Using ProView to visualize hubs
ProView1 can be used to visualize/plot data and ‘geo map’ them on to the protein structure. Here we use the tool to visualize where the hubs in KE07/KE70 lie as published in Reference 2 (Figure 3/4 and Table 3/4). The default structure shown here is the KE70 design with the hubs data loaded for that particular enzyme.
Viewing Hubs
To view the mutual information (MI) hubs and their position with respect to the substrate, first select what type of hubs you want to see in Plot 1. There is an additional plotting space (Plot 2) that is not necessary for this visualization. The type of hubs can be selected from the dropdown box for Plot 1. Keep Residues in the first box and select one of the three in the 2nd box.
Apo_Hub – Residues with high MI in the apo state of the enzyme
EL_Hub – Residues with high MI in the Enzyme-ligand bound state
TS_Hub – Residues with high MI in the Transition State
For example, in the default setting, Apo_Hub is selected and is displayed on the y-axis (with value 1 for hubs in that particular state) and Residue on the x-axis. To see them on the protein structure, select them by directly clicking on the data point. If you want to select a bunch of them, a resizable rectangular selector can be drawn with the mouse (called a selection brush) to select multiple data points. Once selected, they should be simultaneously colored in the protein structure. The residue numbers that were selected can be seen in the box ‘Summary of Properties’.
Loading new data
New PDB files can be loaded along with new hubs data (Example for KE07) and the options are provided at the top of the webpage. For each of the 4 variants reported in the work published in Ref 2, we have provided the CSV files for viewing the hubs that can be downloaded and then uploaded to the ProView server. We also have provided the PDB files for KE07 and KE70 for structural mapping.
References
1. ProView: Visual Exploratory Analysis of Protein Structure. Yedvabny,E; Head-Gordon,T; Bhowmick,A. In Preparation
2. The Role of Side Chain Entropy and Mutual Information for Improving the De Novo Design of Kemp Eliminases KE07 and KE70. Bhowmick, A; Sharma,S; Honma,H; Head-Gordon,T. Phys. Chem. Chem. Phys., 2016, 18, 19386
Data Files:
CSV: KE70 Design, KE70 Round 6, KE07 Design, KE07 Round 7
Contact: Asmit Bhowmick (asmit [at] berkeley [dot] edu)