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COMPUTATIONAL PREDICTION AND ANALYSIS OF PROTEIN-RNA
INTERFACES
by
Brian Thomas Sutch
A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(PHARMACEUTICAL SCIENCES)
December 2010
Copyright 2010 Brian Thomas Sutch
Object Description
| Title | Computational prediction and analysis of protein-RNA interfaces |
| Author | Sutch, Brian Thomas |
| Author email | sutch@usc.edu; bsutch@gmail.com |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Pharmaceutical Sciences |
| School | School of Pharmacy |
| Date submitted | 2010 |
| Restricted until | Unrestricted |
| Date published | 2010-09-13 |
| Advisor (committee chair) | Haworth, Ian S. |
| Advisor (committee member) |
Duncan, Roger F. Qin, Peter Z. |
| Abstract | Protein-RNA complexes play a central role in many biological processes, including translation, mRNA stabilization, ribosome formation, and viral packaging. The investigation of short nucleic acid polymers (aptamers) and their interactions provides a greater understanding of biological phenomena. By virtue of their molecular characteristics such as high specificity and affinity, nucleic acid aptamers are amenable to being designed for therapeutic and diagnostic applications. The goals of this thesis are to create a non-redundant database of protein-RNA interactions, to generate a mechanism for evaluating the success of computationally predicted nucleic acid aptamers, and implement a method of distilling the evolution of a protein-RNA interface during a molecular dynamics simulation down to only the unique conformations. We hypothesized that this may be achieved by creating an algorithm which would reliably assess the similarity of one protein-RNA interface to another protein-RNA interface. When given a list of protein-RNA complexes or in the case of a molecular dynamics simulation, a dry coordinate file, the algorithm correctly locates each protein-RNA interface, examines the interface contacts, geometry and motifs, and performs an all-to-all comparison. |
| Keyword | protein-RNA; interface solvation; aptamer |
| 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-m3440 |
| Rights | Sutch, Brian Thomas |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | http://www.usc.edu/isd/libraries/services/ask_a_librarian/email/ |
| Filename | etd-Sutch-4126 |
| Archival file | uscthesesreloadpub_Volume32/etd-Sutch-4126.pdf |
Description
| Title | Page 1 |
| Full text | COMPUTATIONAL PREDICTION AND ANALYSIS OF PROTEIN-RNA INTERFACES by Brian Thomas Sutch A Dissertation Presented to the FACULTY OF THE USC GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (PHARMACEUTICAL SCIENCES) December 2010 Copyright 2010 Brian Thomas Sutch |
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