Page 143 |
Save page Remove page | Previous | 143 of 185 | Next |
|
small (250x250 max)
medium (500x500 max)
Large (1000x1000 max)
Extra Large
large ( > 500x500)
Full Resolution
All (PDF)
|
This page
All
|
127
(Part II). The secondary structures are unaffected by the switch. Part III in Fig. 4.22 is
the adsorption simulation result using the atom-based method. Compared to (Part I),
generally the lysozyme molecule lost some -helix structures and there is a smaller
loss in the 3 -sheet domains at the initial stage; however, most of the original levels
were recovered after 1.3 ns.
The amino acid residues (Met 12 - Arg 14) in the domain of -helix A were close
to the surface within the cut-off range of the non-bonded interaction. The -helix
domain in this region partially unwound to 3-helix structure and stretched to a turn
structure after contacting with the Si-H surface for the initial 25 ps. However, the
newly formed 3-helix sub-domain is highly persistent during the process of the
interaction with Si-H surface, as shown in Fig. 4.21 and Fig. 4.22.
The -helix B (Leu 25-Ser38) domain lost structural stability immediately when
the protein was in contact with the Si-H surface. The structures in this -helix region
converted to turn and bend structures during the energy minimization, however, some
helix structure in (Leu 25-Trp 28) was recovered as 3-helix after 250 ps. The newly
formed 3-helix structure appeared with great frequency during the following 1.5 ns of
time steps although there were some transitions between 3-helix and turn structure.
The time needed for the recovery of helix structure was about 250 ps, which
corresponds to the discontinuity in the energy curve, changes in RMSD and Rg shown
in Fig. 4.14, Fig. 4.15 and Fig. 4.16. This showed that the internal structural
rearrangement caused some change in the total shape, configuration and the system
energy.
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 143 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@lib.usc.edu |
| Full text | 127 (Part II). The secondary structures are unaffected by the switch. Part III in Fig. 4.22 is the adsorption simulation result using the atom-based method. Compared to (Part I), generally the lysozyme molecule lost some -helix structures and there is a smaller loss in the 3 -sheet domains at the initial stage; however, most of the original levels were recovered after 1.3 ns. The amino acid residues (Met 12 - Arg 14) in the domain of -helix A were close to the surface within the cut-off range of the non-bonded interaction. The -helix domain in this region partially unwound to 3-helix structure and stretched to a turn structure after contacting with the Si-H surface for the initial 25 ps. However, the newly formed 3-helix sub-domain is highly persistent during the process of the interaction with Si-H surface, as shown in Fig. 4.21 and Fig. 4.22. The -helix B (Leu 25-Ser38) domain lost structural stability immediately when the protein was in contact with the Si-H surface. The structures in this -helix region converted to turn and bend structures during the energy minimization, however, some helix structure in (Leu 25-Trp 28) was recovered as 3-helix after 250 ps. The newly formed 3-helix structure appeared with great frequency during the following 1.5 ns of time steps although there were some transitions between 3-helix and turn structure. The time needed for the recovery of helix structure was about 250 ps, which corresponds to the discontinuity in the energy curve, changes in RMSD and Rg shown in Fig. 4.14, Fig. 4.15 and Fig. 4.16. This showed that the internal structural rearrangement caused some change in the total shape, configuration and the system energy. |
