Advertisement

Fluorination in the Design of Membrane Protein Assemblies

  • Vijay M. Krishnamurthy
  • Krishna Kumar
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1063)

Abstract

Protein design approaches based on the binary patterning of nonpolar and polar amino acids have been successful in generating native-like protein structures of amphiphilic α-helices or idealized amphiphilic β-strands in aqueous solution. Such patterning is not possible in the nonpolar environment of biological membranes, precluding the application of conventional approaches to the design of membrane proteins that assemble into discrete aggregates. This review surveys a promising, new strategy for membrane protein design that exploits the unique properties of fluorocarbons—in particular, their ability to phase separate from both water (due to their hydrophobicity) and hydrocarbons (due to their lipophobicity)—to generate membrane protein assemblies. The ability to design such discrete assemblies should enable the disruption of protein-protein interactions and provide templates for novel biomaterials and therapeutics.

Key words

Fluorine Fluorocarbon Membrane Aggregate Oligomer Assembly Coiled coil Alpha-helix Beta-sheet Antimicrobial peptide 

References

  1. 1.
    Almén MS, Nordström KJV, Fredriksson R et al (2009) Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biol 7:50PubMedCrossRefGoogle Scholar
  2. 2.
    Lunn CA (2012) Membrane proteins as drug targets. Academic, LondonGoogle Scholar
  3. 3.
    Bowie JU (2005) Solving the membrane protein folding problem. Nature 438:581–589PubMedCrossRefGoogle Scholar
  4. 4.
    Walters RFS, DeGrado WF (2006) Helix-packing motifs in membrane proteins. Proc Natl Acad Sci USA 103:13658–13663PubMedCrossRefGoogle Scholar
  5. 5.
    Yin H, Slusky JS, Berger BW et al (2007) Computational design of peptides that target transmembrane helices. Science 315:1817–1822PubMedCrossRefGoogle Scholar
  6. 6.
    Caputo GA, Litvinov RI, Li W et al (2008) Computationally designed peptide inhibitors of protein-protein interactions in membranes. Biochemistry 47:8600–8606PubMedCrossRefGoogle Scholar
  7. 7.
    Choma C, Gratkowski H, Lear JD et al (2000) Asparagine-mediated self-association of a model transmembrane helix. Nat Struct Biol 7:161–166PubMedCrossRefGoogle Scholar
  8. 8.
    DeGrado WF, Gratkowski H, Lear JD (2003) How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. Protein Sci 12:647–665PubMedCrossRefGoogle Scholar
  9. 9.
    Zhou FX, Cocco MJ, Russ WP et al (2000) Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nat Struct Biol 7:154–160PubMedCrossRefGoogle Scholar
  10. 10.
    Therien AE, Grant FEM, Deber CM (2001) Interhelical hydrogen bonds in the CFTR membrane domain. Nat Struct Biol 8:597–601PubMedCrossRefGoogle Scholar
  11. 11.
    Kamtekar S, Schiffer JM, Xiong H et al (1993) Protein design by binary patterning of polar and nonpolar amino-acids. Science 262:1680–1685PubMedCrossRefGoogle Scholar
  12. 12.
    Rees DC, DeAntonio L, Eisenberg D (1989) Hydrophobic organization of membrane-proteins. Science 245:510–513PubMedCrossRefGoogle Scholar
  13. 13.
    Bilgiçer B, Fichera A, Kumar K (2001) A coiled coil with a fluorous core. J Am Chem Soc 123:4393–4399PubMedCrossRefGoogle Scholar
  14. 14.
    Tang Y, Ghirlanda G, Vaidehi N et al (2001) Stabilization of coiled-coil peptide domains by introduction of trifluoroleucine. Biochemistry 40:2790–2796PubMedCrossRefGoogle Scholar
  15. 15.
    Son S, Tanrikulu IC, Tirrell DA (2006) Stabilization of bzip peptides through incorporation of fluorinated aliphatic residues. ChemBioChem 7:1251–1257PubMedCrossRefGoogle Scholar
