This proposal seeks continued support for exploration of structure and function of the ribosome actively engaged in protein synthesis, by cryo-electron microscopy (cryo-EM) and single-particle reconstruction. Protein biosynthesis is one of the most fundamental processes of life, but despite seminal work in solving the structure of the ribosome, this process is not well understood. Cryo-EM is uniquely suited to capture the molecule in functional states under close to native conditions. In this lab, several seminal discoveries regarding the dynamics of this process in both eubacterial and eukaryotic translation have been made in the past;among these the ratchet-like motion during mRNA-tRNA translocation and the large spring-like deformation of the aminoacyl-tRNA as it enters the ribosome during the aminoacyl-tRNA selection process. Special focus of this research program will be the eukaryotic (yeast and mammalian) ribosome.
The aims of the proposed studies are threefold: (1) to make use of tilt pair recoding, novel technology for online data capture in the electron microscope, workflow optimization, and availability of a Titan Krios instrument at Janelia Farm, and other improvements in order to achieve atomic (better than 3.5A) resolution for selected ribosome complexes of special interest, such as ribosomes of trypanosomes and a yeast translocation complex;(2) to study the process of mammalian eukaryotic translation initiation by cryo-EM visualization of selected initiation complexes;(3) to study, with the aid of advanced classification methods, the distribution of states and their structural manifestations in a freely equilibrating, factor-free, eukaryotic ribosome sample as a function of relevant parameters such as temperature and ionic conditions. Samples will be obtained from several collaborating labs that are specialized in eukaryotic translation. Additional important collaborations are in the area of eukaryotic ribosome structure, smFRET, classification of heterogeneous samples by manifold embedding, and atomic modeling. Density maps when obtained at sufficient resolution will be analyzed by flexible fitting and interpreted in the rich context of existing structural, kinetics, single-molecule FRET, and biochemical data.

Public Health Relevance

The ribosome performs protein synthesis in all cells in all life forms. The research proposed will further the understanding of its functional dynamics, and thus contribute to a fundamental understanding of all life processes. Understanding the function of the eukaryotic ribosome on a fundamental level is advancing our ability to combat debilitating human diseases arising from dysfunctions of translation, and viral takeover of the ribosome by the IRES mechanism (e.g., in hepatitis C). This knowledge also helps in developing drugs to fight eukaryotic parasites.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function C Study Section (MSFC)
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Flicker, Paula F
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Columbia University (N.Y.)
Schools of Medicine
New York
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