Team:UChicago/Experiments

Experiment

Docking of ligand in active site

Docking was performed with AutoDock Vina through Chimera
1. 1GYC, laccase from T. versicolor, complexed with triclosan
2. 1GSK, laccase from B. subtilis (CotA), complexed with diclofenac
3. 1KV7, laccase from E. coli (CueO), complexed with diclofenac

CotA and CueO were used for our collaboration with Team Aboa
Our protocol for using AutoDock Vina can be found here

1GYC with triclosan
Below is an image of triclosan docked in the active site of 1GYC. Here, we can see that the hydroxyl group on triclosan is pointing directly towards the histidine in 1GYC. We know that the electron transfer occurs along the his-cys pathway (Mot et al, 2012), so the close distance between the hydrogen and the histidine supports the validity of this structure.



CueO with diclofenac
Here, the magenta residues are Met and Asp amino acids that are expected to bind to the ligand (Wang et al). Indeed, diclofenac fits snugly within those bounds.



CotA with diclofenac



Sources
[1] - Mot AC, Silaghi-Dumitrescu R. Laccases: complex architectures for one-electron oxidations. Biochemistry (Mosc). 2012 Dec;77(12):1395-407. doi: 10.1134/S0006297912120085. PMID: 23244736.
[2] - Wang H, Liu X, Zhao J, Yue Q, Yan Y, Gao Z, Dong Y, Zhang Z, Fan Y, Tian J, Wu N, Gong Y. Crystal structures of multicopper oxidase CueO G304K mutant: structural basis of the increased laccase activity. Sci Rep. 2018 Sep 24;8(1):14252. doi: 10.1038/s41598-018-32446-7. PMID: 30250139; PMCID: PMC6155172.

Protonation

Because we want to compare two pH conditions in our simulations, this would affect the protonation state of each amino acid residue. To do this, we used the web server H++. Below, we have attached the outputs to our protonation:

1gyc_pH5
1gyc_pH7.1

> To use these outputs in our simulation, we created and ran a python script that converted the AMBER coordinate and topology fies to GROMACS coordinate and topology files. The program we used is attached below.

topology_converter.py

MD Simulations

We ran our molecular dynamics simulations through GROMACS 2020.6. The basic steps of an MD simulation are solvation, minimization, equilibration, and then the final MD run. Solvation involves the creation of a box with your molecule of interest, adding solvents (typically water), and adding counterions such that the entire box has a neutral charge. Minimization calls a steep optimization algorithm to seek lowest energy conformation protein under linear restraints. Equilibration stabilizes the system at a constant volume (NVT equilibration) and at a constant pressure (NPT equilibration). Only once solvation, minimization, and equilibration are completed can the MD run be initiated.

Our protocols for MD simulations is attached below. Our MD runs were performed on UChicago’s Midway Cluster in the Research Computing Center.

md-protocol.docx

MD Simulation Analysis

The two files we care about that are outputs to the MD run are the trajectory file (.xtc) and the run topology files (.tpr). From these files, we can view the conformational changes of the molecule over time, calculate the root mean square fluctuation of each residue, compute the radius of gyration, and complete a principal component analysis via eigenvalue decomposition.

Our protocols are attached below

md_analysis.docx