Saturday, September 29, 2007

Modular protein domains (an overdue wrap-up)

I did not even cover 1/3 of the Module Protein Domain workshop in my previous blog post. I will not attempt to do it know after so much time. The organizers were clearly concerned about keeping the information withing the participants so I will just post some of the general impressions that I took from the meeting.

Specificity profiling in high gear
There were several sessions dedicated to particular protein domains (SH3, SH2 and PDZ in particular) and for all of these there are several projects under way (or mostly completed) to determine the binding specificity of a large number of these domains (although in different species) using either phage display, spotted peptides and other methods. We should project ahead and start planning what to do with this information. How to combine this to predict pathways and pathway models with dynamical information. The work of Rune Linding is a a very good start at this (see NetworKIN).
Given that the methods are set up I suspect that the emphasis might shift now on exploring the evolution of binding specificities and the impact of disease causing mutations (i.e. profiling binding specificities of domain variants).

Good integration of different methods
Compared to the same meeting two years ago I had an impression that there was a better integration of different approaches (biochemical, structural, computational, etc). A particularly good example was the work of Michael B. Yaffe. There were plenty of structural talks (probably a bit too much) but I found particularly interesting the work of Ivan Dikic that presented extensive novel work on ubiquitin binding domains and Charalampos Kalodimos that presented his lab's work on potential functional roles of proline isomerization (Pubmed).
The computational part was well represented too and it was fun to see again Gary Bader and to get to know Philip Kim.

I hope to be there again in two years time to see how the field changed.