Research objectives and content
The crystallization procedure of membrane proteins requires the addition of an amphiphile which includes the proteins in quasi-solid cubic phases, sources of nucleation sites. Although an intense experimental effort is devoted to protein crystallization, very little is understood about the thermodynamic stability of the protein-rich cubic phase, or the way in which the cubic bilayer catalyses the formation of the crystal.We propose to perform a numerical study of the thermodynamic stability of the cubic phases in order understand which are the important experimental parameters to make the crystallization procedure more effective. We will compare the numerical results with a phenomenological theory that accounts for intra- and inter-aggregate interaction contributions. Then we will focus on the actual formation of the crystal from the templating membrane-rich cubic phase by comparing the relative stability of the membrane-rich and protein-rich phases, and find the pathway for crystal nucleation. We shall use simple, coarse-grained models for the membrane proteins since a fully atomistic protein-protein interaction simulation is not feasible even with the fastest computers.
Training content (objective, benefit and expected impact)
The numerical simulations will require an integration of several advanced numerical techniques, viz. free-energy calculations for the ordered phase, umbrella sampling to compute nucleation barriers, and dissipative particle dynamics to model the coarse-grained dynamics. The group in Amsterdam has played an important part in the development of several of these techniques Links with industry / industrial relevance (22)