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Volumn 82, Issue 11, 2014, Pages 2982-2997

Virtual screening on an α-helix to β-strand switchable region of the FGFR2 extracellular domain revealed positive and negative modulators

Author keywords

Allosteric modulation; Ambivalence; Bioinformatics; Disease; Drug discovery; Mutation; Protein structure; Receptor function; Secondary structure; Virtual screening

Indexed keywords

FIBROBLAST GROWTH FACTOR RECEPTOR 1; FIBROBLAST GROWTH FACTOR RECEPTOR 2; FIBROBLAST GROWTH FACTOR RECEPTOR 3; FIBROBLAST GROWTH FACTOR RECEPTOR 4; FGFR2 PROTEIN, HUMAN; FGFR2 PROTEIN, RAT; FIBROBLAST GROWTH FACTOR RECEPTOR; MITOGEN ACTIVATED PROTEIN KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE 3;

EID: 84937570315     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24657     Document Type: Article
Times cited : (2)

References (72)
  • 1
    • 0001079105 scopus 로고
    • On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations
    • Kabsch W, Sander C. On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci USA 1984;81:1075-1078.
    • (1984) Proc Natl Acad Sci USA , vol.81 , pp. 1075-1078
    • Kabsch, W.1    Sander, C.2
  • 2
    • 0027448801 scopus 로고
    • Origins of structural diversity within sequentially identical hexapeptides
    • Cohen BI, Presnell SR, Cohen FE. Origins of structural diversity within sequentially identical hexapeptides. Protein Sci 1993;2:2134-2145.
    • (1993) Protein Sci , vol.2 , pp. 2134-2145
    • Cohen, B.I.1    Presnell, S.R.2    Cohen, F.E.3
  • 3
    • 0031871068 scopus 로고    scopus 로고
    • Chameleon sequences in the PDB
    • Mezei M. Chameleon sequences in the PDB. Protein Eng 1998;11:411-414.
    • (1998) Protein Eng , vol.11 , pp. 411-414
    • Mezei, M.1
  • 4
    • 33749681874 scopus 로고    scopus 로고
    • Analysis of chameleon sequences by energy decomposition on a pairwise per-residue basis
    • Yoon S, Jung H. Analysis of chameleon sequences by energy decomposition on a pairwise per-residue basis. Protein J 2006;25:361-368.
    • (2006) Protein J , vol.25 , pp. 361-368
    • Yoon, S.1    Jung, H.2
  • 5
    • 34247223063 scopus 로고    scopus 로고
    • Analysis of chameleon sequences and their implications in biological processes
    • Guo JT, Jaromczyk JW, Xu Y. Analysis of chameleon sequences and their implications in biological processes. Proteins 2007;67:548-558.
    • (2007) Proteins , vol.67 , pp. 548-558
    • Guo, J.T.1    Jaromczyk, J.W.2    Xu, Y.3
  • 6
    • 0029865623 scopus 로고    scopus 로고
    • Context-dependent secondary structure formation of a designed protein sequence
    • Minor JrDL, Kim PS. Context-dependent secondary structure formation of a designed protein sequence. Nature 1996;380:730-734.
    • (1996) Nature , vol.380 , pp. 730-734
    • Minor Jr, D.L.1    Kim, P.S.2
  • 7
    • 80052326726 scopus 로고    scopus 로고
    • Evolutionary bridges to new protein folds: design of C-terminal Cro protein chameleon sequences
    • Anderson WJ, Van Dorn LO, Ingram WM, Cordes MHJ. Evolutionary bridges to new protein folds: design of C-terminal Cro protein chameleon sequences. Protein Eng Des Sel 2011;24:765-771.
