Realistic modeling approaches of structure-function properties of CPPs in non-covalent complexes

Biochimica et Biophysica Acta - Biomembranes

Volumn 1798, Issue 12, 2010, Pages 2217-2222

  Thomas, Annick ^a   Lins, Laurence ^a   Divita, Gilles ^b   Brasseur, Robert ^a  

^a UNIVERSITY OF LIÈGE   (Belgium)

^b Centre National de la Recherche Scientifique   (France)

Author keywords

Arginine; Cargo; Complex; CPPs; Molecular modeling; Nanoparticle; Peptide disorder; Tryptophan

Indexed keywords

ARGININE; CELL PENETRATING PEPTIDE; NANOPARTICLE; PENETRATIN; PROTEGRIN; SMALL INTERFERING RNA; TIOPRONIN; TRANSACTIVATOR PROTEIN; TRANSPORTAN; UNCLASSIFIED DRUG; UVOMORULIN;

AMINO ACID SEQUENCE; COMPLEX FORMATION; COMPUTER MODEL; COVALENT BOND; GLYCOCALYX; MEMBRANE PERMEABILITY; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEIN TRANSPORT; REVIEW; THREE DIMENSIONAL IMAGING;

ANIMALS; CELL-PENETRATING PEPTIDES; COMPUTER SIMULATION; HUMANS; MODELS, MOLECULAR; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77958154021     PISSN: 00052736     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbamem.2010.02.020     Document Type: Review

References (52)

