메뉴 건너뛰기




Volumn 2, Issue 13, 2011, Pages 1510-1519

Simulation of peptide-surface recognition

Author keywords

[No Author keywords available]

Indexed keywords

BINDING EVENTS; COMPUTATIONAL MODELING; DESIGN AND CONTROL; EXPERIMENTAL EVIDENCE; GOLD SURFACES; INORGANIC MATERIALS; NATURAL SYSTEMS; PRESENCE OF WATER; PROTEIN-SURFACE INTERACTIONS; SYNTHETIC SYSTEMS;

EID: 79960178615     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz200297k     Document Type: Review
Times cited : (66)

References (96)
  • 1
    • 1342302795 scopus 로고    scopus 로고
    • The interaction of proteins with solid surfaces
    • DOI 10.1016/j.sbi.2003.12.001
    • Gray, J. J. The Interaction of Proteins with Solid Surfaces Curr. Opin. Struct. Biol. 2004, 14, 110-115 (Pubitemid 38249599)
    • (2004) Current Opinion in Structural Biology , vol.14 , Issue.1 , pp. 110-115
    • Gray, J.J.1
  • 3
    • 33747192713 scopus 로고
    • Control and Design Principles in Biological Mineralization
    • Addadi, L.; Weiner, S. Control and Design Principles in Biological Mineralization Angew. Chem., Int. Ed. Engl. 1992, 31, 153-169
    • (1992) Angew. Chem., Int. Ed. Engl. , vol.31 , pp. 153-169
    • Addadi, L.1    Weiner, S.2
  • 4
    • 0029669273 scopus 로고    scopus 로고
    • Control of Crystal Phase Switching and Orientation by Soluble Mollusc-Shell Proteins
    • Belcher, A. M.; Wu, X. H.; Christensen, R. J.; Hansma, P. K.; Stucky, G. D.; Morse, D. E. Control of Crystal Phase Switching and Orientation by Soluble Mollusc-Shell Proteins Nature 1996, 381, 56-58
    • (1996) Nature , vol.381 , pp. 56-58
    • Belcher, A.M.1    Wu, X.H.2    Christensen, R.J.3    Hansma, P.K.4    Stucky, G.D.5    Morse, D.E.6
  • 6
    • 0038155646 scopus 로고    scopus 로고
    • Protein Components and Inorganic Structure in Shell Nacre in Haliotis Rufescens: Implications for Growth and Mechanical Behavior
    • Belcher, A. M.; Gooch, E. E. Protein Components and Inorganic Structure in Shell Nacre in Haliotis Rufescens: Implications for Growth and Mechanical Behavior Biomineralization 2002, 221-249
    • (2002) Biomineralization , pp. 221-249
    • Belcher, A.M.1    Gooch, E.E.2
  • 8
    • 0032982510 scopus 로고    scopus 로고
    • Structure, function and evolution of antifreeze proteins
    • DOI 10.1007/s000180050289
    • Ewart, K. V.; Lin, Q.; Hew, C. L. Structure, Function and Evolution of Antifreeze Proteins Cell. Mol. Life Sci. 1999, 55, 271-283 (Pubitemid 29118893)
    • (1999) Cellular and Molecular Life Sciences , vol.55 , Issue.2 , pp. 271-283
    • Ewart, K.V.1    Lin, Q.2    Hew, C.L.3
  • 9
    • 0034691568 scopus 로고    scopus 로고
    • Mimicry of ice structure by surface hydroxyls and water of a β-helix antifreeze protein
    • DOI 10.1038/35018604
    • Liou, Y. C.; Tocilj, A.; Davies, P. L.; Jia, Z. Mimicry of Ice Structure by Surface Hydroxyls and Water of a Beta-Helix Antifreeze Protein Nature 2000, 406, 322-324 (Pubitemid 30604412)
    • (2000) Nature , vol.406 , Issue.6793 , pp. 322-324
    • Liou, Y.-C.1    Tocilj, A.2    Davies, P.L.3    Jia, Z.4
  • 10
    • 0027641056 scopus 로고
    • Effect of the conformation and orientation of adsorbed fibronectin on endothelial cell spreading and the strength of adhesion
    • Juliano, D. J.; Saavedra, S. S.; Truskey, G. A. Effect of the Conformation and Orientation of Adsorbed Fibronectin on Endothelial-Cell Spreading and the Strength of Adhesion J. Biomed. Mater. Res. 1993, 27, 1103-1113 (Pubitemid 23206726)
    • (1993) Journal of Biomedical Materials Research , vol.27 , Issue.8 , pp. 1103-1113
    • Iuliano, D.J.1    Saavedra, S.S.2    Truskey, G.A.3
  • 11
    • 77955818652 scopus 로고    scopus 로고
    • Applications of Peptide and Protein-Based Materials in Bionanotechnology
    • De la Rica, R.; Matsui, H. Applications of Peptide and Protein-Based Materials in Bionanotechnology Chem. Soc. Rev. 2010, 39, 3499-3509
    • (2010) Chem. Soc. Rev. , vol.39 , pp. 3499-3509
    • De La Rica, R.1    Matsui, H.2
  • 13
    • 31944451232 scopus 로고    scopus 로고
    • Toxic potential of materials at the nanolevel
    • DOI 10.1126/science.1114397
    • Nel, A.; Xia, T.; Mädler, L.; Li, N. Toxic Potential of Materials at the Nanolevel Science 2006, 311, 622-627 (Pubitemid 43191298)
    • (2006) Science , vol.311 , Issue.5761 , pp. 622-627
    • Nel, A.1    Xia, T.2    Madler, L.3    Li, N.4
  • 14
    • 38949105860 scopus 로고    scopus 로고
