Scott A. Strobel

Professor of Molecular Biophysics & Biochemistry and Chemistry, Biochemistry, Biophysical Chemistry, Bioorganic Chemistry
E-mail: strobel@csb.yale.edu
Web site: http://strobel.csb.yale.edu

Biographical Sketch

B.A. Biochemistry, Brigham Young University, 1987
Ph.D. Biological Chemistry, California Institute of Technology, 1992
Howard Hughes Medical Institute Predoctoral Fellow, Caltech, 1988-1992
Postdoctoral Fellow, Biochemistry, University of Colorado at Boulder, 1992-95
Joined Yale Faculty, 1995
Trustees Scholar, Graduated Summa Cum Laude with Honors, BYU, 1982-87
Life Sciences Research Foundation Fellowship, Sponsored by Howard Hughes Medical Institute, CU Boulder, 1992-95
Junior Faculty Research Award, American Cancer Society, Yale University, 1996-1999
Beckman Young Investigator Award, Yale University, 1997-1999
Searle Scholar Award, Yale University, 1997-2000
Basil O'Connor Starter Scholar Research Award, Yale University, 1998-1999
Beginning Investigator Award, American Cancer Society, Yale University, 2002-2006
Dylan Hixon Prize for Teaching Excellence in the Natural Sciences, Yale University, 2004

Research Description

Research in my lab focuses on how RNA catalyzes biologically essential chemical reactions, including protein synthesis and RNA splicing. We utilize synthetic organic chemistry, X-ray crystallography, thermodynamics, enzyme kinetics and combinatorial chemistry. The mutual use of these powerful techniques allows us to address questions of enzymatic structure and function in atomic detail.

Aminolysis of the peptidyl tRNA by the α-amino group of the A-site tRNA is catalyzed within the pepidyl transferase center, an active site comprised exclusively of RNA. To explore this reaction we are synthesizing novel transition state inhibitors, substrates with pK_a perturbed nucleophiles and leaving groups, and substrates with isotopic substitutions. With these reagents we will characterize the transition state and reaction mechanism of this biologically essential reaction. Questions we wish to address include: What is the chirality of the transition state? How does the nascent peptide move down the ribosomal exit tunnel? Does the reaction utilize substrate assisted catalysis? Are active site metal employed to promote the reaction and if so, what type of metal ions? Does ribosome utilize general acid and/or general base catalysis, and if so is the mechanism concerted or step-wise? The answer to these questions will make it possible to create improved antibiotics and understand one of the earliest steps in the evolution of biological catalysis.

Crystal structure of the intron splicing intermediate in complex with its 5' and 3' exons (red). The four helical domains of the RNA are shown in green, blue, orange and purple.

RNA splicing, the covalent ligation of the two flanking RNA exons with release of the intervening sequence or introns, is an important step in the maturation of RNAs prior to their use in protein synthesis. This process involves two phosphotransfer reactions, the first releases the 5'-exon and the second ligates the exons together. Some introns are able to promote these reactions without the assistance of proteins, and these systems serve as models of the reactions promoted by the spliceosome, which is also likely to have an RNA active site. We have recently determined the X-ray crystal structure of an intron and both of its exons in a complex prior to the exon ligation step. With a molecular structure of the second step complex now available to us, we are focused on several additional questions: How does the intron structure change between the first step and second step to accommodate the different substrates of the two reactions? Does the active site undergo rearrangement in approach to the transition state? How are the two active site metal ions utilized in the reaction and is there a third? Can the active site be converted from a phosphorotransferase to a peptidyl transferase as would be required for the evolutionary progression from an RNA world to the protein-RNA world of today?

Substrate residues at the active site of the intron, highlighting the alignment of the nucleophile and the leaving group of the reaction. Two catalytically essential active site metal ions are also observed within the structure.

Selected References

P. L. Adams, M. R. Stahley, A. B. Kosek, J. Wang and S. A. Strobel. Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45-50 (2004).
J. S. Weinger, D. Kitchen, S. A. Scaringe, S. A. Strobel and G. W. Muth. Solid phase synthesis and binding affinity of peptidyl transition state mimics containing 2'-OH at P-site position A76, Nucleic Acids Res. 32, 1502-1511 (2004).
K. M. Parnell, A. C. Seila and S. A. Strobel. Evidence against stabilization of the transition state oxyanion by a pK_a perturbed RNA base in the peptidyl transferase center. Proc. Natl. Acad. Sci. U.S.A. 99, 11658-63 (2002).
T. M. Schmeing, A. C. Seila, J. L. Hansen, B. Freeborn, J. K. Soukup, S. A. Scaringe, S. A. Strobel, P. B. Moore and T. A. Steitz. A pre-translocation intermediate in peptide bond formation observed in crystals of enzymatically active 50S subunits. Nature Struc. Biol. 9, 225-230 (2002).
A. A. Szewczak, A. B. Kosek, J. A. Piccirilli and S. A. Strobel. Identification of an active site ligand for a group I ribozyme catalytic metal ion. Biochemistry 41, 2516-25 (2002).

Last modified: July 10, 2005 (kp)

Scott A. Strobel
Professor of Molecular Biophysics & Biochemistry and Chemistry