Wave function analysis of MHC-peptide interactions

Journal of Molecular Graphics and Modelling

Volumn 25, Issue 5, 2007, Pages 605-615

  Cárdenas, Constanza ^a,b   Obregón, Mateo ^a   Balbín, Alejandro ^a   Villaveces, José Luis ^b   Patarroyo, Manuel E ^a,b  

^a FUNDACIÓN INSTITUTO DE INMUNOLOGÍA DE COLOMBIA FIDIC   (Colombia)

^b UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

Author keywords

MHC pockets; Molecular interactions; Molecular orbital coefficients; Theoretical study of MHC

Indexed keywords

AMINO ACIDS; ANTIGEN-ANTIBODY REACTIONS; MOLECULAR ORIENTATION; POLYPEPTIDES; QUANTUM THEORY; WAVE EQUATIONS;

ATOMIC ORBITAL COEFFICIENTS; INTERACTION MOLECULAR ORBITALS (IMO); MAJOR HISTOCOMPATIBILITY COMPLEX (MHC); MOLECULAR INTERACTIONS; WAVE FUNCTION ANALYSIS;

PROTEINS;

HLA DR ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN; PEPTIDE;

AMINO ACID COMPOSITION; ARTICLE; COMPLEX FORMATION; COMPUTER PROGRAM; CORRELATION ANALYSIS; MAJOR HISTOCOMPATIBILITY COMPLEX; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; QUANTUM CHEMISTRY;

AMINO ACIDS; BINDING SITES; COMPUTER SIMULATION; HLA ANTIGENS; HUMANS; MODELS, MOLECULAR; PEPTIDES; QUANTUM THEORY; SOFTWARE;

EID: 33846631764     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2006.04.005     Document Type: Article

References (19)

1. In: Paul W.E. (Ed). Fundamental Immunology (1998), Williams & Wilkins, Philadelphia (Lippincott Pwachu Awachu)
2. Dessen A., Lawrence C.M., Cupo S., Zaller D.M., and Wiley D.C. X-ray crystal structure of HLA-DR4 (DRA*0101, DRB1*0401) complexed with a peptide from human collagen II. Immunity 7 (1997) 473-481
3. Hennecke J., and Wiley D.C. Structure of a complex of the human alpha/beta T cell receptor (TCR) HA 1.7, influenza heagglutinin peptide, and major histocompatibility complex class II molecule, HLA-DR4 (DRA*0101 and DRB1*0401): insight into TCR cross-restriction and alloreactivity. J. Exp. Med. 195 (2002) 571-581
4. Stern L.J., Brown J.H., Jardetzky T.S., Gorga J.C., Urban R.G., Strominger J.L., and Wiley D.C. Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 368 (1994) 215-221
5. Bian H., Reidhaar-Olson J.F., and Hammer J. The use of bioinformatics for identifying class II restricted T-cell epitopes. Methods 29 (2003) 299-309
6. Doytchinova I.A., and Flower D.R. Quantitative approaches to computational vaccinology. Immunol. Cell. Biol. 80 (2002) 270-279
7. Logean A., and Rognan D. Recovery of known T-cell epitopes by computational scanning o a viral genome. J. Comput. Aided Mol. Des. 16 (2002) 229-243
8. Schirle M., Weinschenk T., and Stevanovic S. Combining computer algorithms with experimental approaches permit the rapid and accurate identification of T cell epitopes from defined antigens. Methods 257 (2001) 1-16
9. Smith G.R., and Sternberg M.J.E. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12 (2002) 28-35
10. Sturniolo T., Bono E., Ding J., Raddrizzani L., Tuereci O., Sahin U., Braxenthaler M., Gallazi F., Protti M.P., Sinigaglia F., and Hammer J. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat. Biotechnol. 17 (1999) 555-561
11. Cardenas C., Villaveces J.L., Bohorquez H., Llanos E., Suarez C., Obregon M., and Patarroyo M.E. Quantum chemical analysis explains hemagglutinin peptide-MHC class II molecule HLA-DRβ1*0101 interactions. Biochem. Biophys. Res. Commun. 323 (2004) 1265-1277
12. Cardenas C., Villaveces J.L., Suarez C., Obregon M., Ortiz M., and Patarroyo M.E. A comparative study of MHC class II HLA-DRJ31*0401-Col II and HLA-DRβ1*0101-HA complexes: a theoretical point of view. J. Struct. Biol. 149 (2005) 38-52
13. Cardenas C., Ortiz M., Balbin A., Villaveces J.L., and Patarroyo M.E. Allele effects in MHC-peptide interactions: a theoretical analysis of HLA-DRβ1*0101-HA and HLA-DRβ1*0401-HA complexes. Biochem. Biophys. Res. Commun. 330 (2005) 1162-1167
14. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T., Weissig H., Shindyalov I., and Bourne P.E. The protein data bank. Nucl. Acid Res. 28 (2000) 235-242
15. Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F.J., Brice M.D., Rogers J.R., Kennard O., Shimanouch T., and Tasumi M. The protein data bank: a computer based archival file for macromolecular structures. J. Mol. Biol. 112 (1977) 535-542
16. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery V.G.Z.J.A., Stratmann R.E., Burant J.C., Dapprich S., Millam J.M., Daniels A.D., Kudin A.N., Strain M.C., Farkas O., Tornasi J., Barone V., Cossi M., Cammi R., Mennucci B., Pomelli C., Adamo C., Clifford S., Ochterski J., Petterson G.A., Ayala P.Y., Cui Q., Malick K.M.D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Cioslowski J., Ortiz J.V., Stefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Gomperts R., Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkarat A., Gonzalez C., Challacombe M., Gill P.M.W., Johnson B.G., Chen W., Wong M.W., Andres J.L., Head-Gordon M., Replogle E.S., and Pople J.A. Gaussian'98, Revision A.5 (1998), Gaussian Inc., Pittsburgh, PA
17. Szabo A., and Ostlund N.S. Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory (1996), Dover Publications Inc., New York
18. McWeeny R. Methods of Molecular Quantum Mechanics (1989), Academic Press, New York
19. SPSS Inc. SPSS Base 12.0 for Windows (2003), SPSS Inc., Chicago, IL