메뉴 건너뛰기




Volumn 29, Issue 1, 1997, Pages 87-102

A predictive method for the evaluation of peptide binding in pocket 1 of HLA-DRB1 via global minimization of energy interactions

Author keywords

Global optimization; HLA DRB1 class II protein; Peptide docking

Indexed keywords

HLA ANTIGEN; HLA DR ANTIGEN;

EID: 0030923442     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199709)29:1<87::AID-PROT7>3.0.CO;2-C     Document Type: Article
Times cited : (17)

References (42)
  • 2
    • 0024821263 scopus 로고
    • Molecular mechanics: The MM3 force field for hydrocarbons
    • Allinger, N.L., Yuh, Y.H., Liu, J.-H. Molecular mechanics: the MM3 force field for hydrocarbons. J. Am. Chem. Soc. 111:8551, 1989.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 8551
    • Allinger, N.L.1    Yuh, Y.H.2    Liu, J.-H.3
  • 3
    • 0001327501 scopus 로고
    • αBB: A global optimization method for general constrained nonconvex problems
    • Androulakis, I.P., Maranas, C.D., Floudas, C.A. αBB: A global optimization method for general constrained nonconvex problems. J. Global Optimiz. 7:337-363, 1995.
    • (1995) J. Global Optimiz. , vol.7 , pp. 337-363
    • Androulakis, I.P.1    Maranas, C.D.2    Floudas, C.A.3
  • 4
    • 1842639266 scopus 로고    scopus 로고
    • Prediction of oligopeptide conformations via deterministic global optimization
    • Androulakis, I.P., Maranas, C.D., Floudas, C.A. Prediction of oligopeptide conformations via deterministic global optimization. J. Global Optimiz. 11:1-34, 1997.
    • (1997) J. Global Optimiz. , vol.11 , pp. 1-34
    • Androulakis, I.P.1    Maranas, C.D.2    Floudas, C.A.3
  • 5
    • 0026642968 scopus 로고
    • Docking by least-square fitting of molecular surface patterns
    • Bacon, D.J., Moult, J. Docking by least-square fitting of molecular surface patterns. J. Mol. Biol. 225:849-858, 1992.
    • (1992) J. Mol. Biol. , vol.225 , pp. 849-858
    • Bacon, D.J.1    Moult, J.2
  • 7
    • 0026721978 scopus 로고
    • Monte Carlo docking of oligopeptides to proteins
    • Calfisch, A., Niederer, P., Anliker, M. Monte Carlo docking of oligopeptides to proteins. Proteins 13:223-230, 1992.
    • (1992) Proteins , vol.13 , pp. 223-230
    • Calfisch, A.1    Niederer, P.2    Anliker, M.3
  • 8
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly, M.L. Solvent-accessible surfaces of proteins and nucleic acids. Science 221:709, 1983.
    • (1983) Science , vol.221 , pp. 709
    • Connolly, M.L.1
  • 9
    • 0023769808 scopus 로고
    • Structure and energetics of ligand binding to peptides: Escherichia coli dihydrofolate reductase-trimethoprim, a drug receptor system
    • Dauber-Osguthorpe, P., Roberts, V.A., Osguthorpe, D.J., Wolff, J., Genest, M., Hagler, A.T. Structure and energetics of ligand binding to peptides: Escherichia coli dihydrofolate reductase-trimethoprim, a drug receptor system. Proteins 4:31, 1988.
    • (1988) Proteins , vol.4 , pp. 31
    • Dauber-Osguthorpe, P.1    Roberts, V.A.2    Osguthorpe, D.J.3    Wolff, J.4    Genest, M.5    Hagler, A.T.6
  • 12
    • 0025135112 scopus 로고
    • Automated docking of substrates to proteins by simulated annealing
    • Goodsell, D.S., Olson, A.J. Automated docking of substrates to proteins by simulated annealing. Proteins 8:195-202, 1990.
    • (1990) Proteins , vol.8 , pp. 195-202
    • Goodsell, D.S.1    Olson, A.J.2
  • 14
    • 0027937713 scopus 로고
    • Precise prediction of major histocompatibility complex class II-peptide interaction based on peptide side chain scanning
    • Hammer, J., Bono, E., Gallazi, F., Belunis, C., Nagy, Z., Sinigaglia, F. Precise prediction of major histocompatibility complex class II-peptide interaction based on peptide side chain scanning. J. Exp. Med. 180:2353-2358, 1994.
