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Volumn 7, Issue 6, 2011, Pages

Mutation D816V alters the internal structure and dynamics of C-Kit receptor cytoplasmic region: Implications for dimerization and activation mechanisms

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING ENERGY; BINDING SITES; CHEMICAL ACTIVATION; CONFORMATIONS; DIMERIZATION; DISEASES; ENZYMES; FREE ENERGY;

EID: 79959833426     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002068     Document Type: Article
Times cited : (69)

References (115)
  • 1
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, et al. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127: 635-648.
    • (2006) Cell , vol.127 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4    Kumar, C.5
  • 4
    • 0031026008 scopus 로고    scopus 로고
    • The protein kinases of budding yeast: six score and more
    • Hunter T, Plowman GD, (1997) The protein kinases of budding yeast: six score and more. Trends Biochem Sci 22: 18-22.
    • (1997) Trends Biochem Sci , vol.22 , pp. 18-22
    • Hunter, T.1    Plowman, G.D.2
  • 5
    • 0029020282 scopus 로고
    • Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification
    • Hanks SK, Hunter T, (1995) Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J 9: 576-596.
    • (1995) FASEB J , vol.9 , pp. 576-596
    • Hanks, S.K.1    Hunter, T.2
  • 6
    • 77955642537 scopus 로고    scopus 로고
    • Pathogenesis, classification and treatment of mastocytosis: state of the art in 2010 and future perspectives
    • Arock M, Valent P, (2010) Pathogenesis, classification and treatment of mastocytosis: state of the art in 2010 and future perspectives. Expert Rev Hematol 3: 497-516.
    • (2010) Expert Rev Hematol , vol.3 , pp. 497-516
    • Arock, M.1    Valent, P.2
  • 7
    • 0023989811 scopus 로고
    • Primary structure of c-kit: relationship with the CSF-1/PDGF receptor kinase family-oncogenic activation of v-kit involves deletion of extracellular domain and C terminus
    • Qiu FH, Ray P, Brown K, Barker PE, Jhanwar S, et al. (1988) Primary structure of c-kit: relationship with the CSF-1/PDGF receptor kinase family-oncogenic activation of v-kit involves deletion of extracellular domain and C terminus. EMBO J 7: 1003-1011.
    • (1988) EMBO J , vol.7 , pp. 1003-1011
    • Qiu, F.H.1    Ray, P.2    Brown, K.3    Barker, P.E.4    Jhanwar, S.5
  • 8
    • 77953896432 scopus 로고    scopus 로고
    • Cell Signaling by Receptor Tyrosine Kinases
    • Lemmon MA, Schlessinger J, (2010) Cell Signaling by Receptor Tyrosine Kinases. Cell 141: 1117-1134.
    • (2010) Cell , vol.141 , pp. 1117-1134
    • Lemmon, M.A.1    Schlessinger, J.2
  • 9
    • 2742529418 scopus 로고
    • Human Protooncogene C-Kit - A New Cell-Surface Receptor Tyrosine Kinase for An Unidentified Ligand
    • Yarden Y, Kuang WJ, Yangfeng T, Coussens L, Munemitsu S, et al. (1987) Human Protooncogene C-Kit- A New Cell-Surface Receptor Tyrosine Kinase for An Unidentified Ligand. EMBO J 6: 3341-3351.
    • (1987) EMBO J , vol.6 , pp. 3341-3351
    • Yarden, Y.1    Kuang, W.J.2    Yangfeng, T.3    Coussens, L.4    Munemitsu, S.5
  • 10
    • 34548501985 scopus 로고    scopus 로고
    • c-Kit-a hematopoietic cell essential receptor tyrosine kinase
    • Edling CE, Hallberg B, (2007) c-Kit-a hematopoietic cell essential receptor tyrosine kinase. Int J Biochem Cell Biol 39: 1995-1998.
    • (2007) Int J Biochem Cell Biol , vol.39 , pp. 1995-1998
    • Edling, C.E.1    Hallberg, B.2
  • 11
    • 27744551009 scopus 로고    scopus 로고
    • Structure and regulation of Kit protein-tyrosine kinase - The stem cell factor receptor
    • Roskoski R, (2005) Structure and regulation of Kit protein-tyrosine kinase- The stem cell factor receptor. Bioch Biophys Res Commun 338: 1307-1315.
    • (2005) Bioch Biophys Res Commun , vol.338 , pp. 1307-1315
    • Roskoski, R.1
  • 12
    • 0029785474 scopus 로고    scopus 로고
    • The kinase insert domain of interferon-induced protein kinase PKR is required for activity but not for interaction with the pseudosubstrate K3L
    • Craig AWB, Cosentino GP, Donze O, Sonenberg N, (1996) The kinase insert domain of interferon-induced protein kinase PKR is required for activity but not for interaction with the pseudosubstrate K3L. J Biol Chem 271: 24526-24533.
    • (1996) J Biol Chem , vol.271 , pp. 24526-24533
    • Craig, A.W.B.1    Cosentino, G.P.2    Donze, O.3    Sonenberg, N.4
  • 13
    • 0025343230 scopus 로고
    • Signal transduction by receptors with tyrosine kinase activity
    • Ullrich A, Schlessinger J, (1990) Signal transduction by receptors with tyrosine kinase activity. Cell 61: 203-212.
    • (1990) Cell , vol.61 , pp. 203-212
    • Ullrich, A.1    Schlessinger, J.2
  • 14
    • 33846987130 scopus 로고    scopus 로고
    • Structural basis for stem cell factor-KIT signaling and activation of class III receptor tyrosine kinases
    • Liu H, Chen X, Focia PJ, He X, (2007) Structural basis for stem cell factor-KIT signaling and activation of class III receptor tyrosine kinases. EMBO J 26: 891-901.