    • Functionalized Carbon Nanotubes in Drug Design and Discovery
    • Prato, M.; Kostarelos, K.; Bianco, A. Functionalized Carbon Nanotubes in Drug Design and Discovery Acc. Chem. Res. 2008, 41, 60-68
    • (2008) Acc. Chem. Res. , vol.41 , pp. 60-68
    • Prato, M.1    Kostarelos, K.2    Bianco, A.3
  • 15
    • 26944462345 scopus 로고    scopus 로고
    • The role of nanobiotechnology in drug discovery
    • DOI 10.1016/S1359-6446(05)03573-7, PII S1359644605035737
    • Jain, K. K. The Role of Nanobiotechnology in Drug Discovery Drug Discovery Today 2005, 10, 1435-1442 (Pubitemid 41483872)
    • (2005) Drug Discovery Today , vol.10 , Issue.21 , pp. 1435-1442
    • Jain, K.K.1
  • 17
    • 0026669435 scopus 로고
    • Engineered Iron Oxide-Adhesion Mutants of the Escherichia-Coli Phage-Lambda Receptor
    • Brown, S. Engineered Iron Oxide-Adhesion Mutants of the Escherichia-Coli Phage-Lambda Receptor Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 8651-8655
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 8651-8655
    • Brown, S.1
  • 18
    • 0030198861 scopus 로고    scopus 로고
    • Monoclonal antibody recognition of cholesterol monohydrate crystal faces
    • DOI 10.1016/S1074-5521(96)90148-9
    • Perl-Treves, D.; Kessler, N.; Izhaky, D.; Addadi, L. Monoclonal Antibody Recognition of Cholesterol Monohydrate Crystal Faces Chem. Biol. 1996, 3, 567-577 (Pubitemid 26324170)
    • (1996) Chemistry and Biology , vol.3 , Issue.7 , pp. 567-577
    • Perl-Treves, D.1    Kessler, N.2    Izhaky, D.3    Addadi, L.4
  • 19
    • 67249149765 scopus 로고    scopus 로고
    • Molecular Biomimetics: Nanotechnology and Molecular Medicine Utilizing Genetically Engineered Peptides
    • Tamerler, C.; Sarikaya, M. Molecular Biomimetics: Nanotechnology and Molecular Medicine Utilizing Genetically Engineered Peptides Philos. Trans. R. Soc. London, Ser. A 2009, 367, 1705-1726
    • (2009) Philos. Trans. R. Soc. London, Ser. A , vol.367 , pp. 1705-1726
    • Tamerler, C.1    Sarikaya, M.2
  • 20
    • 33749993224 scopus 로고    scopus 로고
    • Materials specificity and directed assembly of a gold-binding peptide
    • DOI 10.1002/smll.200600070
    • Tamerler, C.; Duman, M.; Oren, E. E.; Gungormous, M.; Xiong, X.; Kacar, T.; Parviz, B. A.; Sarikaya, M. Materials Specificity and Directed Assembly of a Gold-Binding Peptide Small 2006, 2, 1372-1378 (Pubitemid 44569184)
    • (2006) Small , vol.2 , Issue.11 , pp. 1372-1378
    • Tamerler, C.1    Duman, M.2    Oren, E.E.3    Gungormus, M.4    Xiong, X.5    Kacar, T.6    Parviz, B.A.7    Sarikaya, M.8
  • 21
    • 33749652802 scopus 로고    scopus 로고
    • Antibody molecules discriminate between crystalline facets of a gallium arsenide semiconductor
    • DOI 10.1021/nl0607636
    • Artzy-Schnirman, A.; Zahavi, E.; Yeger, H.; Rosenfeld, R.; Benhar, I.; Reiter, Y.; Sivan, U. Antibody Molecules Discriminate Between Crystalline Facets of a Gallium Arsenide Semiconductor Nano Lett. 2006, 6, 1870-1874 (Pubitemid 44555223)
    • (2006) Nano Letters , vol.6 , Issue.9 , pp. 1870-1874
    • Schnirman, A.A.1    Zahavi, E.2    Yeger, H.3    Rosenfeld, R.4    Benhar, I.5    Reiter, Y.6    Sivan, U.7
  • 23
    • 0034621827 scopus 로고    scopus 로고
    • Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly
    • DOI 10.1038/35015043
    • Whaley, S. R.; English, D. S.; Hu, E. L.; Barbara, P. F.; Belcher, A. M. Selection of Peptides with Semiconductor Binding Specificity for Directed Nanocrystal Assembly Nature 2000, 405, 665-668 (Pubitemid 30428648)
    • (2000) Nature , vol.405 , Issue.6787 , pp. 665-668
    • Whaley, S.R.1    English, D.S.2    Hu, E.L.3    Barbara, P.F.4    Belcher, A.M.5
  • 24
    • 9744243512 scopus 로고    scopus 로고
    • Binding Specificity of a Peptide on Semiconductor Surfaces
    • Goede, K.; Busch, P.; Grundmann, M. Binding Specificity of a Peptide on Semiconductor Surfaces Nano Lett. 2004, 4, 2115-2120
    • (2004) Nano Lett. , vol.4 , pp. 2115-2120
    • Goede, K.1    Busch, P.2    Grundmann, M.3
  • 26
    • 68649099249 scopus 로고    scopus 로고
    • Probing the Conformation and Orientation of Adsorbed Enzymes Using Side-Chain Modification
    • Wei, Y.; Fears, K. P.; Sivaraman, B.; Powell, G. L.; Wu, Y.; Latour, R. A. Probing the Conformation and Orientation of Adsorbed Enzymes Using Side-Chain Modification Langmuir 2009, 25, 9319-9327
    • (2009) Langmuir , vol.25 , pp. 9319-9327
