메뉴 건너뛰기




Volumn 32, Issue 12-13, 2006, Pages 953-961

Simulations of biomolecule unbinding from protein using DL_POLY

(1)  Chau, P L a  

a CNRS   (France)

Author keywords

Granisetron; Molecular dynamics; Molecular recognition; Retinol; Retinol binding protein; Serotonin

Indexed keywords

BINDING ENERGY; COMPUTER SIMULATION; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PROTEINS; SOFTWARE PACKAGES;

EID: 34548383003     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020600835640     Document Type: Article
Times cited : (1)

References (50)
  • 1
    • 0003655740 scopus 로고    scopus 로고
    • English translation by, Blue Poppy Press, Boulder, Colorado, USA 1998
    • English translation by S.-Z. Yang, Divine Farmer's Materia Medica, Blue Poppy Press, Boulder, Colorado, USA (1998).
    • Divine Farmer's Materia Medica
    • Yang, S.-Z.1
  • 2
    • 34548379715 scopus 로고    scopus 로고
    • Dioscorides Pedanius of Anazarbos, De materia medica, 1518 edition published in Venice by Aldus Manutius.
    • Dioscorides Pedanius of Anazarbos, De materia medica, 1518 edition published in Venice by Aldus Manutius.
  • 3
    • 84977496150 scopus 로고
    • Über das Morphium, eine neue salzfähige Grundlage, und die Mekonsäure, als Hauptbestandteile des Opium
    • F.W.A. Sertürner. Über das Morphium, eine neue salzfähige Grundlage, und die Mekonsäure, als Hauptbestandteile des Opium. Annalen der Physik, 55, 56 (1817).
    • (1817) Annalen der Physik , vol.55 , pp. 56
    • Sertürner, F.W.A.1
  • 5
    • 0013049219 scopus 로고
    • The reflection of X-ray by crystals
    • W.H. Bragg. The reflection of X-ray by crystals. Proc. Royal Soc, Land., 89A, 246 (1913).
    • (1913) Proc. Royal Soc, Land , vol.89 A , pp. 246
    • Bragg, W.H.1
  • 6
    • 0001596033 scopus 로고
    • The structure of some crystals as indicated by their diffraction of X-rays
    • W.L. Bragg. The structure of some crystals as indicated by their diffraction of X-rays. Proc. Royal Soc, Land., 89A, 248 (1913).
    • (1913) Proc. Royal Soc, Land , vol.89 A , pp. 248
    • Bragg, W.L.1
  • 7
    • 34548392944 scopus 로고
    • Crystal structure of oxyhaemoglobin
    • M.F. Perutz. Crystal structure of oxyhaemoglobin. Nature, 150, 324 (1942).
    • (1942) Nature , vol.150 , pp. 324
    • Perutz, M.F.1
  • 8
    • 0003634774 scopus 로고    scopus 로고
    • Computer Techniques for Image Processing in Electron Microscopy, supplement to volume 10 of Advances in Electronics and Electron Physics
    • Academic Press, New York 1978
    • W.O. Saxton. Computer Techniques for Image Processing in Electron Microscopy, supplement to volume 10 of Advances in Electronics and Electron Physics series, Academic Press, New York (1978).
    • series
    • Saxton, W.O.1
  • 9
    • 0027506299 scopus 로고
    • Nicotinic acetylcholine receptor at 9A resolution
    • N. Unwin, Nicotinic acetylcholine receptor at 9A resolution. J. Mol. Biol., 229, 1101 (1993).
    • (1993) J. Mol. Biol , vol.229 , pp. 1101
    • Unwin, N.1
  • 10
    • 0028921479 scopus 로고
    • Acetylcholine receptor channel imaged in the open state
    • N. Unwin. Acetylcholine receptor channel imaged in the open state. Nature, 373, 37 (1995).
    • (1995) Nature , vol.373 , pp. 37
    • Unwin, N.1
  • 11
    • 0038112088 scopus 로고    scopus 로고
    • Structure and gating mechanism of the acetylcholine receptor pore
    • A. Miyazawa, Y. Fujiyoshi, N. Unwin. Structure and gating mechanism of the acetylcholine receptor pore. Nature, 423, 949 (2003).
