메뉴 건너뛰기




Volumn 28, Issue 3, 1997, Pages 421-433

Structural consensus in ligand-protein docking identifies recognition peptide motifs that bind streptavidin

Author keywords

Binding energy landscapes; Minimal frustration principle; Molecular recognition; Recognition nucleus; Structural harmony

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; MATHEMATICAL ANALYSIS; MOLECULAR MODEL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SEQUENCE ANALYSIS;

EID: 0030927639     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199707)28:3<421::AID-PROT11>3.0.CO;2-J     Document Type: Article
Times cited : (12)

References (41)
  • 1
    • 0026730489 scopus 로고
    • Structure-based strategies for drug design and discovery
    • Kuntz, I.D. Structure-based strategies for drug design and discovery. Science 257:1078-1082, 1992.
    • (1992) Science , vol.257 , pp. 1078-1082
    • Kuntz, I.D.1
  • 2
    • 0001650642 scopus 로고
    • A good ligand is hard to find: Automated docking methods
    • Blaney, J.M., Dixon, J.S. A good ligand is hard to find: Automated docking methods. Perspect. Drug Discov. Des. 1:301-319, 1993.
    • (1993) Perspect. Drug Discov. Des. , vol.1 , pp. 301-319
    • Blaney, J.M.1    Dixon, J.S.2
  • 3
    • 16044375105 scopus 로고
    • Crystal structures of HIV-1 protease-inhibitor complexes
    • Appelt, K. Crystal structures of HIV-1 protease-inhibitor complexes. Perspect. Drug Discov. Des. 1:23-48, 1993.
    • (1993) Perspect. Drug Discov. Des. , vol.1 , pp. 23-48
    • Appelt, K.1
  • 4
    • 0027218692 scopus 로고
    • Structure-based inhibitors of HIV-1 protease
    • Wlodawer, A., Erickson, J.W. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62:543-585, 1993.
    • (1993) Annu. Rev. Biochem. , vol.62 , pp. 543-585
    • Wlodawer, A.1    Erickson, J.W.2
  • 5
  • 6
    • 0027439390 scopus 로고
    • Atomic structures of the human immunophilin FKBP12 complexes with FK506 and rapamycin
    • Van Duyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L., Clardy, J. Atomic structures of the human immunophilin FKBP12 complexes with FK506 and rapamycin. J. Mol. Biol. 229:105-124, 1991.
    • (1991) J. Mol. Biol. , vol.229 , pp. 105-124
    • Van Duyne, G.D.1    Standaert, R.F.2    Karplus, P.A.3    Schreiber, S.L.4    Clardy, J.5
  • 7
  • 8
    • 0026673724 scopus 로고
    • Crystal structures of two viral peptides in complex with murine MHC class I H-2K
    • Fremont, D.H., Matsumura, M., Stura, E.A., Peterson, P.A., Wilson, I.A. Crystal structures of two viral peptides in complex with murine MHC class I H-2K. Science 257:919-927, 1992.
    • (1992) Science , vol.257 , pp. 919-927
    • Fremont, D.H.1    Matsumura, M.2    Stura, E.A.3    Peterson, P.A.4    Wilson, I.A.5
  • 9
    • 0026728457 scopus 로고
    • Emerging principles for the recognition of peptide antigens by MHC class I molecules
    • Matsumura, M., Fremont, D.H., Peterson, P.A., Wilson, I.A. Emerging principles for the recognition of peptide antigens by MHC class I molecules. Science 257:927-934, 1992.
    • (1992) Science , vol.257 , pp. 927-934
    • Matsumura, M.1    Fremont, D.H.2    Peterson, P.A.3    Wilson, I.A.4
  • 10
    • 0029310676 scopus 로고
    • A tricyclic system replaces the variable regions of peptides presented by three alleles of human MHC class I molecules
    • Weiss, G.A., Collins, E.J., Garboczi, D.N., Wiley, D.C., Schreiber, S.L. A tricyclic system replaces the variable regions of peptides presented by three alleles of human MHC class I molecules. Chem. Biol. 2:401-407, 1995.
    • (1995) Chem. Biol. , vol.2 , pp. 401-407
    • Weiss, G.A.1    Collins, E.J.2    Garboczi, D.N.3    Wiley, D.C.4    Schreiber, S.L.5
  • 11
    • 0025321903 scopus 로고
    • Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 Å
    • Stanfield, R.L., Fieser, T.M., Lerner, R.A., Wilson, I.A. Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 Å. Science 248:712-719, 1990.