    • Wei, Y.1    Fears, K.P.2    Sivaraman, B.3    Powell, G.L.4    Wu, Y.5    Latour, R.A.6
  • 27
    • 78650183774 scopus 로고    scopus 로고
    • Correlation between Desorption Force Measured by Atomic Force Microscopy and Adsorption Free Energy Measured by Surface Plasmon Resonance Spectroscopy for Peptide-Surface Interactions
    • Latour, R. A. Correlation Between Desorption Force Measured by Atomic Force Microscopy and Adsorption Free Energy Measured by Surface Plasmon Resonance Spectroscopy for Peptide-Surface Interactions Langmuir 2010, 26, 18852-18861
    • (2010) Langmuir , vol.26 , pp. 18852-18861
    • Latour, R.A.1
  • 28
    • 77955562565 scopus 로고    scopus 로고
    • Protein-Nanoparticle Interaction: Identification of the Ubiquitin-Gold Nanoparticle Interaction Site
    • Calzolai, L.; Franchini, F.; Gilliland, D.; Rossi, F. Protein-Nanoparticle Interaction: Identification of the Ubiquitin-Gold Nanoparticle Interaction Site Nano Lett. 2010, 10, 3101-3105
    • (2010) Nano Lett. , vol.10 , pp. 3101-3105
    • Calzolai, L.1    Franchini, F.2    Gilliland, D.3    Rossi, F.4
  • 34
    • 3142735054 scopus 로고    scopus 로고
    • Brownian Dynamics Simulations of Simplified Cytochrome C Molecules in the Presence of a Charged Surface
    • Gorba, C.; Geyer, T.; Helms, V. Brownian Dynamics Simulations of Simplified Cytochrome C Molecules in the Presence of a Charged Surface J. Chem. Phys. 2004, 121, 457-464
    • (2004) J. Chem. Phys. , vol.121 , pp. 457-464
    • Gorba, C.1    Geyer, T.2    Helms, V.3
  • 35
    • 0037013360 scopus 로고    scopus 로고
    • A Brownian Dynamics Study of the Initial Stages of Hen Egg-White Lysozyme Adsorption at a Solid Interface
    • Ravichandran, S.; Madura, J. D.; Talbot, J. A Brownian Dynamics Study of the Initial Stages of Hen Egg-White Lysozyme Adsorption at a Solid Interface J. Phys. Chem. B 2011, 105, 3610-3613
    • (2011) J. Phys. Chem. B , vol.105 , pp. 3610-3613
    • Ravichandran, S.1    Madura, J.D.2    Talbot, J.3
  • 36
    • 67650159736 scopus 로고    scopus 로고
    • GolP: An Atomistic Force-Field to Describe the Interaction of Proteins with Au(111) Surfaces
    • Iori, F.; Di Felice, R.; Molinari, E.; Corni, S. GolP: An Atomistic Force-Field to Describe the Interaction of Proteins with Au(111) Surfaces J. Comput. Chem. 2009, 30, 1465-1476
    • (2009) J. Comput. Chem. , vol.30 , pp. 1465-1476
    • Iori, F.1    Di Felice, R.2    Molinari, E.3    Corni, S.4
  • 37
    • 46449115547 scopus 로고    scopus 로고
    • Including Image Charge Effects in the Molecular Dynamics Simulations of Molecules on Metal Surfaces
    • Iori, F.; Corni, S. Including Image Charge Effects in the Molecular Dynamics Simulations of Molecules on Metal Surfaces J. Comput. Chem. 2008, 29, 1656-1666
    • (2008) J. Comput. Chem. , vol.29 , pp. 1656-1666
    • Iori, F.1    Corni, S.2
  • 38
    • 52649166799 scopus 로고    scopus 로고
    • Unraveling the Interaction between Histidine Side Chain and the Au(111) Surface: A DFT Study
    • Iori, F.; Corni, S.; Di Felice, R. Unraveling the Interaction Between Histidine Side Chain and the Au(111) Surface: A DFT Study J. Phys. Chem. C 2008, 112, 13540-13545
    • (2008) J. Phys. Chem. C , vol.112 , pp. 13540-13545
    • Iori, F.1    Corni, S.2    Di Felice, R.3
  • 39
    • 77952378812 scopus 로고    scopus 로고
    • ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Solvent
    • Kokh, D. B.; Corni, S.; Winn, P. J.; Hoefling, M.; Gottschalk, K. E.; Kay, E.; Wade, R. C. ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Solvent J. Chem. Theory Comput 2010, 6, 1753-1768
    • (2010) J. Chem. Theory Comput , vol.6 , pp. 1753-1768
    • Kokh, D.B.1    Corni, S.2    Winn, P.J.3    Hoefling, M.4    Gottschalk, K.E.5    Kay, E.6    Wade, R.C.7
  • 40
    • 77954562476 scopus 로고    scopus 로고
    • Interaction of Amino Acids with the Au(111) Surface: Adsorption Free Energies from Molecular Dynamics Simulations
    • Hoefling, M.; Iori, F.; Corni, S.; Gottschalk, K. E. Interaction of Amino Acids with the Au(111) Surface: Adsorption Free Energies from Molecular Dynamics Simulations Langmuir 2010, 26, 8347-8351
    • (2010) Langmuir , vol.26 , pp. 8347-8351
    • Hoefling, M.1    Iori, F.2    Corni, S.3    Gottschalk, K.E.4
  • 41
    • 33645807591 scopus 로고    scopus 로고
    • 2 Surface Interaction in Solution by Ab Initio and Molecular Dynamics Simulations
