Protein structure discovery - (Jul/22/2009 )
My first post here. I was wondering what kind of structure analysis has been done on protein interactions. For example, if a set of proteins are known to react to/interact with each other, have there been studies to find out whether such proteins have a graphical structure of connectivity, whether the sequence of the interaction can be mathematically modelled and whether discovery of structure (potentially leading to model-based prediction of structures) makes any sense in this area.
Sure it's been done, and still being done on new protein interactions. The fields of crystallography and NMR dynamics are devoted to this field of study, as well as theoretical biophysics and bioinformatics. Even most molecular biology laboratories deal with this to some extent. For instance, if a lab discovers an interesting or novel interaction with their protein, they will often do studies to determine which fragments of the protein are binding. If the structures are known (due to crystal or NMR) molecular modeling and docking may be done to simulate how the interaction is accomplished.
Some interactions are quite complex and form aggregates which are linked in complicated manners. Modeling of this is often useful to determine the ramifications of mutations in the proteins that make up the complex (ie. if a crucial scaffold protein is mutated then the rest of the aggregate may no longer function)