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35
the b−sheet content changes from less than 10% to 30-40% while the a−helix/random
coil content decreased from over 50% to 30-40%) implying that lysozyme secondary
structures are more easily perturbed.
2.3.3 The Effect of Buffer Concentration on Protein Adsorption
Since the type of buffer significantly affects the adsorption behavior, it is
expected that buffer concentration will also have an effect. Here we demonstrate the
magnitude of this effect for BSA adsorption. Fig. 2.8(a) shows BSA adsorption on Ge
at three Tris-HCl concentrations (0, 10 and 100mM). Corresponding results for BSA
in PBS buffer are shown in Fig. 2.8 (b). The observed effect of buffer concentration is
rather complex. Tris-HCl depresses the initial adsorption of BSA on Ge, but enhances
the adsorption in the quasi-linear regime. The enhancement slope of the quasi-linear
regime increases monotomically with Tris-HCl concentration. In PBS buffer, the
initial adsorption is also depressed as in the Tris-HCl buffer, however, in the
quasi-linear regime, the adsorption rate varies non-monotonically with the PBS
concentration. The adsorption rate is increased when the PBS concentration was
changed from 0 mM to 10 mM, but when the PBS concentration was further increased
to 100 mM, the adsorption rate is drastically reduced. We expect this to be due to the
complex dependence of the driving force ( μi
b - μi
s ) on PBS concentration. This
complex behavior is perhaps to be expected for a number of reasons: (a) phosphate
ions adsorbs on solid surfaces and can compete with protein adsorption; (b)
phosphoric acid has three states of deprotonation resulting in three types of phosphate
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 51 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | 35 the b−sheet content changes from less than 10% to 30-40% while the a−helix/random coil content decreased from over 50% to 30-40%) implying that lysozyme secondary structures are more easily perturbed. 2.3.3 The Effect of Buffer Concentration on Protein Adsorption Since the type of buffer significantly affects the adsorption behavior, it is expected that buffer concentration will also have an effect. Here we demonstrate the magnitude of this effect for BSA adsorption. Fig. 2.8(a) shows BSA adsorption on Ge at three Tris-HCl concentrations (0, 10 and 100mM). Corresponding results for BSA in PBS buffer are shown in Fig. 2.8 (b). The observed effect of buffer concentration is rather complex. Tris-HCl depresses the initial adsorption of BSA on Ge, but enhances the adsorption in the quasi-linear regime. The enhancement slope of the quasi-linear regime increases monotomically with Tris-HCl concentration. In PBS buffer, the initial adsorption is also depressed as in the Tris-HCl buffer, however, in the quasi-linear regime, the adsorption rate varies non-monotonically with the PBS concentration. The adsorption rate is increased when the PBS concentration was changed from 0 mM to 10 mM, but when the PBS concentration was further increased to 100 mM, the adsorption rate is drastically reduced. We expect this to be due to the complex dependence of the driving force ( μi b - μi s ) on PBS concentration. This complex behavior is perhaps to be expected for a number of reasons: (a) phosphate ions adsorbs on solid surfaces and can compete with protein adsorption; (b) phosphoric acid has three states of deprotonation resulting in three types of phosphate |