    • (2007) EMBO J , vol.26 , pp. 891-901
    • Liu, H.1    Chen, X.2    Focia, P.J.3    He, X.4
  • 15
    • 34447531743 scopus 로고    scopus 로고
    • Structural basis for activation of the receptor tyrosine kinase KIT by stem cell factor
    • Yuzawa S, Opatowsky Y, Zhang Z, Mandiyan V, Lax I, et al. (2007) Structural basis for activation of the receptor tyrosine kinase KIT by stem cell factor. Cell 130: 323-334.
    • (2007) Cell , vol.130 , pp. 323-334
    • Yuzawa, S.1    Opatowsky, Y.2    Zhang, Z.3    Mandiyan, V.4    Lax, I.5
  • 16
    • 0032493859 scopus 로고    scopus 로고
    • Switching signals on or off by receptor dimerization
    • Weiss A, Schlessinger J, (1998) Switching signals on or off by receptor dimerization. Cell 94: 277-280.
    • (1998) Cell , vol.94 , pp. 277-280
    • Weiss, A.1    Schlessinger, J.2
  • 17
    • 0034644539 scopus 로고    scopus 로고
    • Cell signaling by receptor tyrosine kinases
    • Schlessinger J, (2000) Cell signaling by receptor tyrosine kinases. Cell 103: 211-225.
    • (2000) Cell , vol.103 , pp. 211-225
    • Schlessinger, J.1
  • 18
    • 0032857449 scopus 로고    scopus 로고
    • The biology of stem cell factor and its receptor C-kit
    • Ashman LK, (1999) The biology of stem cell factor and its receptor C-kit. International J Biochem Cell Biol 31: 1037-1051.
    • (1999) International J Biochem Cell Biol , vol.31 , pp. 1037-1051
    • Ashman, L.K.1
  • 19
    • 0037013143 scopus 로고    scopus 로고
    • The conformational plasticity of protein kinases
    • Huse M, Kuriyan J, (2002) The conformational plasticity of protein kinases. Cell 109: 275-282.
    • (2002) Cell , vol.109 , pp. 275-282
    • Huse, M.1    Kuriyan, J.2
  • 20
    • 4444353636 scopus 로고    scopus 로고
    • Regulation of protein kinases; controlling activity through activation segment conformation
    • Nolen B, Taylor S, Ghosh G, (2004) Regulation of protein kinases; controlling activity through activation segment conformation. Mol Cell 15: 661-675.
    • (2004) Mol Cell , vol.15 , pp. 661-675
    • Nolen, B.1    Taylor, S.2    Ghosh, G.3
  • 21
    • 0842310394 scopus 로고    scopus 로고
    • The structural basis for autoinhibition of FLT3 by the juxtamembrane domain
    • Griffith J, Black J, Faerman C, Swenson L, Wynn M, et al. (2004) The structural basis for autoinhibition of FLT3 by the juxtamembrane domain. Mol Cell 13: 169-178.
    • (2004) Mol Cell , vol.13 , pp. 169-178
    • Griffith, J.1    Black, J.2    Faerman, C.3    Swenson, L.4    Wynn, M.5
  • 22
    • 0034614490 scopus 로고    scopus 로고
    • Signaling - 2000 and beyond
    • Hunter T, (2000) Signaling- 2000 and beyond. Cell 100: 113-127.
    • (2000) Cell , vol.100 , pp. 113-127
    • Hunter, T.1
  • 23
    • 0028838971 scopus 로고
    • Protein-Kinases and Phosphatases - the Yin and Yang of Protein-Phosphorylation and Signaling
    • Hunter T, (1995) Protein-Kinases and Phosphatases- the Yin and Yang of Protein-Phosphorylation and Signaling. Cell 80: 225-236.
    • (1995) Cell , vol.80 , pp. 225-236
    • Hunter, T.1
  • 24
    • 0028796630 scopus 로고
    • W/Kit Gene Required for Interstitial-Cells of Cajal and for Intestinal Pacemaker Activity
    • Huizinga JD, Thuneberg L, Kluppel M, Malysz J, Mikkelsen HB, et al. (1995) W/Kit Gene Required for Interstitial-Cells of Cajal and for Intestinal Pacemaker Activity. Nature 373: 347-349.
    • (1995) Nature , vol.373 , pp. 347-349
    • Huizinga, J.D.1    Thuneberg, L.2    Kluppel, M.3    Malysz, J.4    Mikkelsen, H.B.5
  • 25
    • 0018344526 scopus 로고
    • Decreased Production of Mast-Cells in S1-S1D Anemic Mice
    • Kitamura Y, Go S, (1979) Decreased Production of Mast-Cells in S1-S1D Anemic Mice. Blood 53: 492-497.
    • (1979) Blood , vol.53 , pp. 492-497
    • Kitamura, Y.1    Go, S.2
  • 26
    • 0018596155 scopus 로고
    • Distribution of Mast-Cell Precursors in Hematopoietic and Lymphopoietic Tissues of Mice
    • Kitamura Y, Shimada M, Go S, Matsuda H, Hatanaka K, et al. (1979) Distribution of Mast-Cell Precursors in Hematopoietic and Lymphopoietic Tissues of Mice. J Exp Med 150: 482-490.
    • (1979) J Exp Med , vol.150 , pp. 482-490
    • Kitamura, Y.1    Shimada, M.2    Go, S.3    Matsuda, H.4    Hatanaka, K.5
  • 27
    • 0018096538 scopus 로고
    • Decrease of Mast-Cells in W-W Nu Mice and Their Increase by Bone-Marrow Transplantation
    • Kitamura Y, Go S, Hatanaka K, (1978) Decrease of Mast-Cells in W-W Nu Mice and Their Increase by Bone-Marrow Transplantation. Blood 52: 447-452.