  16. 16.
    Lee K-H, Lee H-Y, Slutsky MM et al (2004) Fluorous effect in proteins: de novo design and characterization of a four-alpha-helix bundle protein containing hexafluoroleucine. Biochemistry 43:16277–16284PubMedCrossRefGoogle Scholar
  17. 17.
    Lee H-Y, Lee K-H, Al-Hashimi HM et al (2006) Modulating protein structure with fluorous amino acids: increased stability and native-like structure conferred on a 4-helix bundle protein by hexafluoroleucine. J Am Chem Soc 128:337–343PubMedCrossRefGoogle Scholar
  18. 18.
    Buer BC, de la Salud-Bea R, Al-Hashimi HM et al (2009) Engineering protein stability and specificity using fluorous amino acids: the importance of packing effects. Biochemistry 48:10810–10817PubMedCrossRefGoogle Scholar
  19. 19.
    Buer BC, Meagher JL, Stuckey JA et al (2012) Structural basis for the enhanced stability of highly fluorinated proteins. Proc Natl Acad Sci USA 109:4810–4815PubMedCrossRefGoogle Scholar
  20. 20.
    Bilgiçer B, Xing X, Kumar K (2001) Programmed self-sorting of coiled coils with leucine and hexafluoroleucine cores. J Am Chem Soc 123:11815–11816PubMedCrossRefGoogle Scholar
  21. 21.
    Bilgiçer B, Kumar K (2002) Synthesis and thermodynamic characterization of self-sorting coiled coils. Tetrahedron 58:4105–4112CrossRefGoogle Scholar
  22. 22.
    Gottler LM, de la Salud-Bea R, Marsh ENG (2008) The fluorous effect in proteins: properties of alpha F-4(6), a 4-alpha-helix bundle protein with a fluorocarbon core. Biochemistry 47:4484–4490PubMedCrossRefGoogle Scholar
  23. 23.
    Bilgiçer B, Kumar K (2004) De novo design of defined helical bundles in membrane environments. Proc Natl Acad Sci USA 101: 15324–15329PubMedCrossRefGoogle Scholar
  24. 24.
    Naarmann N, Bilgiçer B, Meng H et al (2006) Fluorinated interfaces drive self-association of transmembrane α helices in lipid bilayers. Angew Chem Int Ed 45:2588–2591CrossRefGoogle Scholar
  25. 25.
    Scott RL (1948) The solubility of fluorocarbons. J Am Chem Soc 70:4090–4093PubMedCrossRefGoogle Scholar
  26. 26.
    Hildebrand JH, Cochran D (1949) Liquid-liquid solubility of perfluoromethylcyclohexane with benzene, carbon tetrachloride, chlorobenzene, chloroform and toluene. J Am Chem Soc 71:22–25CrossRefGoogle Scholar
  27. 27.
    Dunitz JD (2004) Organic fluorine: odd man out. ChemBioChem 5:614–621PubMedCrossRefGoogle Scholar
  28. 28.
    Muir TW (2003) Semisynthesis of proteins by expressed protein ligation. Annu Rev Biochem 72:249–289PubMedCrossRefGoogle Scholar
  29. 29.
    Muralidharan V, Muir TW (2006) Protein ligation: an enabling technology for the biophysical analysis of proteins. Nat Methods 3:429–438PubMedCrossRefGoogle Scholar
  30. 30.
    Montclare JK, Son S, Clark GA et al (2009) Biosynthesis and stability of coiled-coil peptides containing (2 S,4 R)-5,5,5-trifluoroleucine and (2 S,4 S)-5,5,5-trifluoroleucine. ChemBioChem 10:84–86PubMedCrossRefGoogle Scholar
  31. 31.
    Wang P, Fichera A, Kumar K et al (2004) Alternative translations of a single RNA message: an identity switch of (2S,3R)-4,4,4-trifluorovaline between valine and isoleucine codons. Angew Chem Int Ed 43: 3664–3666CrossRefGoogle Scholar
  32. 32.
    Lupas AN, Gruber M (2005) The structure of α-helical coiled coils. Adv Protein Chem 70: 37–38PubMedCrossRefGoogle Scholar
  33. 33.
    Woolfson DN (2005) The design of coiled-coil structures and assemblies. Adv Protein Chem 70:79–112PubMedCrossRefGoogle Scholar
  34. 34.
    Harbury PB, Zhang T, Kim PS et al (1993) A switch between 2-stranded, 3-stranded and 4-stranded coiled coils in Gcn4 leucine-zipper mutants. Science 262:1401–1407PubMedCrossRefGoogle Scholar