    • (1990) Science , vol.248 , pp. 712-719
    • Stanfield, R.L.1    Fieser, T.M.2    Lerner, R.A.3    Wilson, I.A.4
  • 12
    • 0026587998 scopus 로고
    • Structural evidence for induced fit as a mechanism for antibody-antigen recognition
    • Rini, J.M., Schulze-Gahmen, U., Wilson, I.A. Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science 255:959-965, 1992.
    • (1992) Science , vol.255 , pp. 959-965
    • Rini, J.M.1    Schulze-Gahmen, U.2    Wilson, I.A.3
  • 13
    • 0027994352 scopus 로고
    • Predicting molecular interactions and inducible complementarity: Fragment docking of Fab-peptide complexes
    • Friedman, A.R., Roberts, V.A., Tainer, J.A. Predicting molecular interactions and inducible complementarity: Fragment docking of Fab-peptide complexes. Proteins 20: 15-24, 1994.
    • (1994) Proteins , vol.20 , pp. 15-24
    • Friedman, A.R.1    Roberts, V.A.2    Tainer, J.A.3
  • 14
    • 0028243847 scopus 로고
    • Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries
    • Gallop, M.A., Barrett, R.W., Dower, W.J., Fodor, S.P.A., Gordon, E.M. Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries. J. Med. Chem. 37:1233-1250, 1994.
    • (1994) J. Med. Chem. , vol.37 , pp. 1233-1250
    • Gallop, M.A.1    Barrett, R.W.2    Dower, W.J.3    Fodor, S.P.A.4    Gordon, E.M.5
  • 15
    • 0028318863 scopus 로고
    • Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies and future directions
    • Gordon, E.M., Barrett, R.W., Dower, W.J., Fodor, S.P.A., Gallop, M.A. Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies and future directions. J. Med. Chem. 37:1385-1400, 1994.
    • (1994) J. Med. Chem. , vol.37 , pp. 1385-1400
    • Gordon, E.M.1    Barrett, R.W.2    Dower, W.J.3    Fodor, S.P.A.4    Gallop, M.A.5
  • 16
    • 0025004285 scopus 로고
    • Random peptide libraries: A source of specific protein binding molecules
    • Devlin, J.J., Panganiban, L.C., Devlin, P.E. Random peptide libraries: A source of specific protein binding molecules. Science 249:404-406, 1990.
    • (1990) Science , vol.249 , pp. 404-406
    • Devlin, J.J.1    Panganiban, L.C.2    Devlin, P.E.3
  • 17
    • 0026419328 scopus 로고
    • A new type of synthetic peptide library for identifying ligand-binding activity
    • Lam, K.S., Salmon, S.E., Hersh, E.M., Hruby, V.J., Kazmierski, W.M., Knapp, R.J. A new type of synthetic peptide library for identifying ligand-binding activity. Nature 354: 82-84, 1991.
    • (1991) Nature , vol.354 , pp. 82-84
    • Lam, K.S.1    Salmon, S.E.2    Hersh, E.M.3    Hruby, V.J.4    Kazmierski, W.M.5    Knapp, R.J.6
  • 18
    • 0028808005 scopus 로고
    • Screening of cyclic peptide phage libraries identifies ligands that bind streptavidin with high affinities
    • Giebel, L.B., Cass, R.T., Milligan, D.L., Young, D.C., Arze, R., Johnson, C.R. Screening of cyclic peptide phage libraries identifies ligands that bind streptavidin with high affinities. Biochemistry 34:15430-15435, 1995.
    • (1995) Biochemistry , vol.34 , pp. 15430-15435
    • Giebel, L.B.1    Cass, R.T.2    Milligan, D.L.3    Young, D.C.4    Arze, R.5    Johnson, C.R.6
  • 19
    • 0029152204 scopus 로고
    • Structure-based design of high affinity streptavidin binding cyclic peptide ligands containing thioether cross-links
    • Katz, B.A., Johnson, C.R., Cass, R.T. Structure-based design of high affinity streptavidin binding cyclic peptide ligands containing thioether cross-links. J. Am. Chem. Soc. 117:8541-8547, 1995.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 8541-8547
    • Katz, B.A.1    Johnson, C.R.2    Cass, R.T.3
  • 20
    • 0026807019 scopus 로고
    • Crystal structure and ligand-binding studies of a screened peptide complexed with streptavidin
    • Weber, P.C., Pantoliano, M.W., Thompson, L.D. Crystal structure and ligand-binding studies of a screened peptide complexed with streptavidin. Biochemistry 31:9350-9354, 1992.
    • (1992) Biochemistry , vol.31 , pp. 9350-9354
