The Nuts and Bolts of Cell Machinery
Walter Kolch, Professor of Molecular Cell Biology and Scientific Director of the Sir Henry Wellcome Functional Genomics Facility at Glasgow University, is intent on explaining the interactions between proteins to provide new levels of detail in our understanding of disease…
"Almost paradoxically the success of the genome projects has highlighted the need to analyse the proteome" says Kolch. "The genome may be the blueprint for life; however, it is the proteins encoded by the genes that are the nuts and bolts of all the cellular machinery." The modest number of approximately 40,000 genes in the human genome gives rise to a bewildering variety of an estimated 1 million different types of proteins, due to the processes of RNA splicing and editing, proteolytic processing and posttranslational modification. These modifications can alter the function of a protein and change its interactions with other proteins.
While the challenges posed by the complexity of the proteome are enormous, its analysis opens the door to understanding cellular processes that govern health and disease, with huge ramifications for basic research and medicine. The key to this door is the new discipline of proteomics that has emerged thanks to technical breakthroughs in the fields of mass spectrometry and bioinformatics (see “The Protein Code” p4-6 and “Bio-Mining” p10-12). These developments have allowed the identification and analysis of new proteins with unprecedented speed and sensitivity.
Professor Kolch explains, "It used to take many months to identify a single cellular protein. However, the important recent advances made in mass spectrometry and related methods mean that hundreds of proteins can now be identified in one afternoon – 15 years ago, this would have been seen as the work of centuries."
The next step, beyond identifying individual proteins, is to study how they interact and function within a cell. Professor Kolch explains, "Proteins assemble into complexes that carry out a particular function, so you can think of such protein complexes as a machine with a purpose. Many proteins are assembled into molecular machines that either generate energy, or else maintain and control the cell’s shape and movement. The protein complexes may be quite dynamic and their life-span can vary greatly." Studying these molecular machines raises many questions. As is so often the case in modern science, the answers lie in bringing different disciplines together to work on the complex problems.
Facility Unique in Europe
The Sir Henry Wellcome Functional Genomics Facility (SHWFGF) in Glasgow has been established to respond to this challenge. The Centre is embedded in the Biomedical Faculties of the University of Glasgow and uniquely in Europe brings together a raft of core skills – Proteomics, Gene Arrays, DNA Analysis, Robotics, Bioinformatics and Laser Micro-dissection. It is both a service facility and a research centre. The proteomics unit is equipped with state-of-the-art instrumentation for protein separation, identification and analysis. Kolch comments, "The provision of the specialist facilities demands the involvement of experts and it is therefore appropriate that the facility also undertakes its own research, ensuring that its services remain at the cutting edge of requirements in this field.
In future, the need to study smaller and smaller amounts of protein complexes will require the development of micro-devices for protein analysis. The lab-ona- chip concept (see “Lab-on-a Chip” p13-14) is an important route for isolating a single copy of a protein complex, which can then be analysed using a highly sensitive mass spectrometer.
Scotland at Forefront of Proteomics
Scotland has a longstanding reputation as a leader in protein analysis, built on her strengths in biochemistry and structural biology. Scotland is now also at the forefront of the new discipline of proteomics. According to Professor Kolch, "Our strength in Scotland lies in applying these recent breakthroughs in protein analysis to the understanding of cancer, heart disease and infection and inflammation. This is not an esoteric study, but one which is expected to bring real benefit in terms of medical developments in the coming years".
The Molecular Pathology of Cancer
Professor Kolch also leads a research group at the Cancer Research UK’s Beatson Institute, Scotland’s leading Cancer Research facility, which is located on the Bearsden Campus of the University of Glasgow. "Employing methods spanning molecular cell biology, biochemistry, bioinformatics and proteomics, we are analysing multi-protein signalling complexes and working at understanding their function in signalling networks. Our aim is to understand the molecular mechanisms of cancer development."
"Cancer can be considered a disease of communication at the molecular level. Cellular communication uses biochemical networks that receive and integrate extracellular cues into specific cellular responses. We try to understand how a communication pathway can convert numerous input signals into specific responses that control such diversified functions as cell growth, survival and differentiation."
The Beatson Institute is one of 11 European institutions, collaborating on Interaction Protome, an integrated project to establish Europe as the international scientific leader in the analysis of protein-protein interactions. Major objectives include the establishment of a broadly applicable platform of routine methods for the analysis of protein interaction networks.
EU funding under the Framework Programme has been provided for five years to enable Interaction Proteome to develop novel technology, including a high-end mass spectrometer with a large dynamic range, high-density peptide arrays, and improved visualisation technology for light and electron microscopy. Using the novel technology, the interaction partners of more than 100 relevant protein domains and more than 3,000 peptides will be characterised.
The particular contribution of the Beatson scientists to this project will be to field test the application of these new technologies in the biology laboratory and develop them into useful tools for untangling the complicated wiring of the "signal transduction pathways" that control cell differentiation, proliferation and death. Kolch’s team will be involved at many levels in the project from identifying the protein components of the molecular machines that drive these pathways by mass spectrometry, to visualising the subcellular localisation of proteins using novel microscopic techniques, and to the computational modelling of the signalling pathways. This project aims to set an experimental paradigm for how we can obtain comprehensive understanding of complex biological processes and will be a contribution to the new field of "Systems Biology".