  35. 35.
    Acharya A, Ruvinov SB, Gal J et al (2002) A heterodimerizing leucine zipper coiled coil system for examining the specificity of a position interactions: amino acids I, V, L, N, A, and K. Biochemistry 41:14122–14131PubMedCrossRefGoogle Scholar
  36. 36.
    Mecinovic J, Snyder PW, Mirica KA et al (2011) Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the “hydrophobic wall” of carbonic anhydrase. J Am Chem Soc 133:14017–14026PubMedCrossRefGoogle Scholar
  37. 37.
    Curran DP (2001) Fluorous reverse phase silica gel. A new tool for preparative separations in synthetic organic and organofluorine chemistry. Synlett 9:1488–1496CrossRefGoogle Scholar
  38. 38.
    Horvath IT, Rabai J (1994) Facile catalyst separation without water—fluorous biphase hydroformylation of olefins. Science 266: 72–75PubMedCrossRefGoogle Scholar
  39. 39.
    Hancock REW, Sahl H-G (2006) Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat Biotechnol 24: 1551–1557PubMedCrossRefGoogle Scholar
  40. 40.
    Marr AK, Gooderham WJ, Hancock REW (2006) Antibacterial peptides for therapeutic use: obstacles and realistic outlook. Curr Opin Pharmacol 6:468–472PubMedCrossRefGoogle Scholar
  41. 41.
    Zasloff M (2002) Antimicrobial peptides of multicellular organisms. Nature 415:389–395PubMedCrossRefGoogle Scholar
  42. 42.
    Tossi A, Sandri L, Giangaspero A (2000) Amphipathic, alpha-helical antimicrobial peptides. Biopolymers 55:4–30PubMedCrossRefGoogle Scholar
  43. 43.
    Niemz A, Tirrell DA (2001) Self-association and membrane-binding behavior of melittins containing trifluoroleucine. J Am Chem Soc 123:7407–7413PubMedCrossRefGoogle Scholar
  44. 44.
    Meng H, Kumar K (2007) Antimicrobial activity and protease stability of peptides containing fluorinated amino acids. J Am Chem Soc 129:15615–15622PubMedCrossRefGoogle Scholar
  45. 45.
    Gottler LM, Lee H-Y, Shelburne CE et al (2008) Using fluorous amino acids to modulate the biological activity of an antimicrobial peptide. ChemBioChem 9:370–373PubMedCrossRefGoogle Scholar
  46. 46.
    Gottler LM, de la Salud-Bea R, Shelburne CE et al (2008) Using fluorous amino acids to probe the effects of changing hydrophobicity on the physical and biological properties of the beta-hairpin antimicrobial peptide protegrin-1. Biochemistry 47:9243–9250PubMedCrossRefGoogle Scholar
  47. 47.
    Hellmann N, Schwarz G (1998) Peptide-liposome association. A critical examination with mastoparan-X. Biochim Biophys Acta 1369:267–277PubMedCrossRefGoogle Scholar
  48. 48.
    Daniels DS, Petersson EJ, Qiu JX et al (2007) High-resolution structure of a beta-peptide bundle. J Am Chem Soc 129:1532–1533PubMedCrossRefGoogle Scholar
  49. 49.
    Molski MA, Goodman JL, Craig CJ et al (2010) beta-peptide bundles with fluorous cores. J Am Chem Soc 132:3658–3659PubMedCrossRefGoogle Scholar
  50. 50.
    Barton AFM (1991) CRC handbook of solubility parameters and other cohesion parameters. CRC, Boca Raton, FLGoogle Scholar
  51. 51.
    Bates FS, Wignall GD, Koehler WC (1985) Critical behavior of binary liquid mixtures of deuterated and protonated polymers. Phys Rev Lett 55:2425–2428PubMedCrossRefGoogle Scholar
  52. 52.
    Hildebrand JH, Scott RL (1949) Solubility of non-electrolytes, 3rd edn. Reinhold, New York, NYGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Vijay M. Krishnamurthy
    • 1
  • Krishna Kumar
    • 1
    • 2
  1. 1.Department of ChemistryTufts UniversityMedfordUSA
  2. 2.Cancer Center, Tufts Medical CenterBostonUSA

Personalised recommendations