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25. Sun, Y.; Welsh, W. J.; Latour, R. A., Prediction of the orientations of adsorbed
protein using an empirical energy function with implicit salvation. Langmuir 2005, 21,
(12), 5616-5626.
26. Zhang, J.; Li, L. Y.; Chen, S. F.; Jiang, S. Y., Molecular simulation study of water
interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled
monolayers. Langmuir 2004, 20, 8931-8938.
27. Snow, C. D.; Sorin, E. J.; Rhee, Y. M.; Pande, V. S., How well can simulation
predict protein folding kinetics and thermodynamics? Annu. Rev. Biophys. Struct.
2005, 34, 43-69.
28. Zagrovic, B.; Pande, V., Solvent viscosity dependence of the folding rate of a
small protein: distributed computing study. J. Comp. Chem. 2003, 24, 1432-1436.
29. Blake, C. C.; Koenig, D. F.; Mair, G. A.; North, A.; Phillips, D. C.; Sarma, V. R.,
Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2
Angstrom resolution. Nature 1965, 206, (986), 757-761.
30. Smith, L. J.; Sutcliffe, M. J.; Redfield, C.; Dobson, C. M., Analysis of and 1
torsion angles for hen lysozyme in solution from 1H NMR spin, spin coupling
constants. Biochemistry 1991, 30, 986-996.
31. Smith, L. J.; Sutcliffe, M. J.; Redfield, C.; Dobson, C. M., Structure of hen
lysozyme in solution. J. Mol. Biol. 1993, 229, 930-944.
32. Smith, L. J.; Mark, A. E.; Dobson, C. M.; van Gunsteren, W. F., Comparison of
MD simulations and NMR experiments for hen lysozyme—analysis of local
fluctuations, cooperative motions, and global changes. Biochemistry 1995, 34,
10918–10931.
33. Schwalbe, H.; Grimshaw, S. B.; Spencer, A.; Buck, M.; Boyd, J.; Dobson, C. M.;
Redfield, C.; Smith, L. J., A refined solution structure of hen lysozyme determined
using residual dipolar coupling data. Protein Sci. 2001, 10, (4), 677-688.
34. Hattori, T.; Aiba, T.; Iijima, E.; Okube, Y.; Nohira, H.; Tate, N.; Katayama, M.,
Initial stage of oxidation of hydrogen-terminated silicon surface. Applied Surface
Science 1996, 104/105, 323-328.
35. Strother, T.; Hamers, R. J.; Smith, L. M., Covalent attachment of
oligodeoxyribonucleotides to amine-modified Si (001) surfaces. Nucleic Acids Res.
2000, 28, (18), 3535-3541.
Object Description
| Title | Experimental study and atomic simulation of protein adsorption |
| Author | Wei, Tao |
| Author email | twei2004@gmail.com; dnaafm@yahoo.com.cn |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Chemical Engineering |
| School | Viterbi School of Engineering |
| Date defended/completed | 2008-07-29 |
| Date submitted | 2008 |
| Restricted until | Unrestricted |
| Date published | 2008-10-07 |
| Advisor (committee chair) | Shing, Katherine |
| Advisor (committee member) |
Nakano, Aiichiro Goo, Edward K. |
| Abstract | The studies of protein adsorption at solid-liquid interface are important in various applications. Multilayer and irreversible adsorption behaviors are commonly observed. In this work, protein adsorption behavior at the solid-liquid interface was investigated by a combination of experimental Fourier transform infrared/attenuated total reflectance (FTIR/ATR) studies and computer simulations: Molecular Dynamics (MD) simulation and hybrid Genetic-Algorithm (GA) schemes.; BSA, lysozyme, IgG and fibrinogen adsorption was studied with FTIR/ATR in tris(hydroxymethyl)-aminomethane hydrochloride (Tris-HCl) and phosphate buffered saline (PBS) buffers on a Ge surface. Buffer choice was shown to drastically affect adsorption kinetics. In comparison with Tris-HCl, PBS buffer depresses the adsorption of BSA, IgG and fibrinogen in the prolonged quasi-linear kinetic region while lysozyme adsorption is relatively insensitive to buffer choice. Buffer concentration can also significantly affect protein adsorption. The secondary structures in the adsorbed phase are generally quite different from the bulk structure; however, buffer choice has negligible effect on structural evolution. Significant secondary structure changes occur during adsorption. The secondary structures in the adsorbed phase are inhomogeneous. The role of phosphate ions in PBS buffer and their effect on protein adsorption are rather complex. Phosphate ions adsorb competitively against protein molecules and their deprotonation equilibrium can be altered at the solid-liquid interface due to the adsorbed protein.; The effect of surface on adsorption is examined by adsorbing IgG on various polymer-coated surfaces. IgG adsorption is higher on more hydrophobic surface. IgG molecules adsorbed in layers near hydrophilic solid