    • (2003) Nature , vol.423 , pp. 949
    • Miyazawa, A.1    Fujiyoshi, Y.2    Unwin, N.3
  • 12
    • 13444271681 scopus 로고    scopus 로고
    • Refined structure of the nicotinic acetylcholine receptor at 4A resolution
    • N. Unwin. Refined structure of the nicotinic acetylcholine receptor at 4A resolution. J. Mol. Biol, 346, 967 (2005).
    • (2005) J. Mol. Biol , vol.346 , pp. 967
    • Unwin, N.1
  • 13
    • 0022419169 scopus 로고    scopus 로고
    • R. Kaptein, E.R.P. Zuiderweg, R.M. Scheek, R. Boelens, W.F. van Gunsteren. A. protein structure from NMR data, lac repressor headpiece. J. Mol. Biol, 182, 179 (1985).
    • R. Kaptein, E.R.P. Zuiderweg, R.M. Scheek, R. Boelens, W.F. van Gunsteren. A. protein structure from NMR data, lac repressor headpiece. J. Mol. Biol, 182, 179 (1985).
  • 15
    • 0029450365 scopus 로고
    • Hydration in drug design. l. Multiple hydrogenbonding features of water molecules in mediating proteinligand interactions
    • CS. Poornima, P.M. Dean. Hydration in drug design. l. Multiple hydrogenbonding features of water molecules in mediating proteinligand interactions. J. Comput.-Aided Mol. Des., 9, 500 (1995).
    • (1995) J. Comput.-Aided Mol. Des , vol.9 , pp. 500
    • Poornima, C.S.1    Dean, P.M.2
  • 16
    • 0029160486 scopus 로고
    • High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA
    • D.S. Wilson, B. Guenther, C. Desplan, J. Kuriyan. High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. Cell, 82, 709 (1995).
    • (1995) Cell , vol.82 , pp. 709
    • Wilson, D.S.1    Guenther, B.2    Desplan, C.3    Kuriyan, J.4
  • 17
    • 0029364787 scopus 로고
    • Conservation of water molecules in an antibody-antigen interaction
    • B.C. Braden, B.A. Fields, R.J. Poljak. Conservation of water molecules in an antibody-antigen interaction. J. Mol. Recogn., 8, 317(1995).
    • (1995) J. Mol. Recogn , vol.8 , pp. 317
    • Braden, B.C.1    Fields, B.A.2    Poljak, R.J.3
  • 18
    • 0029165754 scopus 로고
    • Thrombinthrombomodulin interaction-energetics and potential role of water as an allosteric effector
    • R. de Cristofaro, M. Picozzi, E. de Candia, B. Rocca, R. Landolfi. Thrombinthrombomodulin interaction-energetics and potential role of water as an allosteric effector. Biochem. J., 310, 49 (1995).
    • (1995) Biochem. J , vol.310 , pp. 49
    • de Cristofaro, R.1    Picozzi, M.2    de Candia, E.3    Rocca, B.4    Landolfi, R.5
  • 19
    • 0000493265 scopus 로고    scopus 로고
    • D.N. Dubins, R. Filfil, R.B. MacGregor, TV. Chalikian. Role of water in protein-ligand interactions: volumetric characterisation of the binding of 2′-CMP and 3′-CMP to ribonuclease A. J. Phys. Chem. B, 104, 390 (2000).
    • D.N. Dubins, R. Filfil, R.B. MacGregor, TV. Chalikian. Role of water in protein-ligand interactions: volumetric characterisation of the binding of 2′-CMP and 3′-CMP to ribonuclease A. J. Phys. Chem. B, 104, 390 (2000).
  • 21
    • 0024278057 scopus 로고
    • Protein-ligand dynamics: A 96-ps simulation of a myoglobin-xenon complex
    • R.F. Tilton, U.C. Singh, I.D. Kuntz, P.A. KoUman. Protein-ligand dynamics: a 96-ps simulation of a myoglobin-xenon complex. J. Mol. Biol., 199, 195 (1988).
    • (1988) J. Mol. Biol , vol.199 , pp. 195
    • Tilton, R.F.1    Singh, U.C.2    Kuntz, I.D.3    KoUman, P.A.4
  • 23
    • 85176693826 scopus 로고    scopus 로고
