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7 Major Histocompatibility Complex Class I Protein-Peptide Interactions 197Figure 7-15. (a) Overlay of 5 conformers from the dynamics trajectory demonstrating thestability of the structure of the peptide in the cleft. (b) Initial and final conformations of theflu peptide from the molecular dynamics trajectory compared to the peptide observed in thecrystal structure of HLA-B27.
198 Christopher .l Thorpe and David S. Moss7.7 Modelling of an Epstein Barr Virus NuclearAntigen Peptide with HLA-B27 Sub-TypeMoleculesHLA-B27 is an enigma in the field of immunology, in both its disease associations,and the primary structure of the peptides which it presents. It is to date the onlyhuman class I molecule to have a strong genetic linkage to an autoimmune disease,in its well known, but poorly characterised, association with ankylosing spondylitis(AS) [43, 441. In contrast to the link between HLA-B27 and AS the majority oforgan specific T-cell mediated autoimmune diseases display a strong association tothe class I1 genes of the MHC and a weak association to class I genes via linkagedisequilibria (see Table 7-1).Table 7-1. The MHC class I associations to autoimmune diseases known to date.Disorder HLA allele Relative riskHodgkin’s diseaseIdiopathic hemochromatosisBechet’s diseaseCongenital adrenal hyperplasiaAnkylosing spondylitisReiter’s diseaseAcute anterior uveitisSubacute thyroiditisPsoriasis vugarisHLA-A1HLA-A3HLA-B14HLA-B5HLA-B47HLA-B27HLA-B27HLA-B27HLA-B35HLA-Cw61.48.24.26.315.487.437.010.413.713.3In addition to these associations HLA-B7, HLA-A3 and HLA-Cw7 have been demonstratedto be linked to narcolepsy, probably through their linkage disequilibrium with haplotypes containingthe class I1 HLA-DR2 alleles that have been observed in all narcoleptics typed to date.Another class I allele HLA-BlS has been weaklv linked to C2 comulement deficiencv.The structure of the HLA-B27 molecule determined by X-ray crystallography isvirtually identical to that of HLA-A2. However the initial structure of HLA-B*2705was the first to define the shape of the peptide in the cleft. In the structures of HLA-A2 and HLA-Aw68 with collections of endogenous peptides, electron density for thepeptide was visible but was not interpretable. This feature was suggested to be causedby the vast diversity of peptides bound; diverse both in length and sequence. All ofthe peptides eluted from HLA-B*2705 were nonamers and had an identical residueat position P2. It was considered to be these features which allowed the visualisationof an average backbone peptide conformation in the 3.0 A structure. However octamerand decamer HLA-B27 epitopes have been characterised but all have arginine
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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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2.3.3 Available Modelling Programs2
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38 D. J Osmthorue and I? K. C Paul3
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4 Molecular Dynamics and Free Energ
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5 Modelling Nucleic Acids 105and it
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5 Modelling Nucleic Acids 129simula
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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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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
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Page 174 and 175: 164 Benoft RouxTable 6-3. Pre-expon
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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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