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Index 403 pRB proteins, Tat-E1A binding of, 370 Predictive and proteome analyses, 310–313 artificial neural network-based methods, 311–312 global structure-based methods, 312–313 prediction algorithms, 310 from proteome to secretome, 313 weight matrix methods, 311 Proline-rich peptides as translocating, 130 Protein fibroblast growth factor-1 (FGF-1), 119 Proteins, transportan and, 61–66 Protein transport, 365–375 delivery of PTD-conjugated macromolecules, 369–373 applications in cell culture, 369–371 applications in vivo, 371–373 development of PTD fusion proteins, 367–369 cloning and purification of Tat fusion proteins, 368–369 principles of protein transduction, 365–366 protein transduction technology, 366–367 Proteome analyses, 310–313 artificial neural network-based methods, 311–312 global structure-based methods, 312–313 prediction algorithms, 310 from proteome to secretome, 313 weight matrix methods, 311 PR-39 protein, 129 pVEC, 356 Q Quantification, 263–275 of CPPs via reporter groups, 266–272 biotinylation and cell-ELISA, 267 enzyme activity assays, 270 fluorescence microscopy, spectrometry, and FACS, 267–269 fluorogenic construct assay (resonance energy transfer, RET quenching), 270–272 fluorogenic construct assay (resonance energy transfer, RET), 270–272 HPLC detection, 269–270 immunodetection, 270 radiolabeling, 266–267 of peptide cargo bioactivity, 272–274 DNA/PNA antisense effects, 273 drug activity, 273–274 epidermal growth factor receptor (EGFR), 272–273 principles and background, 263–266 R Rac GTPases, 370 Radiolabeling quantification by, 266–267 for uptake kinetics assays, 280–281 125 I-radiolabeling, for uptake kinetics assays, 280–281 Reagents, for solution phase conjugation, 332–336 amine-reactive reagents, 332–333 example: superparamagnetic iron oxide particle–Tat conjugate, 334–336 heterobifunctional conjugation, 333–334 sulfhydryl-reactive reagents, 333 Receptors, internalization by, 177–179 Resonance energy transfer (RET) quenching, quantification by, 270–272 Rhodamine membrane uptake assay, 251–252 Rho GTPases, 370 S Sec6α, 304 Sec61β, 304 Sec61gamma, 304 SecA-dependent bacterial protein secretion pathways, 299 SecA protein, 299 SecB-dependent bacterial protein secretion pathways, 298–299 SecB protein, 297–298 SecDFyajC protein, 300 SecE protein, 300 SecG protein, 300 Sec62p, 304 Sec63p, 304–305, 305 Sec71p, 304 SecYEG and related protein-dependent bacterial protein secretion pathways, 300 SecYEG channel, 297 SecYEG protein, 300 SecY (PrlA) protein, 300 Side effects, 255–256, see also Toxicity Tat, 256 transportan, 255–256 Signal anchors, 306 Signal peptidases, 306–308 PiHD (XcpA), 307 type I distribution, 306 specificity, 307 type II, 307 Signal peptides, 295–324 bacterial protein secretion pathways, 297–303 Ffh and 4.5S RNA-dependent, 300–301
404 Cell-Penetrating Peptides: Processes and Applications FtsY-dependent, 301 secA-dependent, 299 secB-dependent, 298–299 SecYEG and related protein-dependent, 300 SRP-dependent, 300 Tat-dependent, 301–302 unknown or factor-independent, 302–303 energetic aspects, 302–303 insertion of procoat proteins, 302 eukaryotic secretion pathways, 303–305 cotranslational, 303–304 targeting to ER, 303–304 translocon complex, 304 post-translational, 304–305 chaperone proteins, 305 membrane proteins in addition to Sec, 304–305 historical considerations, 296–297 predictive and proteome analyses, 310–313 artificial neural network–based methods, 311–312 global structure–based methods, 312–313 prediction algorithms, 310 from proteome to secretome, 313 weight matrix methods, 311 sequence features and specificity, 305–310 determinants of specificity, 308–310 eubacterial signal peptides, 308–309 eukaryotic signal peptides, 309–310 general features, 305–306 signal anchors, 306 tripartite structure, 305 signal peptidases, 306–308 PiHD (XcpA), 307 type I distribution, 306 specificity, 307 type II, 307 Signal recognition particles (SRPs), 297, see also Signal peptides Signal sequence-based CPPs, 93–113 design and evaluation, 105–108 cell delivery mechanism, 105–106 nuclear transport mechanism, 106–108 as gene delivery vectors, 102–105 challenges in gene delivery, 102 covalent linkage to condensing agents, 104 direct linkage to DNA, 104–105 noncovalent incorporation of NLS, 102–103 NLS-containing CPPs, 99–102 applications, 100–102 import signal sequences, 99–100 nuclear localization sequence (NLS) in active cargo delivery, 97–98 principles, 94–95 transport mechanism, 95–97 Single time point experiments, 283–284 SIV fusion peptide, 202–204 Small unicellular vesicles (SUVs), 227 SN50 peptide, 118–119 Solution phase conjugation, 332–336 amine-reactive reagents, 332–333 example: superparamagnetic iron oxide particle–Tat conjugate, 334–336 heterobifunctional conjugation, 333–334 sulfhydryl-reactive reagents, 333 Solvent mixtures, 228–229 Specificity determinants of, 308–310 eubacterial signal peptides, 308–309 eukaryotic signal peptides, 309–310 sequence features and, 305–310 general features, 305–306 signal anchors, 306 tripartite structure, 305 signal peptidases, 306–308 PiHD (XcpA), 307 type I distribution, 306 specificity, 307 type II, 307 Spectrometry, quantification by, 267–269 Spectroscopy circular dichroism, 167, 232, 235 electron paramagnetic resonance (EPR), 177, 233 Fourier transform infrared, 167–168, 232 transverse relaxation optimized (TROSY), 235 SR-α, 301 7S RNA, 303 SRP-dependent bacterial protein secretion pathways, 300 STAT1 transcription factor, 118 Stern layer, 229–230 Stretavidin, transportan and, 64–66 Structural organization, of transportans, 67–69 Structure–activity relationships, of transportans, 58–59 Structure prediction modeling, 187–222 conclusions, 215–218 methods, 190–202 atomic surface hydrophobicity (first restraint), 191–193 charge simulation (third restraint), 194–197 description of water–bilayer interface, 190–191
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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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Interactions of Cell-Penetrating Pe
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Structure Prediction of CPPs and It
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FIGURE 9.7 (Color Figure 9.7 follow
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FIGURE 9.8 The center of the figure
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Biophysical Studies of Cell-Penetra
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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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Cell-Penetrating Peptides as Vector
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Cell-Penetrating Peptides as Vector
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Page 400 and 401: Microbial Membrane-Permeating Pepti
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