    • Weber, P.C.1    Pantoliano, M.W.2    Thompson, L.D.3
  • 21
    • 0028841829 scopus 로고
    • Binding to protein targets of peptidic leads discovered by phage display: Crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence
    • Katz, B.A. Binding to protein targets of peptidic leads discovered by phage display: Crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence. Biochemistry 34:15421-15429, 1995.
    • (1995) Biochemistry , vol.34 , pp. 15421-15429
    • Katz, B.A.1
  • 22
    • 0029865819 scopus 로고    scopus 로고
    • Molecular interaction between the Strep-tag affinity peptide and its cognate target, streptavidin
    • Schmidt, T.G.M., Koepke, J., Frank, R., Skerra, A. Molecular interaction between the Strep-tag affinity peptide and its cognate target, streptavidin. J. Mol. Biol. 255:753-766, 1996.
    • (1996) J. Mol. Biol. , vol.255 , pp. 753-766
    • Schmidt, T.G.M.1    Koepke, J.2    Frank, R.3    Skerra, A.4
  • 23
    • 0027499708 scopus 로고
    • The random peptide library-assisted engineering of a C-terminal affinity peptide, useful for the detection and purification of a functional Ig Fv fragment
    • Schmidt, T.G.M., Skerra, A. The random peptide library-assisted engineering of a C-terminal affinity peptide, useful for the detection and purification of a functional Ig Fv fragment, Protein Eng. 6:109-122, 1993.
    • (1993) Protein Eng. , vol.6 , pp. 109-122
    • Schmidt, T.G.M.1    Skerra, A.2
  • 24
    • 0028148629 scopus 로고
    • Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains
    • Lim, W.A., Richards, F.M., Fox, R.O. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature 372:375-379, 1994.
    • (1994) Nature , vol.372 , pp. 375-379
    • Lim, W.A.1    Richards, F.M.2    Fox, R.O.3
  • 25
    • 0027962645 scopus 로고
    • Two binding orientations for peptides to the Src SH3 domain: Development of a general model for SH3-ligand interactions
    • Feng, S., Chen, J.K., Yu, H., Simon, J.A., Schreiber, S.L. Two binding orientations for peptides to the Src SH3 domain: Development of a general model for SH3-ligand interactions. Science 266:1241-1247, 1994.
    • (1994) Science , vol.266 , pp. 1241-1247
    • Feng, S.1    Chen, J.K.2    Yu, H.3    Simon, J.A.4    Schreiber, S.L.5
  • 26
    • 0029109272 scopus 로고
    • Combinatorial synthesis and multidimensional NMR spectroscopy: An approach to understanding protein-ligand interactions
    • Chen, J.K., Schreiber, S.L. Combinatorial synthesis and multidimensional NMR spectroscopy: An approach to understanding protein-ligand interactions. Angew. Chem. Int. Ed. Engl. 34:953-969, 1995.
    • (1995) Angew. Chem. Int. Ed. Engl. , vol.34 , pp. 953-969
    • Chen, J.K.1    Schreiber, S.L.2
  • 27
    • 0029829066 scopus 로고    scopus 로고
    • Unraveling principles of lead discovery: From unfrustrated energy landscapes to novel molecular anchors
    • Rejto, P.A., Verkhivker, G.M. Unraveling principles of lead discovery: From unfrustrated energy landscapes to novel molecular anchors. Proc. Natl. Acad. Sc. USA 93:8945-8950, 1996.
    • (1996) Proc. Natl. Acad. Sc. USA , vol.93 , pp. 8945-8950
    • Rejto, P.A.1    Verkhivker, G.M.2
  • 28
    • 0030058373 scopus 로고    scopus 로고
    • A mean field model of ligand-protein interactions: Implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding
    • Verkhivker, G.M., Rejto, P.A. A mean field model of ligand-protein interactions: Implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding. Proc. Natl. Acad. Sc. USA 93:60-64, 1996.
    • (1996) Proc. Natl. Acad. Sc. USA , vol.93 , pp. 60-64
    • Verkhivker, G.M.1    Rejto, P.A.2
  • 29
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HFV-1 protease: Conformationally flexible docking by evolutionary programming
    • Gehlhaar, D.K., Verkhivker, G.M., Rejto, P.A., Sherman, C.J., Fogel, D.B., Fogel, L.J., Freer, S.T. Molecular recognition of the inhibitor AG-1343 by HFV-1 protease: Conformationally flexible docking by evolutionary programming. Chem. Biol. 2:317-324, 1995.
