Peptide-TiO2 interaction in aqueous solution: Conformational dynamics of RGD using different water models

Journal of Physical Chemistry B

Volumn 114, Issue 13, 2010, Pages 4692-4701

  Wu, Chunya ^a   Chen, Mingjun ^a   Guo, Chuangqiang ^a   Zhao, Xin ^a   Yuan, Changsong ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADSORPTION; AMIDES; BINDING ENERGY; HYDROGEN BONDS; MOLECULAR DYNAMICS; OXIDE MINERALS; OXYGEN; PEPTIDES;

ADSORPTION BEHAVIOR; AMIDE GROUPS; AQUEOUS SOLUTIONS; ARG GLY ASPS; BINDING MODES; CONFORMATIONAL DYNAMICS; CONFORMATIONAL STABILITIES; DIHEDRAL ANGLES; HYDRATION LAYERS; HYDROGEN BONDING INTERACTIONS; INTERMOLECULAR POTENTIALS; MOLECULAR DYNAMICS SIMULATIONS; PEPTIDE-SURFACE INTERACTIONS; RGD SEQUENCES; RUTILE TIO; SIMPLE POINT CHARGE; SIMULATION RESULT; SOLVENT MODEL; SPC/E WATER; SURFACE OXYGEN; TIO; TRI-PEPTIDES; WATER MODELS; WATER SOLUTIONS;

ATOMS;

EID: 77950556887     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp9109223     Document Type: Article

References (42)