    • (1978) Blood , vol.52 , pp. 447-452
    • Kitamura, Y.1    Go, S.2    Hatanaka, K.3
  • 28
    • 12144278434 scopus 로고    scopus 로고
    • Normal and oncogenic forms of the receptor tyrosine kinase kit
    • Lennartsson J, Jelacic T, Linnekin D, Shivakrupa R, (2005) Normal and oncogenic forms of the receptor tyrosine kinase kit. Stem Cells 23: 16-43.
    • (2005) Stem Cells , vol.23 , pp. 16-43
    • Lennartsson, J.1    Jelacic, T.2    Linnekin, D.3    Shivakrupa, R.4
  • 29
    • 12144257058 scopus 로고    scopus 로고
    • Kit as a human oncogenic tyrosine kinase
    • Kitamura Y, Hirotab S, (2004) Kit as a human oncogenic tyrosine kinase. Cell Mol Life Sci 61: 2924-2931.
    • (2004) Cell Mol Life Sci , vol.61 , pp. 2924-2931
    • Kitamura, Y.1    Hirotab, S.2
  • 30
    • 0036769966 scopus 로고    scopus 로고
    • Pathology and diagnostic criteria of gastrointestinal stromal tumors (GISTs): a review
    • Miettinen M, Majidi M, Lasota J, (2002) Pathology and diagnostic criteria of gastrointestinal stromal tumors (GISTs): a review. Eur J Cancer 38: S39-S51.
    • (2002) Eur J Cancer , vol.38 , pp. 39-51
    • Miettinen, M.1    Majidi, M.2    Lasota, J.3
  • 31
    • 0141836914 scopus 로고    scopus 로고
    • FLT3: ITDoes matter in leukemia
    • Levis M, Small D, (2003) FLT3: ITDoes matter in leukemia. Leukemia 17: 1738-1752.
    • (2003) Leukemia , vol.17 , pp. 1738-1752
    • Levis, M.1    Small, D.2
  • 32
    • 0027359443 scopus 로고
    • Identification of Mutations in the Coding Sequence of the Protooncogene C-Kit in A Human Mast-Cell Leukemia-Cell Line Causing Ligand-Independent Activation of C-Kit Product
    • Furitsu T, Tsujimura T, Tono T, Ikeda H, Kitayama H, et al. (1993) Identification of Mutations in the Coding Sequence of the Protooncogene C-Kit in A Human Mast-Cell Leukemia-Cell Line Causing Ligand-Independent Activation of C-Kit Product. J Clin Invest 92: 1736-1744.
    • (1993) J Clin Invest , vol.92 , pp. 1736-1744
    • Furitsu, T.1    Tsujimura, T.2    Tono, T.3    Ikeda, H.4    Kitayama, H.5
  • 33
    • 0032873349 scopus 로고    scopus 로고
    • KIT protein expression and analysis of c-kit gene mutation in adenoid cystic carcinoma
    • Holst VA, Marshall CE, Moskaluk CA, Frierson HF, (1999) KIT protein expression and analysis of c-kit gene mutation in adenoid cystic carcinoma. Mod Pathol 12: 956-960.
    • (1999) Mod Pathol , vol.12 , pp. 956-960
    • Holst, V.A.1    Marshall, C.E.2    Moskaluk, C.A.3    Frierson, H.F.4
  • 35
    • 67649950344 scopus 로고    scopus 로고
    • Mechanisms of secondary resistance to tyrosine kinase inhibitors in gastrointestinal stromal tumours (Review)
    • Maleddu A, Pantaleo MA, Nannini M, Di BM, Saponara M, et al. (2009) Mechanisms of secondary resistance to tyrosine kinase inhibitors in gastrointestinal stromal tumours (Review). Oncol Rep 21: 1359-1366.
    • (2009) Oncol Rep , vol.21 , pp. 1359-1366
    • Maleddu, A.1    Pantaleo, M.A.2    Nannini, M.3    Di, B.M.4    Saponara, M.5
  • 36
    • 0034993741 scopus 로고    scopus 로고
    • Classes of c-KIT activating mutations: proposed mechanisms of action and implications for disease classification and therapy
    • Longley BJ, Reguera MJ, Ma Y, (2001) Classes of c-KIT activating mutations: proposed mechanisms of action and implications for disease classification and therapy. Leuk Res 25: 571-576.
    • (2001) Leuk Res , vol.25 , pp. 571-576
    • Longley, B.J.1    Reguera, M.J.2    Ma, Y.3
  • 37
    • 0035320853 scopus 로고    scopus 로고
    • Gastrointestinal stromal tumor with a novel mutation of KIT proto-oncogene
    • Fukuda R, Hamamoto N, Uchida Y, Furuta K, Katsube T, et al. (2001) Gastrointestinal stromal tumor with a novel mutation of KIT proto-oncogene. Int Med 40: 301-303.
    • (2001) Int Med , vol.40 , pp. 301-303
    • Fukuda, R.1    Hamamoto, N.2    Uchida, Y.3    Furuta, K.4    Katsube, T.5
  • 38
    • 0028959163 scopus 로고
    • Constitutively activating mutations of c-kit receptor tyrosine kinase confer factor-independent growth and tumorigenicity of factor-dependent hematopoietic cell lines
    • Kitayama H, Kanakura Y, Furitsu T, Tsujimura T, Oritani K, et al. (1995) Constitutively activating mutations of c-kit receptor tyrosine kinase confer factor-independent growth and tumorigenicity of factor-dependent hematopoietic cell lines. Blood 85: 790-798.
    • (1995) Blood , vol.85 , pp. 790-798
    • Kitayama, H.1    Kanakura, Y.2    Furitsu, T.3    Tsujimura, T.4    Oritani, K.5
  • 39
    • 0035871889 scopus 로고    scopus 로고
    • Activating mutation of D835 within the activation loop of FLT3 in human hematologic malignancies
    • Yamamoto Y, Kiyoi H, Nakano Y, Suzuki R, Kodera Y, et al. (2001) Activating mutation of D835 within the activation loop of FLT3 in human hematologic malignancies. Blood 97: 2434-2439.
