Bulletin of the American Physical Society
APS March Meeting 2024
Monday–Friday, March 4–8, 2024; Minneapolis & Virtual
Session N00: Poster Session II (11:30am-2:30pm CST)
11:30 AM,
Wednesday, March 6, 2024
Room: Hall BC
Sponsoring
Unit:
APS/SPS
Abstract: N00.00258 : Structural ensemble determination of intrinsically disordered protein, NUPR1, by replica-exchange molecular dynamics simulation
Presenter:
Seonghun Jang
(PharmCADD)
Authors:
Seonghun Jang
(PharmCADD)
Sangwook Woo
(PharmCADD)
In this study, we report the configurational ensembles of NUPR1 employing all-atom molecular dynamics simulation with a replica-exchange method. In particular, CHARMM36m and a99SB-disp, well-known and validated force fields for IDP, were employed. To check the convergence of our simulation, we started the simulation from different initial conformation, one from extended and another from folded (highly helical state). In addition, we performed the simulation using the initial conformation from Alphafold’s predicted structure.
For the analysis of trajectories, we estimated a radius of gyration (Rg) for structural compactness and residue helicity for dynamically generated conformations. We estimated the ensemble-averaged theoretical SAXS data and compared it with experimental data to check the accuracy of our simulation.
This study predicts the configurational ensemble of NUPR1. Our simulation and analysis can be applied to other IDPs and provide a clue to screening of IDP-targeting drugs.
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