Structurally sound: deciphering protein structures 31/08/07. By Chrissie Giles The Structural Genomics Consortium is deciphering the structures of hundreds of proteins relevant to human health and disease.

Thanks to the Human Genome Project, scientists now know the amino acid sequence of every human protein. But it's not just a protein's make-up that affects its function: how it folds in three dimensions is key. As a result, many researchers dedicate their time to solving three-dimensional protein structures - a laborious and often frustrating enterprise. The results of their endeavours - detailed models of how protein chains are folded - are not only often beautiful but also extremely useful, helping to explain how a particular protein works, and allowing the design of drugs that can alter the protein's activity.

In 2004, the Structural Genomics Consortium (SGC) began operations. Described by its Chief Executive Aled Edwards as a "son of the Human Genome Project", the Consortium set out to determine the structure of 386 proteins with medical relevance, predominantly human, in just three years. This is no mean feat when you consider that, according to the Protein Data Bank (an online database), only around 3400 of the 23 000 or so different human proteins have been solved structurally. However, some three years, 75 publications and over 100 collaborations later, the SGC has easily exceeded its target, releasing its 450th protein structure in June 2007.

The SGC operates out of three sites - Oxford in the UK, Toronto in Canada and Stockholm in Sweden - and has taken a high-throughput approach to the difficult tasks of purifying and crystallising proteins, and firing X-rays at the crystals to determine their structure. Thanks to this strategy, the Consortium banked around 22 per cent of all new human protein entries into the Protein Data Bank in 2006, despite commanding well under 5 per cent of the world's total structural biology budget.

The decision to target only human proteins was seen by some as too challenging. "There's a general feeling among scientists that human proteins are trickier to handle than those from prokaryotes," explains Johan Weigelt, Chief Scientist at SGC Stockholm. "Possibly because of the tightly controlled internal environment of eukaryotes."

Michael Sundstrom, Chief Scientist at SGC Oxford, says that the Consortium was often classified with other projects dealing with the purest form of structural genomics. "These programmes are mandated to solve very diverse types of structures and it doesn't necessarily matter what organisms the proteins come from," he explains. "Some people call that stamp collecting, and although we disagree with that view, it's not what we're doing." Dr Edwards agrees: "In terms of the SGC, 'structural genomics' is almost a misnomer."

It's not only the SGC's approach that differs from most other structural genomics programmes, but the way it is funded is also unusual. Like the SNP (single nucleotide polymorphism) Consortium, which searched for variations in the human genome, the SGC is a not-for-profit organisation that receives funding from both the public and private sectors. Sponsors include the Wellcome Trust (which contributed £18 million to the three-year phase I budget of £48m), GlaxoSmithKline, and Canadian and Swedish funding organisations.

The structures produced by the SGC become freely available on the internet without delay, unlike those from other groups, which may be protected for commercial reasons or withheld until papers about the research have been published in a scientific journal. Details of the laboratory protocols and techniques are also shared, on the SGC website and often in open-access journals; the Toronto and Stockholm sites host open courses on laboratory techniques; and there are plans for a 'visiting scientists' scheme.

Spoilt for choice

With the majority of human protein structures still unsolved, how did the researchers choose which proteins to work on? "The SGC works on targets that are nominated by the funders; these represent both probable targets for medicine and proteins of interest to the academic community," says Dr Edwards. Unsurprisingly, there's often a strong overlap between the two.

Proteins exist in families, which means that, for some targets, it's a case of guilt by association. "If one member of a particular protein family is a drug target, it's likely that others will be too," says Dr Weigelt. To ensure a drug is selective for its target, researchers also have to examine the structures of closely related proteins.

A key focus of the Oxford site has been a family of enzymes called the protein kinases, which are vital for a range of functions, including the regulation of cell signalling and cell growth. The SGC's work accounts for around half the world's output for human protein kinase structures, which are likely to become increasingly valuable for the development of new drugs. Of the 518 known protein kinases, 30 or more are already validated drug targets. "If I were a betting man, I'd be pretty sure the other 488 could be targets to make new medicines," says Dr Edwards.

The SGC is now entering phase 2: between 2007 and 2011, the researchers aim to determine 650 new protein structures relevant to human health. The Consortium, which has been joined by pharmaceutical companies Novartis and Merck (see box, below), is providing more than £50m funding for the second phase.

scheme.

A fifth of the SGC's resources is being put forward to solve the structures of nine human integral membrane proteins. These proteins nestle in the fatty bilayer that surrounds our cells and are notoriously difficult to purify and crystallise. "These proteins like a fatty environment," says Dr Edwards. "In the lab you strip them away and purify them in a water-rich environment. History shows that not many proteins can survive that brutality." However, many feel that the time is right to crack this type of protein. "The SGC cut its teeth on membrane proteins from bacteria¹ and scientific developments over the last four to five years mean that structural determination of human membrane proteins could now be possible," Dr Sundstrom explains.

An added benefit for the Oxford team is its proximity to the newly opened Diamond synchrotron (see X-ray vision ). Synchrotrons generate very powerful X-rays, which means that lots of structural data can be collected quickly. "We have a very successful collaboration with the Swiss Light Source [a synchrotron], but it's obviously easier to take a 20-minute car ride to Diamond than a flight to Switzerland," explains Dr Sundstrom. "It's also less likely that our proteins will get lost or our liquid-nitrogen-containing containers will arouse the curiosity of a customs official."

While the short-term aims of the SGC are clear, what challenges does the wider structural genomics community face? "We're still just scratching the surface in terms of the numbers of structures solved," says Dr Sundstrom. "It will be many years before we can talk about any kind of completion."

This is particularly true as proteins exist in many forms - due to mutations, post-translational modification and splicing. They also occur as complexes with each other, small molecules and various ligands and substrates. "There are probably millions of variations needed to perform biological functions," says Dr Sundstrom.

Dr Edwards is looking further ahead: "In the future I would like to see everyone to be thinking of the world in terms of shape rather than [genetic] code." As in all scientific fields, he is confident that structural genomicists' expertise will continue to develop rapidly. "Hopefully, what we're doing now will be so routine in the future that it won't even be part of the scientific challenge of the day."

Reference

1 Lunin VV et al. Crystal structure of the CorA Mg2+ transporter. Nature 2006;440(7085):833-7. Abstract .

Reference

1 Vedadi M et al. Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc Natl Acad Sci USA 2006;103(43):15835-40. Full text .

Chrissie Giles is a writer at the Wellcome Trust