    • (2001) Blood , vol.97 , pp. 2434-2439
    • Yamamoto, Y.1    Kiyoi, H.2    Nakano, Y.3    Suzuki, R.4    Kodera, Y.5
  • 40
    • 0042357240 scopus 로고    scopus 로고
    • Structure of a c-kit product complex reveals the basis for kinase transactivation
    • Mol CD, Lim KB, Sridhar V, Zou H, Chien EY, et al. (2003) Structure of a c-kit product complex reveals the basis for kinase transactivation. J Biol Chem 278: 31461-31464.
    • (2003) J Biol Chem , vol.278 , pp. 31461-31464
    • Mol, C.D.1    Lim, K.B.2    Sridhar, V.3    Zou, H.4    Chien, E.Y.5
  • 41
    • 4444311694 scopus 로고    scopus 로고
    • Analysis of the activating mutations within the activation loop of leukemia targets Flt-3 and c-Kit based on protein homology modeling
    • Torrent M, Rickert K, Pan BS, Sepp-Lorenzino L, (2004) Analysis of the activating mutations within the activation loop of leukemia targets Flt-3 and c-Kit based on protein homology modeling. J Mol Graph Model 23: 153-165.
    • (2004) J Mol Graph Model , vol.23 , pp. 153-165
    • Torrent, M.1    Rickert, K.2    Pan, B.S.3    Sepp-Lorenzino, L.4
  • 42
    • 0035469886 scopus 로고    scopus 로고
    • Phosphatidylinositol 3 kinase contributes to the transformation of hematopoietic cells by the D816V c-Kit mutant
    • Chian RJ, Young S, Danilkovitch-Miagkova A, Ronnstrand L, Leonard E, et al. (2001) Phosphatidylinositol 3 kinase contributes to the transformation of hematopoietic cells by the D816V c-Kit mutant. Blood 98: 1365-1373.
    • (2001) Blood , vol.98 , pp. 1365-1373
    • Chian, R.J.1    Young, S.2    Danilkovitch-Miagkova, A.3    Ronnstrand, L.4    Leonard, E.5
  • 43
    • 70349507344 scopus 로고    scopus 로고
    • The aberrant localization of oncogenic kit tyrosine kinase receptor mutants is reversed on specific inhibitory treatment
    • Bougherara H, Subra F, Crepin R, Tauc P, Auclair C, et al. (2009) The aberrant localization of oncogenic kit tyrosine kinase receptor mutants is reversed on specific inhibitory treatment. Mol Cancer Res 7: 1525-1533.
    • (2009) Mol Cancer Res , vol.7 , pp. 1525-1533
    • Bougherara, H.1    Subra, F.2    Crepin, R.3    Tauc, P.4    Auclair, C.5
  • 44
    • 0033557589 scopus 로고    scopus 로고
    • Activating mutation in the catalytic domain of c-kit elicits hematopoietic transformation by receptor self-association not at the ligand-induced dimerization site
    • Tsujimura T, Hashimoto K, Kitayama H, Ikeda H, Sugahara H, et al. (1999) Activating mutation in the catalytic domain of c-kit elicits hematopoietic transformation by receptor self-association not at the ligand-induced dimerization site. Blood 93: 1319-1329.
    • (1999) Blood , vol.93 , pp. 1319-1329
    • Tsujimura, T.1    Hashimoto, K.2    Kitayama, H.3    Ikeda, H.4    Sugahara, H.5
  • 45
    • 23644452511 scopus 로고    scopus 로고
    • Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component?
    • Kannan N, Neuwald AF, (2005) Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component? J Mol Biol 351: 956-972.
    • (2005) J Mol Biol , vol.351 , pp. 956-972
    • Kannan, N.1    Neuwald, A.F.2
  • 46
    • 55749102720 scopus 로고    scopus 로고
    • A helix scaffold for the assembly of active protein kinases
    • Kornev AP, Taylor SS, Ten Eyck LF, (2008) A helix scaffold for the assembly of active protein kinases. Proc Natl Acad Sci U S A 105: 14377-14382.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 14377-14382
    • Kornev, A.P.1    Taylor, S.S.2    Ten Eyck, L.F.3
  • 47
    • 77951270272 scopus 로고    scopus 로고
    • Large conformational changes in proteins: signaling and other functions
    • Grant BJ, Gorfe AA, McCammon JA, (2010) Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol 20: 142-147.
    • (2010) Curr Opin Struct Biol , vol.20 , pp. 142-147
    • Grant, B.J.1    Gorfe, A.A.2    McCammon, J.A.3
  • 48
    • 77954913405 scopus 로고    scopus 로고
    • Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor
    • Laine E, Goncalves C, Karst JC, Lesnard A, Rault S, et al. (2010) Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor. Proc Natl Acad Sci U S A 107: 11277-11282.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 11277-11282
    • Laine, E.1    Goncalves, C.2    Karst, J.C.3    Lesnard, A.4    Rault, S.5
  • 49
    • 64849113665 scopus 로고    scopus 로고
    • Trapping moving targets with small molecules
    • Lee GM, Craik CS, (2009) Trapping moving targets with small molecules. Science 324: 213-215.
    • (2009) Science , vol.324 , pp. 213-215
    • Lee, G.M.1    Craik, C.S.2
  • 50
    • 27644462900 scopus 로고    scopus 로고
    • The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation
    • Banavali NK, Roux B, (2005) The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation. Structure 13: 1715-1723.
    • (2005) Structure , vol.13 , pp. 1715-1723
    • Banavali, N.K.1    Roux, B.2
  • 51
    • 34248532092 scopus 로고    scopus 로고
    • Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck
    • Banavali NK, Roux B, (2007) Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Proteins 67: 1096-1112.
