Data for: Energetics of substrate transport in proton-dependent oligopeptide transporters

The PepTSo transporter mediates the transport of peptides across biological membranes. Despite advancements in structural biology, including cryogenic electron microscopy structures resolving PepTSo in different states, the molecular basis of peptide recognition and transport by PepTSo is not fully elucidated. In this study, we used molecular dynamics simulations, Markov State Models (MSMs), and Transition Path Theory (TPT) to investigate the transport mechanism of an alanine-alanine peptide (Ala-Ala) through the PepTSo transporter. Our simulations revealed conformational changes and key intermediate states involved in peptide translocation. We observed that the presence of the Ala-Ala peptide substrate lowers the free energy barriers associated with transition to the inward-facing state. We also show a proton transport model and analyzed the pharmacophore features of intermediate states, providing insights for rational drug design. These findings highlight the significance of substrate..., , , README: Energetics of substrate transport in proton-dependent oligopeptide transporters

This dataset includes data from Markov State Model (MSM) and Transition Path Theory (TPT) analyses conducted on molecular dynamics simulations for this study. The code for generating figures using the provided numeric files (NumPy and pickle formats) can be found on GitHub at the following link: [https://github.com/ShuklaGroup/Selvam_et_al_Communications_Chemistry_2024/tree/main](https://github.com/ShuklaGroup/Selvam_et_al_Communications_Chemistry_2024/tree/main).

Descriptions

Fig1_Data.zip

1.apo_count_mat.dat:

* ```
Count matrix for the apo (without substrate) system.
```
* ```
Represents transition counts between states, used for constructing the MSM.
```
* This data can be viewed using the following commands:
* ```
import numpy as np
```
* ```
np.loadtxt(\"apo_count_mat.dat\")
```

2.apo_data_x.npy:

* ```
Array of extracellular distances for the apo (without su...