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FIGURE 9.7 (Color Figure 9.7 follows p. 14.) AntHD–DNA complex from 9ent (A) and its constitutive helices (B). Column C represents molecular hydrophobicity potentials of each helix. Structure Prediction of CPPs and Iterative Development of Novel CPPs 207
208 Cell-Penetrating Peptides: Processes and Applications hydrophobicity potential (MHP) (Figure 9.7.C) provides an idea about the hydrophobicity distribution. Figure 9.7.C shows the partition of the hydrophilic (green) and the hydrophobic (orange) areas for each of the homeodomain helices. All helices are amphiphilic. The hydrophilic and hydrophobic partition is balanced for the first helix; a first hydrophilic domain is made of Arg1, Tyr2, and Cys3, followed by an important hydrophobic domain flanking a next hydrophilic domain defined by Glu6, Glu8, Lys9, and Glu10. For the second helix, there is an evident segregation between a bulking hydrophilic domain (Arg1, Arg2, Arg3, and Arg4) and a C-terminal hydrophobic domain (Ile7, Ala8, Ala10, and Leu11). Finally, the penetratin helix (pAntp) has numerous hydrophilic domains spread all along the sequence. At the beginning of the sequence, one is due to Arg1 and Gln3. Then, a smaller hydrophilic domain is formed by the polar residues (Gln8, Asn9); charged residues are defining an important hydrophilic domain at the pAntp C-terminal extremity (Lys13, Lys15, and Lys16). An important hydrophobic domain is contributed by Trp6 and Phe7. 9.3.2.1 Uncharged Membrane Model Figure 9.8 shows the Monte Carlo simulation results obtained for AntHD–DNA, AntHD, and the three homeodomain helices. The graph in the middle of the figure shows evolution of the global energetic restraint (hydrophobic and lipid perturbation restraints are summed) for each molecule or complex as a function of their mass center penetration Z ordinate. The two dotted lines mark the boundary of the phospholipid polar heads of the membrane external leaflets (between 18 and 13.5 Å) and the bilayer center corresponds to the 0 Å Z ordinate. The simulations were started with the molecule mass center located at 35 Å. At the end of the calculation, the lowest value of global energy restraint indicates the most probable position of the molecules in the bilayer. Therefore, it is revealed from simulations that the AntHD–DNA complex stabilizes when its mass center is located at 34.5 Å from the bilayer center. When it approaches the bilayer, the energy restraint slowly, then severely, increases as the complex reaches 28.5 Å. Closer to the membrane, the restraint values are tremendous; the Monte Carlo procedure predicts that the complex cannot enter the bilayer. A similar profile is obtained for the homeodomain alone, even if the energy restraint is higher. The AntHD stabilizes at almost the same position as it does when in the AntHD–DNA complex (i.e., 27.5 Å). If the energy restraint evolution curves for AntHD–DNA and AntHD penetrations are similar, the position of each subdomain (Figure 9.8A and 9.8B) are different at the restraint minimum value: for the AntHD–DNA complex, the third helix is in interaction with the double-strand DNA, and the other two helices, especially the first one (Figure 9.8C) are near the external sheet phospholipid polar heads. Conversely, when the DNA is removed, the third helix is close to the phospholipid heads; the other helices lie more distantly. This preferential interaction between the third helix and the phospholipids may be attributed to its amphiphilicity. In order to go further in our analysis and to evaluate the contribution of each helix to interaction with the bilayer and, even more, to provide a model for penetratin
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CELL- PENETRATING PEPTIDES Processe
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Pharmacology and Toxicology: Basic
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Library of Congress Cataloging-in-P
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to the handbook are prominent resea
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REFERENCES 1. Green, M. and Loewens
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Contributors Mats Andersson Microbi
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Erin T. Pelkey Department of Chemis
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Contents Section I Classes of Cell-
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Chapter 16 Cell-Penetrating Peptide
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The Tat-Derived Cell-Penetrating Pe
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24 Cell-Penetrating Peptides: Proce
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3 Transportans Margus Pooga, Mattia
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Transportans 55 Indeed, galparan is
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Transportans 57 especially the endo
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Transportans 59 In the penetration
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Transportans 61 A 21-mer antisense
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Transportans 63 Commonly, the prote
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Transportans 65 antibiotin antibodi
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Transportans 67 For cross-linking o
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Transportans 69 and still retain ef
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Model Amphipathic Peptides 73 its D
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Model Amphipathic Peptides 75 pmol/
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TABLE 4.1 Internalization of Peptid
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TABLE 4.2 Internalization of Peptid
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Model Amphipathic Peptides 81 relat
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Model Amphipathic Peptides 87 A cat
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Model Amphipathic Peptides 89 At th
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Model Amphipathic Peptides 91 16. H
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Signal Sequence-Based Cell-Penetrat
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116 Cell-Penetrating Peptides: Proc
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Page 186 and 187: Interactions of Cell-Penetrating Pe
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Page 210 and 211: Structure Prediction of CPPs and It
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Page 268 and 269: Toxicity and Side Effects of Cell-P
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Toxicity and Side Effects of Cell-P
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Kinetics of Uptake of Cell-Penetrat
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Cell-Penetrating Peptide Conjugatio
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FIGURE 15.9 (Color Figure 15.9 foll
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Cell-Penetrating Peptides as Vector
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TABLE 16.1 Examples of Transport of
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CPP 2 Cargo or mRNA CAP Antisense A
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Microbial Membrane-Permeating Pepti
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Index A Abaecin, 129 Abz radiolabel
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Index 399 Diffraction, 168 Disulphi
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Index 401 structure prediction, 187
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Index 403 pRB proteins, Tat-E1A bin
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Index 405 lipid perturbation (secon
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