The mechanism of protein synthesis is first observed directly

Research by molecular biologist Harry Noller and colleagues at UC Santa Cruz has led to success in directly observing the mechanism of protein synthesis in living cells.

Their new findings on the ribosome, which form the protein molecule in all cells, were published on the cover of the April 3, 2008, issue of the international journal Nature.

Researchers have used a laser device called 'optical tweezers' to probe every step of the ribosome apparatus as it converts gene codes into protein molecules.

Noller, Sinsheimer's Professor of Molecular Biology at UCSC, has been studying ribosomes for more than 30 years. His latest discovery was the result of a six-year collaboration of three research groups at the California Institute of Quantitative Biology (QB3). The collaboration team includes Noller, postdoctoral researcher Laura Lancaster at UCSC, UC Berkeley biophysics scientist Carlos Bustamante and biochemist chemist Ignacio Tinoco, Jr.

The image of a ribosome moving along an informative RNA strand (yellow) is fixed by two optical tweezers.(Photo: Laura Lancaster and Courtney Hodges)

Noller said: 'This is a collaboration between optical tweezers researchers at Berkeley and ribosome researchers at UCSC. We worked together to find out if this method could be used to measure the effect of ribosomes on protein synthesis' .

To create a new protein, the first genetic instructions are copied from a DNA sequence of a gene into a messenger RNA molecule. The ribosome then reads the genetic code from the information RNA and converts these codes into the structure of a protein.

Noller's lab performed technical manipulations of the ribosome containing the messenger RNA molecule with two DNA strands attached to the two ends acting as 'handles'. DNA strands, in turn, are attached to small particles. These particles are fixed by laser from the 'optical tweezers', the laser from each end creates the opposite force on the metabolic system.

Thanks to this system, researchers are able to monitor the metabolism in individual ribosomes. They found that protein synthesis has a fixed rhythm: bop, bop, bop, stop; bop, bop, bop, stop; and so on. Three times 'bop' is equivalent to once the ribosome reads a set of three encodings - a sequence of three super-molecular RNAs informing the ribosome to add an amino acid to the protein chain.

Noller said: 'The Ribosome moves along the signaling code in a series of stops and stops - stopping and moving. Stop, move, stop '.

Noller's team were the first to explain the full structure of a ribosome using X-ray crystallography. That was the first step to answer the bigger question: How does the Ribosome work?

'So far, we have just stopped observing trillions of ribosomes, and they are not synchronized - the details are unclear. We can now observe only one ribosome at a time, ' he said.

Noller, directing the Center for Molecular Biology of RNA at UCSC, announced that the project's next step was to select analysis. 'We have not yet completely directly measured the effects created by ribosomes,' he said. 'Now we have more sensitive optical tweezers at UC Berkeley. We also devised a way to hold the ribosome with an optical tweezers and hold the information chain with the other. We can see that the ribosome has pulled that chain of information. '

The first author of the Nature paper was Jin-Der Wen of UC Berkeley.In addition to Noller, Lancaster, Bustamante, and Tinoco, other co-authors include Courtney Hodges of UC Berkeley;Ana-Carolina belongs to the Brazilian Cretaceous Laboratory;and Shige Yoshimura of Kyoto University.