#Script and Macros Used for Analysis of MD Trajectories of YidC Studied in Article: Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase Authors: Adithya Polasa, Shadi A Badiee and Mahmoud Moradi

#Dynamic Network Analysis (calc_correlation_custom.py)

This is done using python package MD-TASK, software suite of MD analysis tools, was used to calculate the correlation coefficient for the motion of each C_alpha atom relative to the other C_alpha atoms. A correlation matrix M was generated for each of the three protomers in all the simulated trajectories. Additionally, a correlation matrix for the entire trimer was calculated for each simulation to explore correlations between structures of different protomers.

#Hydrogen Bond Analysis (hbond.tcl)

Hydrogen bond analysis script calculatest the hydrogen bond distance between two residues.

#Principal Component analysis (PCA) (PCA.py)

PCA performed with ProDy using this python script to quantify the persistent conformational changes and relative motions of the active and inactive states.

#Root Mean Square Deviation (RMSD) (RMSD.tcl)

Calculates the RMSD of the protein. All the atoms are aligned onto a reference structure intial frame of the protein.

#Salt-Bridge Analysis (salt.tcl)

This script finds saltbridges in the system and calculates distance of the saltbridge for entire trajectory.

#Transmembrane Helical Angle (inter_helical_angle.tcl)

These are VMD scripts For the inter helical angle calculations, we chose residues of indivual helices of YidC Transmembrane region. The angle script measures, vector angle between the helix 1 and Helix 2 and computed angle was subtracted from 180◦.

#Water Analysis (water.tcl)

The amount of solvent water inside the groove quantified using water analysis VMD script. This calculates the number of water molecules within 5 ̊A of the R366 for every frame of trajectory.

#Simulation files structure coordinate files of all YidC systems studied in this research are provided here in PDB format. The NAMD configuration file and PSF file are also available for the system without the C2 loop in the YidC_Delta_C2 folder. The Anton 2 configuration file can be found in the Anton 2 folder.