New routes to acceleration of directed evolution in Synthetic Biology
Cost-effective and environmentally-sustainable catalytic methods for the separation into enantiomerically pure chiral molecules are urgently needed (almost half of drug candidates have a chiral amine). Directed evolution (DE) aims to meet this need by re-engineering enzyme specificities and turnover rate by repeated laboratory mutagenesis and selection. However, DE struggles to produce mutant enzymes with sufficiently high turnover rates for industrial use. The problem is that beneficial mutations occur not just at active sites but all over enzymes and the number of possible mutants to search is astronomical. We aim to integrate computer simulations into the predict-design-test-build-learn cycle of DE to allow the crucial few beneficial mutations to be found at each iterative step. Our vision is to fundamentally change how DE is performed, and reduce the optimisation time, not incrementally, but by millions of times to facilitate rapid evolution of enzymes with high turnover rates, and a produce a methodology that can be generalised to other enzymes.
New techniques for investigating the 3D-shape of sugars
Sugars were the first biomolecules to be identified and extracted from living organisms, but our understanding of proteins and DNA is far advanced. This situation is due to a revolution stemming from 1950s observations that proteins and DNA have shapes that enable them to perform as micro-machines (from probing crystalline biological matter with x-rays). Unfortunately, sugar research has not yet produced a similar revolution, e.g., the heparin sugar has been used surgically for a century, but its shape and function is not understood. Most sugars (other than the simplest) resist crystallisation and other techniques to investigate their shape are under development. Carbohydrates, therefore, represent an unexplored frontier in Biochemistry and have fundamental industrial importance (food, paper, wood, pharmaceuticals, biomaterials). This research aims to link sugar-composition and function by developing new techniques for investigating microscopic shape. Rather than using crystals and x-rays, we use precise and extensive computer simulations, advanced methods for refining carbohydrates and a molecular microscope (similar to a MRI-scanner) to achieve this goal. To date our research has focused on large sugars called glycosaminoglycans, which fill space between cells, bonding them together, conferring strength to organs, joints and skin.
The role of molecular dynamics in extracellular matrix organisation.
Interactions with water provide the impetus for all molecular self-organisation, from protein-folding and membrane assembly to molecular associations. An understanding of water-biomolecule interplay is at the centre of a new biology where dynamics is included, and detailed predictions are possible. Over the last decade we have been using combined experimental and theoretical approaches to study water and dynamics in biology. This led to a study of self-dynamics in the vertebrate polysaccharide, hyaluronan. This substance is worth $500 million annually as a medical tool, but for which the solution behaviour, both at the macro- and microscopic level, is poorly understood. Hyaluronan is an ideal model system for studying water interaction, and is being used to devise theories for how water interacts with biomolecules, and the emergence of structure and dynamics both at the molecular and supramolecular scale. In particular these approaches are being used to understand how subtle interactions between hyaluronan chains and proteins result in the formation of extracellular matrices and tissue. This research requires the use of a wide variety of both computational and experimental techniques.