Research
The biological physics group aims to apply techniques and ideas from physics to biological problems. Current research activities in the group are described under the following topics:
- Biointerface
- Biocomputing & Integrative Systems Biology
- Biomolecular structure and dynamics
- Intracellular Particle Tracking and self-assembly
Biointerface
Our work has centred on studying molecular structure and dynamics at wet interfaces under conditions mimicking biological and biomedical applications. We are well established in applying leading physical techniques to access direct information at molecular and cellular levels from various biointerfacial processes. The highlight of our recent work has been to apply spectroscopic ellipsometry (SE) and neutron reflection to reveal protein molecular features underlying surface biocompatibility, a topic highly relevant to biomaterials development, tissue engineering, controlled local drug and gene delivery and medical implant deployment.
We often conduct these research activities in close collaboration with life scientists and medical experts. Within the Biological Physics Group, we place a strong emphasis to seek integrated approaches between theoreticians, computational experts and experimentalists and try to approach research topics with the balanced skills and expertise. Current research topics are:
Antibody-antigen binding
The in situ structural conformations of antibody molecules immobilised at the solid/solution interface are widely thought to affect their ability to bind antigen from solution, but few techniques have the structural sensitivity to unravel them. In our work neutron reflection has been applied to studying the structure and composition of a monoclonal antibody and its specific recognition by human chorionic gonadotrophin (hCG), a hormonal protein. Our results show that under most physiological mimicking conditions, antibodies adsorb flat-on, with their fragments lying flat on the substrate surface and that the antigen binding capacity decreases with increasing antibody surface packing density. The model system provides an important platform for assessing the effect of surface chemistry and solution environment on antibody immobilisation and bioactivity (see Fig 1, for example).
Fig. 1 A schematic representation to show the gradual pH dependent transition of antibody structural conformation and hCG binding. Electrostatic repulsions at higher pH cause the layer to twist and open up. The opening up of the antibody’s constituent fragments, within a predominantly “flat-on” orientation, leads to the increase in AgBC. Color coding: Fc in blue, Fab in green and hCG in red (to appear in Biomacromolecules).
Tissue Engineering
Study of interactions between biomaterial and vascular cells is highly relevant to the control of cell seeding and tissue growth. In this project, we emphasise the understanding of the mediation of representative ECM proteins on the attachment, spreading and growth of vascular cells. In parallel, the up and down regulations of key proteins excreted by cells are also monitored. Using well fabricated planar surfaces and polymeric films as model biomaterial, the different biointerfaces are interrogated by a combined approach of biochemical and biophysical techniques. The information so obtained is highly useful towards future model development and growth of 3D tissue constructs.
Controlled Local Gene Delivery
In collaboration with colleagues from Biocompatibles UK Ltd and the Manchester Medical School we exploit molecular interactions to the benefit of loading bioactive genes into biocompatible surfaces and thin films. We aim at developing the new technology towards the coating of vascular stents. Controlled local drug or gene release could help mediate the local biological environment leading to the healthy integration of the implants. Physical studies using neutron reflection, SANS and spectroscopic ellipsometry help tune nanoporous network and surface chemistry, leading to the effective manipulation of gene loading and release kinetics.
Fig. 2 shows how film thickness and cationic charge density (in CAT%) affects the loading of a FAM-labelled oligodeoxynucleutide loaded in different PC polymers with single (x1) or multiplayer (x3) fabrication.
Biomaterials Development
We apply our extensive expertise in polymer and surfactant research to design short peptide sequences as biomaterials. There are some 20 natural amino acids that are polar (hydrophilic), non-polar (hydrophobic) and charged (positive and negative). They offer almost endless choices for novel peptide surfactant design and synthesis. Neutron reflection and small angle neutron scattering (SANS) are well suited for revealing the nano-structures of these peptides assembled at interfaces and their aggregates formed in bulk solution.
Fig. 3 Schematic of end (left) and side (right) views of a pair of 15-mer peptides forming α-helical configuration via the strong hydrophobic interdigitation of three tryptophans between them. The α-helical backbone is illustrated as a ribbon. W groups are labelled in green, Y in cyan, R in red, and K in blue. The α-helical structure was revealed at the silicon oxide/water interface (J. Am. Chem. Soc. 2004, 126, 8940).
Biocomputing & Systems Biology
In the last decade, advances in life sciences have gathered a vast amount of experimental information about biological systems at cellular and sub-cellular levels. Now we are facing two big challenges:
- How do we interpret, analyse the experimental information and relate it to the functions of life?
- Can we reconstruct biological systems from such detailed information?
There is a strong motivation to address these challenges. As a biological system is an integral system, within which components interact with each other. The interaction coordinates the simple behaviours of a biological system at cellular and sub-cellular levels into more complicated behaviours at tissue and organ levels. To understand the functions of a biological system, one has to synthesize the detailed, but isolated biological information obtained at cellular and sub-cellular systems into an interactive system at tissue and organ levels.
To tackle the two challenges requires multidisciplinary approaches. Recently, developments in non-linear science, modern physics of excitable medium, applied mathematics, together with availability of supercomputing power, have provided powerful tools to integrate detailed biological information into an interactive system. This forms a new exciting research area – reconstruction of virtual biological systems: from cell to organ.
Biomolecular structure and dynamics
The interaction of water with proteins with respect to their structure and function is a recently emerging field. We have recently studied water around DNA, proteins and biopolymers using various neutron sources around the world. These studies have shed new light towards the understanding of the structure and dynamics of water in the biological environments. In order to make further progress in this field, we have recently concentrated our effort on the basic building block of proteins - amino acids using inelastic and quasi-elastic neutron scattering techniques and computational methods (molecular dynamics and ab initio quantum mechanics).
Inelastic neutron scattering of hydrogen bonding in ices is of considerable relevance to a range of disciplines where water is considered to be important. It not only provides the foundation for us to understand a range of thermodynamical properties of ices and associated anomalies (e.g. providing the basic experimental information for theoretical modelling, e.g. ab initio quantum chemistry calculations, molecular and lattice dynamical calculations for ice and water), but also equally important for us to understand the role (or interaction) of water around biological systems.
However, the complex structures of DNA/proteins and the conformational arrangements of water molecules around them make it very hard to gain a clear picture of the spatial arrangements, as often only averaged (time and molecule) positions are given. In addition, neutron fluxes are typically weak compared to X-ray sources and this necessitates both long collection times and extremely large crystals. However, using vibrational spectroscopy (including neutron, IR and Raman), we can determine the local structures of water in biological environments by comparing the spectra of known structures, such as exotic phases of ice with those in biological systems. We can thus deduce the interactions between water molecules and DNA/proteins.
Intracellular Particle Tracking and self-assembly
The mechanical properties of cells are intimately connected with their form of locomotion, signalling and misfunctioning in diseased states e.g. malaria, heart disease and cancers. We are examining a number of new microrheology methods to examine the viscoelasticity inside live cells and relate these properties to the structure and dynamics of the constituent cellular biomolecules. Fast particle tracking allows us to probe the viscoelasticity at the cellular level over a wide range of time scales (0.01-10,000Hz) and allows intracellular hydrodynamics to be studied.
Self-assembly is a generic mechanism through which biological molecules explore their free energy landscapes and spontaneously arrange themselves in functional structures. Examples include the construction of blood clots, smectic nanostructures in carbohydrates, fibrous peptides, comb structures in proteoglycans, globular instabilities in glycoproteins and motor protein architectures. A range of experimental techniques are used to examine this behaviour including magnetic tweezers, optical coherence tomography picorheology, X-ray scattering and neutron scattering.