Project Director

Whitson, Kristin B.

Department Examiner

Allen, Tatiana; Marlowe, Bob; Carter, Pam; Whitson, Stefanie

Department

Dept. of Physics, Geology, and Astronomy

Publisher

University of Tennessee at Chattanooga

Place of Publication

Chattanooga (Tenn.)

Abstract

The heterogeneous nuclear ribonucleoprotein C (hnRNP C) performs a critical role in the processing of nascent pre-messenger ribonucleic acid (pre-mRNA) transcripts as they exit DNA polymerase II. As the pre-mRNA transcripts emerge from the polymerase complex, they are bound by hnRNP C only if its nucleotide (NT) chain is longer than a certain nucleotide length. If the chain is long enough and binding occurs, the nucleotide strand is exported and processed as mRNA, whereas if the length requirement is not met, the RNA sequence is directed along a pathway to become small nuclear RNA (snRNA). The functional form of hnRNP C is a four-copy tetramer, with four C proteins associating at their leucine zipper-like oligomerization domains (CLZ) to form the complex. The CLZ domains form a coiled-coil tetramer, a very stable structural motif in biological macromolecules. This work studies the thermodynamic properties of the CLZ domain of hnRNP C. Fluorescence resonance energy transfer (FRET) assays were conducted using fluorescently labeled CLZ peptides to determine the equilibrium dissociation constant (KD) as well as the rate of tetramer formation (k-on). The experimental data was used in conjunction with computational simulations to gain a more coherent picture of CLZ interactions.

Acknowledgments

I would like to acknowledge the major efforts given by Dr. Kristin Whitson on this project. Without her mentorship, guidance, and inspiring passion for science this project would never have been finished. I want to acknowledge our collaborators at Vanderbilt University, Dr. Carlos Lopez and James Pino, for their work on the computational facet of this project. I also would like to acknowledge the efforts of Bomi Kim and Dr. Stephanie R. Whitson for help on the project as well. A special thanks also is needed for the Provost Student Research Awards for funding this project.

Degree

B. S.; An honors thesis submitted to the faculty of the University of Tennessee at Chattanooga in partial fulfillment of the requirements of the degree of Bachelor of Science.

Date

5-2015

Subject

Thermodynamics; Proteins -- Analysis; Oligomers

Keyword

CLZ; hnRNP C; FRET; Biological modeling; Molecular dynamics; Umbrella sampling

Discipline

Physics

Document Type

Theses

Extent

xi, 55 leaves

Language

English

Rights

Under copyright.

License

http://creativecommons.org/licenses/by-nc-nd/3.0/

Date Available

9-15-2015

Included in

Physics Commons

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