    • (2011) Protein Eng Des Sel , vol.24 , pp. 765-771
    • Anderson, W.J.1    Van Dorn, L.O.2    Ingram, W.M.3    Cordes, M.H.J.4
  • 9
    • 0032509980 scopus 로고    scopus 로고
    • Crystal structure of the yeast MATα2/MCM1/DNA ternary complex
    • Tan S, Richmond TJ. Crystal structure of the yeast MATα2/MCM1/DNA ternary complex. Nature 1998;391:660-666.
    • (1998) Nature , vol.391 , pp. 660-666
    • Tan, S.1    Richmond, T.J.2
  • 10
    • 35348916034 scopus 로고    scopus 로고
    • Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains
    • Troffer-Charlier N, Cura V, Hassenboehler P, Moras D, Cavarelli J. Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains. EMBO J 2007;26:4391-4401.
    • (2007) EMBO J , vol.26 , pp. 4391-4401
    • Troffer-Charlier, N.1    Cura, V.2    Hassenboehler, P.3    Moras, D.4    Cavarelli, J.5
  • 11
    • 36549050792 scopus 로고    scopus 로고
    • MAD contortions: conformational dimerization boosts spindle checkpoint signalling
    • Mapelli M, Musacchio A. MAD contortions: conformational dimerization boosts spindle checkpoint signalling. Curr Opin Struct Biol 2007;17:716-725.
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 716-725
    • Mapelli, M.1    Musacchio, A.2
  • 12
    • 55249120526 scopus 로고    scopus 로고
    • Protein metamorphosis: the two-state behavior of Mad2
    • Luo X, Yu H. Protein metamorphosis: the two-state behavior of Mad2. Structure 2008;16:1616-1625.
    • (2008) Structure , vol.16 , pp. 1616-1625
    • Luo, X.1    Yu, H.2
  • 17
    • 58149299775 scopus 로고    scopus 로고
    • The Mad2 partial unfolding model: regulating mitosis through Mad2 conformational switching
    • Skinner JJ, Wood S, Shorter J, Englander SW, Black BE. The Mad2 partial unfolding model: regulating mitosis through Mad2 conformational switching. J Cell Biol 2008;183:761-768.
    • (2008) J Cell Biol , vol.183 , pp. 761-768
    • Skinner, J.J.1    Wood, S.2    Shorter, J.3    Englander, S.W.4    Black, B.E.5
  • 19
    • 84861315209 scopus 로고    scopus 로고
    • High-resolution structure of infectious prion protein: the final frontier
    • Diaz-Espinoza R, Soto C. High-resolution structure of infectious prion protein: the final frontier. Nat Struct Mol Biol 2012;19:370-377.
    • (2012) Nat Struct Mol Biol , vol.19 , pp. 370-377
    • Diaz-Espinoza, R.1    Soto, C.2
  • 20
    • 77953126861 scopus 로고    scopus 로고
    • Serotonin derivatives as a new class of non-ATP-competitive receptor tyrosine kinase inhibitors
    • Büttner A, Cottin T, Xu J, Tzagkaroulaki L, Giannis A. Serotonin derivatives as a new class of non-ATP-competitive receptor tyrosine kinase inhibitors. Bioorgan Med Chem 2010;18:3387-3402.
    • (2010) Bioorgan Med Chem , vol.18 , pp. 3387-3402
    • Büttner, A.1    Cottin, T.2    Xu, J.3    Tzagkaroulaki, L.4    Giannis, A.5
  • 21
    • 79953658137 scopus 로고    scopus 로고
    • Drug discovery and the human kinome: recent trends
    • Eglen R, Reisine T. Drug discovery and the human kinome: recent trends. Pharmacol Therapeut 2011;130:144-156.
    • (2011) Pharmacol Therapeut , vol.130 , pp. 144-156
    • Eglen, R.1    Reisine, T.2
  • 23
    • 0017873321 scopus 로고
    • Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
    • Garnier J, Osguthorpe DJ, Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 1978;120:97-120.
