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Structure Prediction of CPPs and Iterative Development of Novel CPPs 211 TABLE 9.2 Internalization of Simulated Peptides as a Function of the Inner Sheet Superficial Charge Density Inner sheet charge (e – /Å 2 ) AntHD + DNA AntHD 1st helix 2nd helix pAntp No charge – – – – – 0.005 – – – – – 0.01 – – – – + 0.02 – – – – + 0.04 – ± ± + ++ The AntHD–DNA complex stabilizes when its mass center is located at a distance of 28 Å, where the minimum value of the total restraint is reached. This is closer to the bilayer than when this one is uncharged, due to the charge restraint, which tends to bring the complex close to the membrane. Nevertheless, there is no membrane insertion because the hydrophobic restraint increases, thus impairing any insertion. From 28 to 25 Å, the total restraint increases, suggesting that a localization of the complex close to the membrane is unlikely. The lipid perturbation restraint is low (maximum value: 8 kJ/mol.Å 2 ) compared with the other restraints. This is consistent since the complex only partially penetrates within the polar head domain; therefore, it does not disturb the acyl chains of the phospholipids. When the homeodomain is not associated with the DNA (Figure 9.9B), its mass center comes near the external bilayer leaflet because of the charge distribution in the internal leaflet. Here again, the hydrophilic and hydrophobic balance of the homeodomain prevents the crossing: the hydrophobic restraint is unfavorable from 28 Å and increases when the homeodomain mass center approaches the bilayer. The same graphics have been made for simulations of the isolated helices (Figure 9.9C, D, E, bottom). Moreover, in every helix we chose two reference atoms to draw a segment parallel to the helix axis. This allowed us to follow the evolution of the total restraint as a function of the positions of the mass center and of the angles of the helix axis vs. the bilayer plane center (Figure 9.9C, D, E, top). Now, considering each helix separately, it appears that, for the first helix, which is the less charged, the most probable position is reached when its mass center is located at 20 Å. When the mass center gets closer to the membrane both hydrophobic and charge restraints increase. At the energy minimum, the helix makes an angle of –5° (from the N-term to the C-term) with respect to the bilayer plane; several residues (Gln3, Leu7, Phe11) therefore enter within the polar heads domain (results not shown). For the second helix observations are similar, but the charge restraint is more favorable (this helix has a charge of +4.00). The mass center is then located at the external limit of the polar heads of the external leaflet (18 Å). Here again, hydrophobic restraint prevents the penetration of the second helix into the hydrophobic
212 Cell-Penetrating Peptides: Processes and Applications A B C (top) Total Restraints (kJ/mol Å 2 ) 1st Helix (inner leaflet charge: -0.02) Mass Center Penetration (Å) FIGURE 9.9 Evolution of the total restraint vs. mass center penetration of all simulated compounds in a charged bilayer model (inner leaflet charge: 0.02 e – /Å –2 ). (See text for details.) Angle(°)
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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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