    • (2007) Proteins , vol.67 , pp. 1096-1112
    • Banavali, N.K.1    Roux, B.2
  • 52
    • 59449100832 scopus 로고    scopus 로고
    • Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases
    • Banavali NK, Roux B, (2009) Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins 74: 378-389.
    • (2009) Proteins , vol.74 , pp. 378-389
    • Banavali, N.K.1    Roux, B.2
  • 53
    • 67649781716 scopus 로고    scopus 로고
    • Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics
    • Kastner J, Loeffler HH, Roberts SK, Martin-Fernandez ML, Winn MD, (2009) Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics. J Struct Biol 167: 117-128.
    • (2009) J Struct Biol , vol.167 , pp. 117-128
    • Kastner, J.1    Loeffler, H.H.2    Roberts, S.K.3    Martin-Fernandez, M.L.4    Winn, M.D.5
  • 54
    • 69049106642 scopus 로고    scopus 로고
    • New insights into the activation of Escherichia coli tyrosine kinase revealed by molecular dynamics simulation and biochemical analysis
    • Lu T, Tan H, Lee D, Chen G, Jia Z, (2009) New insights into the activation of Escherichia coli tyrosine kinase revealed by molecular dynamics simulation and biochemical analysis. Biochemistry 48: 7986-7995.
    • (2009) Biochemistry , vol.48 , pp. 7986-7995
    • Lu, T.1    Tan, H.2    Lee, D.3    Chen, G.4    Jia, Z.5
  • 55
    • 70149117469 scopus 로고    scopus 로고
    • Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations
    • Dixit A, Verkhivker GM, (2009) Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations. PLoS Comput Biol 5: e1000487.
    • (2009) PLoS Comput Biol , vol.5
    • Dixit, A.1    Verkhivker, G.M.2
  • 56
    • 61549094352 scopus 로고    scopus 로고
    • Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability
    • Dixit A, Torkamani A, Schork NJ, Verkhivker G, (2009) Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability. Biophys J 96: 858-874.
    • (2009) Biophys J , vol.96 , pp. 858-874
    • Dixit, A.1    Torkamani, A.2    Schork, N.J.3    Verkhivker, G.4
  • 57
    • 33749002274 scopus 로고    scopus 로고
    • Impact of EGFR point mutations on the sensitivity to gefitinib: insights from comparative structural analyses and molecular dynamics simulations
    • Liu B, Bernard B, Wu JH, (2006) Impact of EGFR point mutations on the sensitivity to gefitinib: insights from comparative structural analyses and molecular dynamics simulations. Proteins 65: 331-346.
    • (2006) Proteins , vol.65 , pp. 331-346
    • Liu, B.1    Bernard, B.2    Wu, J.H.3
  • 58
    • 70149090164 scopus 로고    scopus 로고
    • The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
    • Bakan A, Bahar I, (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci U S A 106: 14349-14354.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 14349-14354
    • Bakan, A.1    Bahar, I.2
  • 59
    • 21644473891 scopus 로고    scopus 로고
    • Representing receptor flexibility in ligand docking through relevant normal modes
    • Cavasotto CN, Kovacs JA, Abagyan RA, (2005) Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 127: 9632-9640.
    • (2005) J Am Chem Soc , vol.127 , pp. 9632-9640
    • Cavasotto, C.N.1    Kovacs, J.A.2    Abagyan, R.A.3
  • 60
    • 45749139232 scopus 로고    scopus 로고
    • Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking
    • May A, Zacharias M, (2008) Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking. J Med Chem 51: 3499-3506.
    • (2008) J Med Chem , vol.51 , pp. 3499-3506
    • May, A.1    Zacharias, M.2
  • 61
    • 30044434744 scopus 로고    scopus 로고
    • Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
    • Tobi D, Bahar I, (2005) Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci U S A 102: 18908-18913.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 18908-18913
    • Tobi, D.1    Bahar, I.2
  • 62
    • 77957241496 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation
    • Cheng S, Niv MY, (2010) Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation. J Chem Inf Model 50: 1602-1610.
    • (2010) J Chem Inf Model , vol.50 , pp. 1602-1610
    • Cheng, S.1    Niv, M.Y.2
  • 63
    • 26444598487 scopus 로고    scopus 로고
    • Molecular modeling of wild-type and D816V c-kit inhibition based on ATP-competitive binding of ellipticine derivatives to tyrosine kinases
    • Vendome J, Letard S, Martin F, Svinarchuk F, Dubreuil P, et al. (2005) Molecular modeling of wild-type and D816V c-kit inhibition based on ATP-competitive binding of ellipticine derivatives to tyrosine kinases. J Med Chem 48: 6194-6201.
    • (2005) J Med Chem , vol.48 , pp. 6194-6201
    • Vendome, J.1    Letard, S.2    Martin, F.3    Svinarchuk, F.4    Dubreuil, P.5
  • 64
    • 4444230149 scopus 로고    scopus 로고
    • Molecular basis of the constitutive activity and STI571 resistance of Asp816Val mutant KIT receptor tyrosine kinase
    • Foster R, Griffith R, Ferrao P, Ashman L, (2004) Molecular basis of the constitutive activity and STI571 resistance of Asp816Val mutant KIT receptor tyrosine kinase. J Mol Graph Model 23: 139-152.
    • (2004) J Mol Graph Model , vol.23 , pp. 139-152
    • Foster, R.1    Griffith, R.2    Ferrao, P.3    Ashman, L.4
  • 65
    • 46449120133 scopus 로고    scopus 로고
    • Induced disorder in protein-ligand complexes as a drug-design strategy
    • Crespo A, Fernandez A, (2008) Induced disorder in protein-ligand complexes as a drug-design strategy. Mol Pharm 5: 430-437.
