Biochemistry; Biophysics; DNA Replication; Nucleic Acids; Recombination, Genetic; Crystallography, X-Ray
Our major interests are in the structural bases of the molecular mechanisms by which the proteins and nucleic acids involved in DNA replication, transcription, translation, and genetic recombination achieve their biological function. The maintenance, rearrangement, and expression of information stored in the genome all involve interactions between proteins and nucleic acids, and we have established crystal structures of macromolecules involved in all steps of gene expression. Future directions will increasingly focus on the complex macromolecular assemblies that are the functional machines in these processes, including the ribosome and the replisome. For example, we wish to establish the atomic structures of the ribosome captured in the act of protein synthesis in each of its conformational states with elongation and termination factors as well as interacting with the proteins and RNAs involved in protein secretion and membrane insertion. Likewise, a mechanistic understanding of replication and recombination will require structures of the assemblies in each step of the process. These macromolecular mechanisms are being investigated using X-ray crystal structure determination of appropriate macromolecular complexes, as well as testing of hypotheses using site directed mutagenesis and biochemical studies to relate structure to function.
Specialized Terms: Protein Structure; Proteins and Macromolecules; Protein Nucleic Acid Complexes; X-ray Crystallography
Extensive Research Description
Structure and function of biological macromolecules
Our general goal is to understand the biological functions of macromolecules in terms of their detailed molecular structure. Of particular interest are the molecular mechanisms by which those proteins and nucleic acids involved in the central dogma of molecular biology (DNA replication, transcription, translation and genetic recombination) achieve their biological function. Virtually all aspects of the maintenance, rearrangement and expression of information stored in the genome involve interactions between proteins and nucleic acids.
Our recent accomplishments have included the determination of the atomic structure of the 50S ribosomal subunit and its complexes with substrate, intermediate and product analogues as well as complexes with more than a dozen antibiotics. These structures establish that the ribosome is a ribozyme, provide insights into the mechanism of peptide bond formation and show how several classes of antibiotics function. In the area of transcription, six structures of T7 RNA polymerase captured in various functional states show the structural basis of the transition from the initiation to elongation phase, which involves a large protein structural rearrangement. They explain the basis of promoter clearance, processivity of the elongation phase, translocation and strand separation. The structures of the CCA-adding enzyme captured in each state of CCA incorporation onto tRNA explain the enzyme's specificity for nucleotide incorporation in the absence of a nucleic acid template. The structure of a recombination intermediate of gamma delta resolvase suggests that site specific recombination by this enzyme is achieved by subunit rotation.
Future directions will focus on the complex macromolecular assemblies that are the functional machines in these processes, including the ribosome and the replisome. For example, we wish to establish the atomic structures of the ribosome captured in the act of protein synthesis in each of its conformational states with elongation factors as well as interacting with the proteins involved in protein secretion. Likewise, a mechanistic understanding of replication and recombination will require structures of the assemblies in each step of their functioning. Hypotheses arising from these structures will be tested using site directed mutagenesis and biochemical studies to relate structure to function.
- Bailey, S., Wing, R.A., and Steitz, T.A. (2006). The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases. Cell 126:893-904.
- Schmeing, T.M., Huang, K.S., Strobel, S.A., and Steitz, T.A. (2005). An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 438:520-524.
- Blaha G, Stanley RE, Steitz TA. Science. 2009 Aug 21;325(5943):966-70
- Palioura S, Sherrer RL, Steitz TA, Söll D, Simonovic M. Science. 2009 Jul 17;325(5938):321-5.
- Simonovic M, Steitz TA. Biochim Biophys Acta. 2009 Jul 9. [Epub ahead of print]