Structure prediction of cpps and iterative development of novel CPPs

Cell-Penetrating Peptides: Processes and Applications

Volumn , Issue , 2002, Pages 187-222

  Bouffioux, Olivier ^a   Basyn, Frédéric ^a   Rezsohazy, René ^b   Brasseur, Robert ^a  

^a UNIVERSITY OF LIÈGE   (Belgium)

^b UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0013094825     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (69)

1. Banerjee-Basu, S., Ryan, J.F., and Baxevanis, A.D., The homeodomain resource: a prototype database for a large protein family, Nucleic Acids Res., 28, 329, 2000.
2. Krumlauf, R., Hox genes in vertebrate development, Cell, 78, 191, 1994.
3. Wolberger, C., Homeodomain interactions, Curr. Opin. Struct. Biol., 6, 62, 1996.
4. Passner, J.M. et al., Structure of a DNA-bound ultrabithorax-extradenticle homeodomain complex, Nature, 397, 714, 1999.
5. Piper, D.E. et al., Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation, Cell, 96, 587, 1999.
6. Niessing, D. et al., Homeodomain position 54 specifies transcriptional vs. translational control by Bicoid, Mol. Cell, 5, 395, 2000.
7. Schnabel, C.A. and Abate-Shen, C., Repression by HoxA7 is mediated by the homeodomain and the modulatory action of its N-terminal-arm residues, Mol. Cell Biol., 16, 2678, 1996.
8. Zhang, H., Catron, K.M., and Abate-Shen, C., A role for the Msx-1 homeodomain in transcriptional regulation: residues in the N-terminal arm mediate TATA binding protein interaction and transcriptional repression, Proc. Natl. Acad. Sci. U.S.A., 93, 1764, 1996.
9. Zhang, N. et al., Three distinct domains in the HOX-11 homeobox oncoprotein are required for optimal transactivation, Oncogene, 13, 1781, 1996.
10. Kim, Y.H. et al., Homeodomain-interacting protein kinases, a novel family of corepressors for homeodomain transcription factors, J. Biol. Chem, 273, 25875, 1998.
11. Li, X., Murre, C., and McGinnis, W., Activity regulation of a Hox protein and a role for the homeodomain in inhibiting transcriptional activation, EMBO J., 18, 198, 1999.
12. Zappavigna, V. et al., HMG1 interacts with HOX proteins and enhances their DNA binding and transcriptional activation, EMBO J., 15, 4981, 1996.
13. Zappavigna, V., Sartori, D., and Mavilio, F., Specificity of HOX protein function depends on DNA-protein and protein-protein interactions, both mediated by the homeodomain, Genes Dev., 8, 732, 1994.
14. Ohneda, K. et al., The homeodomain of PDX-1 mediates multiple protein-protein interactions in the formation of a transcriptional activation complex on the insulin promoter, Mol. Cell Biol., 20, 900, 2000.
15. Zhang, H. et al., Heterodimerization of Msx and Dlx homeoproteins results in functional antagonism, Mol. Cell Biol., 17, 2920, 1997.
16. Le Roux, I. et al., Neurotrophic activity of the Antennapedia homeodomain depends on its specific DNA-binding properties, Proc. Natl. Acad. Sci. U.S.A., 90, 9120, 1993.
17. Derossi, D. et al., The third helix of the Antennapedia homeodomain translocates through biological membranes, J. Biol. Chem, 269, 10444, 1994.
18. Joliot, A. et al., Identification of a signal sequence necessary for the unconventional secretion of engrailed homeoprotein, Curr. Biol., 8, 856, 1998.
19. Maizel, A. et al., A short region of its homeodomain is necessary for engrailed nuclear export and secretion, Development, 126, 3183, 1999.
20. Chatelin, L. et al., Transcription factor hoxa-5 is taken up by cells in culture and conveyed to their nuclei, Mech. Dev., 55, 111, 1996.
21. Prochiantz, A., Messenger proteins: homeoproteins, TAT and others, Curr. Opin. Cell Biol., 12, 400, 2000.
22. Derossi, D. et al., Cell internalization of the third helix of the Antennapedia homeodomain is receptor-independent, J. Biol. Chem, 271, 18188, 1996.