    • (2008) Mol Pharm , vol.5 , pp. 430-437
    • Crespo, A.1    Fernandez, A.2
  • 66
    • 34249290776 scopus 로고    scopus 로고
    • Rational drug redesign to overcome drug resistance in cancer therapy: imatinib moving target
    • Fernandez A, Sanguino A, Peng Z, Crespo A, Ozturk E, et al. (2007) Rational drug redesign to overcome drug resistance in cancer therapy: imatinib moving target. Cancer Res 67: 4028-4033.
    • (2007) Cancer Res , vol.67 , pp. 4028-4033
    • Fernandez, A.1    Sanguino, A.2    Peng, Z.3    Crespo, A.4    Ozturk, E.5
  • 67
    • 60849113175 scopus 로고    scopus 로고
    • KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients
    • Gajiwala KS, Wu JC, Christensen J, Deshmukh GD, Diehl W, et al. (2009) KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients. Proc Natl Acad Sci U S A 106: 1542-1547.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 1542-1547
    • Gajiwala, K.S.1    Wu, J.C.2    Christensen, J.3    Deshmukh, G.D.4    Diehl, W.5
  • 68
    • 44949190466 scopus 로고    scopus 로고
    • Detailed conformational dynamics of juxtamembrane region and activation loop in c-Kit kinase activation process
    • Zou J, Wang YD, Ma FX, Xiang ML, Shi B, et al. (2008) Detailed conformational dynamics of juxtamembrane region and activation loop in c-Kit kinase activation process. Proteins 72: 323-332.
    • (2008) Proteins , vol.72 , pp. 323-332
    • Zou, J.1    Wang, Y.D.2    Ma, F.X.3    Xiang, M.L.4    Shi, B.5
  • 69
    • 2942542387 scopus 로고    scopus 로고
    • Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase
    • Mol CD, Dougan DR, Schneider TR, Skene RJ, Kraus ML, et al. (2004) Structural basis for the autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase. J Biol Chem 279: 31655-31663.
    • (2004) J Biol Chem , vol.279 , pp. 31655-31663
    • Mol, C.D.1    Dougan, D.R.2    Schneider, T.R.3    Skene, R.J.4    Kraus, M.L.5
  • 70
    • 77950617070 scopus 로고    scopus 로고
    • Function of activation loop tyrosine phosphorylation in the mechanism of c-Kit auto-activation and its implication in sunitinib resistance
    • DiNitto JP, Deshmukh GD, Zhang Y, Jacques SL, Coli R, et al. (2010) Function of activation loop tyrosine phosphorylation in the mechanism of c-Kit auto-activation and its implication in sunitinib resistance. J Biochem 147: 601-609.
    • (2010) J Biochem , vol.147 , pp. 601-609
    • DiNitto, J.P.1    Deshmukh, G.D.2    Zhang, Y.3    Jacques, S.L.4    Coli, R.5
  • 71
    • 33745759471 scopus 로고    scopus 로고
    • Ensemble-based convergence analysis of biomolecular trajectories
    • Lyman E, Zuckerman DM, (2006) Ensemble-based convergence analysis of biomolecular trajectories. Biophys J 91: 164-172.
    • (2006) Biophys J , vol.91 , pp. 164-172
    • Lyman, E.1    Zuckerman, D.M.2
  • 72
    • 44349088854 scopus 로고    scopus 로고
    • The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis
    • Laine E, Yoneda JD, Blondel A, Malliavin TE, (2008) The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis. Proteins 71: 1813-1829.
    • (2008) Proteins , vol.71 , pp. 1813-1829
    • Laine, E.1    Yoneda, J.D.2    Blondel, A.3    Malliavin, T.E.4
  • 73
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • Kollman PA, Massova I, Reyes C, Kuhn B, Huo SH, et al. (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc Chem Res 33: 889-897.
    • (2000) Acc Chem Res , vol.33 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.H.5
  • 74
    • 0002611483 scopus 로고
    • Estimation of statistical errors in molecular simulation calculations
    • Straatsma TP, Berendsen HJC, Stam AJ, (1986) Estimation of statistical errors in molecular simulation calculations. Mol Phys 57: 89-95.
    • (1986) Mol Phys , vol.57 , pp. 89-95
    • Straatsma, T.P.1    Berendsen, H.J.C.2    Stam, A.J.3
  • 75
    • 2342648012 scopus 로고    scopus 로고
    • Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions
    • Blondel A, (2004) Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions. J Comput Chem 25: 985-993.
    • (2004) J Comput Chem , vol.25 , pp. 985-993
    • Blondel, A.1
  • 76
    • 77958451570 scopus 로고    scopus 로고
    • Activation of the edema factor of Bacillus anthracis by Calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding
    • Laine E, Martinez L, Blondel A, Malliavin TE, (2010) Activation of the edema factor of Bacillus anthracis by Calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding. Biophys J 99: 2264-2272.
    • (2010) Biophys J , vol.99 , pp. 2264-2272
    • Laine, E.1    Martinez, L.2    Blondel, A.3    Malliavin, T.E.4
  • 77
    • 49649108911 scopus 로고    scopus 로고
    • Solution conformations and dynamics of ABL kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib
    • Vajpai N, Strauss A, Fendrich G, Cowan-Jacob SW, Manley PW, et al. (2008) Solution conformations and dynamics of ABL kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib. J Biol Chem 283: 18292-18302.
    • (2008) J Biol Chem , vol.283 , pp. 18292-18302
    • Vajpai, N.1    Strauss, A.2    Fendrich, G.3    Cowan-Jacob, S.W.4    Manley, P.W.5
  • 78
    • 77949382914 scopus 로고    scopus 로고
    • Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis-application to the HIV-1 protease
    • Batista PR, Robert CH, Marechal JD, Hamida-Rebai MB, Pascutti PG, et al. (2010) Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis-application to the HIV-1 protease. Phys Chem Chem Phys 12: 2850-2859.
