eBriefing

A Beautiful Machine: Investigating the Inner Workings of the Ribosome

A Beautiful Machine
Reported by
Megan Stephan

Posted July 16, 2009

Overview

Protein translation is the elegant process by which the genetic code is used to produce enzymes, structural proteins, and other working components of the cell. This process is carried out by ribosomes, intracellular organelles composed of RNA and protein that are charged with making polypeptides quickly and accurately, using messenger RNAs (mRNAs) as templates.

On April 1, 2009, three ribosome researchers came together at the Academy to present their findings on the workings of this molecular machine. Marina V. Rodnina and her colleagues at the Max Planck Institute for Biophysical Chemistry are studying the mechanisms by which ribosomes select the mRNA templates that they will translate. Hani Zaher and his colleagues of the Johns Hopkins School of Medicine are investigating the process by which mistakes are kept out of the final peptide. Ruben L. Gonzalez, Jr. and his group at Columbia University are researching how the dynamics of ribosomal conformational changes control the process of protein synthesis.

Use the tabs above to find a meeting report and multimedia from this event.

Web Sites

NCBI Entrez Structure Database
Searchable database includes ribosomal subunit, tRNA, and related structures.

Protein Translation Animation
Animation produced by Said Sannuga of the MRC Laboratory of Molecular Biology.

Ribosomal Database Project
Web site based at Michigan State University providing ribosome-related data and services to the scientific community.

Ribosome Structure and Function
Structures and movies from the Ramakrishnan laboratory at the MRC Laboratory of Molecular Biology.

Rib-X Pharmaceuticals
Small molecule drug discovery and development company focused on the structure-based design of new classes of antibiotics.


Articles

Marina Rodnina

Milon P, Konevega AL, Gualerzi CO, Rodnina MV. 2008. Kinetic checkpoint at a late step in translation initiation. Mol. Cell. 30: 712-720.

Rodnina MV. 2009. Long-range signalling in activation of the translational GTPase EF-Tu. EMBO J. 28: 619-620. Full Text

Rodnina MV. 2009. Visualizing the protein synthesis machinery: new focus on the translational GTPase elongation factor Tu. Proc. Natl. Acad. Sci. USA 106: 969-970.

Savelsbergh A, Rodnina MV, Wintermeyer W. 2009. Distinct functions of elongation factor G in ribosome recycling and translocation. RNA 15: 772-780.

Wohlgemuth I, Brenner S, Beringer M, Rodnina MV. 2008. Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates. J. Biol. Chem. 283: 32229-32235.

Hani Zaher

Zaher HS, Green R. 2009. Fidelity at the molecular level: lessons from protein synthesis. Cell 136: 746-762.

Zaher HS, Green R. 2009. Quality control by the ribosome following peptide bond formation. Nature 457: 161-166.

Zaher HS, Unrau PJ. 2007. Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA 13: 1017-1026. Full Text

Zaher HS, Unrau PJ. 2006. A general RNA-capping ribozyme retains stereochemistry during cap exchange. J. Am. Chem. Soc. 128: 13894-13900.

Zaher HS, Watkins RA, Unrau PJ. 2006. Two independently selected capping ribozymes share similar substrate requirements. RNA 12: 1949-1958. Full Text

Ruben Gonzalez

Sternberg, SH, Fei J, Prywes, N, McGrath, KA, Gonzalez RL Jr. 2009. Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling. Nat. Struct. Molec. Biol. DOI 10.1038/nsmb.1622.

Gonzalez RL Jr. 2008. Navigating the RNA folding landscape. Nat. Chem. Biol. 4: 451-452.

Fei J, Kosuri P, MacDougall DD, Gonzalez RL Jr. 2008. Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol. Cell 30: 348-359.

Gonzalez RL Jr, Chu S, Puglisi JD. 2007. Thiostrepton inhibition of tRNA delivery to the ribosome. RNA 13: 2091-2097. Full Text

Blanchard SC, Kim HD, Gonzalez RL Jr, et al. 2004. tRNA dynamics on the ribosome during translation. Proc. Natl. Acad. Sci. USA 101: 12893-12898. Full Text

Speakers

Marina Rodnina

Marina Rodnina, PhD

Max Planck Institute for Biophysical Chemistry
e-mail | web site | publications

Marina Rodnina is director of the Department of Physical Biochemistry at the Max Planck Institute of Biophysical Chemistry in Göttingen, Germany. Rodnina received her PhD from the Institute of Molecular Biology and Genetics in Kiev, Ukraine. She did her postdoctoral work in biochemistry at the University of Witten/Herdecke in Witten, Germany. Rodnina is an elected member of the European Molecular biology Organization, the director of the RNA Society for the 2007–2009 term, and has been a member of the German Academy of Sciences Leopoldina since 2008.

Hani Zaher

Hani Zaher, PhD

The Johns Hopkins University School of Medicine
e-mail | web site | publications

Hani Zaher obtained his graduate degree from Simon Fraser University, Canada, working under the supervision of Peter Unrau. There, Zaher used in vitro selection techniques to expand the repertoire of RNA's catalytic abilities, most notably an RNA polymerase ribozyme that is capable of extending an RNA primer by up to 20 nucleotides in a template-dependent manner. In the summer of 2007, he moved to Rachel Green's lab at Johns Hopkins School of Medicine for his postdoctoral studies, where he has been interested in dissecting the mechanism of translation regulation on the ribosome. Since then, he has discovered a novel post-peptidyl quality control mechanism that contributes to high-fidelity protein synthesis.

Ruben Gonzalez

Ruben Gonzalez, PhD

Columbia University
e-mail | web site | publications

Ruben Gonzalez is an assistant professor in the Department of Chemistry at Columbia University. He earned his PhD from the Department of Chemistry at the University of California, Berkeley under the advisement of Ignacio Tinoco. At Berkeley, Gonzalez's doctoral studies focused on the structure and thermodynamics of divalent metal ion binding sites in RNA. He then initiated a postdoctoral fellowship with Joseph Puglisi in the Department of Structural Biology and Steven Chu in the Department of Physics at Stanford University. While at Stanford, Gonzalez adapted and applied single-molecule fluorescence spectroscopies to mechanistic studies of protein synthesis, one of the most fundamental biochemical reactions in the cell and, to date, the most complex biological system that has been mechanistically analyzed with single-molecule resolution. Gonzalez has been awarded an American Cancer Society Postdoctoral Fellowship, a Burroughs Wellcome Fund Career Award in the Biomedical Sciences, a National Science Foundation CAREER Award, and an American Cancer Society Research Scholar Award.


Megan Stephan

Megan Stephan studied transporters and ion channels at Yale University for nearly two decades before giving up the pipettor for the pen. She specializes in covering research at the interface between biology, chemistry, and physics. Her work has appeared in The Scientist and Yale Medicine. Stephan holds a PhD in biology from Boston University.