Docking of ubiquitin to gold nanoparticles

ACS Nano

Volumn 6, Issue 11, 2012, Pages 9863-9878

  Brancolini, Giorgia ^a   Kokh, Daria B ^b   Calzolai, Luigi ^c   Wade, Rebecca C ^b,d   Corni, Stefano ^a  

^a CNR   (Italy)

^b HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

^c JOINT RESEARCH CENTRE   (Italy)

^d UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

circular dichroism; docking; gold; molecular dynamics; nanoparticles; ubiquitin

Indexed keywords

AB INITIO; ASSOCIATION PROCESS; BROWNIAN DYNAMICS; CLASSICAL MOLECULAR DYNAMICS; DRIVING FORCES; FUNCTIONALIZATIONS; GOLD NANOPARTICLES; MICROSCOPIC LEVELS; MOLECULAR BASIS; MULTIPLE LEVELS; NANOSCIENCE AND NANOTECHNOLOGIES; NMR CHEMICAL SHIFTS; SURFACE COMPLEX; TARGETED DRUG DELIVERY; THERANOSTICS; UBIQUITIN;

AMINO ACIDS; BROWNIAN MOVEMENT; DICHROISM; DOCKING; DRUG DELIVERY; GOLD; METAL NANOPARTICLES; MOLECULAR DYNAMICS; NANOPARTICLES; NANOSCIENCE; QUANTUM THEORY;

PROTEINS;

GOLD; METAL NANOPARTICLE; UBIQUITIN;

ADSORPTION; ARTICLE; BINDING SITE; CHEMICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; MATERIALS TESTING; MOLECULAR DYNAMICS; PROTEIN BINDING; SURFACE PROPERTY; ULTRASTRUCTURE;

ADSORPTION; BINDING SITES; COMPUTER SIMULATION; GOLD; MATERIALS TESTING; METAL NANOPARTICLES; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; SURFACE PROPERTIES; UBIQUITIN;

EID: 84870415772     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn303444b     Document Type: Article

References (80)

