Parallel protein purification workstation is a world first

The ability of Australian scientists to study the molecular structure and function of proteins has taken a leap forward with the announcement that the world's largest parallel protein purification workstation is to be housed at Monash University in Victoria.

The ÄKTAxpress ­ from GE Healthcare ­ allows up to 48 proteins to be produced simultaneously, giving Australian scientists the materials they need to conduct life-saving protein-based research.

Victorian Bioinformatics Consortium scientific director and Monash University researcher James Whisstock said that protein research is currently focused on understanding how proteins function or dysfunction, and in particular understanding the atomic structure of these molecules.

One such project at Monash involves the structural biology of novel domains. The major problem raised by whole genome projects is that many novel putative proteins of unknown function are identified.

For example, it is estimated that more that 40percent of human proteins identified as a result of the human genome remain to be structurally and functionally characterised.

One method of attacking this problem is to use database-searching techniques such as PSI-BLAST to identify similarity between a protein of unknown function and a well-characterised family.

However, if such a relationship cannot be identified what alternatives are there? One solution is to use structural genomics in order to determine the structure of a domain of unknown function in order to provide clues as to its biochemical function.

So a team at Monash will express and purify various novel protein domains with the aim of determining their three-dimensional structure via

X-ray crystallography.

“If we understand the molecular shape of a protein, we can begin to understand how it works,“ said Whisstock. “Heart disease, cancers, osteoporosis and immune deficiencies are just some examples of illnesses that manifest through the actions of proteins, so knowing how proteins function not only gives us a better understanding of these illnesses, but also points the way to effective therapies.

“Currently our ability to study the molecular structure and function of proteins is constrained by the rate at which we can produce proteins for analysis,“ he added.

The arrival of the protein purification workstation is closely linked to Victoria's AUS$180million synchrotron facility due to open in 2007.

Australia is currently one of the only developed nations in the world without its own synchrotron, a modern circular particle accelerator used to study the atomic composition of molecules such as proteins.

“The more we can produce, the more we can study, the more we can learn,“ explained Whisstock. “That's why the marriage of technologies like protein production and the synchrotron is so exciting.

Parallel protein production will give us the means to produce large amounts of different proteins in a high-throughput fashion, and the synchrotron will allow us to rapidly collect diffraction data right here in Australia, something that was simply not possible before.“

The ÄKTAxpress is a modular system developed for the high-throughput purification of protein samples, automating the multi-step purification process to yield highly purified protein.

At present, one scientist basically produces one protein at a time. This process involves growing bacteria in the lab, disrupting the cells, washing the samples and finally extracting and purifying the proteins. It can take up to a week to complete. Owing to equipment and personnel constraints, the department often has to wait for one production run to end before it can start another one.

“That's where the ÄKTAxpress comes in: it allows us to produce 48 different proteins in parallel, in genuine production scale.

A typical scientist would be hard pushed to produce large scale quantities of 48 different proteins in a year, let alone in the eight hours it takes for the Äktaxpress to do its work,“ noted Whisstock.

Monash has invested in a 12-module ÄKTAxpress system, the largest configuration of its kind anywhere in the world.

The equipment has been funded via the Australian Research Council LIEF and will provide enormous capacity for the ARC Centre for Structural and Functional Microbial Genomics and the National Health and Medical Research Council programme for protease systems biology.

“Big science is done on a big scale overseas, and the ÄKTAxpress gives us the means to compete on a world scale and be involved in major projects such as structural genomics initiatives,“ said Whisstock.

Peter Simpson, general manager Australasia, GE Healthcare Bio-sciences, said the system would not only improve Australia's medical resources, but would be useful in other areas such as agriculture.

“Numerous vaccine development programmes also require the production of proteins,“ said Simpson. “Finding vaccines for major livestock diseases, for example, can have a direct impact on Australian farmers, the quality of Australian produce, and the Australian economy as a whole. The uses for protein analysis are many and varied.“

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