    • 2 Surface Interaction in Solution by Ab Initio and Molecular Dynamics Simulations J. Phys. Chem. B 2006, 110, 6160-6169
    • (2006) J. Phys. Chem. B , vol.110 , pp. 6160-6169
    • Carravetta, V.1    Monti, S.2
  • 42
    • 36749039258 scopus 로고    scopus 로고
    • RAD16II β-sheet filaments onto titanium dioxide: Dynamics and adsorption properties
    • DOI 10.1021/jp075154g
    • Monti, S. RAD16II β-Sheet Filaments onto Titanium Dioxide: Dynamics and Adsorption Properties J. Phys. Chem. C 2007, 111, 16962-16973 (Pubitemid 350207458)
    • (2007) Journal of Physical Chemistry C , vol.111 , Issue.45 , pp. 16962-16973
    • Monti, S.1
  • 44
    • 0345708206 scopus 로고    scopus 로고
    • A Combined Atomic Force Microscopy and Molecular Dynamics Simulation Study on a Plastocyanin Mutant Chemisorbed on a Gold Surface
    • Bizzarri, A. R.; Costantini, G.; Cannistraro, S. A Combined Atomic Force Microscopy and Molecular Dynamics Simulation Study on a Plastocyanin Mutant Chemisorbed on a Gold Surface ChemPhysChem 2003, 4, 1189-1195
    • (2003) ChemPhysChem , vol.4 , pp. 1189-1195
    • Bizzarri, A.R.1    Costantini, G.2    Cannistraro, S.3
  • 45
    • 0025857852 scopus 로고
    • The Interaction of a Point-Charge with an Aluminum(111) Surface
    • Finnis, M. W. The Interaction of a Point-Charge with an Aluminum(111) Surface Surf. Sci. 1991, 241, 61-72
    • (1991) Surf. Sci. , vol.241 , pp. 61-72
    • Finnis, M.W.1
  • 46
    • 62249214187 scopus 로고    scopus 로고
    • Long-Range Interactions between Polar Molecules and Metallic Surfaces: A Comparison of Classical and Density Functional Theory Based Models
    • Fernandez-Torre, D.; Kupiainen, O.; Pyykko, P.; Halonen, L. Long-Range Interactions Between Polar Molecules and Metallic Surfaces: A Comparison of Classical and Density Functional Theory Based Models Chem. Phys. Lett. 2009, 471, 239-243
    • (2009) Chem. Phys. Lett. , vol.471 , pp. 239-243
    • Fernandez-Torre, D.1    Kupiainen, O.2    Pyykko, P.3    Halonen, L.4
  • 47
    • 4243943295 scopus 로고    scopus 로고
    • Generalized gradient approximation made simple
    • Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple Phys. Rev. Lett. 1996, 77, 3865-3868 (Pubitemid 126631804)
    • (1996) Physical Review Letters , vol.77 , Issue.18 , pp. 3865-3868
    • Perdew, J.P.1    Burke, K.2    Ernzerhof, M.3
  • 50
    • 0035997080 scopus 로고    scopus 로고
    • Supramolecular structure in full-length Alzheimer's β-amyloid fibrils: Evidence for a parallel β-sheet organization from solid-state nuclear magnetic resonance
    • Balbach, J. J.; Petkova, A. T.; Oyler, N. A.; Antzutkin, O. N.; Gordon, D. J.; Meredith, S. C.; Tycko, R. Supramolecular Structure in Full-Length Alzheimers β-Amyloid Fibrils: Evidence for a Parallel β-Sheet Organization from Solid-State Nuclear Magnetic Resonance Biophys. J. 2002, 83, 1205-1216 (Pubitemid 34803651)
    • (2002) Biophysical Journal , vol.83 , Issue.2 , pp. 1205-1216
    • Balbach, J.J.1    Petkova, A.T.2    Oyler, N.A.3    Antzutkin, O.N.4    Gordon, D.J.5    Meredith, S.C.6    Tycko, R.7
  • 51
    • 0031873102 scopus 로고    scopus 로고
    • β-sheet breaker peptides inhibit fibrillogenesis in a rat brain model of amyloidosis: Implications for Alzheimer's therapy
    • DOI 10.1038/nm0798-822
    • Soto, C.; Sigurdsson, E. M.; Morelli, L.; Kumar, R. A.; Castano, E.; Frangione, B. β-Sheet Breaker Peptides Inhibit Fibrillogenesis in a Rat Brain Model of Amyloidosis: Implications for Alzheimers Therapy Nat. Med. 1998, 4, 822-826 (Pubitemid 28331024)
    • (1998) Nature Medicine , vol.4 , Issue.7 , pp. 822-826
    • Soto, C.1    Sigurdsson, E.M.2    Morelli, L.3    Kumar, R.A.4    Castano, E.M.5    Frangione, B.6
  • 52
    • 0021481142 scopus 로고
    • Wettability of Clean Metal Surfaces
    • Schrader, M. E. Wettability of Clean Metal Surfaces J. Colloid Interface Sci. 1984, 100, 372-380
    • (1984) J. Colloid Interface Sci. , vol.100 , pp. 372-380
    • Schrader, M.E.1
  • 53
    • 34547207176 scopus 로고    scopus 로고
    • Large area, molecularly smooth (0.2 nm rms) gold films for surface forces and other studies
    • DOI 10.1021/la063738o
    • Chai, L.; Klein, J. Large Area, Molecularly Smooth (0.2 nm rms) Gold Films for Surface Forces and Other Studies Langmuir 2007, 23, 7777-7783 (Pubitemid 47116445)
    • (2007) Langmuir , vol.23 , Issue.14 , pp. 7777-7783
    • Chai, L.1    Klein, J.2
  • 55
