Analysis of interactions between potent inhibitors of ATP sulfurylase via molecular dynamics

Abstract

The dynamic behaviour of adenosine triphosphate sulfurylase (ATPs) is analysed to investigate its energetic interactions with inhibitors recently studied theoretically and tested experimentally. The interactions between ATPs and three inhibitors namely, 2,2 0 -azino-di-(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS), butylated hydroxytoluene (BHT), and 3-tert-butyl-4-hydroxyanisole (BHA) in aqueous solution were studied via molecular dynamics simulations. The results of the absolute and relative free energies reveal the existence of synergism in the system. Additionally, the system demonstrates strong steric effect between ABTS and BHA that is not only due to the size of these inhibitors but also their surroundings.

Multiepitope glycan based laser assisted fluorescent nanocomposite with dual functionality for sensing and ablation ofPseudomonas aeruginosa

“…Several studies employed the ATB server for the parameterization of ligands and described the effectiveness as well as the reliability of parameters generated by the ATB server. 34–37…”

“…Several studies employed the ATB server for the parameterization of ligands and described the effectiveness as well as the reliability of parameters generated by the ATB server. [34][35][36][37] To illuminate the interactions of GM and GT with LecA, molecular docking was performed using AutoDock Vina. 38 The dimensions of the grid box were set at 96 Å × 80 Å × 96 Å in x, y, and z dimensions, respectively.…”

Conformational dynamics of superoxide dismutase (SOD1) in osmolytes: a molecular dynamics simulation study

“…† The ATB generated parameters were found to be reliable and have been widely used in several current studies. [48][49][50][51][52][53] However, the effectiveness of ATB parameters was also justied by calculating the transport properties (i.e. self-diffusion coefficient), structural properties (RDF and number of hydrogen bonds) and thermodynamic properties (density) of the TMAO box, and the results were compared with the Shea force eld 54 and the united atom force eld (generated from ATB) of TMAO as a benchmark test; 55 these are reported in the ESI.…”

Effect of Osmolytes on Conformational Behavior of Intrinsically Disordered Protein α-Synuclein

“…The topology for urea and TMAO was built from Automated Topology Builder (ATB) (25). The parameters generated from ATB are found to be reliable and is extensively used in a number of current studies (26)(27)(28)(29)(30)(31). However, to justify the effectiveness of ATB parameters, we have calculated the thermodynamic property (i.e., density), transport property (self-diffusion coefficient), and structural property (RDF and number of hydrogen bonds) of a 3 M TMAO box and compared our result with the shea force field and united atom force field (generated from ATB) of TMAO as a benchmark test (32), which is provided in the Supporting Materials and Methods.…”