23. Berlose, J.P. et al., Conformational and associative behaviours of the third helix of antennapedia homeodomain in membrane-mimetic environments, Eur. J. Biochem., 242, 372, 1996.
24. Drin, G. et al., Physico-chemical requirements for cellular uptake of pAntp peptide. Role of lipid-binding affinity, Eur. J. Biochem., 268, 1304, 2001.
25. Scheller, A. et al., Evidence for an amphipathicity independent cellular uptake of amphipathic cell-penetrating peptides, Eur. J. Biochem., 267, 6043, 2000.
26. Pooga, M. et al., Cell penetration by transportan, FASEB J., 12, 67, 1998.
27. Pooga, M. et al., Cell penetrating PNA constructs regulate galanin receptor levels and modify pain transmission in vivo, Nat. Biotechnol., 16, 857, 1998.
28. Prochiantz, A., Getting hydrophilic compounds into cells: lessons from homeopeptides, Curr. Opin. Neurobiol., 6, 629, 1996.
29. Schwarze, S.R., Hruska, K.A., and Dowdy, S.F., Protein transduction: unrestricted delivery into all cells? Trends Cell Biol., 10, 290, 2000.
30. Williams, E.J. et al., Selective inhibition of growth factor-stimulated mitogenesis by a cell-permeable Grb2-binding peptide, J. Biol. Chem, 272, 22349, 1997.
31. Ducarme, P., Rahman, M., and Brasseur, R., IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies, Proteins, 30, 357, 1998.
32. La Rocca, P., Shai, Y., and Sansom, M.S., Peptide-bilayer interactions: simulations of dermaseptin B, an antimicrobial peptide, Biophys. Chem., 76, 145, 1999.
33. Vogt, B. et al., The topology of lysine-containing amphipathic peptides in bilayers by circular dichroism, solid-state NMR, and molecular modeling, Biophys. J., 79, 2644, 2000.
34. Lins, L. and Brasseur, R., The hydrophobic effect in protein folding, FASEB J., 9, 535, 1995.
35. Basyn, F. et al., Prediction of membrane protein orientation in lipid bilayer: a theoretical approach, J. Mol. Graph. Model., 20, 235, 2001.
36. Wiener, M.C. and White, S.H., Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure, Biophys. J., 61, 437, 1992.
37. Bradshaw, J.P. et al., Oblique membrane insertion of viral fusion peptide probed by neutron diffraction, Biochemistry, 39, 6581, 2000.
38. Saiz, L. and Klein, M.L., Structural properties of a highly polyunsaturated lipid bilayer from molecular dynamics simulations, Biophys. J., 81, 204, 2001.
39. Sankararamakrishnan, R. and Weinstein, H., Molecular dynamics simulations predict a tilted orientation for the helical region of dynorphin A(1-17) in dimyristoylphosphatidylcholine bilayers, Biophys. J., 79, 2331, 2000.
40. Milik, M. and Skolnick, J., Insertion of peptide chains into lipid membranes: an offlattice Monte Carlo dynamics model, Proteins, 15, 10, 1993.
41. White, S.H., Hydropathy plots and the prediction of membrane topology, in Membrane Protein Structure: Experimental Approaches, White, S.H., Eds., Oxford University Press, New York, 1994.
42. Popot, J.L., De Vitry, C., and Atteia, A., Folding and assembly of integral membrane proteins: an introduction, in Membrane Protein Structure: Experimental Approaches, White, S.H., Eds., Oxford University Press, New York, 2001.
43. Shrake, A. and Rupley J.A., Environment and exposure to solvent of proteins atoms. Lysozyme and insulin, J. Mol. Biol., 79, 351, 1973.
44. Flower, D.R., SERF: a program for accessible surface area calculations, J. Mol. Graph. Model., 15, 238, 1997.
45. Brasseur, R., Differentiation of lipid-associating helices by use of three- dimensional molecular hydrophobicity potential calculations, J. Biol. Chem., 266, 16120, 1991.
46. Eisenberg, D. and McLachlan, A.D., Solvation energy in protein folding and binding, Nature, 319, 199, 1986.