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • DOI 10.1016/S0959-440X(02)00285-3
    • Smith, G. R.; Sternberg, M. J. E. Prediction of Protein-Protein Interactions by Docking Methods Curr. Opin. Struct. Biol. 2002, 12, 28-35 (Pubitemid 34142717)
    • (2002) Current Opinion in Structural Biology , vol.12 , Issue.1 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.E.2
  • 56
    • 0036468396 scopus 로고    scopus 로고
    • Protein-protein association kinetics and protein docking
    • DOI 10.1016/S0959-440X(02)00286-5
    • Camacho, C. J.; Vajda, S. Protein-Protein Association Kinetics and Protein Docking Curr. Opin. Struct. Biol. 2002, 12, 36-40 (Pubitemid 34142718)
    • (2002) Current Opinion in Structural Biology , vol.12 , Issue.1 , pp. 36-40
    • Camacho, C.J.1    Vajda, S.2
  • 57
    • 0036468995 scopus 로고    scopus 로고
    • Kinetic studies of protein-protein interactions
    • DOI 10.1016/S0959-440X(02)00287-7
    • Schreiber, G. Kinetic Studies of Protein-Protein Interactions Curr. Opin. Struct. Biol. 2002, 12, 41-47 (Pubitemid 34142719)
    • (2002) Current Opinion in Structural Biology , vol.12 , Issue.1 , pp. 41-47
    • Schreiber, G.1
  • 58
    • 79952108731 scopus 로고    scopus 로고
    • Ligand Macromolecule Interactions: Theoretical Principles of Molecular Recognition
    • Nolan, T.; Singh, N.; McCurdy, C. R. Ligand Macromolecule Interactions: Theoretical Principles of Molecular Recognition Methods Mol. Biol. 2009, 572, 13-29
    • (2009) Methods Mol. Biol. , vol.572 , pp. 13-29
    • Nolan, T.1    Singh, N.2    McCurdy, C.R.3
  • 59
    • 0030891436 scopus 로고    scopus 로고
    • Simulation of the diffusional association of barnase and barstar
    • Gabdoulline, R. R.; Wade, R. C. Simulation of the Diffusional Association of Barnase and Barstar Biophys. J. 1997, 72, 1917-1929 (Pubitemid 27184422)
    • (1997) Biophysical Journal , vol.72 , Issue.5 , pp. 1917-1929
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 60
    • 0031714012 scopus 로고    scopus 로고
    • Brownian Dynamics Simulation of Protein-Protein Encounter
    • Gabdoulline, R. R.; Wade, R. C. Brownian Dynamics Simulation of Protein-Protein Encounter Methods 1998, 3, 329-341
    • (1998) Methods , vol.3 , pp. 329-341
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 62
    • 4243606192 scopus 로고
    • Unified Approach for Molecular Dynamics and Density Functional Theory
    • Car, R.; Parrinello, M. Unified Approach for Molecular Dynamics and Density Functional Theory Phys. Rev. Lett. 1985, 55, 2471-2474
    • (1985) Phys. Rev. Lett. , vol.55 , pp. 2471-2474
    • Car, R.1    Parrinello, M.2
  • 63
    • 77950830266 scopus 로고    scopus 로고
    • Hydroxyl-Rich β-Sheet Adhesion to the Gold Surface in Water by First-Principle Simulations
    • Calzolari, A.; Cicero, G.; Cavazzoni, C.; Di Felice, R.; Catellani, A.; Corni, S. Hydroxyl-Rich β-Sheet Adhesion to the Gold Surface in Water by First-Principle Simulations J. Am. Chem. Soc. 2010, 132, 4790-4795
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 4790-4795
    • Calzolari, A.1    Cicero, G.2    Cavazzoni, C.3    Di Felice, R.4    Catellani, A.5    Corni, S.6
  • 64
    • 51449087199 scopus 로고    scopus 로고
    • New Insights on Growth Mechanisms of Protein Clusters at Surfaces: An AFM and Simulation Study
    • Pellenc, D.; Bennet, R. A.; Green, R. J.; Sperrin, M.; Mulheran, P. A. New Insights on Growth Mechanisms of Protein Clusters at Surfaces: An AFM and Simulation Study Langmuir 2008, 24, 9648-9655
    • (2008) Langmuir , vol.24 , pp. 9648-9655
    • Pellenc, D.1    Bennet, R.A.2    Green, R.J.3    Sperrin, M.4    Mulheran, P.A.5
  • 65
    • 39749192202 scopus 로고    scopus 로고
    • Phenylalanine near inorganic surfaces: Conformational statistics vs specific chemistry
    • DOI 10.1021/ja077817d
    • Ghiringhelli, L. M.; Delle Site, L. Phenylalanine near Inorganic Surfaces: Conformational Statistics vs Specific Chemistry J. Am. Chem. Soc. 2008, 130, 2634-2638 (Pubitemid 351304778)
    • (2008) Journal of the American Chemical Society , vol.130 , Issue.8 , pp. 2634-2638
    • Ghiringhelli, L.M.1    Delle Site, L.2
  • 66
    • 34248653737 scopus 로고    scopus 로고
    • Interaction of hydrated amino acids with metal surfaces: A multiscale modeling description
    • DOI 10.1021/jp065568u
    • Schravendijk, P.; Ghiringhelli, L. M.; Delle Site, L.; van der Vegt, N. F. A. Interaction of Hydrated Amino Acids with Metal Surfaces: A Multiscale Modeling Description J. Phys. Chem. C 2007, 111, 2631-2642 (Pubitemid 46774502)
