This week in the lab we continued working with two more analyses to run on our Hsp90 systems. These will be the last analyses that our mentors will teach us. The main purpose of all of these analyses we have learned are to see if there’s any correlation between each system and their IC50 value.
The last two analyses we learned about are called Hydrogen Bond Analysis and POVME Analysis. The Hydrogen Bond Analysis calculates the amount of hydrogen bonds between the ligand and the protein. Each system has a different amount of hydrogen bonds because each has a different ligand.
The Hsp90 system with the highest binding pocket volume(showed in purple)
The POVME Analysis is short for the Pocket Volume Measurer. This analysis was created by Jeff Wagner, one of our mentors. This analysis is ran in a program that is often used in computational chemistry, which is called Visual Molecular Dynamics(VMD). POVME will analyze the whole simulation from the perspective of the binding pocket and find unique conformations. Then it will calculate the volume of the pocket. After running this analysis on the systems I found the average volume for the 6 systems. Then, I compared those values with their IC50 values. After analyzing my data, I found that the system with the lower IC50 had the smallest volume and the highest IC50 value had the highest volume.
On Thursday, our mentors explained to us what we would be doing for the next 3 weeks. They call it the “BioChemCoRe Grand Challenge.” We were split up into groups and the goal for the “BioChemCoRe Grand Challenge” is to correlate the 6 Hsp90 systems with 6 new ones, and predict the rank order of ligands by the IC50 value. We already know the IC50 values for 6 of them because we worked with those in the previous weeks. For the remainder of the week we did a lot of research on new methods we can use to help us predict the rank order.
Scripps Coastal Reserve Biodiversity Trail
Friday afternoon, the lab took us on a hike that was about one mile on the Scripps Coastal Reserve Biodiversity Trail. It is a short but very scenic loop with views of the pier and the La Jolla coastline.
Outside the lab this week, we only went to the beach once because the weather wasn’t the best in the first half of the week. Also, I spent a lot of my time exploring La Jolla Shores and finding new hiking trails around the area. Overall, I am having an amazing time here and I am eager to see what I will be able to accomplish for the remainder of my time here.
Great update Emmanuel – I don’t understand much of it but it sounds like you do (: Enjoy the last few weeks.