Knowledge about the three dimensional structure of ribonucleic acids (RNAs) and ribonucleoprotein particles (RNPs) is essential for understanding how they carry out their biological functions, which include RNA processing and the translation of the genetic information of messenger RNA (mRNA) into protein sequences. Such understanding could offer opportunities for pharmacological or genetic intervention in these critical processes. This proposal describes the development of three dimensional models for RNAs and RNPs, with emphasis on the ribosome and tmRNA. The ribosome is the site of protein synthesis in the cell, while tmRNA is the product of the ssrA gene in bacteria. tmRNA combines functions of both transfer RNA (tRNA) and mRNA and is used to terminate translation of messages lacking a stop codon, to release the ribosome for recycling, and to tag the truncated protein product for degradation by cellular proteases. The studies on ribosomal structure/function relationships will incorporate all available high resolution data from x-ray crystallography and nuclear magnetic resonance into models matching the density maps from cryo-electron microscopic (cryo-EM) reconstructions of ribosomes trapped at various points in the translational cycle. Dr. Harvey seeks to understand the structural, energetic and kinetic basis of translational fidelity and of translocation. The tmRNA research will include studies of the molecule free in solution, using transient electric birefringence and molecular modeling, along with cryo-EM investigations of tmRNA structure / function relationships on the ribosome. This research will include development of a library of RNA structural motifs derived from the Nucleic Acid Database, along with tools for incorporating these motifs into structural models.
| Taylor, Derek J; Devkota, Batsal; Huang, Andrew D et al. (2009) Comprehensive molecular structure of the eukaryotic ribosome. Structure 17:1591-1604 |
| Mears, Jason A; Sharma, Manjuli R; Gutell, Robin R et al. (2006) A structural model for the large subunit of the mammalian mitochondrial ribosome. J Mol Biol 358:193-212 |
| Stagg, Scott M; Harvey, Stephen C (2005) Exploring the flexibility of ribosome recycling factor using molecular dynamics. Biophys J 89:2659-66 |
| Stagg, Scott M; Mears, Jason A; Harvey, Stephen C (2003) A structural model for the assembly of the 30S subunit of the ribosome. J Mol Biol 328:49-61 |
| Gao, Haixiao; Sengupta, Jayati; Valle, Mikel et al. (2003) Study of the structural dynamics of the E coli 70S ribosome using real-space refinement. Cell 113:789-801 |
| Mears, Jason A; Cannone, Jamie J; Stagg, Scott M et al. (2002) Modeling a minimal ribosome based on comparative sequence analysis. J Mol Biol 321:215-34 |
| Stagg, Scott M; Valle, Mikel; Agrawal, Rajendra K et al. (2002) Problems with the transorientation hypothesis. RNA 8:1093-4 |
| Stagg, S M; Frazer-Abel, A A; Hagerman, P J et al. (2001) Structural studies of the tRNA domain of tmRNA. J Mol Biol 309:727-35 |
| VanLoock, M S; Agrawal, R K; Gabashvili, I S et al. (2000) Movement of the decoding region of the 16 S ribosomal RNA accompanies tRNA translocation. J Mol Biol 304:507-15 |
| Wang, R; Alexander, R W; VanLoock, M et al. (1999) Three-dimensional placement of the conserved 530 loop of 16 S rRNA and of its neighboring components in the 30 S subunit. J Mol Biol 286:521-40 |
Showing the most recent 10 out of 13 publications