    • (2007) Journal of Physical Chemistry C , vol.111 , Issue.6 , pp. 2631-2642
    • Schravendijk, P.1    Ghiringhelli, L.M.2    Site, L.D.3    Van Der Vegt, N.F.A.4
  • 67
    • 34249102684 scopus 로고    scopus 로고
    • Atomistic simulation of alkanethiol self-assembled monolayers on different metal surfaces via a quantum, first-principles parametrization of the sulfur-metal interaction
    • DOI 10.1021/jp067347u
    • Alexiadis, O.; Harmandaris, V. A.; Mavrantzas, V. G.; Delle Site, L. Atomistic Simulation of Alkanethiol Self-Assembled Monolayers on Different Metal Surfaces via a Quantum, First-Principles Parameterization of the Sulfur-Metal Interaction J. Phys. Chem. C 2007, 111, 6380-6391 (Pubitemid 46787859)
    • (2007) Journal of Physical Chemistry C , vol.111 , Issue.17 , pp. 6380-6391
    • Alexiadis, O.1    Harmandaris, V.A.2    Mavrantzas, V.G.3    Site, L.D.4
  • 68
    • 33746650444 scopus 로고    scopus 로고
    • Adsorption of Alanine on a Ni(111) Surface: A Multiscale Modeling Oriented Density Functional Study
    • Ghiringhelli, L. M.; Schravendijk, P.; Delle Site, L. Adsorption of Alanine on a Ni(111) Surface: A Multiscale Modeling Oriented Density Functional Study Phys. Rev. B 2006, 74, 035437/1-035437/8
    • (2006) Phys. Rev. B , vol.74
    • Ghiringhelli, L.M.1    Schravendijk, P.2    Delle Site, L.3
  • 69
    • 13844298226 scopus 로고    scopus 로고
    • Multiscale modeling of polymers on a surface: From ab initio density functional calculations of molecular adsorption to large-scale properties
    • DOI 10.1002/qua.20330, Proceedings of the Tenth International Conference on the Applications of Density Functional Theory in Chemistry and Physics - Part II of II
    • Delle Site, L.; Kremer, K. Multiscale Modeling of Polymers on a Surface: From Ab Initio Density Functional Calculations of Molecular Adsorption to Large Scale Properties Int. J. Quantum Chem. 2005, 101, 733-739 (Pubitemid 40253448)
    • (2005) International Journal of Quantum Chemistry , vol.101 , Issue.6 , pp. 733-739
    • Delle Site, L.1    Kremer, K.2
  • 70
    • 53549123870 scopus 로고    scopus 로고
    • Competing Adsorption between Hydrated Peptides and Water onto Metal Surfaces: From Electronic to Conformational Properties
    • Ghiringhelli, L. M.; Hess, B.; van der Vegt, N. F. A.; Delle Site, L. Competing Adsorption Between Hydrated Peptides and Water onto Metal Surfaces: From Electronic to Conformational Properties J. Am. Chem. Soc. 2008, 130, 13460-13464
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 13460-13464
    • Ghiringhelli, L.M.1    Hess, B.2    Van Der Vegt, N.F.A.3    Delle Site, L.4
  • 71
    • 79951502137 scopus 로고    scopus 로고
    • A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces
    • Schneider, J.; Colombi Ciacchi, L. A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces J. Chem. Theory Comput 2011, 7, 473-484
    • (2011) J. Chem. Theory Comput , vol.7 , pp. 473-484
    • Schneider, J.1    Colombi Ciacchi, L.2
  • 72
    • 71749085441 scopus 로고    scopus 로고
    • Water Structuring and Collagen Adsorption at Hydrophilic and Hydrophobic Silicon Surfaces
    • Cole, D. J.; Payne, M. C.; Colombi Ciacchi, L. Water Structuring and Collagen Adsorption at Hydrophilic and Hydrophobic Silicon Surfaces Phys. Chem. Chem. Phys. 2009, 11, 11395-11399
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 11395-11399
    • Cole, D.J.1    Payne, M.C.2    Colombi Ciacchi, L.3
  • 73
    • 65249180872 scopus 로고    scopus 로고
    • Affinity Scale for the Interaction of Amino Acids with Silica Surfaces
    • Rimola, A.; Sodupe, M.; Ugliengo, P. Affinity Scale for the Interaction of Amino Acids with Silica Surfaces J. Phys. Chem. C 2009, 113, 5741-5750
    • (2009) J. Phys. Chem. C , vol.113 , pp. 5741-5750
    • Rimola, A.1    Sodupe, M.2    Ugliengo, P.3
  • 74
    • 66649120341 scopus 로고    scopus 로고
    • The Role of Defective Silica Surfaces in Exogenous Delivery of Prebiotic Compounds: Clues from First Principles Calculations
    • Rimola, A.; Ugliengo, P. The Role of Defective Silica Surfaces in Exogenous Delivery of Prebiotic Compounds: Clues from First Principles Calculations Phys. Chem. Chem. Phys. 2009, 11, 2497-2506
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 2497-2506
    • Rimola, A.1    Ugliengo, P.2
  • 75
