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Volumn 35, Issue 10-11, 2009, Pages 974-985

Coarse grain molecular dynamics simulation for the prediction of tertiary conformation of lysozyme adsorbed on silica surface

Author keywords

All atom molecular dynamics simulation; Coarse grain molecular dynamics simulation; Lysozyme; Molecular dynamics simulation; Silica surface; Tertiary conformation

Indexed keywords

COARSE GRAINS; MOLECULAR DYNAMICS SIMULATIONS; SILICA SURFACE; TERTIARY CONFORMATION;

EID: 73149113587     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020903015338     Document Type: Conference Paper
Times cited : (6)

References (45)
  • 1
    • 44249089305 scopus 로고    scopus 로고
    • Characterization of secondary and tertiary conformational changes of b lactoglobulin on silica nanoparticle surfaces
    • X. Wu and G. Narsimhan, Characterization of secondary and tertiary conformational changes of b lactoglobulin on silica nanoparticle surfaces, Langmuir 24 (2008), pp. 4989-4998.
    • (2008) Langmuir , vol.24 , pp. 4989-4998
    • Wu, X.1    Narsimhan, G.2
  • 2
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • C.B. Anfinsen, Principles that govern the folding of protein chains, Science 181 (1973), pp. 223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 3
    • 0033613255 scopus 로고    scopus 로고
    • Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
    • E. Alm and D. Baker, Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures, Proc. Natl Acad. Sci. USA 96 (1999), pp. 11305-11310.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 11305-11310
    • Alm, E.1    Baker, D.2
  • 4
    • 0032842870 scopus 로고    scopus 로고
    • The fundamentals of protein folding: Bringing together theory and experiment
    • C.M. Dobson and M. Karplus, The fundamentals of protein folding: bringing together theory and experiment, Curr. Opin. Struct. Biol. 9 (1999), pp. 92-101.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 92-101
    • Dobson, C.M.1    Karplus, M.2
  • 5
    • 34147177151 scopus 로고    scopus 로고
    • Improved sampling methods for molecular simulation
    • H. Lei and Y. Duan, Improved sampling methods for molecular simulation, Curr. Opin. Struct. Biol. 17 (2007), pp. 187-191.
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 187-191
    • Lei, H.1    Duan, Y.2
  • 6
    • 0034602807 scopus 로고    scopus 로고
    • Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and e domains
    • D.O. Alonso and V. Daggett, Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains, Proc. Natl Acad. Sci. USA 97 (2000), pp. 133-138.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 133-138
    • Alonso, D.O.1    Daggett, V.2
  • 7
    • 0034979318 scopus 로고    scopus 로고
    • Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and proteinnucleic acid noncovalent interactions
    • W. Wang, O. Donnii, C.M. Reyes, and P.A. Kollman, Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and proteinnucleic acid noncovalent interactions, Annu. Rev. Biophys. Biomol. Struct. 30 (2001), pp. 211-243.
    • (2001) Annu. Rev. Biophys. Biomol. Struct. , vol.30 , pp. 211-243
    • Wang, W.1    Donnii, O.2    Reyes, C.M.3    Kollman, P.A.4
  • 9
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • M. Karplus and J.A. McCammon, Molecular dynamics simulations of biomolecules, Nat. Struct. Biol. 9 (2002), pp. 646-652.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 10
    • 34249298006 scopus 로고    scopus 로고
    • Two-stage folding of HP-35 from ab initio simulations
    • H.X. Lei and Y. Duan, Two-stage folding of HP-35 from ab initio simulations, J. Mol. Biol. 370 (2007), pp. 196-206.
    • (2007) J. Mol. Biol. , vol.370 , pp. 196-206
    • Lei, H.X.1    Duan, Y.2
  • 11
    • 0141627542 scopus 로고    scopus 로고