    • J. Leech, J. Prins, J. Hermans. SMD: visual steering of molecular dynamics for protein design. IEEE Comput. Sci. Eng., 3, 38 (1996).
    • J. Leech, J. Prins, J. Hermans. SMD: visual steering of molecular dynamics for protein design. IEEE Comput. Sci. Eng., 3, 38 (1996).
  • 24
    • 0030059225 scopus 로고    scopus 로고
    • Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
    • H. Grubmüller, B. Heymann, P. Tavan. Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science, 271, 997 (1996).
    • (1996) Science , vol.271 , pp. 997
    • Grubmüller, H.1    Heymann, B.2    Tavan, P.3
  • 25
  • 26
    • 0032906662 scopus 로고    scopus 로고
    • Unbinding of retinoie acid from its receptor studied by steered molecular dynamics
    • D. Kosztin, S. Izrailev, K. Schulten. Unbinding of retinoie acid from its receptor studied by steered molecular dynamics. Biophys. J., 76, 188 (1999).
    • (1999) Biophys. J , vol.76 , pp. 188
    • Kosztin, D.1    Izrailev, S.2    Schulten, K.3
  • 28
    • 0034874258 scopus 로고    scopus 로고
    • Molecular dynamics force probe simulations of antibody/antigen unbinding: Entropie control, and non-additivity of unbinding forces
    • B. Heymann, H. Grubmüller. Molecular dynamics force probe simulations of antibody/antigen unbinding: entropie control, and non-additivity of unbinding forces. Biophys. J., 81, 1295 (2001).
    • (2001) Biophys. J , vol.81 , pp. 1295
    • Heymann, B.1    Grubmüller, H.2
  • 29
    • 0037380955 scopus 로고    scopus 로고
    • Forced detachment of the CD2-CD58 complex
    • M.V. Bayas, K. Schulten, D. Leckband. Forced detachment of the CD2-CD58 complex. Biophys. J., 84, 2223 (2003).
    • (2003) Biophys. J , vol.84 , pp. 2223
    • Bayas, M.V.1    Schulten, K.2    Leckband, D.3
  • 30
    • 0000179672 scopus 로고    scopus 로고
    • Process and thermodynamics of ligand-receptor interaction studied using a novel simulation method
    • P.-L. Chau. Process and thermodynamics of ligand-receptor interaction studied using a novel simulation method. Chem. Phys. Lett., 334, 343 (2001).
    • (2001) Chem. Phys. Lett , vol.334 , pp. 343
    • Chau, P.-L.1
  • 31
    • 0027302351 scopus 로고
    • Crystal-structure of liganded and unliganded forms of bovine plasma retinol-binding protein
    • G. Zanotti, R. Bemi, H.L. Monaco. Crystal-structure of liganded and unliganded forms of bovine plasma retinol-binding protein. J. Biol. Chem., 268, 10728 (1993).
    • (1993) J. Biol. Chem , vol.268 , pp. 10728
    • Zanotti, G.1    Bemi, R.2    Monaco, H.L.3
  • 34
    • 0030175155 scopus 로고    scopus 로고
    • DL_POLY 2.0-a general-purpose parallel molecular dynamics package
    • T.R. Forester, W. Smith. DL_POLY 2.0-a general-purpose parallel molecular dynamics package. J. Mol. Graph., 14, 136 (1996).
    • (1996) J. Mol. Graph , vol.14 , pp. 136
    • Forester, T.R.1    Smith, W.2
  • 35
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics methods
    • S. Nosé. A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys., 81, 511 (1984).
    • (1984) J. Chem. Phys , vol.81 , pp. 511
    • Nosé, S.1
  • 36
    • 0001538909 scopus 로고
    • Canonical dynamics-equilibrium, phase space distributions
    • W.G. Hoover. Canonical dynamics-equilibrium, phase space distributions. Phys. Rev. A, 31, 1695 (1985).
    • (1985) Phys. Rev. A , vol.31 , pp. 1695
    • Hoover, W.G.1
  • 37
    • 84925711387 scopus 로고
    • Hoover NPT dynamics for systems varying in size and shape