1. Sarikaya, M.; Tamerler, C.; Jen, A. K.; Schulten, K.; Baneyx, F. Molecular Biomimetics: Nanotechnology through Biology Nat. Mater. 2003, 2, 577-585
2. Keren, K.; Berman, R. S.; Buchstab, E.; Sivan, U.; Braun, E. DNA-Templated Carbon Nanotube Field-Effect Transistor Science 2003, 302, 1380-1382
3. Nam, K. T.; Kim, D.-W.; Yoo, P. J.; Chiang, C.-Y.; Meethong, N.; Hammond, P. T.; Chiang, Y.-M.; Belcher, A. M. Virus-Enabled Synthesis and Assembly of Nanowires for Lithium Ion Battery Electrodes Science 2006, 312, 885-888
4. Naik, R. R.; Stringer, J. S.; Agarwal, G.; Jones, S. E.; Stone, M. O. Biomimetic Synthesis and Patterning of Silver Nanoparticles Nat. Mater. 2002, 1, 169-172
5. Crookes-Goodson, W. J.; Slocik, J. M.; Naik, R. R. Bio-directed Synthesis and Assembly of Nanomaterials Chem. Soc. Rev. 2008, 37, 2403-2412
6. Dickerson, M. B.; Sandhage, K. H.; Naik, R. R. Protein- and Peptide-Directed Syntheses of Inorganic Materials Chem. Rev. 2008, 108, 4935-4978
7. Mahmoudi, M.; Lynch, I.; Ejtehadi, M. R.; Monopoli, M. P.; Bombelli, F. B.; Laurent, S. Protein-Nanoparticle Interactions: Opportunities and Challenges Chem. Rev. 2011, 111, 5610-5637
8. Lacerda, S. H. D. P.; Park, J. J.; Meuse, C.; Pristinski, D.; Becker, M. L.; Karim, A.; Douglas, J. F. Interaction of Gold Nanoparticles with Common Human Blood Proteins ACS Nano 2010, 4, 365-379
9. Maiorano, G.; Sabella, S.; Sorce, B.; Brunetti, V.; Malvindi, M. A.; Cingolani, R.; Pompa, P. P. Effects of Cell Culture Media on the Dynamic Formation of Protein-Nanoparticle Complexes and Influence on the Cellular Response ACS Nano 2010, 4, 7481-7491
10. Cedervall, T.; Lynch, I.; Lindman, S.; Berggøard, T.; Thulin, E.; Nilsson, H.; Dawson, K. A.; Linse, S. Understanding the Nanoparticle-Protein Corona Using Methods to Quantify Exchange Rates and Affinities of Proteins for Nanoparticles Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 2050-2055
11. Lundqvist, M.; Stigler, J.; Elia, G.; Lynch, I.; Cedervall, T.; Dawson, K. A. Nanoparticle Size and Surface Properties Determine the Protein Corona with Possible Implications for Biological Impacts Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 14265-14270
12. Dutta, D.; Sundaram, S. K.; Teeguarden, J. G.; Riley, B. J.; Fifield, L. S.; Jacobs, J. M.; Addleman, S. R.; Kaysen, G. A.; Moudgil, B. M.; Weber, T. J. Adsorbed Proteins Influence the Biological Activity and Molecular Targeting of Nanomaterials Toxicol. Sci. 2007, 100, 303-315
13. Lynch, I.; Dawson, K. A.; Linse, S. Detecting Cryptic Epitopes created by Nanoparticles Sci. STKE 2006, 327, pe14
14. Treuel, L.; Malissek, M.; Gebauer, J. S.; Zellner, R. The Influence of Surface Composition of Nanoparticles on Their Interactions with Serum Albumin ChemPhysChem 2010, 11, 3093-3099
15. Casals, E.; Pfaller, T.; Duschl, A.; Oostingh, G. J.; Puntes, V. Time Evolution of the Nanoparticle Protein Corona ACS Nano 2010, 4, 3623-3632
16. Tsai, D.-H.; DelRio, F. W.; Keene, A. M.; Tyner, K. M.; MacCuspie, R. I.; Cho, T. J.; Zachariah, M. R.; Hackley, V. A. Adsorption and Conformation of Serum Albumin Protein on Gold Nanoparticles Investigated Using Dimensional Measurements and in Situ Spectroscopic Methods Langmuir 2011, 27, 2464-2477
17. Monopoli, M. P.; Walczyk, D.; Campbell, A.; Elia, G.; Lynch, I.; Bombelli, F. B.; Dawson, K. A. Physical-Chemical Aspects of Protein Corona: Relevance to in Vitro and in Vivo Biological Impacts of Nanoparticles J. Am. Chem. Soc. 2011, 133, 2525-2534
