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116
provides the information on the gyration radius change of lysozyme molecule on Si-H
surface. After the initial minimization, lysozyme gyration radius underwent very small
shrink by 0.024 Å from the value obtained from the bulk simulation as tabulated in
Table 4.1. Fig. 4.16, showed that after the initial rapid reduction in the radius of
gyration during energy minimization, lysozyme spread gradually during the following
540 ps of time steps, reached around 14.350 Å, and followed, however, by gradual
contraction. The initial quick and large increase in the radius of gyration, which were
caused by the relaxation of protein when brought into close contact with solid Si-H
surface, correspond to the sharp energy drop and quick increase of RMSD value, as
discussed previous in Fig. 4.14 and Fig. 4.15. However, the radius of gyration
fluctuated and reached to some plateau value in the subsequent 1 ns, suggesting that
the lysozyme molecule has retreated from the surface and reached an energetically
favorable distance from the surface. The small magnitude of the change in the value of
Rg shows that lysozyme is relatively rigid.
Table 4.1. Comparisons of lysozyme gyration radius Rg: conformation of initial pdb
file (state 18), after re-hydration (bulk simulation) and after the interaction with Si-H
surface for 2.45 ns.
NMR data Re-hydration a Adsorption b
Rg (Å) 14.097 14.361 ±0.0415 14.339±0.0031
a Standard deviation obtained from the simulation of the final 50 ps during the
re-hydration with the atom-based method. The data were collected every 1 ps.
b Standard deviation obtained from the simulation of the final 100 ps of the adsorption.
The data were collected every 2 ps.
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 132 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | 116 provides the information on the gyration radius change of lysozyme molecule on Si-H surface. After the initial minimization, lysozyme gyration radius underwent very small shrink by 0.024 Å from the value obtained from the bulk simulation as tabulated in Table 4.1. Fig. 4.16, showed that after the initial rapid reduction in the radius of gyration during energy minimization, lysozyme spread gradually during the following 540 ps of time steps, reached around 14.350 Å, and followed, however, by gradual contraction. The initial quick and large increase in the radius of gyration, which were caused by the relaxation of protein when brought into close contact with solid Si-H surface, correspond to the sharp energy drop and quick increase of RMSD value, as discussed previous in Fig. 4.14 and Fig. 4.15. However, the radius of gyration fluctuated and reached to some plateau value in the subsequent 1 ns, suggesting that the lysozyme molecule has retreated from the surface and reached an energetically favorable distance from the surface. The small magnitude of the change in the value of Rg shows that lysozyme is relatively rigid. Table 4.1. Comparisons of lysozyme gyration radius Rg: conformation of initial pdb file (state 18), after re-hydration (bulk simulation) and after the interaction with Si-H surface for 2.45 ns. NMR data Re-hydration a Adsorption b Rg (Å) 14.097 14.361 ±0.0415 14.339±0.0031 a Standard deviation obtained from the simulation of the final 50 ps during the re-hydration with the atom-based method. The data were collected every 1 ps. b Standard deviation obtained from the simulation of the final 100 ps of the adsorption. The data were collected every 2 ps. |
