EU-funded researchers have made a film showing cells' protein factories, ribosomes, in action. The work offers an unprecedented glimpse of the workings of these essential pieces of cellular machinery and could aid the development of new drugs.
The study, published in the journal Nature, received EU support through the 3D-REPERTOIRE ('A multidisciplinary approach to determine the structures of protein complexes in a model organism') project, which was funded under the Life sciences, genomics and biotechnology for health Thematic area of the Sixth Framework Programme (FP6).
If DNA is the blueprint for life, then ribosomes are the factories where the blueprint is turned into the proteins which make up our muscles, transport substances around and between cells, send and receive signals, trigger chemical reactions, and much more.
The whole process starts with DNA. The stretch of DNA that bears the genetic code for a given protein is copied into a single strand of messenger ribonucleic acid (mRNA). The mRNA becomes attached to a ribosome, which moves over the mRNA molecule. Each block of three letters in the mRNA represents the genetic code for a specific amino acid. Molecules of a different kind of RNA, called transfer RNA (tRNA), 'read' this genetic code and bring the appropriate amino acid to the ribosome. Amino acids are the building blocks of proteins; as the ribosome moves along the mRNA, a chain of amino acids is created and the protein starts to take shape.
Ribosomes are extremely small - at just 25 nanometres long, they are about the same size as the smallest viruses. Studying their structure is therefore far from easy and the team that eventually succeeded in clarifying their form won the 2009 Nobel Prize for Chemistry for their efforts. Previous studies have also elucidated how ribosomes link up amino acids to form a chain, and how tRNAs read the information encoded in the mRNA.
However, ribosomes are essentially machines with moving parts and, until now, the only images of ribosomes were still. As a result, many aspects of the way ribosomes work have remained a mystery.
In this study, scientists at the Max Planck Institute for Biophysical Chemistry in Germany and the Petersburg Nuclear Physics Institute in Russia came up with a cunning way of 'filming' ribosomes in action.
'The trick is that we first of all got the ribosomes working in a solution,' explained Holger Stark, head of the 3D (three-dimensional) Electron Cryomicroscopy Group at the Max Planck Institute for Biophysical Chemistry. Samples of the solution were taken at different times and frozen rapidly. This effectively stopped the molecular machinery during different steps of the process.
'From these samples, the electron microscope delivers a series of images of ribosomes during different phases of protein production, in which the ribosomes differ in their three-dimensional structure,' said Professor Stark.
In total, the team snapped over two million pictures of ribosomes at work. A computer programme was used to categorise the images; the resulting groups of pictures correspond to different stages of protein production. Next, the computer calculated the 3D structure of these groups. Finally, the images were put in order to create a film which shows how the mRNA is passed through the ribosome like a conveyer belt, and how the tRNAs deliver their amino acid cargo to the ribosome before being released.
'We can follow the path of the tRNAs through the ribosome step-by-step, and observe how the movements of the tRNAs are coupled to the dynamic changes of the ribosome,' commented Niels Fischer, who works in Professor Stark's laboratory.
Marina Rodnina of the Department of Physical Biochemistry at the Max Planck Institute for Biophysical Chemistry added: 'An analysis of this coupling shows that nanomachines like the ribosome work differently to mechanically coupled machines in our everyday life. Spontaneous movements of the ribosome and the tRNA molecules are relatively weakly coupled.'
In addition, the team discovered that ribosomes work optimally at body temperature, around 37°C, using our body heat to power their activities.
'The ribosome can convert thermal energy directly into movement,' said Professor Stark. 'The thermal energy that is available under physiological conditions is fully sufficient for the ribosomes to carry out all the movements required for protein production.'
The work could also aid in the development of new drugs. Human ribosomes are different from bacterial ribosomes, and some antibiotics are effective because they block protein production in bacterial ribosomes but leave human ribosomes unharmed. Increasing our understanding of the structure and function of ribosomes is therefore key to the development of new antibiotics.