1. Heitz F., Morris M.C., Divita G. Twenty years of cell-penetrating peptides: from molecular mechanism to therapeutics. Br. J. Pharmacol. 2009, 157:195-206.
2. Thomas A., Deshayes S., Decaffmeyer M., Van Eyck M.-H., Charloteaux B., Brasseur R. Prediction of peptide structure: how far are we?. Proteins 2006, 65:889-897.
3. Uversky V.N., Oldfield C.J., Dunker A.K. Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu. Rev. Biophys. 2008, 37:215-246.
4. Alexandrescu A.., Kammerer R.A. Structure and disorder in the ribonuclease S-peptide probed by NMR residual dipolar couplings. Protein Sci. 2003, 12:2132-2140.
5. Mendoza-Espinosa A., Moreno A., Castillo R., Mas-Oliva J. Lipid dependant disorder-to-order conformational transitions in apolipoprotein CI derived peptides. Biochem. Biophys. Res. Commun. 2008, 365:8.
6. A. Thomas, B. Joris, R. Brasseur, Standardized evaluation of protein stability, Biochim Biophys Acta (in press), doi:10.1016/j.bbapap.2010.02.008.
7. Deshayes S., Decaffmeyer M., Brasseur R., Thomas A. Structural polymorphism of two CPP: an important parameter of activity. Biochim. Biophys. Acta Biomembr. 2008, 1778:1197-1205.
8. Lazaridis T. Binding affinity and specificity from computational studies. Curr. Org. Chem. 2002, 6:1319-1332.
9. Goldblum G.M. A novel energy-based stochastic model for positioning polar protons in protein structure from X-rays. Proteins 2000, 38:273-287.
10. Etchebest C., Benros C., Hazout S., de Brevern A.G. A structural alphabet for local protein structure: improved prediction methods. Proteins 2005, 59:810-827.
11. Leach J.R. Van der Waals interactions. Molecular Modelling: Principles and Applications 1996, 171-177. Addison-Wesley, Essex England. A.R. Leach (Ed.).
12. Lins L., Charloteaux B., Heinen C., Thomas A., Brasseur R. «De novo» design of peptides with specific lipid binding properties. Biophys. J. 2006, 90:470-479.
13. Brasseur R. Simulating the folding of small proteins using the local minimum energy and the free solvation energy yields native-like structures. J. Mol. Graph. Model. 1995, 13:312-322.
14. Brasseur R. Differentiation of lipid-associating helices by use of 3-dimensional molecular hydrophobicity potential calculations. J. Biol. Chem. 1991, 266:16120-16127.
15. R. Brasseur, Molecular Description of Biological Membrane Components by Computer Aided Conformational Analysis. R. Brasseur, editor, Vols. I-II. 1990 CRC PRSS, INC. 2000 Corporate Blvd., N.W., Boca Raton, Florida 33431.
16. Herce H.D., Garcia A.E. Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes. Proc. Natl. Acad. Sci. USA 2007, 104:20805-20810.
17. Yesylecskyy S., Marrink S.J., Mark A.E. Alternative mechanisms for the interaction of the cell-penetrating peptides Penetratin and the TAT peptide with lipid bilayers. Biophys. J. 2009, 97:40-49.
18. Brasseur R., Lorge P., Espion D., Goormaghtigh E., Burny A., Ruysschaert J.M. The mode of insertion of the paramyxovirus F1 N-terminus into lipid matrix, an initial step in host cell-virus fusion. Virus Genes 1988, 1:325-332.
19. Vonèche V., Portetelle D., Kettmann R., Willems L., Limbach K., Paoletti E., Ruysschaert J.M., Burny A., Brasseur R. Fusogenic segments of bovine leukemia virus and simian immunodeficiency virus are interchangeable and mediate fusion via oblique insertion in the lipid bilayer or their target cells. Proc. Natl. Acad. Sci. USA 1992, 89:3810-3814.
20. Thomas A., Brasseur R. Tilted peptides: the history. Curr. Protein Pept. Sci. 2006, 7:523-527.
21. Epand R.F., Thomas A., Brasseur R., Vishwanathan S.A., Hunter E., Epand R.M. Juxtamembrane protein segments that contribute to recruitment of cholesterol into domains. Biochemistry 2006, 45:6105-6114.
22. Snyder E.L., Dowdy S.F. Recent advances in the use of protein transduction domain for the delivery of peptides, proteins and nucleic acids in vivo. Expert. Opin. Drug Deliv. 2005, 2:43-51.
23. Schwarze S.R., Ho A., Vocero-Akbani A., Dowdy S.F. In vivo protein transduction: delivery of a biologically active protein into the mouse. Science 1999, 285:1569-1572.
24. Eguchi A., Meade B.R., Chang Y.C., Fredrickson C.T., Willert K., Puri N., Dowdy S.F. Efficient siRNA delivery into primary cells by a peptide transduction domain-dsRNA binding domain fusion protein. Nat. Biotechnol. 2009, 27:567-571.
25. Joliot A., Prochiantz A. Transduction peptides: from technology to physiology. Nat. Cell Biol. 2004, 6:189-196.
26. Pooga M., Soomets U., Hallbrink M., Valkna A., Saar K., Rezaei K. Cell penetrating PNA constructs regulate galanin receptor levels and modify pain transmission in vivo. Nat. Biotechnol. 1998, 16:857-861.
27. EL-Andaloussi, Johansson H., Magnusdottir A., Järver P., Lundberg P., Langel Ü. TP10, a delivery vector for decoy oligonucleotides targeting the Myc protein. J. Control. Release 2005, 110:189-201.
28. Elliott G., O'Hare P. Intercellular trafficking and protein delivery by a Herpes virus structural protein. Cell 1997, 88:223-233.
