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7 Major Histocompatibility Complex Class I Protein-Peptide Interactions 1950 : i : : : : : : : : : : : : : : : I l : I : / : : i . : : : : : : : : l : : : : : : : I : : : : : I.. .--- -.._.. __ _... .. .. .. .--0--2mFigure 7-13. (a) Plot of time vs. kinetic energy (top), temperature (second from top), totalenergy (second from bottom) and potential energy (bottom) for the equilibration of the influenzavirus nucleoprotein peptide with HLA-A*6801. (b) Plot of time vs. kinetic energy(top), temperature (second from top), total energy (second from bottom) and potential energy(bottom) for the simulation of the influenza virus nucleoprotein peptide with HLA-A*6801.
196 Christopher .I Thorpe and David S. MossFigure 7-14. Series of snapshots of the peptide bound to HLA-A*6801 at 10 ps intervals,demonstrating the progression of conformers, and the formation of the pronounced bulgeformed in this peptide.
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Computer Modellingin Molecular Biol
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Professor Julia M. GoodfellowDepart
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ContentsColour Illustrations ......
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XContributorsBenoit RouxGroupe de R
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Colour IllustrationsXI11Figure 4-4.
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XVIColour IllustrationsFigure 7-18.
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2 Julia M. Goodfellow and Mark A. W
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Computer Modelling in Molecular Bio
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2 Modellinn Protein Structures 11su
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2 Modelling Protein Structures 13St
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2 Modelling Protein Structures 15Th
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2 Modelling Protein Structures 17Th
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2 Modelling Protein Structures 19Fa
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2 Modellinn Protein Structures 21th
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2 Modelling Protein Structures 23ho
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2 Modelling Protein Structures 25Wo
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2 Modelling Protein Structures 271.
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2.3.3 Available Modelling Programs2
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2 Modelling Protein Structures 31sp
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2 Modellina Protein Structures 33Ac
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2 Modelling Protein Structures 35[8
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38 D. J Osmthorue and I? K. C Paul3
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40 D. J; Osnuthorue and I? K. C. Pa
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42 D. J. OsPuthorDe and J? K. C Pau
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~443.3.1D. J. Osnuthorpe and I? K.
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46 D. 1 Osnuthorpe and r! K. C. Pau
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48 D. J. Osguthorpe and I? K. C. Pa
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50 D. J. Osguthorpe and I? K. C. Pa
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52 D. J. Osguthorpe and I! K. C. Pa
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54 D. L Osguthorpe and I! K. C Paul
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56 D. J Osguthorpe and I? K. C. Pau
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58 D. J. Osguthorpe and r! K. C. Pa
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4 Molecular Dynamics and Free Energ
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4 Molecular Dvnamics and Free Enera
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4 Molecular Dynamics and Free Enerw
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4 Molecular Dynamics and Free Enern
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5 Modelling Nucleic Acids 105and it
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5 Modelling Nucleic Acids 107of the
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5 Modelling Nucleic Acids 109ElFigu
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5 Modelling Nucleic Acids 11 1Figur
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5 Modellinn Nucleic Acids 1135.7 Ch
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5 Modelling Nucleic Acids 115With i
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5 Modellinn Nucleic Acids 117Figure
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5 Modelling Nucleic Acids 119Figure
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5 Modelling Nucleic Acids 1211.0mod
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5 Modelling Nucleic Acids 1235.12 M
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5 Modelling Nucleic Acids 125rotati
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5 Modellinp Nucleic Acids 1275.14 M
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5 Modelling Nucleic Acids 129simula
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5 Modellinn Nucleic Acids 131[40] G
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134 Benoft Roux6.1 IntroductionThe
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136 Benoit Roux[18-201. The gramici
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138 Benoft Rouxwhere D (x) is the l
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140 Benoft Roux“one-ion” conduc
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142 Benoft RouxTable 6-1. Interacti
Page 154 and 155: 144 Benoit RouxFigure 6-2. Solvated
Page 156 and 157: 146 Benoit Rouxwater box equilibrat
Page 158 and 159: 148 Benoit Roux-I I I I II I I I II
Page 160 and 161: 150 Benoi’t Rouxbulk waters. A st
Page 162 and 163: 152 Benoit RouxOne advantage of thi
Page 164 and 165: 154 Benoft Roux-.3.-15-c 10 -h5 5 -
Page 166 and 167: 156 Benoft Rouxwhere x and v are th
Page 168 and 169: 158 Benoit RouxReactant to ProductO
Page 170 and 171: 160 Benoit Rouxremain in close cont
Page 172 and 173: 162 Benoit Rouxis the deviation of
Page 174 and 175: 164 Benoft RouxTable 6-3. Pre-expon
Page 176 and 177: 166 Benoft RouxThis chapter demonst
Page 178 and 179: 168 Benoft Rouxproximately one Kf c
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Page 182 and 183: 7 Major Histocompatibility Complex
Page 184 and 185: 7 Major HistocompatibiIity Complex
Page 186 and 187: 7 Maior Histocompatibility Complex
Page 192 and 193: 7 Maior Histocomuatibilitv Cornulex
Page 210 and 211: HLA-B*270 IHLA-B*2702HLA-B*2703HLA-
Page 212 and 213: 7 Maior Histocomvatibilitv Comrdex
Page 224 and 225: 216 Oliver S. Smart8.1 Introduction
Page 226 and 227: 218 Oliver S. Smartvolving large mo
Page 228 and 229: 220 Oliver S. Smart8.2 TheoryConsid
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Page 232 and 233: 224 Oliver S. SmartThe repulsion te
Page 234 and 235: 226 Oliver S. Smart8.4 Applications
Page 236 and 237: 228 Oliver S. Smartrigid-body penal
Page 238 and 239: 230 Oliver S. Smart216 252 200 324
Page 240 and 241: 232 Oliver S. SmartrbFigure 8-5. A
Page 242 and 243: 234 Oliver S. Smartlink the eoc and
Page 244 and 245: 236 Oliver S. Smarttermediates mark
Page 246 and 247: 238 Oliver S. Smartmoving conformat
Page 248 and 249: 240 Oliver S. Smart[39] Halgren, T.
Page 250 and 251: 242 IndexGGramicidin A 134- NMR dat
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