| Contributors |
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xi | |
| Preface |
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xvii | |
| Volumes in Series |
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xix | |
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1 Intracellular Production of Recombinant Serpins in Yeast |
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1 | (12) |
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1 | (1) |
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2 Selection of Strain and Expression Plasmid |
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2 | (1) |
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3 | (1) |
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4 Transformation of Yeast |
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4 | (1) |
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5 Screening Transformants |
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4 | (1) |
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6 Large-Scale Growth and Induction |
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5 | (1) |
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6 | (1) |
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7 | (2) |
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9 Assessing Serpin Activity and Removing Inactive Forms |
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9 | (1) |
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10 Production of Polymerogenic Serpins |
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10 | (3) |
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12 | (1) |
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2 Production of Recombinant Serpins in Escherichia coli |
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13 | (16) |
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14 | (6) |
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2 Experimental Procedures for the Production of Serpins in E. coli |
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20 | (1) |
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3 Some Common Variations Used for Expression of Other Serpins |
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21 | (2) |
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4 Preparation of AT from Inclusion Bodies |
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23 | (1) |
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5 Preparation of Soluble AT |
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24 | (5) |
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27 | (2) |
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3 Isolation and Characterization of the Nuclear Serpin MENT |
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29 | (20) |
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30 | (1) |
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2 Purification of the MENT Protein |
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31 | (3) |
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3 Protease Inhibition/Serpin Activity |
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34 | (2) |
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4 MENT Interaction with DNA and Chromatin In Vitro |
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36 | (6) |
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5 Analysis of MENT Association with Native Chromatin In Situ |
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42 | (7) |
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46 | (1) |
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46 | (3) |
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4 Solving Serpin Crystal Structures |
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49 | (14) |
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50 | (1) |
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2 Protein Production and Purification |
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50 | (1) |
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3 Modifications to Aid Crystallization |
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51 | (1) |
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51 | (1) |
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52 | (1) |
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53 | (4) |
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7 Phase Improvement by Density Modification |
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57 | (1) |
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8 Refinement and Validation |
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58 | (5) |
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59 | (4) |
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5 Crystallography of Serpins and Serpin Complexes |
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63 | (26) |
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64 | (1) |
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2 First Glimpses of Serpin Structures |
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64 | (1) |
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3 The Serpin-Enzyme Complex |
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64 | (12) |
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76 | (1) |
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5 Conformational Control of Serpins |
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77 | (1) |
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6 Nonconventional Serpin Complexes |
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77 | (1) |
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7 Conformational Change and the Formation of the Latent Conformation |
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78 | (1) |
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8 Abnormal Conformational Change---The δ-Form |
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79 | (1) |
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79 | (2) |
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10 Crystallization of Serpins and Serpin Complexes |
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81 | (1) |
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82 | (7) |
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82 | (7) |
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6 Serpins as Hormone Carriers: Modulation of Release |
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89 | (16) |
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1 Serpins and Allosteric Modulation |
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89 | (1) |
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2 Hormone Carriage-TBG and CBG |
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90 | (5) |
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3 Temperature Response: A Protein Thermocouple |
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95 | (1) |
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4 Angiotensinogen and Its Interaction with Renin |
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96 | (9) |
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100 | (1) |
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101 | (4) |
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7 Serpin-Glycosaminoglycan Interactions |
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105 | (34) |
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106 | (15) |
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121 | (6) |
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127 | (12) |
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131 | (1) |
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131 | (8) |
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8 Targeting Serpins in High-Throughput and Structure-Based Drug Design |
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139 | (38) |
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140 | (2) |
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2 Targeting the s4A Site with Peptides in a Pathogenic Variant of α1-antitrypsin |
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142 | (6) |
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3 Computational Approaches |
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148 | (7) |
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4 In vitro Screening of Small Molecules |
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155 | (11) |
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5 Mammalian Cell Models and Beyond |
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166 | (2) |
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168 | (9) |
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169 | (8) |
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9 Development of Inhibitors of Plasminogen Activator Inhibitor-1 |
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177 | (32) |
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178 | (1) |
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2 Serpins as Drug Targets |
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179 | (5) |
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3 Development of PAI-1 Inhibitors |
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184 | (16) |
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200 | (9) |
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200 | (9) |
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10 Bioinformatic Approaches for the Identification of Serpin Genes with Multiple Reactive Site Loop Coding Exons |
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209 | (14) |
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210 | (1) |
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2 Procedure for Identification of Serpin Genes with mRSL Cassette Exons |
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211 | (8) |
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219 | (4) |
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220 | (1) |
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220 | (3) |