    • S. Melchionna, G. Ciccotti, B.L. Holian. Hoover NPT dynamics for systems varying in size and shape. Mol. Phys., 78, 533 (1993)
    • (1993) Mol. Phys , vol.78 , pp. 533
    • Melchionna, S.1    Ciccotti, G.2    Holian, B.L.3
  • 38
    • 0000760421 scopus 로고
    • Direct dynamical calculation of entropy and free energy by adlabatic switching
    • M. Watanabe, W.P. Reinhardt. Direct dynamical calculation of entropy and free energy by adlabatic switching. Phys, Rev. Lett., 65, 3301 (1990).
    • (1990) Phys, Rev. Lett , vol.65 , pp. 3301
    • Watanabe, M.1    Reinhardt, W.P.2
  • 39
    • 0025344397 scopus 로고
    • Thermodynamic parameters of the binding of retinol to binding proteins and to membranes
    • N. Noy, Z.J. Xu. Thermodynamic parameters of the binding of retinol to binding proteins and to membranes. Biochemistry, 29, 3888 (1990).
    • (1990) Biochemistry , vol.29 , pp. 3888
    • Noy, N.1    Xu, Z.J.2
  • 41
    • 84961983475 scopus 로고    scopus 로고
    • Molecular surface generation using marching tetrahedra
    • S.L. Chan, E.O. Purisima. Molecular surface generation using marching tetrahedra. J. Comput Chem., 19, 1268 (1998).
    • (1998) J. Comput Chem , vol.19 , pp. 1268
    • Chan, S.L.1    Purisima, E.O.2
  • 42
    • 3042813453 scopus 로고    scopus 로고
    • Water movement during ligand unbinding from receptor site
    • P.-L. Chau. Water movement during ligand unbinding from receptor site. Biophys. J, 87, 121 (2004).
    • (2004) Biophys. J , vol.87 , pp. 121
    • Chau, P.-L.1
  • 44
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics Studies of proteins
    • A.D. MacKerell, et al. All-atom empirical potential for molecular modeling and dynamics Studies of proteins. J. Phys. Chem. B, 102, 3586 (1998).
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3586
    • MacKerell, A.D.1
  • 45
    • 0037381989 scopus 로고    scopus 로고
    • 3 receptor agonist-binding residues using homology modelling. Biophys. J., 84, 2338 (2003).
    • 3 receptor agonist-binding residues using homology modelling. Biophys. J., 84, 2338 (2003).
  • 46
    • 20144380360 scopus 로고    scopus 로고
    • 3 receptor binding site: a modeling and radioligand binding study. J. Biol. Chem., 280, 20476 (2005).
    • 3 receptor binding site: a modeling and radioligand binding study. J. Biol. Chem., 280, 20476 (2005).
  • 47
    • 33645978140 scopus 로고    scopus 로고
    • Unbinding pathways of an agonist and an antagonist from the 5-HT3 receptor
    • A.J. Thompson, P.-L. Chau, S.L. Chan, S.C.R. Lummis. Unbinding pathways of an agonist and an antagonist from the 5-HT3 receptor. Biophys. J., 90, 1979 (2006).
    • (2006) Biophys. J , vol.90 , pp. 1979
    • Thompson, A.J.1    Chau, P.-L.2    Chan, S.L.3    Lummis, S.C.R.4
  • 48
    • 34548391194 scopus 로고    scopus 로고
    • Private communication with Søren Toxværd in 1996
    • Private communication with Søren Toxværd in 1996.
  • 49
    • 0034634393 scopus 로고    scopus 로고
    • How do substrates enter and products exit the buried active site of cytochrome P450cam? l. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms
    • S.K. Lüdemann, V. Lounnas, R.C. Wade. How do substrates enter and products exit the buried active site of cytochrome P450cam? l. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. J. Mol. Biol., 303, 797 (2000).
    • (2000) J. Mol. Biol , vol.303 , pp. 797
    • Lüdemann, S.K.1    Lounnas, V.2    Wade, R.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.