James M. Nolan

RNA-protein interactions, RNA structure

Assistant Professor of Biochemistry
Ph.D. (Duke, 1988)
Phone: (504) 584-2453
FAX: (504) 584-2739
Address:
1430 Tulane Ave., Box SL-43
New Orleans LA 70112
Email: JNolan@tulane.edu

Research Interests

The RNase P Holoenzyme. We are examining structural aspects of RNA-protein interactions using the bacterial ribonuclease P (RNase P) holoenzyme as a model system. RNase P consists of a large RNA and a small protein subunit which together cleave 5'-precursor sequences from tRNA transcripts. In vitro at high ionic strength, the RNA subunit is the catalytic moiety and the protein is dispensable for catalysis. Thus, RNase P is a member of an unusual class of enzyme known as ribozymes, which use an RNA molecule, rather than a protein, as a catalyst. Although the RNase P protein is not required for activity in vitro, it is essential for viability in vivo. In addition, the kinetics of the holoenzyme reaction in vitro differs dramatically from the RNA-alone reaction in salt requirement, substrate specificity, and reaction rate. While much is known about the RNA subunit of the enzyme, little is known about the mechanism by which the protein moiety mediates its pleiotropic effects on the enzymatic reaction, which are required for function in vivo.

We are using a detailed structural analysis of the RNase P RNA-protein complex to investigate the how the protein binds to RNase P RNA, and how this binding affects the reaction mechanism, including changes in how the RNase P RNA interacts with its tRNA substrate in the presence of RNase P protein. These problems are being studied by a variety of techniques. The site of RNase P RNA with which the protein interacts is being studied by chemical and enzymatic footprinting of the holoenzyme complex. We are incorporating crosslinking reagents at specific sites of both the RNA and protein subunits to further characterize the sites of interaction between the two subunits. Regions of the RNase P protein important for interaction with RNase P RNA will also be identified by in vitro and in vivo analyses of mutations in the RNase P protein.

The results of these studies will shed light on the RNase P protein and its function in the holoenzyme which, in turn, will enhance understanding of RNA enzyme mechanism, and RNA-protein as well as RNA-RNA interactions.


RNA Modeling. We are also interested in modeling the structure of the RNase P RNA. This is a primary research interest in the laboratory of Norm Pace. I have modeled a tertiary structural element of RNase P RNA structure using the MC-SYM modeling program based upon phylogenetic comparative analysis done by Jim Brown (see the abstract). You can see the model of this structure if you have the Chime plug-in for viewing PDB files.

Publications

List of recent publications.

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