Materials World Network: Protein Phase Behavior - Experiments and Simulations

A key objective of computational materials science is to relate molecular structure to material properties. In many areas of materials science this approach now provides a standard tool for the controlled design of novel materials. However, the prediction of the structural and thermodynamic properties of protein-based materials is much more challenging because in this case all-atom models are too expensive to be viable for the prediction of phase behavior and kinetics.
The aim of the present work is to use an integration of experiments (US partners Fraden and Lenhoff) and simulation (UK partner Frenkel and US partner Lenhoff) to develop and validate an approach that will make it possible to predict the phase behaviour and crystallisation pathways of proteins in solution.

This proposed research is motivated by the observation that protein-based materials play a key role in science and technology.
To start with a simple observation: our bodies contain high concentrations of proteins and these proteins have evolved to perform either "biochemical" or "structural" tasks (the division is not always sharp).
In science, the preparation of high-quality protein crystals is a crucial step in the elucidation of 3D protein structures by X-ray or neutron diffraction. In addition, the thermodynamic and structural properties of protein-based products are of key importance for the shelf life and bio-avalability of many pharmaceuticals and food products.

It is therefore clearly desirable to be able to predict the phase behaviour and structural properties of protein-based materials on the basis of microscopic information. At present, our ability to make such predictions is limited by the absence of reliable predictive tools.

The objective of the proposed research is to pool the expertise of three world-leading groups in the area of protein crystallization and gelation, to develop modelling techniques that will allow us to predict structure, crystal nucleation and phase stability of protein systems. The project will combine the expertise of two US groups and one UK group. The US groups comprise an expert on experimental studies of protein phase behaviour (Lenhoff, Delaware) and a leader in the field of microfluidics-based protein crystallization (Fraden, Brandeis). The UK group (Frenkel, Cambridge) has a strong track record in the numerical modelling of protein phase behaviour and crystal nucleation.

The key objective of the proposal is develop a systematic procedure that allows us to construct simplified, but physically meaningful, molecular models of proteins for computer simulations. These models should be sufficiently refined that they will allow us to predict/elucidate experimental studies of the equilibrium phase diagrams and phase separation kinetics of protein solutions. Clearly such a model will need to be validated extensively. Our project will therefore be based on a tight coupling between modelling and experimental validation. Measurements of nucleation rates will be interpreted in the context of the classical nucleation model and measurements of the growth of individual precritical nuclei will be used to test the assumptions of that model. The effect of kinetically arrested states, such as non-equilibrium gels and precipitates, on crystallization will be studied in both experiment and simulation.

The broader impact of the proposed research will be that it will enable a better control of the properties of protein-based materials. In particular, it should allow us to improve the rate of protein crystallization for structural biology and to control protein aggregation for pharmaceutical applications.

This work will have impact on various levels: first of all, the tools to be developed will be of basic and practical interest for the academic community that aims to relate the properties of bio-molecular materials to the underlying molecular details. Secondly, the work should lead to strategies to facilitate to crystallization of protein-based materials - or, where relevant, the suppression of crystallization. In this context it should be stressed that the poor crystallisability of many proteins is, at present, the main bottleneck in the determination (by diffraction) of the tertiary protein structure. Any insights that would substantially increase the success of protein crystallization are likely to have a profound impact on protein crystallography and thereby on our ability to understand protein function and, where relevant, to develop drugs that would influence these functions. But the impact of the proposed research would not be limited to academia alone: the shelf-life and bio-availability of protein-based pharmaceuticals depends crucially on the stability and structure of these products. Again, a rational approach to control these morphologies is sorely lacking.

In view of the potential practical importance (and hence, economic relevance) of the proposed work, it is important to have good lines of communication with industries for which this research could become potentially interesting. Both the US and the UK PI's have considerable experience with industrial collaborations. To focus on the UK impact: DF is, at present, involved in a collaborative projects with Unilever. Earlier (whilst in the Netherlands) he was involved in several collaborations with Unilever, Shell an DSM.. In all cases, the focus of this interaction with industry was/is on the exchange information in such a way that scientific advances can be translated into useful tools for industry.

On a longer timescale, the insights in crystallization of proteins that would be the result of the proposed research are likely to have an impact on strategies to develop novel self-assembling materials. Conversely, a better understanding of factors that interfere with crystallization (e.g. the formation of protein fibrils) may have an impact on the life sciences where protein-aggregation diseases are a major (and growing) issue. The same tools that will be developed for the proposed research are likely to have a substantial impact on this field.

In summary, we expect that the UK and US PI's have both the skills and the contacts to ensure that the proposed work will have impact in many academic fields, in a wide range of technological applications, and in other areas that affect directly our society.