29. Morris M.C., Deshayes S., Heitz F., Divita G. Cell-penetrating peptides: from molecular mechanisms to therapeutics. Biol. Cell 2008, 100:201-217.
30. Crombez L., Morris M.C., Dufort S., Aldrian-Herrada G., Nguyen Q., Mc Master G., Coll J.L., Heitz F., Divita G. Targeting cyclin B1 through peptide-based delivery of siRNA prevents tumour growth. Nucleic Acids Res. 2009, 37:4559-4569.
31. Gros E., Deshayes S., Morris M.C., Aldrian-Herrada G., Depollier J., Heitz F. A non-covalent peptide-based strategy for protein and peptide nucleic acid delivery. Biochim. Biophys. Acta 2006, 1758:384-393.
32. Oehlke J., Lorenz D., Wiesner B., Bienert M. Studies on the cellular uptake of substance P and lysine-rich, KLA-derived model peptides. J. Mol. Recognit. 2005, 18:50-59.
33. Pujals S., Fernandez-Carneado J., Lopez-Iglesias C., Kogan M.J., Giralt E. Mechanistic aspects of CPP-mediated intracellular drug delivery: relevance of CPP self-assembly. Biochim. Biophys. Acta 2006, 1758:264-279.
34. Rittner K., Benavente A., Bompard-Sorlet A., Heitz F., Divita G., Brasseur R. New basic membrane-destabilizing peptides for plasmid-based gene delivery in vitro and in vivo. Mol. Ther. 2002, 5:104-114.
35. Wender P.A., Mitchell D.J., Pattabiraman K., Pelkey E.T., Steinman L., Rothbard J.B. The design, synthesis and evaluation of molecules that enable or enhance cellular uptake: peptoid molecular transporters. Proc. Natl. Acad. Sci. USA 2000, 97:13003-13008.
36. Futaki S., Suzuki T., Ohashi W., Yagami T., Tanaka S., Ueda K. Arginine-rich peptides, an abundant source of membrane permeable peptides having potential as carriers for intracellular protein delivery. J. Biol. Chem. 2001, 276:5836-5840.
37. Schmidt M.C., Rothen-Rutishauser B., Rist B., Beck-Sickinger A., Wunderli-Allenspach H., Rubas W. Translocation of human calcitonin in respiratory nasal epithelium is associated with self assembly in lipid membrane. Biochemistry 1998, 37:16582-16590.
38. Rousselle C., Smirnova M., Clair P., Lefauconnier J.M., Chavanieu A., Calas B. Enhanced delivery of doxorubicin into the brain via a peptide-vector-mediated strategy: saturation kinetics and specificity. J. Pharmacol. Exp. Ther. 2001, 296:124-131.
39. Elmquist A., Lindgren M., Bartfai T., Langel Ü. VE-cadherin-derived cell-penetrating peptide, pVEC, with carrier functions. Exp. Cell Res. 2001, 269:237-244.
40. Mano M., Teodósio C., Paiva A., Simões S., Pedroso de Lima M.C. On the mechanisms of the internalization of S4(13)-PV cell-penetrating peptide. Biochem. J. 2006, 390:603-612.
41. Lins L., Thomas A., Brasseur R. Analysis of accessible surface of residues in proteins. Protein Sci. 2003, 12:1406-1417.
42. Sakai N., Matile S. Anion-mediated transfer of polyarginine across lipid and bilayer membranes. J. Am. Chem. Soc. 2003, 125:14348-14356.
43. Ziegler A., Blatter X.L., Seelig A., Seelig J. Protein transduction domains of HIV-1 and SIV TAT interact with charged lipid vesicles binding mechanism and thermodynamic analysis. Biochemistry 2003, 42(30):9185-9194.
44. Ziegler A. Interaction of the protein transduction domain of HIV-1 TAT with heparan sulfate: binding mechanism and thermodynamic parameters. Biophys. J. 2004, 86:254-263.
45. K. Konate, L. Crombez, S. Deshayes, A. Thomas, R. Brasseur, M. Decaffmeyer, G. Aldrian-Herrada, F. Heitz, G. Divita, Insight into the cellular uptake mechanism of a secondary amphipathic cell penetrating peptide for siRNA delivery. (2010) in revision.
46. Crombez L., Aldrian-Herrada G., Konate K., Nguyen Q.N., McMaster G.K., Brasseur R., Heitz F., Divita G. A new potent secondary amphipathic cell-penetrating peptide for siRNA delivery into mammalian cells. Mol. Ther. 2009, 17(1):95-103.
47. Pooga M., Kut C., Kihlmark M., Hällbrink M., Fernaeus S., Raid R., Land T., Hallberg E., Bartfai T., Langel U. Cellular translocation of proteins by transportan. FASEB J. 2001, 15:1451-1453.
48. Meade B.R., Dowdy S.F. Enhancing the cellular uptake of siRNA duplexes following noncovalent packaging with protein transduction domain peptides. Adv. Drug Deliv. Rev. 2008, 60:530-536.
49. Simeoni F., Morris M.C., Heitz F., Divita G. Insight into the mechanism of the peptide-based gene delivery system MPG: implications for delivery of siRNA into mammalian cells. Nucleic Acids Res. 2003, 31:2717-2724.
50. Morris M.C., Depollier J., Mery J., Heitz F., Divita G. A peptide carrier for the delivery of biologically active proteins into mammalian cells. Nat. Biotechnol. 2001, 19:1173-1176.
51. Munoz M.A., Heitz F., Divita G., Morris M.C. The peptide carrier Pep-1 forms biologically efficient nanoparticle complexes. Biochem. Biophys. Res. Commun. 2007, 355:877-882.
52. Fotin-Mlecek M., Fischer R., Brock R. Endocytosis and cationic cell-penetrating peptides: a merger of concepts and methods: cell-penetrating peptides, mechanisms and applications. Curr. Pharm. Des. 2005, 11:3613-3628.