Electronic Theses and Dissertations

Identifier

1065

Date

2014

Date of Award

4-22-2014

Document Type

Dissertation

Degree Name

Doctor of Philosophy

Major

Chemistry

Concentration

Physical Chemistry

Committee Chair

Yongmei Wang

Committee Member

Abby Parrill

Committee Member

Daniel Baker

Committee Member

Ramin Homayouni

Abstract

Ribosomes are complex cellular machines that synthesize new proteins in the cell. The accurate and efficient assembly of ribosomal proteins (r-proteins) and ribosomal RNA (rRNA) to form a functional ribosome is important for cell growth, metabolic reactions, and other cellular processes. Ribosomal assembly has been an active research topic for many years because understanding the assembly mechansims can provide insight into protein/RNA recognitions that are important in many other cellular processes, as well as help optimize the development of antibacterial therapeutics. Experimental and computational sutdies thus far have greatly improved our understanding of assembly, yet many questions remain unanswered regarding the complex behaviors of r-proteins and rRNA during the process. To further understand ribosome assembly, we have computationally studied the sequences, structures, and dynamic properties of r-proteins from the 30S subunit and their relationships to RNA binding. We discuss the statistically greater amount of positively charged residues in r-proteins compared to other housekeeping proteins and observe a high level of charged interactions between r-proteins and rRNA in the assembled structure. We also detect a significant correlation between the overall flexibility of a protein and the number of contact points it makes with its rRNA binding site. Protein residues contacting with rRNA are observed to be more mobile in solution when compared to the non-contacting residues. We also describe common modes of structural dynamics, revealing likely conformational changes the proteins make prior to binding, how they relate to possible binding mechanisms used during the assembly and to the location of the protein in the fully assembled ribosome.

Comments

Data is provided by the student.

Library Comment

dissertation or thesis originally submitted to the local University of Memphis Electronic Theses & dissertation (ETD) Repository.

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