    • 70350029656 scopus 로고    scopus 로고
    • Ab Initio Modeling of Protein/Biomaterial Interactions: Competitive Adsorption between Glycine and Water onto Hydroxyapatite Surfaces
    • Rimola, A.; Corno, M.; Zicovich-Wilson, C. M.; Ugliengo, P. Ab Initio Modeling of Protein/Biomaterial Interactions: Competitive Adsorption Between Glycine and Water onto Hydroxyapatite Surfaces Phys. Chem. Chem. Phys. 2009, 11, 9005-9007
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 9005-9007
    • Rimola, A.1    Corno, M.2    Zicovich-Wilson, C.M.3    Ugliengo, P.4
  • 76
    • 0036392715 scopus 로고    scopus 로고
    • Genetically Engineered Gold-Binding Polypeptides: Structure Prediction and Molecular Dynamics
    • Braun, R.; Sarikaya, M.; Schulten, K. S. Genetically Engineered Gold-Binding Polypeptides: Structure Prediction and Molecular Dynamics J. Biomater. Sci. 2002, 13, 747-758
    • (2002) J. Biomater. Sci. , vol.13 , pp. 747-758
    • Braun, R.1    Sarikaya, M.2    Schulten, K.S.3
  • 77
    • 56549109784 scopus 로고    scopus 로고
    • Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12-6 and 9-6 Lennard-Jones Potentials
    • Heinz, H.; Vaia, R. A.; Farmer, B. L.; Naik, R. R. Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12-6 and 9-6 Lennard-Jones Potentials J. Phys. Chem. C 2008, 112, 17281-17290
    • (2008) J. Phys. Chem. C , vol.112 , pp. 17281-17290
    • Heinz, H.1    Vaia, R.A.2    Farmer, B.L.3    Naik, R.R.4
  • 78
    • 67650457696 scopus 로고    scopus 로고
    • Nature of Molecular Interactions of Peptides with Gold, Palladium, and Pd-Au Bimetal Surfaces in Aqueous Solution
    • Heinz, H.; Farmer, B. L.; Pandey, R. B.; Slocik, J. M.; Patnaik, S. S.; Pachter, R.; Naik, R. R. Nature of Molecular Interactions of Peptides with Gold, Palladium, and Pd-Au Bimetal Surfaces in Aqueous Solution J. Am. Chem. Soc. 2009, 131, 9704-9714
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 9704-9714
    • Heinz, H.1    Farmer, B.L.2    Pandey, R.B.3    Slocik, J.M.4    Patnaik, S.S.5    Pachter, R.6    Naik, R.R.7
  • 79
    • 67649187881 scopus 로고    scopus 로고
    • Towards Understanding Amino Acid Adsorption at Metallic Interfaces: A Density Functional Theory Study
    • Hong, G.; Heinz, H.; Naik, R. R.; Farmer, B. L.; Pachter, R. Towards Understanding Amino Acid Adsorption at Metallic Interfaces: A Density Functional Theory Study ACS Appl. Mater. Interf. 2009, 1, 388-392
    • (2009) ACS Appl. Mater. Interf. , vol.1 , pp. 388-392
    • Hong, G.1    Heinz, H.2    Naik, R.R.3    Farmer, B.L.4    Pachter, R.5
  • 80
    • 68849090298 scopus 로고    scopus 로고
    • Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations
    • Vila Verde, A.; Acres, J. M.; Maranas, J. K. Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations Biomacromolecules 2009, 10, 2118-2128
    • (2009) Biomacromolecules , vol.10 , pp. 2118-2128
    • Vila Verde, A.1    Acres, J.M.2    Maranas, J.K.3
  • 81
    • 33947397117 scopus 로고    scopus 로고
    • Atomistic Modelling of the Interaction between Peptides and Carbon Nanotubes
    • de Miranda Tomasio, S.; Walsh, T. R. Atomistic Modelling of the Interaction Between Peptides and Carbon Nanotubes Mol. Phys. 2007, 105, 221
    • (2007) Mol. Phys. , vol.105 , pp. 221
    • De Miranda Tomasio, S.1    Walsh, T.R.2
  • 82
    • 67649216262 scopus 로고    scopus 로고
    • Modeling the Binding Affinity of Peptides for Graphitic Surfaces. Influences of Aromatic Content and Interfacial Shape
    • Tomaésio, S. M.; Walsh, T. R. Modeling the Binding Affinity of Peptides for Graphitic Surfaces. Influences of Aromatic Content and Interfacial Shape J. Phys. Chem. C 2009, 113, 8778-8785
    • (2009) J. Phys. Chem. C , vol.113 , pp. 8778-8785
    • Tomaésio, S.M.1    Walsh, T.R.2
  • 84
    • 34248598110 scopus 로고    scopus 로고
    • Interaction of liquid water with the rutile TiO2 (110) surface
    • DOI 10.1080/17441690701191693, PII 778683673
    • 2 (110) Surface Mol. Simul. 2007, 33, 379-389 (Pubitemid 46761307)
    • (2007) Molecular Simulation , vol.33 , Issue.4-5 , pp. 379-389
    • Skelton, A.A.1    Walsh, T.R.2
  • 85
    • 34248353968 scopus 로고    scopus 로고
    • Molecular dynamics simulations of collagen-like peptide adsorption on titanium-based material surfaces
    • DOI 10.1021/jp070266t
    • Monti, S. Molecular Dynamics Simulations of Collagen-Like Peptide Adsorption on Titanium-Based Material Surfaces J. Phys. Chem. C 2007, 111, 6086-6094 (Pubitemid 46732909)