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11 Methods to Measure the Kinetics of Protease Inhibition by Serpins |
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223 | (14) |
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223 | (3) |
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2 Determining the Rate of Protease Inhibition (ka) |
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226 | (4) |
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3 Efficiency of the Serpin Inhibitory Reaction |
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230 | (7) |
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233 | (1) |
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233 | (4) |
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12 Predicting Serpin/Protease Interactions |
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237 | (38) |
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238 | (4) |
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242 | (14) |
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3 Sequence Analysis Methods |
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256 | (13) |
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4 Concluding Remarks and Perspective |
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269 | (6) |
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270 | (1) |
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270 | (5) |
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13 Amino-Terminal Oriented Mass Spectrometry of Substrates (ATOMS): N-Terminal Sequencing of Proteins and Proteolytic Cleavage Sites by Quantitative Mass Spectrometry |
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275 | (20) |
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276 | (1) |
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277 | (4) |
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3 Control Experiment to Determine the Ratio Cutoff and Identify Natural N-Termini, Basal Proteolytic Products, and Outliers |
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281 | (1) |
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4 Limited Proteolytic Processing of the Target Protein by the Test Protease In Vitro |
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282 | (1) |
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5 Isotopic Labeling and Tryptic Digestion |
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283 | (3) |
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6 Identification of Peptides by Liquid Chromatography-Tandem Mass Spectrometry |
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286 | (1) |
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7 Mass Spectrometry Data Analysis |
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287 | (4) |
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8 Discussion: Measuring the Effect of Protease Inhibitors on the Generation of Proteolytic Fragments |
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291 | (4) |
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292 | (1) |
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292 | (3) |
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14 Computational Methods for Studying Serpin Conformational Change and Structural Plasticity |
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295 | (30) |
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296 | (3) |
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2 Local to Global Dynamics Simulations |
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299 | (5) |
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3 Pushing the Limits---Improving Conformational Sampling |
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304 | (3) |
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4 I Know Where to Go---Directed Simulations |
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307 | (1) |
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308 | (1) |
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309 | (2) |
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311 | (2) |
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313 | (1) |
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314 | (2) |
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316 | (9) |
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319 | (6) |
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15 Probing Serpin Conformational Change Using Mass Spectrometry and Related Methods |
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325 | (26) |
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326 | (5) |
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331 | (5) |
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3 Determination of Thermodynamic Stability Using Hydrogen-Deuterium Exchange Combined with Mass Spectrometry |
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336 | (7) |
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4 "Functional Unfolding" During the Native → Cleaved Transition |
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343 | (1) |
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5 Investigating the Polymerization Pathway and Polymer Structure of α1-AT by HXMS and Ion Mobility MS |
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344 | (4) |
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348 | (3) |
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348 | (3) |
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16 Determining Serpin Conformational Distributions with Single Molecule Fluorescence |
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351 | (28) |
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353 | (1) |
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2 Labeling Serpins and Proteases with Fluorophores |
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354 | (1) |
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3 Overview of Single Molecule Fluorescence Techniques |
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355 | (3) |
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358 | (10) |
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5 Conformational Distributions of Protease-Serpin Complexes |
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368 | (5) |
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6 Conclusions and Future Directions |
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373 | (6) |
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373 | (1) |
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374 | (5) |
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17 Serpin Polymerization In Vitro |
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379 | (42) |
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380 | (3) |
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2 Methods of Inducing Polymerization |
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383 | (12) |
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3 Kinetics of Polymerization |
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395 | (7) |
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4 Effect of Mutations and "Drugs" on Polymerization |
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402 | (6) |
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5 Mechanisms of Polymerization |
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408 | (7) |
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415 | (6) |
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416 | (1) |
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417 | (4) |
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18 The Serpinopathies: Studying Serpin Polymerization In Vivo |
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421 | (46) |
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1 Introduction to Serpin Polymers and the Serpinopathies |
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423 | (1) |
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2 Biophysical Techniques to Assess Serpin Polymers Formed In Vivo |
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424 | (4) |
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3 Assessment of Serpin Polymers by Electron Microscopy |
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428 | (8) |
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4 Development of mAbs to Aberrant Conformers of α1-Antitrypsin and Neuroserpin |
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436 | (5) |
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5 Development of Cell Models to Assess the Polymerization of Antitrypsin |
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441 | (2) |
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6 Development of Cell Models to Assess the Polymerization of Neuroserpin |
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443 | (2) |
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7 Detection of the UPR and the OPR in the Serpinopathies |
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445 | (3) |
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8 Characterization of the Interaction Between Serpin Polymers and Neutrophils |
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448 | (3) |
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9 The Use of Transgenic Mice to Assess the Hepatic Consequences of Serpin Polymerization. Jeff Teckman |
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451 | (2) |
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10 The Use of Transgenic Mice to Assess the Pulmonary Consequences of Serpin Polymerization |
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453 | (4) |
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11 Characterization of Serpin Polymerization Using iPS to Generate Hepatocyte-Like Cell Lines |
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457 | (10) |
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461 | (1) |
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461 | (6) |
| Author Index |
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467 | (26) |
| Subject Index |
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493 | |
