Modelling the Protein-DNA Interface

Sammanfattning: Protein-DNA interactions are crucial to life. Several millions of DNA base pair steps are organ- ised, read and protected by proteins in every cell. Protein-DNA interactions must be specific, controllable and reasonably fast. Understanding how these features coexist is one of the great challenges for biochemists and molecular biologists. Great interest has been directed towards the fast association rates measured for DNA-binding proteins such as bacterial transcription factors. These interactions have been described as proceeding by ‘facilitated diffusion’, which means that the non-specific interaction of a protein with DNA guides its way towards the target site. This can be studied using fluorescent labels and high resolution microscopes. This tech- niques can record traces of proteins, that diffuse along DNA until they bind their target sites and stop diffusion. But, which role the conformation of the protein or the DNA play a during the pro- cess of non-specific binding and recognition cannot be revealed. It is still unclear how proteins recognise their target sites. It is likely that conformational changes in both, the protein and in the DNA, play important roles. We can solve structures of protein-DNA complexes in molecular detail using crystallography or nuclear magnetic resonance. With all-atom molecular dynamic simulations we can elucidating their dynamics and obtain insights about conformational vari- ability. But some, large conformational changes and especially diffusion are processes that can be out of reach for the time-scales of normal all-atom simulations. Simplified representations of large biomolecules, so called coarse-grained models, can be used to study diffusion instead. The repressor of the lac operon is a well studied model system for understanding protein-DNA interactions. In this study, we applied coarse-grained simulations to define the search confor- mation of the protein, answering how it can sample the DNA effectively and how it recognises the target site sequence. Additionally we applied all-atom molecular dynamics to understand the stabilisation of the specific complex.