    • (2010) Phys Chem Chem Phys , vol.12 , pp. 2850-2859
    • Batista, P.R.1    Robert, C.H.2    Marechal, J.D.3    Hamida-Rebai, M.B.4    Pascutti, P.G.5
  • 79
    • 70449379413 scopus 로고    scopus 로고
    • Sequence and structure signatures of cancer mutation hotspots in protein kinases
    • Dixit A, Yi L, Gowthaman R, Torkamani A, Schork NJ, et al. (2009) Sequence and structure signatures of cancer mutation hotspots in protein kinases. PLoS One 4: e7485.
    • (2009) PLoS One , vol.4
    • Dixit, A.1    Yi, L.2    Gowthaman, R.3    Torkamani, A.4    Schork, N.J.5
  • 80
    • 67049154293 scopus 로고    scopus 로고
    • The crystal structure of BRAF in complex with an organoruthenium inhibitor reveals a mechanism for inhibition of an active form of BRAF kinase
    • Xie P, Streu C, Qin J, Bregman H, Pagano N, et al. (2009) The crystal structure of BRAF in complex with an organoruthenium inhibitor reveals a mechanism for inhibition of an active form of BRAF kinase. Biochemistry 48: 5187-5198.
    • (2009) Biochemistry , vol.48 , pp. 5187-5198
    • Xie, P.1    Streu, C.2    Qin, J.3    Bregman, H.4    Pagano, N.5
  • 81
    • 78349232462 scopus 로고    scopus 로고
    • Asymmetric tyrosine kinase arrangements in activation or autophosphorylation of receptor tyrosine kinases
    • Bae JH, Schlessinger J, (2010) Asymmetric tyrosine kinase arrangements in activation or autophosphorylation of receptor tyrosine kinases. Mol Cells 29: 443-448.
    • (2010) Mol Cells , vol.29 , pp. 443-448
    • Bae, J.H.1    Schlessinger, J.2
  • 82
    • 77649251478 scopus 로고    scopus 로고
    • Asymmetric receptor contact is required for tyrosine autophosphorylation of fibroblast growth factor receptor in living cells
    • Bae JH, Boggon TJ, Tome F, Mandiyan V, Lax I, et al. (2010) Asymmetric receptor contact is required for tyrosine autophosphorylation of fibroblast growth factor receptor in living cells. Proc Natl Acad Sci U S A 107: 2866-2871.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 2866-2871
    • Bae, J.H.1    Boggon, T.J.2    Tome, F.3    Mandiyan, V.4    Lax, I.5
  • 83
    • 77951557992 scopus 로고    scopus 로고
    • Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases
    • Aleksandrov A, Simonson T, (2010) Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases. J Biol Chem 285: 13807-13815.
    • (2010) J Biol Chem , vol.285 , pp. 13807-13815
    • Aleksandrov, A.1    Simonson, T.2
  • 84
    • 0020997912 scopus 로고
    • Dictionary of Protein Secondary Structure - Pattern-Recognition of Hydrogen-Bonded and Geometrical Features
    • Kabsch W, Sander C, (1983) Dictionary of Protein Secondary Structure- Pattern-Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 85
    • 0034663597 scopus 로고    scopus 로고
    • Application of multiple sequence alignment profiles to improve protein secondary structure prediction
    • Cuff JA, Barton GJ, (2000) Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins Struct Funct Genet 40: 502-511.
    • (2000) Proteins Struct Funct Genet , vol.40 , pp. 502-511
    • Cuff, J.A.1    Barton, G.J.2
  • 86
    • 0028304962 scopus 로고
    • Satisfying Hydrogen-Bonding Potential in Proteins
    • Mcdonald IK, Thornton JM, (1994) Satisfying Hydrogen-Bonding Potential in Proteins. J Mol Biol 238: 777-793.
    • (1994) J Mol Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 87
    • 79959855072 scopus 로고    scopus 로고
    • The PyMOL Molecular Grapics System, Delano Scientific, San Carlos, CA, USA
    • DeLano WL, (2002) The PyMOL Molecular Grapics System, Delano Scientific, San Carlos, CA, USA.
    • (2002)
    • DeLano, W.L.1
  • 88
    • 0026696669 scopus 로고
    • Definition and Display of Steric, Hydrophobic, and Hydrogen-Bonding Properties of Ligand-Binding Sites in Proteins Using Lee and Richards Accessible Surface - Validation of A High-Resolution Graphical Tool for Drug Design
    • Bohacek RS, Mcmartin C, (1992) Definition and Display of Steric, Hydrophobic, and Hydrogen-Bonding Properties of Ligand-Binding Sites in Proteins Using Lee and Richards Accessible Surface- Validation of A High-Resolution Graphical Tool for Drug Design. J Med Chem 35: 1671-1684.
    • (1992) J Med Chem , vol.35 , pp. 1671-1684
    • Bohacek, R.S.1    McMartin, C.2
  • 89
    • 0346458811 scopus 로고    scopus 로고
    • N - H...O, O - H...O, and C - H...O hydrogen bonds in protein-ligand complexes: Strong and weak interactions in molecular recognition
    • Sarkhel S, Desiraju GR, (2004) N- H...O, O- H...O, and C- H...O hydrogen bonds in protein-ligand complexes: Strong and weak interactions in molecular recognition. Proteins Struct Funct Genet 54: 247-259.
    • (2004) Proteins Struct Funct Genet , vol.54 , pp. 247-259
    • Sarkhel, S.1    Desiraju, G.R.2
  • 91
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser A, Do RKG, Sali A, (2000) Modeling of loops in protein structures. Protein Science 9: 1753-1773.
    • (2000) Protein Science , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.G.2    Sali, A.3
  • 93
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • Ponder JW, Case DA, (2003) Force fields for protein simulations. Adv Protein Chem 66: 27-85.
