapeptide. Biopolymers 33, 827–837.

    Article  PubMed  CAS  Google Scholar 

  22. Datta, S., Kaul, R., Rao, R. B., Shamala, N., and Balaram, P. (1997) Stereochemistry of linking segments in the design of helix-helix motifs in peptides. Crystallographic comparison of a glycyl-dipropylglycyl-glycyl segment in a tripeptide and a 14-residue peptide. J. Chem. Soc. Perkin Trans. 2, 1659–1664.

    Google Scholar 

  23. Karle, I. L., Flippen-Anderson, J. L., Uma, K., and Balaram, P. (1993) Peptide mimics for structural features in proteins. Crystal structures of three heptapeptide helices with a C-terminal 6→1 hydrogen bond. Int. J. Peptide Protein Res. 42, 401–410.

    Article  CAS  Google Scholar 

  24. Datta, S., Shamala, N., Banerjee, A., Pramanik, A., Bhattacharjya, S., and Balaram, P. (1997) Characterization of helix-terminating Schellman motifs in peptides. Crystal structure and nuclear Overhauser effect analysis of a synthetic hexapeptide helix. J. Am. Chem. Soc. 119, 9246–9251.

    Article  CAS  Google Scholar 

  25. Babu, M. M., Singh, S. K., and Balaram, P. (2002) A C-H-O hydrogen bond stabilized polypeptide chain reversal motif at the C-terminus helices in proteins. J. Mol. Biol. 322, 871–880.

    Article  Google Scholar 

  26. Banerjee, A., Raghothama, S., Karle, I. L., and Balaram, P. (1996) Ambidextrous molecules: cylindrical peptide structures formed by fusing left-and right-handed helices. Biopolymers 39, 279–285.

    Article  PubMed  CAS  Google Scholar 

  27. Karle, I. L. (2001) Controls exerted by the Aib residue: helix formation and helix reversal. Biopolymers (Pept. Sci.) 60, 351–365.

    Article  CAS  Google Scholar 

  28. Aravinda, S., Shamala, N., Desiraju, S., and Balaram, P. (2002) A right handed peptide helix containing a central double D-amino acid segment. Chem. Commun. 2454–2455.

    Google Scholar 

  29. Karle, I. L., Gopi, H. N., and Balaram, P. (2003) Crystal structure of a hydrophobic 19-residue peptide helix containing three centrally located D amino acids. Proc. Natl. Acad. Sci. USA 100, 13946–13951.

    Article  PubMed  CAS  Google Scholar 

  30. Awasthi, S. K., Raghothama, S., and Balaram, P. (1995) A designed β-hairpin peptide. Biochem. Biophys. Res. Commun. 216, 375–381.

    Article  PubMed  CAS  Google Scholar 

  31. Karle, I. L., Awasthi, S. K., and Balaram, P. (1996) A designed β-hairpin peptide in crystals. Proc. Natl. Acad. Sci. USA 93, 8189–8193.

    Article  PubMed  CAS  Google Scholar 

  32. Raghothama, S., Awasthi, S. K., and Balaram, P. (1998) β-hairpin nucleation by Pro-Gly β-turns. Comparison of D-Pro-Gly and L-Pro-Gly sequences in apolar octapeptides. J. Chem. Soc. Perkin Trans. 2, 137–143.

    Google Scholar 

  33. Das, C., Naganagowda, G. A., Karle, I. L., and Balaram, P. (2001) Designed β-hairpin peptides with defined tight turn stereochemistry. Biopolymers 58, 335–346.

    Article  PubMed  CAS  Google Scholar 

  34. Haque, T. S. and Gellman, S. H. (1997) Insights on β-hairpin stability in aqueous solution from peptides with enforced type I’ and type II’ β-turns. J. Am. Chem. Soc. 119, 2303–2304.

    Article  CAS  Google Scholar 

  35. Espinosa, J. F. and Gellman, S. H. (2000) A designed β-hairpin containing a natural hydrophobic cluster. Angew. Chem. Int. Ed. Engl. 39, 2330–33.

    Article  PubMed  CAS  Google Scholar 

  36. Stanger, H. E. and Gellman, S. H. (1998) Rules for antiparallel β-sheet design: D-Pro-Gly is superior to L-Asn-Gly for β-hairpin nucleation. J. Am. Chem. Soc. 120, 4236–4237.

    Article  CAS  Google Scholar 

  37. Aravinda, S., Harini, V. V., Shamala, N., Das, C., and Balaram, P. (2004) Structure and assembly of designed β-hairpin peptides in crystals as models for β-sheet aggregation. Biochemistry 43, 1832–1846.

    Article  PubMed  CAS  Google Scholar 

  38. Gellman, S. H. (1998) Minimal model systems for β-sheet secondary structure in proteins. Curr. Opin. Chem. Biol. 2, 717–725.