1. Diebold, U. The Surface Science of Titanium Dioxide Surf. Sci. Rep. 2003, 48, 53 - 229
2. Yao, K. D.; Yin, Y. J. Biomaterials Related to Tissue Engineering; Chemical Industry Press: Beijing, 2003.
3. 1-integrin Cell. Biochem. 2007, 100, 1288 - 1300
4. Pierschbacher, M. D.; Ruoslahti, E. Cell Attachment Activity of Fibronectin Can Be Duplicated by Small Synthetic Fragments of the Molecule Nature 1984, 309, 30 - 33
5. Ruoslahti, E.; Pierschbacher, M. D. New Perspectives in Cell Adhesion: RGD and Integrins Science 1987, 238, 491 - 497
6. Kasemo, B. Biological Surface Science Surf. Sci. 2002, 500, 656 - 677
7. Wu, Y. J.; Tepper, H. L.; Voth, G. A. Flexible Simple Point-charge Water Model with Improved Liquid-state Properties J. Chem. Phys. 2006, 124, 1 - 12
8. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926 - 960
9. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The Missing Term in Effective Pair Potentials J. Phys. Chem. 1987, 91, 6269 - 6271
10. Monti, S. Molecular Dynamics Simulations of Collagen-like Peptide Adsorption on Titanium-based Material Surfaces J. Phys. Chem. C 2007, 111, 6086 - 6094
11. 2 Surface Interaction in Solution by Ab Initio and Molecular Dynamics Simulations J. Phys. Chem. B 2006, 110, 6160 - 6169
12. Smith E.; Pettitt, B. M. Modeling Solvent in Biomolecular Systems J. Phys. Chem. 1994, 98, 9700 - 9711
13. Löffler, G.; Schreiber, H.; Steinhauser, O. Calculation of the Dielectric Properties of a Protein and Its Solvent: Theory and a Case Study J. Mol. Biol. 1997, 270, 520 - 534
14. Predota, M; Bandura, A. V; Cummings T. Electric Double Layer at the Rutile (110) Surface. 1. Structure of Surfaces and Interfacial Water from Molecular Dynamics by Use of Ab Initio Potential J. Phys. Chem. B 2004, 108, 12049 - 12060
15. Abrahams, S. C.; Bernstein, J. L. Gutile: Normal Probability Plot Analysis and Accurate Measurement of Crystal Structure J. Chem. Phys. 1971, 55, 3206 - 3211
16. Andersson, S.; Collen, B.; Kuylenstierna, U.; Magneli, A. Phase Analysis Studies on the Titanium-oxygen System Acta Chem. Scand. 1957, 11, 1641 - 1652
17. Dickinson, C. D.; Veerapandian, B.; Dai, X. P. Crystal Structure of the Tenth Type III Cell Adhesion Module of Human Fibronectin J. Mol. Biol. 1994, 236, 1079 - 1092
18. Hoover, W. G. Canonical Dynamics: Equilibrium Phase-space Distributions Phys. Rev. A 1985, 31, 1695 - 1701
19. 2 Mol. Simul. 1991, 6, 239 - 244
20. Cornell, W. D.; Cieplak; Bayly, C. I. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179 - 5197
21. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerial Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-alkanes J. Comp. Phys. 1977, 23, 327 - 341
22. Massaro, C.; Rotolo; Riccardis, F. D. Comparative Investigation of the Surface Properties of Commercial Titanium Dental Implants. Part I: Chemical Composition J. Mater. Sci.: Mater. Med. 2002, 13, 535 - 548
23. Shen, J. W.; Wu, T.; Wang, Q.; Pan, H. H. Molecular Simulation of Protein Adsorption and Desorption on Hydroxyapatite Surfaces Biomaterials 2008, 29, 513 - 532
24. Chen, M. J.; Wu, C. Y.; Song, D. P. Li, Kai. RGD Tripeptide onto Perfect and Grooved Rutile Surfaces in Aqueous Solution: Adsorption Behaviors and Dynamics Phys. Chem. Chem. Phys. 2010, 12, 406 - 415
25. Gilli, G.; Gilli Towards an Unified Hydrogen-bond Theory J. Mol. Struct. 2000, 552, 1 - 15
26. García, A. E.; Stiller, L. Computation of the Mean Residence Time of Water in the Hydration Shells of Biomolecules J. Comput. Chem. 1993, 14, 1396 - 1406
27. Obst, S.; Bradaczek, H. Molecular Dynamics Study of the Structure and Dynamics of the Hydration Shell of Alkaline and Alkaline-earth Metal Cations J. Phys. Chem. 1996, 100, 15677 - 15687
28. 2 Nanotopography Surface in Aqueous Solution Acta Biomater. 2010, 6, 684 - 694
29. Stöckelmann, E.; Hentschke, R. A Molecular-dynamics Simulation Study of Water on NaCl (100) Using a Polarizable Water Model J. Chem. Phys. 1999, 110, 12097 - 12107
30. Jung, S. Y.; Lim, S. M.; Albertorio, F.; Kim, G.; Garau, M. C.; Yang, R. D.; Holden, M. A.; Cremer S. The Vroman Effect: A Molecular Level Description of Fibrinogen Displacement J. Am. Chem. Soc. 2003, 125, 12782 - 12786
31. Zhang, Z.; Fenter; Cheng, L. Ion Adsorption at the Rutile-water Interface: Linking Molecular and Macroscopic Properties Langmuir 2004, 20, 4954 - 4969
32. Pekka, M; Lennart, N. Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K J. Phys. Chem. A 2001, 105, 9954 - 9960
33. Soper, A. K.; Phillips, M. G. A New Determination of the Structure of Water at 25°C Chem. Phys. 1986, 107, 47 - 60
34. Svishchev, I. M.; Kusalik G. Structure in Liquid Water: A Study of Spatial Distribution Functions J. Chem. Phys. 1993, 99, 3049 - 3058
35. Hess, B.; van der Vegt, N. F. A. 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
36. Sadeghi, M.; Naderi-Manesh, H.; Zarrabi, M.; Ranjbar, B. Effective Factors in Thermostability of Thermophilic Proteins Biophys. Chem. 2006, 119, 256 - 270
37. Wagner, W.; Prusse, A. The IAPWS Formulation 1995 for the Thermodynamic Properties of Ordinary Water Substance for General and Scientific Use J. Phys. Chem. Ref. Data 2002, 31, 387 - 535
38. Sciortino, F.; Fornili, S. L. Hydrogen Bond Cooperativity in Simulated Water: Time Dependence Analysis of Pair Interactions J. Chem. Phys. 1989, 90, 2786 - 2792
39. Kowall, T.; Geiger, A. Molecular Dynamics Simulation Study of 18-crown-6 in Aqueous Solution. 1. Structure and Dynamics of the Hydration Shell J. Phys. Chem. 1994, 98, 6216 - 6224
40. Smith E.; van Gunsteren, W. F. The Viscosity of SPC and SPC/E Water at 277 and 300 K Chem. Phys. Lett. 1993, 215, 315 - 318
41. 2 (110) Appl. Surf. Sci. 2009, 255, 5702 - 5708
42. 2 (110) Surface: Towards a Realistic Modeling by Molecular Dynamics J. Chem. Phys. 2004, 121, 3722 - 3726