    • (1978) J Mol Biol , vol.120 , pp. 97-120
    • Garnier, J.1    Osguthorpe, D.J.2    Robson, B.3
  • 24
    • 0029884694 scopus 로고    scopus 로고
    • GOR method for predicting protein secondary structure from amino acid sequence
    • Garnier J, Gibrat JF, Robson B. GOR method for predicting protein secondary structure from amino acid sequence. Method Enzymol 1996;266:540-553.
    • (1996) Method Enzymol , vol.266 , pp. 540-553
    • Garnier, J.1    Gibrat, J.F.2    Robson, B.3
  • 26
    • 0032822088 scopus 로고    scopus 로고
    • Predicting allosteric switches in myosins
    • Kirshenbaum K, Young M, Highsmith S. Predicting allosteric switches in myosins. Prot Sci 1999;8:1806-1815.
    • (1999) Prot Sci , vol.8 , pp. 1806-1815
    • Kirshenbaum, K.1    Young, M.2    Highsmith, S.3
  • 29
    • 48649109470 scopus 로고    scopus 로고
    • Secondary structure conversions of Mycobacterium tuberculosis ribonucleotide reductase protein R2 under varying pH and temperature conditions
    • Georgieva ER, Narvaez AJ, Hedin N, Gräslund A. Secondary structure conversions of Mycobacterium tuberculosis ribonucleotide reductase protein R2 under varying pH and temperature conditions. Biophys Chem 2008;137:43-48.
    • (2008) Biophys Chem , vol.137 , pp. 43-48
    • Georgieva, E.R.1    Narvaez, A.J.2    Hedin, N.3    Gräslund, A.4
  • 31
    • 1642494905 scopus 로고    scopus 로고
    • Successful design and synthesis of a polarity-triggered β --> α conformational switch using the side chain interaction index (SCII) as a measure of local structural stability
    • Gehenn K, Pipkorn R, Reed J. Successful design and synthesis of a polarity-triggered β --> α conformational switch using the side chain interaction index (SCII) as a measure of local structural stability. Biochemistry 2004;43:607-612.
    • (2004) Biochemistry , vol.43 , pp. 607-612
    • Gehenn, K.1    Pipkorn, R.2    Reed, J.3
  • 32
    • 77952617181 scopus 로고    scopus 로고
    • Towards understanding secondary structure transitions: phosphorylation and metal coordination in model peptides
    • Broncel M, Wagner SC, Paul K, Hackenberger CPR, Koksch B. Towards understanding secondary structure transitions: phosphorylation and metal coordination in model peptides. Org Biomol Chem 2010;8:2575-2579.
    • (2010) Org Biomol Chem , vol.8 , pp. 2575-2579
    • Broncel, M.1    Wagner, S.C.2    Paul, K.3    Hackenberger, C.P.R.4    Koksch, B.5
  • 34
    • 29444445833 scopus 로고    scopus 로고
    • Sequence determinants of a conformational switch in a protein structure
    • Anderson TA, Cordes MHJ, Sauer RT. Sequence determinants of a conformational switch in a protein structure. Proc Natl Acad Sci USA 2005;102:18344-18349.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 18344-18349
    • Anderson, T.A.1    Cordes, M.H.J.2    Sauer, R.T.3
  • 35
  • 36
    • 84863012003 scopus 로고    scopus 로고
    • Mutational tipping points for switching protein folds and functions
    • He Y, Chen Y, Alexander PA, Bryan PN, Orban J. Mutational tipping points for switching protein folds and functions. Structure 2012;20:283-291.
    • (2012) Structure , vol.20 , pp. 283-291
    • He, Y.1    Chen, Y.2    Alexander, P.A.3    Bryan, P.N.4    Orban, J.5
  • 37
    • 61749083187 scopus 로고    scopus 로고
    • A thermodynamic approach to the conformational preferences of the 180-195 segment derived from the human prion protein α2-helix
    • Ronga L, Palladino P, Ragone R, Benedetti E, Rossi F. A thermodynamic approach to the conformational preferences of the 180-195 segment derived from the human prion protein α2-helix. J Pept Sci 2009;15:30-35.