18. Nel, A.; Xia, T.; Mädler, L.; Li, N. Toxic Potential of Materials at the Nanolevel Science 2006, 311, 622-627
19. Vecchio, G.; Galeone, A.; Brunetti, V.; Maiorano, G.; Sabella, S.; Cingolani, R.; Pompa, P. P. Concentration-Dependent, Size-Independent Toxicity of Citrate-Capped AuNPs in Drosophila Melanogaster PLoS One 2012, 7, e29980
20. Vecchio, G.; Galeone, A.; Brunetti, V.; Maiorano, G.; Rizzello, L.; Sabella, S.; Cingolani, R.; Pompa, P. P. Mutagenic Effects of Gold Nanoparticles Induce Aberrant Phenotypes in Drosophila Melanogaster Nanomed. Nanotechnol. Biol. Med. 2012, 8, 1-7
21. Chen, X.; Gambhir, S. S.; Cheon, J. Theranostic Nanomedicine Acc. Chem. Res. 2011, 44 (10) 841-841
22. Aubin-Tam, M.-E.; Hwang, W.; Hamad-Schifferli, K. Site-Directed Nanoparticle Labeling of Cytochrome C Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 4095-4100
23. Goobes, G.; Goobes, R.; Schueler-Furman, O.; Baker, D.; Stayton, P. S.; Drobny, G. P. Folding of the C-Terminal Bacterial Binding Domain in Statherin upon Adsorption onto Hydroxyapatite Crystals Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 16083-16088
24. Gray, J. J. The Interaction of Proteins with Solid Surfaces Curr. Opin. Struct. Biol. 2004, 14, 110-115
25. Harding, M. M.; Nowicki, M. W.; Walkinshaw, M. D. Metals in Protein Structures: A Review of Their Principal Features Crystallogr. Rev. 2010, 16, 247-302
26. Latour, R. A. Molecular Simulation of Protein-Surface Interactions: Benefits, Problems, Solutions, and Future Directions Biointerphases 2008, it 3, FC2-FC12
27. Cohavi, O.; Corni, S.; De Rienzo, F.; Di Felice, R.; Gottschalk, K. E.; Hoefling, M.; Kokh, D.; Molinari, E.; Schreiber, G.; Vaskevich, A.; Wade, R. C. Protein-Surface Interactions: Challenging Experiments and Computations J. Mol. Recognit. 2009, 23, 259-262
28. Bachmann, M.; Goede, K.; Beck-Sickinger, A. G.; Grundmann, M.; Irbäck, A.; Janke, W. Microscopic Mechanism of Specific Peptide Adhesion to Semiconductor Substrates Angew. Chem., Int. Ed. 2010, 49, 9530-9533
29. Di Felice, R.; Corni, S. Simulation of Peptide-Surface Recognition J. Phys. Chem. Lett. 2011, 2, 1510-1519
30. Makrodimitris, K.; Masica, D. L.; Kim, E. T.; Gray, J. J. Structure Prediction of Protein-Solid Surface Interactions Reveals a Molecular Recognition Motif of Statherin for Hydroxyapatite J. Am. Chem. Soc. 2007, 129, 13713-13722
31. 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
32. Hong, G.; Heinz, H.; Naik, R. R. R.; Farmer, B. L.; Pachter, R. Toward Understanding Amino Acid Adsorption at Metallic Interfaces: A Density Functional Theory Study ACS Appl. Mater. Interfaces 2009, 1, 388-392
33. 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
34. Vila Verde, A.; Beltramo, P. J.; Maranas, J. K. Adsorption of Homopolypeptides on Gold Investigated Using Atomistic Molecular Dynamics Langmuir 2011, 27 (10) 5918-5926
35. Coppage, R.; Slocik, J. M.; Briggs, B. D.; Frenkel, A. I.; Heinz, H.; Naik, R. R.; Knecht, M. R. Crystallographic Recognition Controls Peptide Binding for Bio-based Nanomaterials J. Am. Chem. Soc. 2011, 133, 12346-12349
36. Calzolari, A.; Cicero, G.; Cavazzoni, C.; Felice, R. D.; Catellani, A.; Corni, S. Hydroxyl-rich Sheet Adhesion to the Gold Surface in Water by First-Principle Simulations J. Am. Chem. Soc. 2010, 132, 4790-4795