    • 3D-LatticeMonte Carlo simulations of model proteins. Size effects on folding thermodynamics and kinetics
    • K. Leonhard, J.M. Prausnitz, and C.J. Radke, 3D-LatticeMonte Carlo simulations of model proteins. Size effects on folding thermodynamics and kinetics, Biophys. Chem. 106 (2003), pp. 81-89.
    • (2003) Biophys. Chem. , vol.106 , pp. 81-89
    • Leonhard, K.1    Prausnitz, J.M.2    Radke, C.J.3
  • 12
    • 1642534616 scopus 로고    scopus 로고
    • Solvent-amino acid interaction energies in three-dimensional-lattice Monte Carlo simulations of a model 27-mer protein: Folding thermodynamics and kinetics
    • K. Leonhard, J.M. Prausnitz, and C.J. Radke, Solvent-amino acid interaction energies in three-dimensional-lattice Monte Carlo simulations of a model 27-mer protein: folding thermodynamics and kinetics, Protein Sci. 13 (2004), pp. 358-369.
    • (2004) Protein Sci. , vol.13 , pp. 358-369
    • Leonhard, K.1    Prausnitz, J.M.2    Radke, C.J.3
  • 13
    • 33645517317 scopus 로고    scopus 로고
    • Three-dimensional lattice Monte Carlo simulations of model proteins. IV. Proteins at an oil-water interface
    • K. Leonhard, J.M. Prausnitz, and C.J. Radke, Three-dimensional lattice Monte Carlo simulations of model proteins. IV. Proteins at an oil-water interface, Langmuir 22 (2006), pp. 3265-3272.
    • (2006) Langmuir , vol.22 , pp. 3265-3272
    • Leonhard, K.1    Prausnitz, J.M.2    Radke, C.J.3
  • 14
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grain model for semiquantitative lipid simulations
    • S.J. Marrink, A.H. de Vrij, and A.E. Mark, Coarse grain model for semiquantitative lipid simulations, J. Phys. Chem. B 108 (2004), pp. 750-760.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 750-760
    • Marrink, S.J.1    Vrij De, A.H.2    Mark, A.E.3
  • 15
    • 34548020295 scopus 로고    scopus 로고
    • A coarse-grained protein-protein potential derived from an all-atom force field
    • N. Basdevant, D. Borgis, and T. Ha-Duong, A coarse-grained protein-protein potential derived from an all-atom force field, J. Phys. Chem. B 111 (2007), pp. 9390-9399.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 9390-9399
    • Basdevant, N.1    Borgis, D.2    Ha-Duong, T.3
  • 16
    • 33644893631 scopus 로고    scopus 로고
    • Coarse grained protein-lipid model with application to lipoprotein particles
    • A.Y. Shih, A. Arkhipov, P.L. Freddolino, and K. Schulten, Coarse grained protein-lipid model with application to lipoprotein particles, J. Phys. Chem. B 110 (2006), pp. 3674-3684.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 3674-3684
    • Shih, A.Y.1    Arkhipov, A.2    Freddolino, P.L.3    Schulten, K.4
  • 17
    • 33644644163 scopus 로고    scopus 로고
    • Insertion and assembly of membrane proteins via simulation
    • P.J. Bond and M.S. Sansom, Insertion and assembly of membrane proteins via simulation, J. Am. Chem. Soc. 128 (2006), pp. 2697-2704.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 2697-2704
    • Bond, P.J.1    Sansom, M.S.2
  • 18
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Y. Sugita and Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chem. Phys. Lett. 314 (1999), pp. 141-151.
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 19
    • 0000646464 scopus 로고
    • On a remarkable bacteriolytic element found in tissues and secretions
    • A. Fleming, On a remarkable bacteriolytic element found in tissues and secretions, Proc. R. Soc. Ser. B 93 (1922), pp. 306-317.
    • (1922) Proc. R. Soc. Ser. B , vol.93 , pp. 306-317
    • Fleming, A.1
  • 20
    • 0013852463 scopus 로고
    • Structure of hen egg-white lysozyme. A threedimensional Fourier synthesis at 2A ° ngstrom resolution