surfaces suffer less secondary structure changes.; The behavior of lysozyme during adsorption on a hydrogen-terminated Si surface (Si-H) is studied using MD simulations. Although atomistic simulations are highly time-consuming for direct observations of complete secondary structure changes, indications of molecular deformations are observed over nanosecond simulation time scale. Lysozyme molecule undergoes deformation onto the Si-H surface, as is evidenced by the reduction in the volume, the increase in solvent accessible surface area, the change of the overall shape, and certain amount of alteration in secondary structures. The main α-helix domains experience some loss while the beta-sheet domains remain almost intact. The hydrophobic character of the surface is believed to contribute to the loss of the organized structures of the amino residues in close proximity to the surface.; An efficient hybrid GA/spatial-grid method was developed to search for low adsorption-energy orientations and locations of a protein molecule on a solid surface. The surface and the protein molecule are treated as rigid bodies, whereas the bulk fluid is represented by spatial grids. The hybrid search procedure consists of two interlinked loops. In 1st loop (A), a GA is employed to identify promising regions for the global energy minimum, whereas a local optimizer with the derivative-free Nelder-Mead method is used to search for the lowest-energy orientation within the identified regions. In 2nd loop (B), new population is generated and competitive solution from loop A is improved. The switching between two loops is adaptively controlled by similarity analysis. We test the method for lysozyme adsorption on a hydrophobic Si-H (110) surface in implicit water. The hybrid search method was shown to have faster convergence and better solution accuracy compared with the conventional GA, which suffered from premature convergence. |
| Keyword | protein adsorption; FTIR/ATR; MD simulation; hybrid genetic algorithm |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m1641 |
| Contributing entity | University of Southern California |
| Rights | Wei, Tao |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | cisadmin@lib.usc.edu |
| Filename | etd-Wei-2367 |
| Archival file | uscthesesreloadpub_Volume14/etd-Wei-2367.pdf |
Description
| Title | Page 150 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | 134 25. Sun, Y.; Welsh, W. J.; Latour, R. A., Prediction of the orientations of adsorbed protein using an empirical energy function with implicit salvation. Langmuir 2005, 21, (12), 5616-5626. 26. Zhang, J.; Li, L. Y.; Chen, S. F.; Jiang, S. Y., Molecular simulation study of water interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled monolayers. Langmuir 2004, 20, 8931-8938. 27. Snow, C. D.; Sorin, E. J.; Rhee, Y. M.; Pande, V. S., How well can simulation predict protein folding kinetics and thermodynamics? Annu. Rev. Biophys. Struct. 2005, 34, 43-69. 28. Zagrovic, B.; Pande, V., Solvent viscosity dependence of the folding rate of a small protein: distributed computing study. J. Comp. Chem. 2003, 24, 1432-1436. 29. Blake, C. C.; Koenig, D. F.; Mair, G. A.; North, A.; Phillips, D. C.; Sarma, V. R., Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution. Nature 1965, 206, (986), 757-761. 30. Smith, L. J.; Sutcliffe, M. J.; Redfield, C.; Dobson, C. M., Analysis of and 1 torsion angles for hen lysozyme in solution from 1H NMR spin, spin coupling constants. Biochemistry 1991, 30, 986-996. 31. Smith, L. J.; Sutcliffe, M. J.; Redfield, C.; Dobson, C. M., Structure of hen lysozyme in solution. J. Mol. Biol. 1993, 229, 930-944. 32. Smith, L. J.; Mark, A. E.; Dobson, C. M.; van Gunsteren, W. F., Comparison of MD simulations and NMR experiments for hen lysozyme—analysis of local fluctuations, cooperative motions, and global changes. Biochemistry 1995, 34, 10918–10931. 33. Schwalbe, H.; Grimshaw, S. B.; Spencer, A.; Buck, M.; Boyd, J.; Dobson, C. M.; Redfield, C.; Smith, L. J., A refined solution structure of hen lysozyme determined using residual dipolar coupling data. Protein Sci. 2001, 10, (4), 677-688. 34. Hattori, T.; Aiba, T.; Iijima, E.; Okube, Y.; Nohira, H.; Tate, N.; Katayama, M., Initial stage of oxidation of hydrogen-terminated silicon surface. Applied Surface Science 1996, 104/105, 323-328. 35. Strother, T.; Hamers, R. J.; Smith, L. M., Covalent attachment of oligodeoxyribonucleotides to amine-modified Si (001) surfaces. Nucleic Acids Res. 2000, 28, (18), 3535-3541. |