    • (2007) Journal of Physical Chemistry C , vol.111 , Issue.16 , pp. 6086-6094
    • Monti, S.1
  • 86
    • 77954023023 scopus 로고    scopus 로고
    • Simulating DNA Hybridization on an Amine-Functionalized Silicon Substrate
    • Monti, S.; Cacelli, I.; Ferretti, A.; Prampolini, G.; Barone, V. Simulating DNA Hybridization on an Amine-Functionalized Silicon Substrate J. Phys. Chem B 2010, 114, 8341-8349
    • (2010) J. Phys. Chem B , vol.114 , pp. 8341-8349
    • Monti, S.1    Cacelli, I.2    Ferretti, A.3    Prampolini, G.4    Barone, V.5
  • 88
    • 20744434424 scopus 로고    scopus 로고
    • Prediction of the orientations of adsorbed protein using an empirical energy function with implicit solvation
    • DOI 10.1021/la046932o
    • Sun, Y.; Welsh, W. J.; Latour, R. A. Prediction of the Orientations of Adsorbed Protein Using an Empirical Energy Function with Implicit Solvation Langmuir 2005, 21, 5616-5626 (Pubitemid 40850653)
    • (2005) Langmuir , vol.21 , Issue.12 , pp. 5616-5626
    • Sun, Yu.1    Welsh, W.J.2    Latour, R.A.3
  • 89
    • 34547267323 scopus 로고    scopus 로고
    • Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface
    • DOI 10.1002/jcc.20716
    • Sun, Y.; Dominy, B. N.; Latour, R. A. Comparison of Solvation-Effect Methods for the Simulation of Peptide Interactions with a Hydrophobic Surface J. Comput. Chem. 2007, 28, 1883-1892 (Pubitemid 47153616)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.11 , pp. 1883-1892
    • Sun, Y.U.1    Dominy, B.N.2    Latour, R.A.3
  • 90
    • 66249119965 scopus 로고    scopus 로고
    • Molecular Dynamics Simulation of Protein-Surface Interactions: Benefits, Problems, Solutions, and Future Directions
    • Latour, R. A. Molecular Dynamics Simulation of Protein-Surface Interactions: Benefits, Problems, Solutions, and Future Directions Biointerphases 2008, 3, FC2-FC12
    • (2008) Biointerphases , vol.3
    • Latour, R.A.1
  • 91
    • 36049046635 scopus 로고    scopus 로고
    • An Improved Replica-Exchange Sampling Method: Temperature Intervals with Global Energy Reassignment (TIGER)
    • /1-164116/10
    • Li, X. F.; OBrien, C. P.; Collier, G.; Vellore, N. A.; Wang, F.; Bruce, D. A.; Stuart, S. J.; Latour, R. A. An Improved Replica-Exchange Sampling Method: Temperature Intervals with Global Energy Reassignment (TIGER) J. Chem. Phys. 2007, 127, 164116 /1-164116/10
    • (2007) J. Chem. Phys. , vol.127 , pp. 164116
    • Li, X.F.1    Obrien, C.P.2    Collier, G.3    Vellore, N.A.4    Wang, F.5    Bruce, D.A.6    Stuart, S.J.7    Latour, R.A.8
  • 92
    • 65549124993 scopus 로고    scopus 로고
    • TIGER2: An Improved Algorithm for Temperature Intervals with Global Exchange of Replicas
    • Li, X.; Stuart, S. J.; Latour, R. A. TIGER2: An Improved Algorithm for Temperature Intervals with Global Exchange of Replicas J. Chem. Phys. 2009, 130, 174106/1-174106/9
    • (2009) J. Chem. Phys. , vol.130
    • Li, X.1    Stuart, S.J.2    Latour, R.A.3
  • 93
    • 77956246697 scopus 로고    scopus 로고
    • De Dovo Design of Peptide-Calcite Biomineralization Systems
    • Masica, D. L.; Schrier, S. B.; Specht, E. A.; Gray, J. J. De Dovo Design of Peptide-Calcite Biomineralization Systems J. Am. Chem. Soc. 2010, 132, 12252-12262
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 12252-12262
    • Masica, D.L.1    Schrier, S.B.2    Specht, E.A.3    Gray, J.J.4
  • 94
    • 57349101729 scopus 로고    scopus 로고
    • Computational Techniques at the Organic-Inorganic Interface in Biomineralization
    • Harding, J. H.; Duffy, D. M.; Sushko, M. L.; Rodger, P. M.; Quigley, D.; Elliot, J. A. Computational Techniques at the Organic-Inorganic Interface in Biomineralization Chem. Rev. 2008, 108, 4823-4854
    • (2008) Chem. Rev. , vol.108 , pp. 4823-4854
    • Harding, J.H.1    Duffy, D.M.2    Sushko, M.L.3    Rodger, P.M.4    Quigley, D.5    Elliot, J.A.6
  • 95
    • 33645725174 scopus 로고    scopus 로고
    • Simulating an electrochemical interface using charge dynamics
    • Guymon, C. G.; Rowley, R. L.; Harb, J. N.; Wheeler, D. R. Simulating an Electrochemical Interface Using Charge Dynamics Condens. Matter Phys. 2005, 8, 335-356 (Pubitemid 43664311)
    • (2005) Condensed Matter Physics , vol.8 , Issue.2 , pp. 335-356
    • Guymon, C.G.1    Rowley, R.L.2    Harb, J.N.3    Wheeler, D.R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.