There are many cool things that can be done when mixing wet “classical” biochemistry and computational biology/biophysics. The virtual ligand screening is one of those things that fall into the major cool category. Nowadays computer have plenty of horsepower that can be put into good use to simulate the binding of libraries of small molecules onto an active site of an enzyme for instance. Following the in silico simulations, the *best* molecules are assessed in the lab for their *experimental* binding/inhibitory properties. In the following video, I used AutodockVina to dock a small subset of 943 compounds into the human SETD1 (NSD1): 20 best docking solutions for each compounds = 18860 docking solutions!

After weeks of ordering lab stuffs, chemicals, equipments, we can finally switch gear and get the research started. Thanks to a grant from the national research foundation of Korea, Masayo joined the lab along with a lab assistant and an undergraduate student. I’m thrilled to see finally the projects taking off. It is really a great feeling. I can’t wait to see the lab accumulate good and solid data. Here a short iPhone video of Masayo taking care of some human gene constructs we got today.

My life just got 10x better. I have been notified that the National Research Foundation of Korea (NRF) will fund one of my project (I’m the sole PI) for the next 3 years with a descent amount of money too. Now, I can hire a tech for 3 years along with a couple of students to work on that project and study the 3D structures of the NSD proteins (transcription co-activators – TCA) along with trying to understand the inter-domain flexibility of TCA during functions.
I’m now seriously thinking of publishing some of my preliminary data.

Here some of the figures of my grant.

A nerdy post after such a long break. Sorry

Zinc fingers is typically a domain of about 60 amino acids that fold around one or more zinc ions and is found in over 400 eukaryotic proteins, many of which are involved in the regulation of gene expression and in the maintenance of chromatin structure. Zinc fingers typically show a C4HC3 signature (four cysteines, one histidine, three cysteines) with characteristic cysteine spacing and with additional conserved residues, most notably a tryptophan or other aromatic amino acid preceding the final cysteine pair. Studies have suggested a role for zinc fingers as nucleosome interaction determinants. However their functions are still elusive and controversial, as a variety of functions have been suggested, including phosphoinositide binding and E3 ubiquitin ligase activity. In addition to their role as a DNA-binding module,  zinc finger have been shown to mediate protein-protein and protein-lipid interactions as well.

What about the electrostatic surface properties of zinc-finger domains? Here an example with the models of the 4 zinc-fingers of one of the histone methyl-transferase I’m working on. On the figures, blue is positively charged, and red is negative. The large positive (blue) area will bind to the DNA. But, on the other face, there is room for binding to some positively charged partners. Fascinating!

Saturday 21st, I ran the Turkey Trot’09 (10K) in Davis. It was fun as usual and a somewhat easy 10K.  However the weather was not so great: foggy, wet, slippery and cold. But what a great crowd to cheers us up! I just love Davis and I will miss it very much. This year I ran it in 43 minutes, beating my last year time of 48 minutes. I’m happy with that!….do you like my hair?

Since I have some time-off for the next few weeks before staring my new exiting job, I took advantage of today’s great weather to spend some time flying around, just for the heck of flying. I took off KEDU (UC Davis airport called University airport) using runway 17 then I made a 90 right-turn to the west and climb to 4500ft.

The climb to cruising altitude was really smooth, thanks to the temperature inversion. However the downside of a temperature inversion is bad to poor visibility of such air masses. After few minutes I was overflying Winters and decided to head north for a little while. No other aircrafts were around me and the radio was quiet. Perfect!

After some time, I headed back to Davis and started my descent while turning over Winters. I overflew KEDU at 1600ft then descended a bit to 1400ft to stay underneath SMF airspace. After few moments of flying south Davis, I overflew the city to take some photos of downtown Davis. Not easy to fly with one hand and take pictures with the other.

As usual I had a great time. I can’t get enough of that!