A Thermodynamic and Kinetic Approach to Determining Cooperative Binding in DEAD-Box Proteins

Albring, Michael J.

A Thermodynamic and Kinetic Approach to Determining Cooperative Binding in DEAD-Box Proteins

Persistent URL

http://hdl.handle.net/10456/15731

Author(s)

Albring, Michael J.

Date Issued

May 1, 2011

Abstract

RNA is a vital component in maintaining biological life, and requires a high level of processing before it can achieve its mature, final strucuture1. It has a high degree of flexibility, and can interact with itself, other molecules of RNA, DNA, and even proteins. Therefore, along its folding path into its mature structure, it can form unwanted interactions that are sometimes energetically more favorable than its final active conformation. Specialized proteins are therefore employed to assist in RNA folding called RNA chaperones. An example of an RNA chaperone is DEAD-box protein A (DbpA) in Escherichia coli. DEAD-box proteins are ATP dependent RNA helicases, thus requiring the energy from ATP hydrolysis to separate a double stranded region of RNA. DbpA exhibits what is known as cooperative binding, which occurs when the binding of its first substrate facilitates the binding of the second. It is currently unknown how DbpA’s observed cooperative binding occurs. Kinetic and thermodynamic parameters of DbpA suggest that an arginine within the ATP binding pocket (R334) is responsible for forming an ionic interaction which protects the ATP and facilitates RNA binding. Direct binding analyses were carried out in an attempt to verify and solidify these findings, but the majority of the experimentation period was spent troubleshooting two new protocols.

Honors

Biochemistry, 2011

First Reader(s)

Garcia, Ivelitza