    Article  PubMed  CAS  Google Scholar 

  39. Blanco, F., Ramirez-Alvarado, M., and Serrano, L. (1998) Formation and stability of β-hairpin structures in polypeptides. Curr. Opin. Struct. Biol. 8, 107–111.

    Article  PubMed  CAS  Google Scholar 

  40. Aravinda, S., Shamala, N., Rai R., Gopi, H. N., and Balaram, P. (2002) A crystalline β-hairpin peptide nucleated by a type I’ Aib-D-Ala β-turn: evidence for crossstrand aromatic interactions. Angew. Chem. Int. Ed. Engl. 41, 3863–3865.

    Article  PubMed  CAS  Google Scholar 

  41. Harini, V. V., Aravinda, S., Rai, R., Shamala, N., and Balaram, P. (2005) Molecular conformation and packing of peptide β-hairpins in crystals. Structures of two synthetic octapeptides containing 1-aminocycloalkane-1-carboxylic acid residues at the i+2 position of the β-turn. Chem. Eur. J. In press.

    Google Scholar 

  42. Das, C., Raghothama, S., and Balaram, P. (1998) A designed three stranded β-sheet peptide. J. Am. Chem. Soc. 120, 5812–5813.

    Article  CAS  Google Scholar 

  43. Das, C., Raghothama, S., and Balaram, P. (1999) A four stranded β-sheet structure in a designed synthetic polypeptide. Chem. Commun. 967–968.

    Google Scholar 

  44. Venkatraman, J., Naganagowda, G. A., Sudha, R., and Balaram, P. (2001) De novo design of a five-stranded β-sheet anchoring a metal-ion binding site. Chem. Commun. 2660–2661.

    Google Scholar 

  45. Venkatraman, J., Naganagowda, G. A., and Balaram, P. (2002) Design and construction of an open multistranded β-sheet polypeptide stabilized by a disulfide bridge. J. Am. Chem. Soc. 124, 4987–4994.

    Article  PubMed  CAS  Google Scholar 

  46. Karle, I. L., Das, C., and Balaram, P. (2000) De novo protein design: crystallographic characterization of a synthetic peptide containing independent helical and hairpin domains. Proc. Natl. Acad. Sci. USA 97, 3034–3037.

    Article  PubMed  CAS  Google Scholar 

  47. Wallimann, P., Kennedy. R. J., Miller, J. S., Shalongo. W., and Kemp, D. S. (2003) Dual wavelength parametric test of two-state models for circular dichroism spectra of helical polypeptides: anomalous dichroic properties of alanine-rich peptides. J. Am. Chem. Soc. 125, 1203–1220.

    Article  PubMed  CAS  Google Scholar 

  48. Aravinda, S., Datta, S., Shamala, N., and Balaram, P. (2004) Hydrogen-bond lengths in polypeptide helices: no evidence for short hydrogen bonds. Angew. Chem. Int. Ed. Engl. 43, 6728–6731.

    Article  PubMed  CAS  Google Scholar 

  49. Mahalakshmi, R., Raghothama, S., and Balaram, P. (2006) NMR analysis of aromatic interactions in designed peptide β-haripins. J. Am. Chem. Soc. 128, 1125–1138.

    Article  PubMed  CAS  Google Scholar 

  50. Bunkoczi, G., Vertesy, L., and Sheldrick, G. M. (2005) The antiviral antibiotic Feglymycin: first direct-methods solution of a 1000+ equal-atom structure. Angew. Chem. Int. Ed. Engl. 44, 1340–1342.

    Article  PubMed  CAS  Google Scholar 

  51. Konnert, J., Karle, J., Karle, I. L., Uma, K., and Balaram, P. (1999) Isomorphous replacement combined with anomalous dispersion in the linear equations: applications to a crystal containing four nonapeptide conformers. Acta Crystallogr. D55, 448–457.

    CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India

    Radhakrishnan Mahalakshmi & Padmanabhan Balaram

Authors
  1. Radhakrishnan Mahalakshmi
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  2. Padmanabhan Balaram
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Editor information

Editors and Affiliations

  1. Département de Biologie Joliot–Curie CEA Saclay, Gif-sur-Yvette, France

    Raphael Guerois

  2. Merz Pharmaceuticals GmbH, Frankfurt am Main, Germany

    Manuela López de la Paz

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© 2006 Humana Press Inc.

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Mahalakshmi, R., Balaram, P. (2006). Non-Protein Amino Acids in the Design of Secondary Structure Scaffolds. In: Guerois, R., de la Paz, M.L. (eds) Protein Design. Methods in Molecular Biology, vol 340. Humana Press. https://doi.org/10.1385/1-59745-116-9:71

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  • DOI: https://doi.org/10.1385/1-59745-116-9:71

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-585-9

  • Online ISBN: 978-1-59745-116-1

  • eBook Packages: Springer Protocols

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