    • (1994) J. Exp. Med. , vol.180 , pp. 2353-2358
    • Hammer, J.1    Bono, E.2    Gallazi, F.3    Belunis, C.4    Nagy, Z.5    Sinigaglia, F.6
  • 15
    • 0028952168 scopus 로고
    • Peptide binding specificity of HLA-DR4 molecules: Correlation with Rheumatoid Arthritis Association
    • Hammer, J., Gallazzi, F., Bono, E., Karr, R., Guenot, J., Valsasnini, Nagy, Z. Peptide binding specificity of HLA-DR4 molecules: correlation with Rheumatoid Arthritis Association. J. Exp. Med. 181:1847-1855, 1995.
    • (1995) J. Exp. Med. , vol.181 , pp. 1847-1855
    • Hammer, J.1    Gallazzi, F.2    Bono, E.3    Karr, R.4    Guenot, J.5    Valsasnini6    Nagy, Z.7
  • 16
    • 0026780930 scopus 로고
    • A multiple-start Monte-Carlo docking method
    • Hart, T.N., Read, R.J. A multiple-start Monte-Carlo docking method. Proteins 13:206-222, 1992.
    • (1992) Proteins , vol.13 , pp. 206-222
    • Hart, T.N.1    Read, R.J.2
  • 18
    • 0025369192 scopus 로고
    • Peptide binding to HLA-DR1: A peptide with most residues substituted to alanine retains MHC binding
    • Jardesky, T.S., Gorga, J.C., Bush, R., Rothbard, J., Strominger, J.L. Wiley, D.C. Peptide binding to HLA-DR1: a peptide with most residues substituted to alanine retains MHC binding. EMBO J. 9:1797, 1990.
    • (1990) EMBO J. , vol.9 , pp. 1797
    • Jardesky, T.S.1    Gorga, J.C.2    Bush, R.3    Rothbard, J.4    Strominger, J.L.5    Wiley, D.C.6
  • 19
    • 0026310932 scopus 로고
    • Soft docking: Matching of molecular surface cubes
    • Jiang, F., Kim, S.H. Soft docking: Matching of molecular surface cubes. J. Mol. Biol. 219:79-102, 1991.
    • (1991) J. Mol. Biol. , vol.219 , pp. 79-102
    • Jiang, F.1    Kim, S.H.2
  • 20
    • 0029078319 scopus 로고
    • Accuracy of a structural homology model for a class II histocompatibility protein, HLA-DR1: Comparison to the crystal structure
    • Nauss, J.L., Reid, R.H., Sadegh-Nasseri, S. Accuracy of a structural homology model for a class II histocompatibility protein, HLA-DR1: comparison to the crystal structure. J. Biomol. Struct. Dyn. 12:1213-1233, 1995.
    • (1995) J. Biomol. Struct. Dyn. , vol.12 , pp. 1213-1233
    • Nauss, J.L.1    Reid, R.H.2    Sadegh-Nasseri, S.3
  • 21
    • 0000895361 scopus 로고    scopus 로고
    • Peptide docking using dynamic programming
    • Gulukota, K., Vajda, S., Delisi, C. Peptide docking using dynamic programming. J. Comp. Chem. 17:418-428, 1996.
    • (1996) J. Comp. Chem. , vol.17 , pp. 418-428
    • Gulukota, K.1    Vajda, S.2    Delisi, C.3
  • 22
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B., Richards, F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400, 1971.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 23
    • 0021095856 scopus 로고
    • Protein folding by restrained energy minimization and molecular dynamics
    • Levitt, M. Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol. 170:723, 1983.
    • (1983) J. Mol. Biol. , vol.170 , pp. 723
    • Levitt, M.1
  • 25
    • 0001203963 scopus 로고
    • Global minimum potential energy conformations of small molecules
    • Maranas, C.D., Floudas, C.A. Global minimum potential energy conformations of small molecules. J. Global Optimiz. 4:135-170, 1994.
    • (1994) J. Global Optimiz. , vol.4 , pp. 135-170
    • Maranas, C.D.1    Floudas, C.A.2
  • 26
    • 5944250450 scopus 로고
    • Energy Parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
    • Momany, F.A., Burgess, A.W., McGuire, R.F., Scheraga, H.A. Energy Parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79:2361, 1975.