37. Yu, J.; Becker, M. L.; Carri, G. The Influence of Amino Acid Sequence and Functionality on the Binding Process of Peptides onto Gold Surfaces Langmuir 2012, 28, 1408-1417
38. Feng, J.; Slocik, J. M.; Sarikaya, M.; Naik, R. R.; Farmer, B. L.; Heinz, H. Influence of the Shape of Nanostructured Metal Surfaces on Adsorption of Single Peptide Molecules in Aqueous Solution Small 2012, 8, 1049-1059
39. Hoefling, M.; Iori, F.; Corni, S.; Gottschalk, K. E. The Conformations of Amino Acids on a Gold(111) Surface ChemPhysChem 2010, 11, 1763-1767
40. 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
41. Hoefling, M.; Monti, S.; Corni, S.; Gottschalk, K. E. Interaction of β -Sheet Folds with a Gold Surface PLoS One 2012, 6, e20925
42. Toroz, D.; Corni, S. Peptide Synthesis of Gold Nanoparticles: The Early Steps of Gold Reduction Investigated by Density Functional Theory Nano Lett. 2011, 11, 1313-1318
43. Boisselier, E.; Astruc, D. Gold Nanoparticles in Nanomedicine: Preparations, Imaging, Diagnostics, Therapies and Toxicity Chem. Soc. Rev. 2009, 38, 1759-1782
44. Personick, M. L.; Langille, M. R.; Zhang, J.; Mirkin, C. Shape Control of Gold Nanoparticles by Silver Underpotential Deposition Nano Lett. 2011, 11, 3394-3398
45. 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
46. Kokh, D. B.; Corni, S; Winn, P. J.; Hoefling, M.; Gottschalk, K. E.; Wade, R. C. ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aqueous Solvent J. Chem. Theory Comput. 2010, 6, 1753-1768
47. Iori, F; Di Felice, R.; Molinari, E.; Corni, S. GolP: An Atomistic Force-Field to Describe the Interaction of Proteins with Au(111) Surfaces in Water J. Comput. Chem. 2009, 30, 1465-1476
48. Elechiguerra, J. L.; Reyes-Gasga, J.; Yacaman, M. J. The Role of Twinning in Shape Evolution of Anisotropic Noble Metal Nanostructures J. Mater. Chem. 2006, 16, 3906-3919
49. SDA, Simulation of Diffusional Association. http://projects.villa-bosch. de/mcmsoft/sda/6.00/. Accessed October 9, 2012.
50. Gabdoulline, R. R.; Wade, R. C. Effective Charges for Macromolecules in Solvent J. Phys. Chem. 1996, 100, 3868-3878
51. Kirkpatrick, S.; Gelatt., C. D.; Vecchi, M. P. Optimization by Simulated Annealing Science 1983, 220, 671-680
52. Brünger, A. T.; Adams, P. D.; Rice, L. M. New Applications of Simulated Annealing in X-ray Crystallography and Solution NMR Structure 1997, 5, 325-336
53. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: Fast, Flexible, and Free J. Comput. Chem. 2005, 26, 1701-1718
54. Lin, Y.; Pan, G.; Su, G.-J.; Fang, X.-H.; Wan, L.-J.; Bai, C.-L. Study of Citrate Adsorbed on the Au(111) Surface by Scanning Probe Microscopy Langmuir 2003, 19, 10000-10003
55. Kunze, J.; Burgess, I.; Nichols, R.; Buess-Herman, I.; Lipkowski, J. Electrochemical Evaluation of Citrate Adsorption on Au(111) and the Stability of Citrate-Reduced Gold Colloids J. Electroanal. Chem. 2007, 599, 147-159
56. Brewer, S. H.; Glomm, W. R.; Johnson, M. C.; Knag, M. K.; Franzen, S. Probing BSA Binding to Citrate-Coated Gold Nanoparticles and Surfaces Langmuir 2005, 62, 9303-9307
57. Cohavi, O.; Reichmann, D.; Abramovich, R.; Tesler, A. B.; Bellapadrona, G.; Kokh, D. B.; Wade, R. C.; Vaskevich, A.; Rubinstein, I.; Schreiber, G. A Quantitative, Real-Time Assessment of Binding of Peptides and Proteins to Gold Surfaces Chem.-Eur. J. 2011, 17, 1327-1336
