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HLA-B*270 IHLA-B*2702HLA-B*2703HLA-B*2704HLA-B*2705HLA-B'2706HLA-B*2707HLA-B*2701HLA-B*2702HLA-B*2703HLA-B*2704HLA-B*2705HLA-B*2706HLA-B*2707HLA-B *2701HLA-B.2702HLA-B'2703HLA-B *2704HLA-B.2705HLA-B*2706HLA-B.2707(a)7 Major Histocompatibility Complex Class I Protein-Peptide Interactions201-60606060606060120120120120120120120182182182182182182182Figure 7-16. (a) Sequence alignment of the seven HLA-B27 subtype molecules. From HLA-B*2705, the archetypal HLA-B27 allele the evolution of all other seven molecules can bedefined. (b) Molecular graphics image of HLA-B*2705 displaying, in dark-grey, patches theregions of polymorphism. The clustering of polymorphic residues in the regions that surroundand chelate the C-terminal residue PC, and the penultimate residue PC-1 (P8 in a nonamersuch as the EBNA 3C epitope) is clearly visible.
202 Christopher 1 Thorpe and David S. MossTable 7-2(a). Lists of contacts and hydrogen bonds displayed by the interaction of the EBNA3C peptide with the clefts of the HLA-27 isotype molecule HLA-B*2702.Position Residues Waters mc hydrogen sc hydrogenin peptide within 4A within 4A bonds bondsArgPlArgP2Y59, R62, TIP461,E63, Y159, TIP465E163, W167,Y171Y7, H9, T24, TIP456,V25, V34, TIP461,E45, R62, E63, TIP465166, C67, Y99,Y159, El63NH-OH(sc) Y171, NH-C=O El63C = O-OH(sc)Y159NH-C = O(SC) NH-C = O(SC)E63, E45 (x2),C = O-NH(sc)R62(x2)NH-OH(sc)T24(x2),IleP35rP4AspP5LeuP6IleP7GluPSLeuP9166, Y99, TIP456,L156, Y159 TIP458,TIP459,TIP465R62, 465, I66 TIP457,TIP458,TIP464,TIP465V152, QlSS,L156T73, V152,Q155, L156T73, N77,H114, W147,V152T73, E76,N77, 180,W147N77, 180, Y84,L95, Y123,T143, W147TIP457,TIP460,TIP464TIP453,TIP454,TIP455,TIP460TIP451,TIP453,TIP460TIP451,TIP452,TIP453NH-OH(sc) Y99C = 0-tipTIP458NH-tipTIP465-(E163, R62)C = 0-tipTIP464C = 0-tip TIP453C = O-NH(sc)W147NH-C = O(SC)N77C=O-OH(sc)Y84C = O-OH(sc)T143C = 0-tipTIP452-K146NH-tipTIP456-(Y99,H9)C = 0-tipTIP451-(N77, LeuP9)
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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
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144 Benoit RouxFigure 6-2. Solvated
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146 Benoit Rouxwater box equilibrat
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148 Benoit Roux-I I I I II I I I II
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Page 162 and 163: 152 Benoit RouxOne advantage of thi
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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
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Page 186 and 187: 7 Maior Histocompatibility Complex
Page 192 and 193: 7 Maior Histocomuatibilitv Cornulex
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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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