    • (2003) Adv Protein Chem , vol.66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2
  • 95
    • 0000035913 scopus 로고    scopus 로고
    • Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density
    • Jorgensen WL, Jenson C, (1998) Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density. J Comput Chem 19: 1179-1186.
    • (1998) J Comput Chem , vol.19 , pp. 1179-1186
    • Jorgensen, W.L.1    Jenson, C.2
  • 97
    • 0026869597 scopus 로고
    • Langevin Dynamics of Peptides - the Frictional Dependence of Isomerization Rates of N-Acetylalanyl-N'-Methylamide
    • Loncharich RJ, Brooks BR, Pastor RW, (1992) Langevin Dynamics of Peptides- the Frictional Dependence of Isomerization Rates of N-Acetylalanyl-N'-Methylamide. Biopolymers 32: 523-535.
    • (1992) Biopolymers , vol.32 , pp. 523-535
    • Loncharich, R.J.1    Brooks, B.R.2    Pastor, R.W.3
  • 98
    • 33846823909 scopus 로고
    • Particle Mesh Ewald - An N.Log(N) Method for Ewald Sums in Large Systems
    • Darden T, York D, Pedersen L, (1993) Particle Mesh Ewald- An N.Log(N) Method for Ewald Sums in Large Systems. J Chem Phys 98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 99
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Sanner MF, Olson AJ, Spehner JC, (1996) Reduced surface: An efficient way to compute molecular surfaces. Biopolymers 38: 305-320.
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 100
    • 0028922586 scopus 로고
    • Ligplot - A Program to Generate Schematic Diagrams of Protein Ligand Interactions
    • Wallace AC, Laskowski RA, Thornton JM, (1995) Ligplot- A Program to Generate Schematic Diagrams of Protein Ligand Interactions. Protein Eng 8: 127-134.
    • (1995) Protein Eng , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 102
    • 35148855766 scopus 로고    scopus 로고
    • Lexical scope and statistical computing
    • Gentleman R, Ihaka R, (2000) Lexical scope and statistical computing. J Comput Graph Stat 9: 491-508.
    • (2000) J Comput Graph Stat , vol.9 , pp. 491-508
    • Gentleman, R.1    Ihaka, R.2
  • 103
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of macromolecular solvation effects
    • Bashford D, Case DA, (2000) Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem 51: 129-152.
    • (2000) Annu Rev Phys Chem , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.A.2
  • 104
    • 20644449471 scopus 로고    scopus 로고
    • Modification of the generalized Born model suitable for macromolecules
    • Onufriev A, Bashford D, Case DA, (2000) Modification of the generalized Born model suitable for macromolecules. J Phys Chem B 104: 3712-3720.
    • (2000) J Phys Chem B , vol.104 , pp. 3712-3720
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 105
    • 1842479952 scopus 로고    scopus 로고
    • Exploring protein native states and large-scale conformational changes with a modified generalized born model
    • DOI 10.1002/prot.20033
    • Onufriev A, Bashford D, Case DA, (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55: 383-394 DOI 10.1002/prot.20033.
    • (2004) Proteins , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 106
    • 0029374782 scopus 로고
    • Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin
    • Perahia D, Mouawad L, (1995) Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin. J Comput Chem 19: 241-246.
    • (1995) J Comput Chem , vol.19 , pp. 241-246
    • Perahia, D.1    Mouawad, L.2
  • 109
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F, Sanejouand YH, (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng 14: 1-6.
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 110
    • 0000216012 scopus 로고
    • Collective Protein Dynamics and Nuclear-Spin Relaxation
    • Bruschweiler R, (1995) Collective Protein Dynamics and Nuclear-Spin Relaxation. J Chem Phys 102: 3396-3403.
    • (1995) J Chem Phys , vol.102 , pp. 3396-3403
    • Bruschweiler, R.1
  • 111
    • 33748759844 scopus 로고    scopus 로고
    • Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors
    • Floquet N, Marechal JD, Badet-Denisot MA, Robert CH, Dauchez M, et al. (2006) Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors. FEBS Lett 580: 5130-5136.
    • (2006) FEBS Lett , vol.580 , pp. 5130-5136
    • Floquet, N.1    Marechal, J.D.2    Badet-Denisot, M.A.3    Robert, C.H.4    Dauchez, M.5
  • 112
    • 58149103168 scopus 로고    scopus 로고
    • Collective motions in glucosamine-6-phosphate synthase: influence of ligand binding and role in ammonia channelling and opening of the fructose-6-phosphate binding site
    • Floquet N, Durand P, Maigret B, Badet B, Badet-Denisot MA, et al. (2009) Collective motions in glucosamine-6-phosphate synthase: influence of ligand binding and role in ammonia channelling and opening of the fructose-6-phosphate binding site. J Mol Biol 385: 653-664.
    • (2009) J Mol Biol , vol.385 , pp. 653-664
    • Floquet, N.1    Durand, P.2    Maigret, B.3    Badet, B.4    Badet-Denisot, M.A.5
  • 113
    • 67649422714 scopus 로고    scopus 로고
    • Fpocket: an open source platform for ligand pocket detection
    • Le GV, Schmidtke P, Tuffery P, (2009) Fpocket: an open source platform for ligand pocket detection. BMC Bioinformatics 10: 168.
    • (2009) BMC Bioinformatics , vol.10 , pp. 168
    • Le, G.V.1    Schmidtke, P.2    Tuffery, P.3
  • 115
    • 48449105393 scopus 로고    scopus 로고
    • The RosettaDock server for local protein-protein docking
    • Lyskov S, Gray JJ, (2008) The RosettaDock server for local protein-protein docking. Nucl Acids Res 36: W233-W238.
    • (2008) Nucl Acids Res , vol.36 , pp. 233-238
    • Lyskov, S.1    Gray, J.J.2


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