58. Fernandez, V. L.; Reimer, J. A.; Denn, M. M. Magnetic Resonance Studies of Polypeptides Adsorbed on Silica and Hydroxyapatite Surfaces J. Am. Chem. Soc. 1992, 114, 9634-9642
59. 17O Nuclear Shielding in Water and in Acetone J. Phys. Chem. B 2005, 109, 9830-9838
60. Zuiderweg, E. R. Mapping Protein-Protein Interactions in Solution by NMR Spectroscopy Biochemistry 2002, 41, 1-7
61. Peng, C.; Unger, S. W.; Filipp, F. V.; Sattler, M.; Szalma, S. Automated Evaluation of Chemical Shift Perturbation Spectra: New Approaches to Quantitative Analysis of Receptor-Ligand Interaction NMR Spectra J. Biomol. NMR 2004, 29, 491-504
62. Hong, G.; Heinz, H.; Naik, R. R. R.; Farmer, B. L.; Pachter, R. Toward Understanding Amino Acid Adsorption at Metallic Interfaces: A Density Functional Theory Study ACS Appl. Mater. Interfaces 2009, 1, 388-392
63. Tomasi, J.; Mennucci, B.; Cammi, R. Quantum Mechanical Continuum Solvation Models Chem. Rev. 2005, 105, 2999-3093
64. Cicero, G.; Calzolari, A.; Corni, S.; Catellani, A. Anomalous Wetting Layer at the Au (111) Surface J. Phys. Chem. Lett. 2011, 2, 2582-2586
65. Cappelli, C.; Mennucci, B. Modeling the Solvation of Peptides. The Case of (s)- N -Acetylproline Amide in Liquid Water J. Phys. Chem. B 2008, 112, 3441-3450
66. Structure-Based Chemical Shift Predictions. http://casegroup.rutgers.edu/ qshifts/qshifts.htm. Accessed October 9, 2012.
67. 13C′ Chemical Shifts in Proteins Using a Density Functional Database J. Biomol. NMR 2001, 21, 321-333
68. Keller, R.; Grace, C. R.; Riek, R. Fast Multidimensional NMR Spectroscopy by Spin-State Selective Off-Resonance Decoupling (SITAR) Magn. Reson. Chem. 2006, 44, S196-S205
69. Schmidt, J. M.; Howard, M. J.; Maestre-Martinez, M.; Perez, C. S.; Lohr, F. Variation in Protein C(alpha)-Related One-Bond J Couplings Magn. Reson. Chem. 2009, 47, 16-30
70. Gabdoulline, R. R.; Wade, R. C. Simulation of the Diffusional Association of Barnase and Barstar Biophys. J. 1997, 72, 1917-1929
71. Molecular and Cellular Modeling. www.h-its.org/mcm. Accessed October 9, 2012.
72. Baker, N. A.; Sept, D.; Joseph, S.; Holst, M. J.; McCammon, J. A. Electrostatics of Nanosystems: Application to Microtubules and the Ribosome Proc. Natl. Acad. Sci. U.S.A 2001, 98, 10037-10041
73. H++. http://biophysics.cs.vt.edu/H++. Accessed October 9, 2012.
74. Elcock, A. H.; Gabdoulline, R. R.; Wade, R. C.; McCammon, J. A. Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase- Fasciculin J. Mol. Biol. 1999, 291, 149-162
75. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
76. Hess, B.; van der Vegt, N. F. Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models J. Phys. Chem. B 2006, 110, 17616-17626
77. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; et al. Gaussian 09, revision C.01; Gaussian, Inc.: Wallingford, CT, 2010.
78. Mennucci, B.; Cancés, E.; Tomasi, J. Evaluation of Solvent Effects in Isotropic and Anisotropic Dielectrics and in Ionic Solutions with a Unified Integral Equation Method: Theoretical Bases, Computational Implementation, and Numerical Applications J. Phys. Chem. B 1997, 101, 10506-10517
79. Cancés, E.; Mennucci, B.; Tomasi, J. A New Integral Equation Formalism for the Polarizable Continuum Model: Theoretical Background and Applications to Isotropic and Anisotropic Dielectrics J. Chem. Phys. 1997, 107, 3032-3041
80. Tomasi, J; Mennucci, B.; Cammi, R. Quantum Mechanical Continuum Solvation Models Chem. Rev. 2005, 105, 2999-3093