International collaboration

Stockholm/Copenhagen 2008-08-05

We would like to inform you of the status of the pilot project on generating affinity reagents towards human proteins in high-throughput format that was launched following the Affinity Reagents workshop held in Stockholm 14-15th of March 2008.

SH2 domains were chosen as the target area mainly based on two important issues: First, the presence of a strong biological community which has made a commitment to take part in evaluation of the binders and second, because the SH2 domains are small and well folded proteins of significant biological importance which would be relatively easy to produce. Available to the pilot project participants is both protein domains with a native fold generated through a structural genomics effort (SGC, http://thesgc.com/) and recombinant protein fragments (PrESTs) selected due to their low homology to other human proteins and generated through a proteomics effort (HPR, http://www.proteinatlas.org/). This allows us to compare and evaluate affinity reagents generated towards folded and unfolded protein domains, respectively. Since there is no dedicated funding for the pilot project, all the activities have to be carried out in research groups funded for other purposes. This fact raises demands on the project activities to be easily carried out as part of 'normal' activities of the participating groups.

Among approximately 60 participants at the workshop, a steering committee consisting of 17 members for the project was formed representing important laboratories and networks on a global basis. The committee meets via teleconferences on a regular basis, so far two meetings have been held in April and June (minutes attached) as two separate meetings to cover different time zones, but with the same topics discussed. The first meeting focused on more practical aspects, such as protein and affinity reagent generation as well as selection of Chairman (M. Sundstrom) and an Operations Committee (S. Graslund, M. Sundstrom and M. Uhlen), and the second meeting was mainly dedicated to a discussion on the wanted biological outcome of the project, an effort which is headed by Tony Kossiakoff and Tony Pawson.

In summary, antigens/proteins were sent to participating laboratories in May and June and generation and selection of affinity reagents will start at various time-points, depending on laboratory and methods used, and validated binders should be ready for biological evaluation in December 2008. A second affinity binders workshop will be held in March in Austria, organised by the ProteomeBinders project.

20 target proteins were chosen based on feasibility as well as from advice from the biological community. To date, seven research groups working with different technologies to generate renewable affinity reagents have joined the project and have received a first batch of proteins comprising 12 folded domains and 11 PrESTs covering 18 targets in total.

The seven groups participating gives the project good coverage of different methods to produce renewable affinity reagents, but there is still an opportunity for further labs to join. Please contact us if you are interested and feel free to forward this information to anyone whom you think might find it interesting.