    • (2009) J Pept Sci , vol.15 , pp. 30-35
    • Ronga, L.1    Palladino, P.2    Ragone, R.3    Benedetti, E.4    Rossi, F.5
  • 38
    • 77958579653 scopus 로고    scopus 로고
    • The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain
    • Weinzierl ROJ. The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain. BMC Biol 2010;8:134.
    • (2010) BMC Biol , vol.8 , pp. 134
    • Weinzierl, R.O.J.1
  • 39
    • 31944435091 scopus 로고    scopus 로고
    • Computational design of a single amino acid sequence that can switch between two distinct protein folds
    • Ambroggio XI, Kuhlman B. Computational design of a single amino acid sequence that can switch between two distinct protein folds. J Am Chem Soc 2006;128:1154-1161.
    • (2006) J Am Chem Soc , vol.128 , pp. 1154-1161
    • Ambroggio, X.I.1    Kuhlman, B.2
  • 40
    • 0034602719 scopus 로고    scopus 로고
    • Structural interactions of fibroblast growth factor receptor with its ligands
    • Stauber DJ, DiGabriele AD, Hendrickson WA. Structural interactions of fibroblast growth factor receptor with its ligands. Proc Natl Acad Sci USA 2000;97:49-54.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 49-54
    • Stauber, D.J.1    DiGabriele, A.D.2    Hendrickson, W.A.3
  • 42
    • 0037212102 scopus 로고    scopus 로고
    • LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
    • Venkatachalam CM, Jiang X, Oldfield T, Waldman M. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Mod 2003;21:289-307.
    • (2003) J Mol Graph Mod , vol.21 , pp. 289-307
    • Venkatachalam, C.M.1    Jiang, X.2    Oldfield, T.3    Waldman, M.4
  • 43
    • 34447524011 scopus 로고    scopus 로고
    • Structure-based virtual ligand screening with LigandFit: pose prediction and enrichment of compound collections
    • Montes M, Miteva MA, Villoutreix BO. Structure-based virtual ligand screening with LigandFit: pose prediction and enrichment of compound collections. Proteins 2007;68:712-725.
    • (2007) Proteins , vol.68 , pp. 712-725
    • Montes, M.1    Miteva, M.A.2    Villoutreix, B.O.3
  • 45
    • 61649100307 scopus 로고    scopus 로고
    • The FGF family: biology, pathophysiology and therapy
    • Beenken A, Mohammadi M. The FGF family: biology, pathophysiology and therapy. Nat Rev Drug Discov 2009;8:235-253.
    • (2009) Nat Rev Drug Discov , vol.8 , pp. 235-253
    • Beenken, A.1    Mohammadi, M.2
  • 46
    • 77956678642 scopus 로고    scopus 로고
    • Genetic alterations of FGF receptors: an emerging field in clinical cancer diagnostics and therapeutics
    • Katoh M. Genetic alterations of FGF receptors: an emerging field in clinical cancer diagnostics and therapeutics. Expert Rev Anticancer Ther 2010;10:1375-1379.
    • (2010) Expert Rev Anticancer Ther , vol.10 , pp. 1375-1379
    • Katoh, M.1
  • 47
    • 84862775159 scopus 로고    scopus 로고
    • Challenges and opportunities in the targeting of fibroblast growth factor receptors in breast cancer
    • Jain VK, Turner NC. Challenges and opportunities in the targeting of fibroblast growth factor receptors in breast cancer. Breast Cancer Res 2012;14:208.
    • (2012) Breast Cancer Res , vol.14 , pp. 208
    • Jain, V.K.1    Turner, N.C.2
  • 48
    • 77957896275 scopus 로고    scopus 로고
    • Statistical analysis and molecular dynamics simulations of ambivalent alpha-helices
    • Bhattacharjee N, Biswas P. Statistical analysis and molecular dynamics simulations of ambivalent alpha-helices. BMC Bioinform 2010;11:519.
