MPŠ MP&Scaron MP&Scaron MP&Scaron Avtorji

Jožef Stefan
Postgraduate School

Jamova 39
SI-1000 Ljubljana

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10


Course Description

Advanced Topics in Protein Synthesis


Nanosciences and Nanotechnologies, third-level study programme


prof. dr. Nenad Ban


Students are expected to evaluate the current state of research in the field of protein synthesis using as a help a script that will be provided. The students are then supposed to prepare a paper in which they propose a research project that would have potential for new discoveries in the field. After hearing the lectures the students present and defend their research proposal paper.


High resolution structure of the small ribosomal subunit
- Overall architecture
- Protein RNA interactions
- Role in translational fidelity - decoding

High resolution structure of the large ribosomal subunit
- Overall structure of the large ribosomal subunit
- The role of the ribosome in the peptidyl transferase reaction
- The tunnel of the ribosome and an example of antibiotic action

High resolution structure of the bacterial 70S ribosome
- Conformation of the mRNA
- Interactions of tRNAs with the ribosome

Co-translational protein targeting
- Signal recognition particle
- Translocon – protein conducting channel

Ribosome associated chaperones and co-translational protein folding and processing
- Trigger factor – bacterial ribosome associated chaperone
- Peptide deformylase – mechanism of co-translational nascent chain processing

Course literature:

1. Copies of lecture notes

2. Jenni, S., and Ban, N., 2003, The chemistry of protein synthesis and voyage through the ribosomal tunnel. Curr. Opin. Struct. Biol. 13: 212-219.

3. Steitz, T.A., and Moore, P.B., 2003, RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem. SCI.:28 411-418.

4. Ogle, J.M., Carter, A.P., and Ramakrishnan, V., 2003, Insights into the decoding mechanism from recent ribosome structures. Trends Biochem. Sci. 28: 259-266.

5. Clemons, W.M., Ménétret, J.-F., Akey, C. W., and Rapoport, T. A., 2004, Structural insight into the protein translocation channel. Curr. Opin. Struct. Biol. 14:390-396.

6. Ramakrishnan, V., 2002, Ribosome Structure and the Mechanism of Translation. Cell 108: 557-572.

Significant publications and references:

1) Ban, N., Nissen, P., Hansen, J., Moore, P. B., and Steitz, T. A., 2000, The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289: 905-920.

2) Wimberly, B. T., Brodersen, D. E., Clemons, W. M., Jr., Morgan-Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch, T., and
Ramakrishnan, V., 2000, Structure of the 30S ribosomal subunit. Nature 407: 327-339.

3) Carter, A. P., Clemons, W. M., Brodersen, D. E., Morgan-Warren, R. J., Wimberly, B. T., and Ramakrishnan, V., 2000, Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407, 340-348.

4) Ferbitz, L., Maier, T., Patzelt, H., Bukau, B., Deuerling, E., and Ban, N., 2004, Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature 431: 590-596.

5) Selmer, M., Dunham, C. M., Murphy IV, F. V., Weixlbaumer, A., Petry, S., Kelley, A. C., Weir, J. R., and Ramakrishnan, V., 2006. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935-1942.

6) Schaffitzel, C., Oswald, M., Berger, I., Ishikawa, T., Abrahams, J.P., Koerten, H.K., Koning, R.I. & Ban, N., 2006, Structure of the E. coli signal recognition particle bound to a translating ribosome. Nature 444, 503-506

7) Bingel-Erlenmeyer R, Kohler R, Kramer G, Sandikci A, Antolić S, Maier T, Schaffitzel C, Wiedmann B, Bukau B, Ban N.
A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing. Nature 452(7183): 108-11


Oral exam and presentation of the research paper.

Students obligations:

Attend lectures and contribute to the discussions.