Toward the atomistic simulation of T cell epitopes. Automated construction of MHC: Peptide structures for free energy calculations

Journal of Molecular Graphics and Modelling

Volumn 26, Issue 6, 2008, Pages 957-961

  Todman, Sarah J ^a   Halling Brown, Mark D ^a   Davies, Matthew N ^b   Flower, Darren R ^b   Kayikci, Melis ^a   Moss, David S ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Free energy calculations; Homology modelling; MHC molecules; Molecular dynamics; T cell epitopes

Indexed keywords

BIOLOGICAL ORGANS; COMPUTER SIMULATION; FREE ENERGY; MOLECULAR DYNAMICS; ONCOLOGY; PEPTIDES;

FREE ENERGY CALCULATIONS; HOMOLOGY MODELLINGS; PEPTIDE STRUCTURES; T CELL EPITOPES;

CELLS;

EPITOPE; PEPTIDE VACCINE; T LYMPHOCYTE RECEPTOR; TUMOR VACCINE;

ADAPTIVE IMMUNITY; ANTIGEN PRESENTATION; ARTICLE; BINDING AFFINITY; ENERGY; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; T LYMPHOCYTE;

ANIMALS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; EPITOPES, T-LYMPHOCYTE; HUMANS; MAJOR HISTOCOMPATIBILITY COMPLEX; MODELS, MOLECULAR; PEPTIDES; REPRODUCIBILITY OF RESULTS; SOFTWARE DESIGN; THERMODYNAMICS;

EID: 37349046359     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2007.07.005     Document Type: Article

References (27)

1. Kersh G.J., and Allen P.M. Essential flexibility in the T-cell recognition of antigen. Nature 380 (1996) 495-498
2. Saper M.A., Bjorkman P.J., and Wiley D.C. Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 Å resolution. J. Mol. Biol. 219 (1991) 277-319
3. Sliz P., Michielin O., Cerottini J.C., Luescher I., Romero P., Karplus M., and Wiley D.C. Crystal structures of two closely related but antigenically distinct HLA-A2/melanocyte-melanoma tumor-antigen peptide complexes. J. Immunol. 167 (2001) 3276-3284
4. McFarland B.J., and Beeson C. Binding interactions between peptides and proteins of the class II major histocompatibility complex. Med. Res. Rev. 22 (2002) 168-203
5. Madden D.R. The three-dimensional structure of peptide-MHC complexes. Annu. Rev. Immunol. 13 (1995) 587-622
6. Rammensee H., Bachmann J., Emmerich N.P., Bachor O.A., and Stevanovic S. SYFPEITHI, database for MHC ligands and peptide motifs. Immunogenetics 50 (1999) 213-219
7. Udaka K., Mamitsuka H., Nakaseko Y., and Abe N. Prediction of MHC class I binding peptides by a query learning algorithm based on hidden Markov models. J. Biol. Phys. 28 (2002) 183-194
8. Doytchinova I.A., Blythe M.J., and Flower D.R. Additive method for the prediction of protein-peptide binding affinity. Application to the MHC Class I molecule HLA-A*0201. J. Proteome Res. 1 (2002) 263-272
9. Donnes P., and Elofsson A. Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 3 (2002) 25
10. Reche P.A., Glutting J.P., and Reinherz E.L. Prediction of MHC class I binding peptides using profile motifs. Hum. Immunol. 63 (2002) 701-709
11. Salomon J., and Flower D.R. Predicting Class II MHC-peptide binding. A kernel based approach using similarity scores. BMC Bioinformatics 7 (2006) 501
12. Schueler-Furman O., Altuvia Y., Sette A., and Margalit H. Structure-based prediction of binding peptides to MHC class I molecules, application to a broad range of MHC alleles. Protein Sci. 9 9 (2000) 1838-1844
13. Davies M.N., Sansom C.E., Beazley C., and Moss D.S. A novel predictive technique for the MHC Class II peptide-binding interaction. Mol. Med. 9 (2003) 220-225
14. Davies M.N., Hattotuwagama C.K., Moss D.S., Drew M.G., and Flower D.R. Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity. BMC Struct. Biol. 6 (2006) 5
15. Sette A., and Sidney J. Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics 50 (1999) 201-212
16. Lund O., Nielsen M., Kesmir C., Christensen J., Lundegaard C., Worning P., and Brunak S. Web-based tools for vaccine design. HIV Mol. Immunol. (2002) 45-51
17. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28 (2000) 235-242
18. Stajich J.E., Block D., Boulez K., Brenner S.E., Chervitz S.A., Dagdigian C., Fuellen G., Gilbert J.G., Korf I., Lapp H., Lehvaslaiho H., Matsalla C., Mungall C.J., Osborne B.I., Pocock M.R., Schattner P., Senger M., Stein L.D., Stupka E., Wilkinson M.D., and Birney E. The Bioperl toolkit, Perl modules for the life sciences. Genome Res. 12 (2002) 1611-1880
19. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kale L., and Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26 (2005) 1781-1802
20. Robinson J., Waller M.J., Parham P., de Groot N., Bontrop R., Kennedy L.J., Stoehr P., and Marsh S.G.E. IMGT/HLA and IMGT/MHC, sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res. 31 (2003) 311-314
21. Chipot C., and Henin J. Exploring the free-energy landscape of a short peptide using an average force. J. Chem. Phys. 123 (2005) 244906
22. Henin J., and Chipot C. Overcoming free energy barriers using unconstrained molecular dynamics simulations. J. Chem. Phys. 121 (2004) 2904-2914
23. ImmunologyGrid Project. http://www.immunologygrid.org.
24. Wan S., Coveney P.V., and Flower D.R. Peptide recognition by the T cell receptor, Comparison of binding free energies from thermodynamic integration. Poisson-Boltzmann and linear interaction energy approximations. Philos. Trans. A: Math. Phys. Eng. Sci. 363 (2005) 2037-2053
25. Wan S., Coveney P.V., and Flower D.R. Molecular basis of peptide recognition by the T-cell receptor. Affinity differences calculated using large scale computing. J. Immunol. 175 (2005) 1715-1723
26. Wan S., Coveney P.V., and Flower D.R. Large scale molecular dynamics simulations of HLA-A*0201 complexed with a tumour-specific antigenic peptide. Can the α3 and β2m domains be neglected?. J. Comput. Chem. 25 (2004) 1803-1810
27. Cohen J., McGough A.S., Darlington J., Furmento N., Kong G., and Mayer A. RealityGrid an integrated approach to middleware through ICENI. Philos. Trans. A: Math. Phys. Eng. Sci. 363 (2005) 1817-1827