    • (1975) J. Phys. Chem. , vol.79 , pp. 2361
    • Momany, F.A.1    Burgess, A.W.2    McGuire, R.F.3    Scheraga, H.A.4
  • 29
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions to use in the ECEPP/3 algorithms, with applications to proline-containing peptides
    • Némethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S., Scheraga, H.A. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions to use in the ECEPP/3 algorithms, with applications to proline-containing peptides. J. Phys. Chem. 96:6472, 1992.
    • (1992) J. Phys. Chem. , vol.96 , pp. 6472
    • Némethy, G.1    Gibson, K.D.2    Palmer, K.A.3    Yoon, C.N.4    Paterlini, G.5    Zagari, A.6    Rumsey, S.7    Scheraga, H.A.8
  • 30
    • 33845550595 scopus 로고
    • Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbinded interactions and hydrogen bond interactions for the naturally occurring amino acids
    • Némethy, G., Pottle, M.S., Scheraga, H.A. Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbinded interactions and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 89:1883, 1983.
    • (1983) J. Phys. Chem. , vol.89 , pp. 1883
    • Némethy, G.1    Pottle, M.S.2    Scheraga, H.A.3
  • 34
    • 0028135684 scopus 로고
    • Molecular Dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes
    • Rogman, D., Scapozza, L., Folkers, G., Daser, A. Molecular Dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes. Biochemistry 33: 11476-11485, 1994.
    • (1994) Biochemistry , vol.33 , pp. 11476-11485
    • Rogman, D.1    Scapozza, L.2    Folkers, G.3    Daser, A.4
  • 35
    • 0027135804 scopus 로고
    • Computing the structure of bound peptides: Applications to antigen recognition by class I major histocompatibility complex receptors
    • Rosenfeld, R., Q. Zheng, Vajda, S., DeLisi, C. Computing the structure of bound peptides: applications to antigen recognition by class I major histocompatibility complex receptors. J. Mol. Biol. 234:515-521, 1993.
    • (1993) J. Mol. Biol. , vol.234 , pp. 515-521
    • Rosenfeld, R.1    Zheng, Q.2    Vajda, S.3    DeLisi, C.4
  • 36
    • 1842344380 scopus 로고
    • Cornell University Department of Chemistry, January
    • Scheraga, H.A. ECEPP/3 USER GUIDE. Cornell University Department of Chemistry, January 1993.
    • (1993) ECEPP/3 USER GUIDE
    • Scheraga, H.A.1
  • 38
    • 0028348369 scopus 로고
    • Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide
    • Stern, L., Brown, J., Jardetzky, T., Gorga, J., Urban, R., Strominger, L., Wiley, D. Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 368:215-221, 1994.
    • (1994) Nature , vol.368 , pp. 215-221
    • Stern, L.1    Brown, J.2    Jardetzky, T.3    Gorga, J.4    Urban, R.5    Strominger, L.6    Wiley, D.7
  • 40
    • 0026076082 scopus 로고
    • Empirical solvation models can be used to differentiate native from non-native conformations of bovine pancreatic trypsin inhibitor
    • Vila, J., Williams, R.L., Vasquez, M., Scheraga, H.A. Empirical solvation models can be used to differentiate native from non-native conformations of bovine pancreatic trypsin inhibitor. Proteins 10:199-218, 1991.
    • (1991) Proteins , vol.10 , pp. 199-218
    • Vila, J.1    Williams, R.L.2    Vasquez, M.3    Scheraga, H.A.4
  • 42
    • 84988053694 scopus 로고
    • An all-atom force field for simulations of proteins and nucleic acids
    • Weiner, S., Kollmann, P., Nguyen, D., Case, D. An all-atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7:230, 1986.
    • (1986) J. Comp. Chem. , vol.7 , pp. 230
    • Weiner, S.1    Kollmann, P.2    Nguyen, D.3    Case, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.