    • (1995) Chem. Biol. , vol.2 , pp. 317-324
    • Gehlhaar, D.K.1    Verkhivker, G.M.2    Rejto, P.A.3    Sherman, C.J.4    Fogel, D.B.5    Fogel, L.J.6    Freer, S.T.7
  • 30
    • 0030055657 scopus 로고    scopus 로고
    • Exploring energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP12 complexes
    • Verkhivker, G.M., Rejto, P.A., Gehlhaar, D.K., Freer, S.T. Exploring energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP12 complexes. Proteins 25:342-353, 1996.
    • (1996) Proteins , vol.25 , pp. 342-353
    • Verkhivker, G.M.1    Rejto, P.A.2    Gehlhaar, D.K.3    Freer, S.T.4
  • 31
    • 1842405625 scopus 로고    scopus 로고
    • New trends in computational structure prediction of ligand-protein complexes for receptor-based drug design
    • van Gunsteren, W., Weiner, P., Wilkinson, A.J. (eds.) Leiden: ESCOM, in press
    • Rejto, P.A., Verkhivker, G.M., Gehlhaar, D.K., Freer, S.T. New trends in computational structure prediction of ligand-protein complexes for receptor-based drug design. In: "Computational Simulation of Biomolecular Systems." van Gunsteren, W., Weiner, P., Wilkinson, A.J. (eds.) Leiden: ESCOM, in press.
    • Computational Simulation of Biomolecular Systems
    • Rejto, P.A.1    Verkhivker, G.M.2    Gehlhaar, D.K.3    Freer, S.T.4
  • 32
    • 9144240095 scopus 로고
    • DREIDING: A generic force field for molecular simulation
    • Mayo, S.L., Olafson, B.D., Goddard, W.A. III. DREIDING: A generic force field for molecular simulation. J. Phys. Chem. 94:8897-8909, 1990.
    • (1990) J. Phys. Chem. , vol.94 , pp. 8897-8909
    • Mayo, S.L.1    Olafson, B.D.2    Goddard III, W.A.3
  • 33
    • 0024588901 scopus 로고
    • Structural origins of high-affinity biotin binding to streptavidin
    • Weber, P.C., Ohlendorf, D.H., Wendoloski, J.J., Salemme, F.R. Structural origins of high-affinity biotin binding to streptavidin. Science 243:85-88, 1989.
    • (1989) Science , vol.243 , pp. 85-88
    • Weber, P.C.1    Ohlendorf, D.H.2    Wendoloski, J.J.3    Salemme, F.R.4
  • 34
    • 0026606240 scopus 로고
    • Crystallographic and thermodynamic comparison of natural and synthetic ligands bound to streptavidin
    • Weber, P.C., Wendoloski, J.J., Pantoliano, M.W., Salemme, F.R. Crystallographic and thermodynamic comparison of natural and synthetic ligands bound to streptavidin. J. Am. Chem. Soc. 114:3197-3200, 1992.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 3197-3200
    • Weber, P.C.1    Wendoloski, J.J.2    Pantoliano, M.W.3    Salemme, F.R.4
  • 36
    • 0020972782 scopus 로고
    • Theoretical studies of protein folding
    • Go, N. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12:183-210, 1983.
    • (1983) Annu. Rev. Biophys. Bioeng. , vol.12 , pp. 183-210
    • Go, N.1
  • 37
    • 1842287603 scopus 로고    scopus 로고
    • Mean field analysis of FKBP12 complexes with FK506 and rapamycin: Implications for a role of crystallographic water molecules in molecular recognition and specificity
    • in press
    • Rejto, P.A., Verkhivker, G.M. Mean field analysis of FKBP12 complexes with FK506 and rapamycin: Implications for a role of crystallographic water molecules in molecular recognition and specificity. Proteins, in press.
    • Proteins
    • Rejto, P.A.1    Verkhivker, G.M.2
  • 39
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • Bryngelson, J.D., Onuchic, J.N., Socci, N.D., Wolynes, P.G. Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 21:167-195, 1995.
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 41
    • 0029027832 scopus 로고
    • On constructing folding heteropolymers
    • Ebeling, M., Nadler, W. On constructing folding heteropolymers. Proc. Natl. Acad. Sci. USA 92:8798-8802, 1995.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 8798-8802
    • Ebeling, M.1    Nadler, W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.