    • C.C. Blake, D.F. Koenig, G.A. Mair, A.C.T. North, D.C. Phillips, and V.R. Sarma, Structure of hen egg-white lysozyme. A threedimensional Fourier synthesis at 2A ° ngstrom resolution, Nature 206 (1965), pp. 757-761.
    • (1965) Nature , vol.206 , pp. 757-761
    • Blake, C.C.1    Koenig, D.F.2    Mair, G.A.3    North, A.C.T.4    Phillips, D.C.5    Sarma, V.R.6
  • 21
    • 0026551529 scopus 로고
    • Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-Acetylchitotriose at 1.75A ° resolution
    • J.C. Cheetham, P.J. Artymiuk, and D.C. Phillips, Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-Acetylchitotriose at 1.75A ° resolution, J. Mol. Biol. 224 (1992), p. 613.
    • (1992) J. Mol. Biol. , vol.224 , pp. 613
    • Cheetham, J.C.1    Artymiuk, P.J.2    Phillips, D.C.3
  • 22
    • 0013852450 scopus 로고
    • Structure of some crystalline lysozyme-inhibitor complexes determined by X-ray analysis at 6Å ngstrom resolution
    • L.N. Johnson and D.C. Phillips, Structure of some crystalline lysozyme-inhibitor complexes determined by X-ray analysis at 6Å ngstrom resolution, Nature 206 (1965), pp. 761-763.
    • (1965) Nature , vol.206 , pp. 761-763
    • Johnson, L.N.1    Phillips, D.C.2
  • 23
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia, SCOP: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol. 247 (1995), pp. 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 24
    • 0035940959 scopus 로고    scopus 로고
    • Cooperative folding of the isolated alphahelical domain of hen egg-white lysozyme
    • P. Bai and Z. Peng, Cooperative folding of the isolated alphahelical domain of hen egg-white lysozyme, J. Mol. Biol. 314 (2001), pp. 321-329.
    • (2001) J. Mol. Biol. , vol.314 , pp. 321-329
    • Bai, P.1    Peng, Z.2
  • 25
    • 0029687176 scopus 로고    scopus 로고
    • Folding of lysozyme
    • B. Fischer, Folding of lysozyme, EXS 75 (1996), pp. 143-161.
    • (1996) EXS , vol.75 , pp. 143-161
    • Fischer, B.1
  • 26
    • 0035941116 scopus 로고    scopus 로고
    • Native-like tertiary structure formation in the alpha-domain of a hen lysozyme twodisulfide variant
    • H. Tachibana, O. Akasaka and K. Takashi, Native-like tertiary structure formation in the alpha-domain of a hen lysozyme twodisulfide variant, J. Mol. Biol. 314 (2001), pp. 311-320.
    • (2001) J. Mol. Biol. , vol.314 , pp. 311-320
    • Tachibana, H.1    Akasaka, O.2    Takashi, K.3
  • 27
    • 0037382047 scopus 로고    scopus 로고
    • Steady state tryptophan fluorescence spectroscopy study to probe tertiary structure of proteins in solid powders
    • V.K. Sharma and D.S. Kalonia, Steady state tryptophan fluorescence spectroscopy study to probe tertiary structure of proteins in solid powders, J. Pharm. Sci. 92 (2003), pp. 890-899.
    • (2003) J. Pharm. Sci. , vol.92 , pp. 890-899
    • Sharma, V.K.1    Kalonia, D.S.2
  • 28
    • 0033563828 scopus 로고    scopus 로고
    • Chymotrypsin adsorption on montmorillonite: Enzymatic activity and kinetic FTIR structural analysis
    • M.H. Baron, M. Revault, S. Servagent-Noinville, J. Abadie and H. Quiquampoix, Chymotrypsin adsorption on montmorillonite: enzymatic activity and kinetic FTIR structural analysis, J. Colloid Interf. Sci. 214 (1999), pp. 319-332.
    • (1999) J. Colloid Interf. Sci. , vol.214 , pp. 319-332
    • Baron, M.H.1    Revault, M.2    Servagent-Noinville, S.3    Abadie, J.4    Quiquampoix, H.5
  • 29
    • 0036299064 scopus 로고    scopus 로고
    • Conformational changes of enzymes adsorbed at liquid-solid interface: Relevance to enzymatic activity
    • S. Noinville, M. Revault, M. Baron, A. Tiss, S. Yapoudjian, M. Ivanova, and R. Verger, Conformational changes of enzymes adsorbed at liquid-solid interface: relevance to enzymatic activity, Biopolymers 67 (2002), pp. 323-326.
    • (2002) Biopolymers , vol.67 , pp. 323-326
