Frank Lab

Welcome to the Frank Lab

We investigate the mechanism of translation on the ribosome by using cryo-electron microscopy and single-particle reconstruction.

Recent Publications

Book: Molecular Machines in Biology: Workshop of the Cell
Publisher: Cambridge University Press
Author: Joachim Frank
Click here to order.
[Description]

Article: Cryo-EM visualization of the ribosome in termination complex
with apo-RF3 and RF1
Journal: eLife
Author: Jesper Pallesen, et al.
[Abstract]

Article: Structure of the mammalian ribosomal 43S preinitiation complex
bound to the scanning factor DHX29
Journal: Cell
Author: Yaser Hashem, et al.
[Summary]

Article: Story in a sample – the potential (and limitations) of cryo-electron microscopy applied to molecular machines
Journal: Biopolymers
Author: Joachim Frank
[Introduction]

Molecular machines are workshops in the cell that bring molecules and substrates together in a coordinated, processive way.1‐2. The molecular complexes acting as molecular machines are often spatially localized and assembled in an ad‐hoc fashion, in response to the demands of the cell’s metabolism. Products of such binding reactions can be RNA or DNA polymers, ATP, or other compounds needed at the site. Well‐known examples are RNA and DNA polymerases, ATP synthase, the ribosome, and the proteasome. Visualizing molecular machines in their various states of processing poses challenges which traditional techniques of structure research find hard to meet. The complexes formed in the course of the work cycle are typically large, relatively unstable, and flexible ‐‐ all properties that disfavor X‐ray crystallography as a means of visualization. In addition, molecular machines can have multiple binding partners and can go through numerous states, characterized by different conformations and binding configurations. Purification of such complexes can be done through two different routes: either from a cell extract or from an in vitro reconstituted system. In either case, it is difficult to isolate the complex by biochemical means in one of its many states with the purity required for structural research. Cryo‐electron microscopy (cryo‐EM) is a fairly new technique for obtaining a 3D image of a molecule from a large set of projections, harvested from micrographs of a field of molecules captured in random orientations.3 In some cases, resolutions in the range of 4 to 5.5 Å have already been achieved for the ribosome, an RNA‐containing molecular machine.4‐6 Purity of the sample in terms of conformation and binding state of the molecule is evidently an absolute requirement for obtaining a meaningful 3D image from the “single particle” projection data set. In certain cases, high purity can be achieved by affinity imaging techniques.7‐9 However, because of inherent difficulties of finding biochemical methods that guarantee 100% purity, it has been a goal in the development of cryo‐EM to accomplish the purification of the molecules after the imaging, at the data processing step. Cryo‐EM projection data have a typical signal‐to‐noise ratio in the order of 0.1 or even less.10 The challenge posed by classification of such noisy data is compounded by the fact that variability stemming from a change in viewing direction is intermingled with variability due to heterogeneity of composition or conformation.

Article: High-resolution cryo-electron microscopy structure of the
Trypanosoma brucei ribosome
Journal: Nature
Author: Yaser Hashem, et al.
[Abstract]

Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and maintenance. The few available structures of the eukaryotic ribosome reveal that it is more complex than its prokaryotic counterpart, owing mainly to the presence of eukaryote-specific ribosomal proteins and additional ribosomal RNA insertions, called expansion segments. The structures also differ among species, partly in the size and arrangement of these expansion segments. Such differences are extreme in kinetoplastids. Here we present a high-resolution (~5Å) cryo-electron microscopy structure of the ribosome of Trypanosoma brucei, the parasite that is transmitted by the tsetse fly and that causes African Sleeping Sickness. The atomic model reveals the unique features of this ribosome, characterized mainly by the presence of unusually large eukaryotic expansion segments and ribosomal protein extensions leading to the formation of four additional inter-subunit bridges. We also find additional rRNA insertions, including one large rRNA domain that is not found in other eukaryotes. Furthermore, the structure reveals the five cleavage sites of the kinetoplastid large ribosomal subunit rRNA chain, which is known to be cleaved uniquely into six pieces, and suggests that the cleavage is important for the maintenance of the T. brucei ribosome in the observed structure. We discuss several possible implications of the large rRNA expansion segments for the translation regulation process, and we show a possible link between the protein translation initiation process and expansion segments 6 and 7 on the small ribosomal subunit. Our structure could serve as a basis for future experiments aimed at understanding the functional importance of these kinetoplastid-specific ribosomal features in protein translation regulation, an essential step towards finding effective and safe kinetoplastid-specific drugs.

Recent Blog

Dr. Frank asked to join Faculty of 1000

May 23, 2013

Dr. Frank is now a member of the Faculty of 1000. F1000 identifies and recommends important articles in biology and medical research publications. Articles are selected by a peer-nominated global 'Faculty' of the world's leading scientists and clinicians who then rate them and explain their importance. From the numerical ratings awarded, F1000 has created a unique system for quantifying the importance of individual articles. Launched in 2002, F1000 was conceived as a collaboration of 1,000 international Faculty Members. The name stuck even...

Welcome to the Frank Lab

Recent Publications

Recent Blog

Dr. Frank asked to join Faculty of 1000

Paper accepted by eLife

Papers accepted by Cell and Biopolymers

Papers accepted by Nature and JSB

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