Structural genomics

Structural genomics involves the determination of the 3-D structure of all proteins and RNA molecules encoded in the genomic sequences of living organisms. Understanding the structure of these macromolecules is critical to understanding their role in complex biological processes, and essential for drug design.

The wealth of information produced by genome sequencing is providing researchers with exceptional opportunities to make links between genes and the functions of their products. Current research into protein and RNA structure aims not only to determine the molecular structure of these products but also to describe and understand the multitude of their interactions in cells and tissues. Indeed, knowledge of a macromolecule’s structure alone is often meaningless if taken out of its biological context: researchers need to understand not only the structure of the ‘worker’ molecule, but also its working environment, to be able to write up its job description.

Building sites

Most molecular interactions can only take place as a result of the molecules’ chemical architecture, creating active sites where they can link together with complementary molecules or latch on to a piece of cellular machinery, ready to perform their programmed tasks. In proteins, these sites depend on the way the long chains of amino acids of which they are constituted are intricately folded to give a final 3-D structure. Based on existing databases of protein structure, researchers estimate that a few thousand possible folding patterns exist naturally, of which around a thousand are already known. Most drugs target particular protein functions, either in the human body, or in the pathogen, and the development of new drugs relies heavily on knowledge of the targeted protein’s structure. Compounds with potential pharmaceutical activity can be tested to see if they can latch on to the protein structure.

Understanding the structure of different types of RNA (ribonucleic acid) molecules is particularly important for virology. Although most organisms use RNA only as a temporary messenger molecule, some viruses – known as RNA viruses – and among them the killer pathogens responsible for ‘flu, hepatitis C and HIV, use RNA to store their genetic information. Because RNA is an unstable molecule which regularly mutates, an RNA virus can evolve very rapidly making it difficult for organisms infected with the virus to develop any kind of lasting immunity. Knowledge of the RNA’s 3-D structure is vital for the development of new anti-viral drugs. Recent increases in the threat of bio-terrorism and newly emergent viral diseases have made research in this field one of the priorities in structural genomics.

Measurement techniques

Another key area of research in structural genomics is the determination of the structure of membrane proteins which play critical roles in cell function and are implicated in many major diseases such as Alzheimer’s. These proteins represent around a third of proteins in known proteomes but, because of difficulties in crystallising them – the main technique used to determine structure – knowledge of their 3-D structure has so far been limited.

To study macromolecule structure effectively from the level of the individual molecule to that of its interactions in cellular complexes, researchers need to use a battery of structural techniques permitting measurement at different scales. These range from X-ray crystallography and nuclear magnetic resonance (NMR) to study individual molecule structure, to electron microscopy to focus on complexes. However, bottlenecks in the technical pipeline from preparing structure samples to analysing structural data have meant that until recently these technologies were not allowing a sufficiently high throughput of samples to optimise determination of the structures of the thousands of macromolecules still to be solved. Research effort has therefore been focused on automisation of many stages in the procedures to reduce bottlenecks and increase throughput.

X-ray crystallography uses the high intensity X-ray beams obtained by synchrotron radiation to produce an atomic diffraction pattern from the protein. This requires producing a purified crystal of the protein, loading it into the beamline and then analysing the diffraction data. By developing user-friendly robotics for mounting and aligning crystals, researchers are obtaining increases in productivity and throughput making it possible for non-expert users in academia and industry to access this vital technology.

NMR spectroscopy, although not as accurate as X-ray crystallography for structure determination, is a useful complementary technique, especially for certain proteins which do not crystallise. An NMR signal is produced when the nuclei of certain atoms are immersed in a static magnetic field and exposed to a second oscillating magnetic field. NMR techniques are increasingly being used as they allow researchers to study proteins and their interactions under natural physiological conditions.

Because of the importance of understanding the ‘working environment’ of a protein, researchers are increasingly using electron, rather than X-ray, diffraction, to visualise, in situ, the structural composition and organisation of cellular components like protein complexes. Developments in 3-D electron microscopy will provide unprecedented opportunities to visualise the cell’s internal architecture at high resolutions.

Projects

Interated Projects
Bioxhit
E-MeP

Network of Excellence
3D-EM

Streps
FSG-V-RNA
3DGenome
Genefun