47. Fauchère, J.L. and Pliska, V., Hydrophobicity parameter π of amino acid side chains from the partitioning of N-acetyl-amino-acid-amides, Eur. J. Med. Chem, 18, 369, 1983.
48. Rees, D.C. et al., Membrane protein structure and stability: implications of the first crystallographic analysis, in Membrane Protein Structure: Experimental Approaches, White, S.H., Ed., Oxford University Press, New York, 1994.
49. Heller, H., Shaefer, M., and Shulten, K., Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase, J. Phys. Chem., 97, 8343, 1993.
50. Flewelling, R.F. and Hubbell, W.L., The membrane dipole potential in a total membrane potential model. Applications to hydrophobic ion interactions with membranes, Biophys. J., 49, 541, 1986.
51. Press, W.H. et al., Numerical recipes in FORTRAN, in The Art of Scientific Computing, Cambridge University Press, 1992.
52. Thomas, A. et al., Pex, analytical tools for PDB files. I. GF-Pex: basic file to describe a protein, Proteins, 43, 28, 2001.
53. Rahman, M. and Brasseur, R., WinMGM: a fast CPK molecular graphics program for analyzing molecular structure, J. Mol. Graph., 12, 212, 1994.
54. Tanford, C., The Hydrophobic Effect: Formation of Micelles and Biological Membranes, 1st ed., John Wiley & Sons, New York, 1973.
55. Lins, L. et al., Computational study of lipid-destabilizing protein fragments: towards a comprehensive view of tilted peptides, Proteins, 44, 435, 2001.
56. Lund-Katz, S. et al., Nuclear magnetic resonance investigation of the interactions with phospholipid of an amphipathic alpha-helix-forming peptide of the apolipoprotein class, J. Biol. Chem., 265, 12217, 1990.
57. Kersh, G.J., Tomich, J.M., and Montal, M., The M2 delta transmembrane domain of the nicotinic cholinergic receptor forms ion channels in human erythrocyte membranes, Biochem. Biophys. Res. Commun., 162, 352, 1989.
58. Martin, I. et al., Fusogenic activity of SIV (simian immunodeficiency virus) peptides located in the GP32 NH2 terminal domain, Biochem. Biophys. Res. Commun., 175, 872, 1991.
59. Ducarme, P., Thomas, A., and Brasseur, R., The optimisation of the helix/helix interaction of a transmembrane dimer is improved by the IMPALA restraint field, Biochim. Biophys. Acta, 1509, 148, 2000.
60. Henderson, R. and Unwin, P.N., Three-dimensional model of purple membrane obtained by electron microscopy, Nature, 257, 28, 1975.
61. Luecke, H., Richter, H.T., and Lanyi, J.K., Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution, Science, 280, 1934, 1998.
62. Popot, J.-L., De Vitry, C., and Atteia, A., Folding and assembly of integral membrane proteins: an introduction, in Membrane Protein Structure: Experimental Approaches, Oxford University Press, White, S.H., Ed., New York, 1994, chap. 3.
63. Kuhlbrandt, W. and Gouaux, E., Membrane proteins, Curr. Opin. Struct. Biol., 9, 445, 1999.
64. Buchanan, S.K., Beta-barrel proteins from bacterial outer membranes: structure, function and refolding [see comments], Curr. Opin. Struct. Biol., 9, 455, 1999.
65. Wang, Y.F. et al., Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin, J. Mol. Biol., 272, 56, 1997.
66. Fraenkel, E. and Pabo, C.O., Comparison of x-ray and NMR structures for the Antennapedia homeodomain-DNA complex, Nat. Struct. Biol., 5, 692, 1998.
67. Cullis, P.R., Fenske, D.B., and Hope, M.J., Physical properties and functional roles of lipids in membranes, in Biochemistry of Lipids Lipoproteins and Membranes, Vance, D.E. and Vance, J., Eds., Elsevier, Amsterdam, 1996, chap. 1.
68. Lindberg, M. and Graslund, A., The position of the cell penetrating peptide penetratin in SDS micelles determined by NMR, FEBS Lett., 497, 39, 2001.
69. Magzoub, M. et al., Interaction and structure induction of cell-penetrating peptides in the presence of phospholipid vesicles, Biochim. Biophys. Acta, 1512, 77, 2001.