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Structure Prediction of CPPs and Iterative Development of Novel CPPs 199 of 200,000 × 27 = 5,400,000 cells. In Figure 9.4B, we plotted all values of the total energetic restraint of a molecule as a function of the position of its mass center during the simulation. In order to facilitate the analysis, a subsequent treatment of these huge files is applied. Since Monte Carlo is a minimization procedure, only the minimum values of the restraints need to be taken into consideration (gray points, Figure 9.4B); their extraction is carried out within a range of the mass center penetration (between +30 and –30 Å in this case). Between these two limits, a resolution step (0.5 Å in this case) is defined and we extract the lowest value of the energetic constraint within each 0.5 Å step (Figure 9.4C). The results can also be plotted in three dimensions. In this case, each axis stands for a parameter of interest. As an example, Figure 9.4D shows evolution of the total energy restraint as a function of the mass center penetration of a molecule and as a function of its angle regarding the bilayer normal. As an alternative we also looked for the envelope minima corresponding to the energy for the mass center penetration axis (between +30 and –30 Å with a step of 0.5 Å) and for the angle between the molecule and the bilayer normal axis (between 0 and 180° with a step of 3°), defining a two-dimensional mesh (Figure 9.4E). 9.2.8 MOLECULAR HYDROPHOBICITY POTENTIAL (MHP) MHP is a three-dimensional plot of the potential of hydrophobicity of a molecule in order to visualize its amphipathy. Molecules and MHPs are drawn with Win- MGM. 53 The hydrophobicity of a molecule is calculated using its partition coefficient between water and octanol. In order to visualize the amphipathy, a three-dimensional molecular plot of hydrophobicity was proposed by Fauchère et al. 47 for small molecules. The MHP approach was then extended to plot the surface of the isopotential contours of larger molecules. 35 We postulate that the hydrophobicity induced by an atom i and measured at a point M of space decreases exponentially with the distance between this point M and the surface of atom i. The molecular hydrophobicity potential at a point M in space is thus estimated according to the equation: N MHP = ∑ E r −d exp M tri i i i= 1 ( ) where N are all the atoms of the molecule, E tri is the transfer energy of the atom i, r i is the radius of the atom i, and d i is the distance between the atom i and the point M. E tri is the energy required to transfer an atom i from an hydrophobic to an hydrophilic medium. Atomic E tri were calculated from the molecular E tr compiled by Tanford, 54 assuming that molecular E tr are the sum of the atomic E tr. Atomic E tr values were derived for seven different types of atoms. The isopotential surfaces of protein hydrophobicity were then calculated by a cross-sectional computational method. A 1-Å-mesh-grid plane was set to sweep across the molecule by steps of 1 Å. At each step, the sum of the hydrophobicity
A FIGURE 9.4 Pex file example (top) and graphic representation (bottom). (See text for details.) 200 Cell-Penetrating Peptides: Processes and Applications
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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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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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