University of Illinois Urbana-Champaign

Simulation and Visualization of Dynamics in RNA·protein Complexes in Translation

Eargle, John

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Description

Title
Simulation and Visualization of Dynamics in RNA·protein Complexes in Translation
Author(s)
Eargle, John
Issue Date
2010
Doctoral Committee Chair(s)
Zaida Luthey-Schulten
Department of Study
Biophysics and Computational Biology
Discipline
Biophysics and Computational Biology
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Chemistry, Biochemistry
Language
eng
Abstract
Finally, ongoing work is presented on the role of ribosomal signatures in the first steps of ribosomal assembly. Ribosomal signatures are features that are completely conserved within one domain of life but absent from the other domains. Correlations between rRNA signatures and signatures in the ribosomal proteins (r-proteins) show that the rRNA signatures coevolved with both domain specific r-proteins and inserts in universal r-proteins. The largest bacterial structural rRNA signature with such a coevolutionary protein partner is found in the five-way junction of the 16S rRNA 5' domain, which is held together by the universal r-protein S4. We characterize the dynamics and flexibility of the free S4 structural signature and rRNA signature helix 16 (h16) as well as the S4·h16 complex. Investigation into the folding and binding of these components will be carried out using Go-like potentials to bias the complex structure towards its native state.
Graduation Semester
2010
Type of Resource
text
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http://hdl.handle.net/2142/85479

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Graduate Dissertations and Theses at Illinois PRIMARY
Graduate Theses and Dissertations at Illinois
Dissertations and Theses - Biophysics and Quantitative Biology