Protein self-assembly, in the form of folding and binding, and aggregation is crucial in biologically relevant systems such as regulation networks but fundamentally of physicochemical nature. Knowledge of these important self-assembly processes leads to new insight in the molecular nature of the functioning of the cell, and eventually toward application in biology and medical sciences. We employ advanced molecular simulation techniques to elucidate the mechanism, kinetics and transition states of such processes in atomistic detail.
Special attention is given to photoreceptors. In particular, we work on PYP and BLUF. These proteins act as experimental model systems. Using advanced methods, we can predict structure and dynamics of the photocylce. These simulations give tremendous insight in the function of signal proteins.
Experimental permeability measurements on pure lipid bilayer membranes reveal that passive ion leakage does occur. The mechanisms by which the ions cross the membrane are not yet understood, mainly because these processes are notoriously hard to investigate, due to the small dimensions and the fluctuating nature of the membrane. Our aim is to overcome this difficulty by employing advanced simulation techniques.
- Protein folding
- Signal transduction in Photoactive Yellow Protein: large scale conformational transitions
- Signal transduction in Photoactive Yellow Protein: chemical reactions at the chromophore binding site
- Self-assembly of peptide aggregates
- Transport properties of charged molecules through bio-membranes
- Allosteric mechanisms of trans-membrane signalling proteins