    • Noinville, S.1    Revault, M.2    Baron, M.3    Tiss, A.4    Yapoudjian, S.5    Ivanova, M.6    Verger, R.7
  • 31
    • 0343907224 scopus 로고    scopus 로고
    • Adsorption to silica nanoparticles of human carbonic anhydrase II and truncated forms induce a molten-globule-like structure
    • P. Billsten, P.O. Freskgard, U. Carlsson, B.H. Jonsson, and H. Elwing, Adsorption to silica nanoparticles of human carbonic anhydrase II and truncated forms induce a molten-globule-like structure, FEBS Lett. 402 (1997), pp. 67-72.
    • (1997) FEBS Lett. , vol.402 , pp. 67-72
    • Billsten, P.1    Freskgard, P.O.2    Carlsson, U.3    Jonsson, B.H.4    Elwing, H.5
  • 32
    • 4043075579 scopus 로고    scopus 로고
    • Silica nanoparticle size influences the structure and enzymatic activity of adsorbed lysozyme
    • A.A. Vertegel, et al., Silica nanoparticle size influences the structure and enzymatic activity of adsorbed lysozyme, Langmuir 20 (2004), pp. 6800-6807.
    • (2004) Langmuir , vol.20 , pp. 6800-6807
    • Vertegel, A.A.1
  • 33
    • 54049144209 scopus 로고    scopus 로고
    • Effect of surface concentration on secondary and tertiary conformational changes of lysozyme adsorbed on silica nanoparticles
    • X. Wu and G. Narsimhan, Effect of surface concentration on secondary and tertiary conformational changes of lysozyme adsorbed on silica nanoparticles, Biochim. Biophys. Acta (BBA) Proteins Proteomics 1784 (2008), pp. 1694-1701.
    • (2008) Biochim. Biophys. Acta (BBA) Proteins Proteomics , vol.1784 , pp. 1694-1701
    • Wu, X.1    Narsimhan, G.2
  • 38
    • 0344824394 scopus 로고    scopus 로고
    • Trp-cage: Folding free energy landscape in explicit water
    • R. Zhou, Trp-cage: folding free energy landscape in explicit water, Proc. Natl Acad. Sci. USA 100 (2003), pp. 13280-13285.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 13280-13285
    • Zhou, R.1
  • 39
    • 0037934616 scopus 로고    scopus 로고
    • Understanding folding and design: Replica-exchange simulations of "trp-cage" miniproteins
    • J.W. Pitera and W. Swope, Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins, Proc. Natl Acad. Sci. USA 100 (2003), pp. 7587-7592.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 7587-7592
    • Pitera, J.W.1    Swope, W.2
  • 40
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • W.C. Still, A. Tempczyk, R.C. Hawley, and T. Hendrickson, Semianalytical treatment of solvation for molecular mechanics and dynamics, J. Am. Chem. Soc. 112 (1990), pp. 6127-6129.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 41
    • 4043171970 scopus 로고    scopus 로고
    • The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii
    • D. Qiu, P.S. Shenkin, F.P. Hollinger, and W.C. Still, The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii, J. Phys. Chem. A 101 (1997), pp. 3005-3014.
    • (1997) J. Phys. Chem. A , vol.101 , pp. 3005-3014
    • Qiu, D.1    Shenkin, P.S.2    Hollinger, F.P.3    Still, W.C.4
  • 42
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • B. Hess, H. Bekker, H.J.C. Berendsen, and J. Fraaije, LINCS: a linear constraint solver for molecular simulations, J. Comput. Chem. 18 (1997), pp. 1463-1472.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.C.3    Fraaije, J.4
  • 45
    • 0001346989 scopus 로고
    • Exploration of structure, electron density distribution, and bonding in coesite with Fourier and pseudoatom refinement methods using single-crystal X-ray diffraction data
    • K.L. Geisinger, et al., Exploration of structure, electron density distribution, and bonding in coesite with Fourier and pseudoatom refinement methods using single-crystal X-ray diffraction data, J. Phys. Chem. 91 (1987), p. 3237.
    • (1987) J. Phys. Chem. , vol.91 , pp. 3237
    • Geisinger, K.L.1


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