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SCOTT STROBEL

Research in the Strobel laboratory focuses on biologically critical reactions catalyzed by RNA. Two systems we study are RNA splicing and ribosomal peptide bond formation. We are also exploring the recently discovered class of RNA riboswitches that regulate gene expression by binding small molecule metabolites. We utilize a multidisciplinary approach that includes biochemistry, enzyme kinetics, X-ray crystallography, organic synthesis, and molecular biology.

Protein Synthesis. Crystallographic studies reveal that the ribosomal peptidyl transferase center is composed exclusively of rRNA, i.e., that the ribosome is a ribozyme. We aim to determine how this biologically fundamental reaction is catalyzed. We are taking several approaches to understand this enzyme, including: (i) synthesis and characterization of transition state inhibitors; (ii) preparation of modified A-site and P-site tRNA substrates to test for substrate assisted catalysis of peptide bond formation by enzyme kinetic analysis; (iii) purification of mutant ribosomes to assess the role of rRNA functional groups; (iv) investigating the reaction transition state by kinetic isotope effect analysis and by determining the Brønsted coefficient for the ester aminolysis reaction.

Intron Splicing. The discovery of the RNA self-splicing group I intron provided the first demonstration that not all enzymes are proteins. We recently reported the X-ray crystal structure of a catalytically active group I intron splicing intermediate. This is the first splicing complex of any kind to include a complete intron, both exons and an organized active site occupied with metal ions. The exon ligation is chemically equivalent for pre-mRNA splicing by the spliceosome. As a result, the chemical themes of splice site selection, exon alignment, and catalytic metal ion positioning, which are manifest in this splicing intermediate complex, are likely to find parallels in pre-mRNA splicing. We are now undertaking several additional structural and biochemical studies to characterize the entire RNA splicing pathway. The overriding goals of these studies are to: (i) understand the mechanism of RNA splicing, (ii) explain how RNA tertiary structure is formed and active sites created in the absence of proteins, (iii) reveal how metal ions contribute to RNA catalysis, and (iv) visualize the nature of the transition state of the phosphoryl transfer reaction promoted during exon ligation.

Selected Publications
Stahley, M. R. and Strobel, S. A. Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science 309, 1587-1590 (2005)

Schmeing, T. M., Huang, K. S., Strobel, S. A. and Steitz, T. A. Induced-fit mechanism for the peptidyl transferase reaction of the large ribosomal subunit. Nature 438, 520-524 (2005)

Seila, A. C., Okuda, K., Nunez, S., Seila, A. F., and Strobel, S. A. Kinetic isotope effect analysis of the ribosomal peptidyl transferase reaction. Biochemistry 44, 4018-4027 (2005)

Huang, K. S., Weinger, J. S., Butler, E. B. and Strobel, S. A. Regiospecificity of the peptidyl tRNA ester within the ribosomal P site. J. Amer. Chem. Soc. 128, 3108-3109 (2006)

Cochrane, J. C., Lipchock, S. V. and Strobel, S. A.  Structural investigation of the GlmS ribozyme bound to its catalytic cofactor.  Chemistry & Biology 14, 97-105 (2007)

Last Updated 06-26-2007