    • (2010) BMC Bioinform , vol.11 , pp. 519
    • Bhattacharjee, N.1    Biswas, P.2
  • 49
    • 0032515975 scopus 로고    scopus 로고
    • Activating mutations in the extracellular domain of the fibroblast growth factor receptor 2 function by disruption of the disulfide bond in the third immunoglobulin-like domain
    • Robertson SC, Meyer AN, Hart KC, Galvin BD, Webster MK, Donoghue DJ. Activating mutations in the extracellular domain of the fibroblast growth factor receptor 2 function by disruption of the disulfide bond in the third immunoglobulin-like domain. Proc Natl Acad Sci USA 1998;95:4567-4572.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 4567-4572
    • Robertson, S.C.1    Meyer, A.N.2    Hart, K.C.3    Galvin, B.D.4    Webster, M.K.5    Donoghue, D.J.6
  • 50
    • 33645144263 scopus 로고    scopus 로고
    • Mutation screening in patients with syndromic craniosynostoses indicates that a limited number of recurrent FGFR2 mutations accounts for severe forms of Pfeiffer syndrome
    • Lajeunie E, Heuertz S, El Ghouzzi V, Martinovic J, Renier D, Le Merrer M, Bonaventure J. Mutation screening in patients with syndromic craniosynostoses indicates that a limited number of recurrent FGFR2 mutations accounts for severe forms of Pfeiffer syndrome. Eur J Hum Genet 2006;14:289-298.
    • (2006) Eur J Hum Genet , vol.14 , pp. 289-298
    • Lajeunie, E.1    Heuertz, S.2    El Ghouzzi, V.3    Martinovic, J.4    Renier, D.5    Le Merrer, M.6    Bonaventure, J.7
  • 51
    • 0031683688 scopus 로고    scopus 로고
    • Apert syndrome mutations in fibroblast growth factor receptor 2 exhibit increased affinity for FGF ligand
    • Anderson J, Burns HD, Enriquez-Harris P, Wilkie AOM, Heath JK. Apert syndrome mutations in fibroblast growth factor receptor 2 exhibit increased affinity for FGF ligand. Hum Mol Genet 1998;7:1475-1483.
    • (1998) Hum Mol Genet , vol.7 , pp. 1475-1483
    • Anderson, J.1    Burns, H.D.2    Enriquez-Harris, P.3    Wilkie, A.O.M.4    Heath, J.K.5
  • 52
    • 0034687699 scopus 로고    scopus 로고
    • Loss of fibroblast growth factor receptor 2 ligand-binding specificity in Apert syndrome
    • Yu K, Herr AB, Waksman G, Ornitz DM. Loss of fibroblast growth factor receptor 2 ligand-binding specificity in Apert syndrome. Proc Natl Acad Sci USA 2000;97:14536-14541.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 14536-14541
    • Yu, K.1    Herr, A.B.2    Waksman, G.3    Ornitz, D.M.4
  • 53
    • 68149157248 scopus 로고    scopus 로고
    • The origin of allosteric functional modulation: multiple pre-existing pathways
    • Del Sol A, Tsai CJ, Ma B, Nussinov R. The origin of allosteric functional modulation: multiple pre-existing pathways. Structure 2009;17:1042-1050.
    • (2009) Structure , vol.17 , pp. 1042-1050
    • Del Sol, A.1    Tsai, C.J.2    Ma, B.3    Nussinov, R.4
  • 63
    • 0034563423 scopus 로고    scopus 로고
    • Prediction of protein segments with the same aminoacid sequence and different secondary structure: a benchmark for predictive methods
    • Jacoboni I, Martelli PL, Fariselli P, Compiani M, Casadio R. Prediction of protein segments with the same aminoacid sequence and different secondary structure: a benchmark for predictive methods. Proteins 2000;41:535-544.
