Skip to Main Content
 

Global Search Box

 
 
 
 

Files

File List


ucin1131483101.pdf (2.35 MB)

ETD Abstract Container

Abstract Header

HOMOLOGY MODELING OF BOVINE RHODOPSIN: INVESTIGATION OF THE EFFECT OF LIPID COMPOSITION AND EQUILIBRATION ON PREDICTED STRUCTURE

BURKHARDT, JONATHAN
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1131483101

Abstract Details

2005, MS, University of Cincinnati, Engineering : Chemical Engineering.
Structure prediction techniques are geared at bridging the gap between protein sequencers, and the more complicated crystallographic techniques for creating three-dimensional protein structures. This work used homology modeling techniques to estimate a structure for bovine rhodopsin, the first G-protein-coupled receptor (GPCR) to have a known 3D structure, using bacteriorhodopsin as a template. Molecular dynamic simulations were performed with DMPC and POPC membranes to investigate the effect of bilayer composition. Homology modeling proved to be too limited for predicting the structure of bovine rhodopsin. The initial model differed from the crystalline structure by a RMSD value of 9.46 Ang for helical heavy atoms, which compares to 4.04 Ang from Memb-Struk, and 8.647 for just alpha carbons within the helices, which compares to 3.87 Ang from PREDICT. Results from simulations with a bilayer suggest that systems that contain DMPC show a minimal improvement relative to their POPC counterparts.
Dr. Joel Fried (Advisor)
67 p.
bovine rhodopsin; rhodopsin; homology modeling; equilibration; POPC; DMPC

Recommended Citations

Citations

  • BURKHARDT, J. (2005). HOMOLOGY MODELING OF BOVINE RHODOPSIN: INVESTIGATION OF THE EFFECT OF LIPID COMPOSITION AND EQUILIBRATION ON PREDICTED STRUCTURE [Master's thesis, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1131483101

    APA Style (7th edition)

  • BURKHARDT, JONATHAN. HOMOLOGY MODELING OF BOVINE RHODOPSIN: INVESTIGATION OF THE EFFECT OF LIPID COMPOSITION AND EQUILIBRATION ON PREDICTED STRUCTURE. 2005. University of Cincinnati, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1131483101.

    MLA Style (8th edition)

  • BURKHARDT, JONATHAN. "HOMOLOGY MODELING OF BOVINE RHODOPSIN: INVESTIGATION OF THE EFFECT OF LIPID COMPOSITION AND EQUILIBRATION ON PREDICTED STRUCTURE." Master's thesis, University of Cincinnati, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1131483101

    Chicago Manual of Style (17th edition)

ucin1131483101
843
© 2005, all rights reserved.
This open access ETD is published by University of Cincinnati and OhioLINK.