    • (2000) Proteins , vol.41 , pp. 535-544
    • Jacoboni, I.1    Martelli, P.L.2    Fariselli, P.3    Compiani, M.4    Casadio, R.5
  • 65
    • 33747816204 scopus 로고    scopus 로고
    • Identifying sequence regions undergoing conformational changes via predicted continuum secondary structure
    • Boden M, Bailey TL. Identifying sequence regions undergoing conformational changes via predicted continuum secondary structure. Bioinformatics 2006;22:1809-1814.
    • (2006) Bioinformatics , vol.22 , pp. 1809-1814
    • Boden, M.1    Bailey, T.L.2
  • 66
    • 44949083561 scopus 로고    scopus 로고
    • Ordered conformational change in the protein backbone: prediction of conformationally variable positions from sequence and low-resolution structural data
    • Kuznetsov IB. Ordered conformational change in the protein backbone: prediction of conformationally variable positions from sequence and low-resolution structural data. Proteins 2008;72:74-87.
    • (2008) Proteins , vol.72 , pp. 74-87
    • Kuznetsov, I.B.1
  • 67
    • 71549157431 scopus 로고    scopus 로고
    • A sequence-based hybrid predictor for identifying conformationally ambivalent regions in proteins
    • Liu YC, Yang MH, Lin WL, Huang CK, Oyang YJ. A sequence-based hybrid predictor for identifying conformationally ambivalent regions in proteins. BMC Genom 2009;10 (Suppl 3):S22.
    • (2009) BMC Genom , vol.10 , Issue.Suppl 3 , pp. S22
    • Liu, Y.C.1    Yang, M.H.2    Lin, W.L.3    Huang, C.K.4    Oyang, Y.J.5
  • 70
    • 84859949261 scopus 로고    scopus 로고
    • A series of α7 nicotinic acetylcholine receptor allosteric modulators with close chemical similarity but diverse pharmacological properties
    • Gill JK, Dhankher P, Sheppard TD, Sher E, Millar NS. A series of α7 nicotinic acetylcholine receptor allosteric modulators with close chemical similarity but diverse pharmacological properties. Mol Pharmacol 2012; 81:710-718.
    • (2012) Mol Pharmacol , vol.81 , pp. 710-718
    • Gill, J.K.1    Dhankher, P.2    Sheppard, T.D.3    Sher, E.4    Millar, N.S.5
  • 71
    • 84857375139 scopus 로고    scopus 로고
    • Allosteric modulation of seven transmembrane spanning receptors: theory, practice and opportunities for central nervous system drug discovery
    • Melancon BJ, Hopkins CR, Wood MR, Emmite KA, Niswender CM, Christopoulos A, Conn PJ, Lindsley CW. Allosteric modulation of seven transmembrane spanning receptors: theory, practice and opportunities for central nervous system drug discovery. J Med Chem 2012;55:1445-1464.
    • (2012) J Med Chem , vol.55 , pp. 1445-1464
    • Melancon, B.J.1    Hopkins, C.R.2    Wood, M.R.3    Emmite, K.A.4    Niswender, C.M.5    Christopoulos, A.6    Conn, P.J.7    Lindsley, C.W.8
  • 72
    • 79953213637 scopus 로고    scopus 로고
    • "Molecular switches" on mGluR allosteric ligands that modulate modes of pharmacology
    • Wood MR, Hopkins CR, Brogan JT, Conn PJ, Lindsley CW. "Molecular switches" on mGluR allosteric ligands that modulate modes of pharmacology. Biochemistry 2011;50:2403-2410.
    • (2011) Biochemistry , vol.50 , pp. 2403-2410
    • Wood, M.R.1    Hopkins, C.R.2    Brogan, J.T.3    Conn, P.J.4    Lindsley, C.W.5


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