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Open AccessArticle

Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation

by 1,2, 1,2, 1,2, 3, 1,* and 1,2,*
1
Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
2
Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
3
Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
*
Authors to whom correspondence should be addressed.
Academic Editor: Quan Zou
Molecules 2018, 23(11), 3018; https://doi.org/10.3390/molecules23113018
Received: 20 August 2018 / Revised: 4 November 2018 / Accepted: 6 November 2018 / Published: 19 November 2018
(This article belongs to the Special Issue Computational Analysis for Protein Structure and Interaction)
The interaction of death-associated protein kinase 1 (DAPK1) with the 2B subunit (GluN2B) C-terminus of N-methyl-D-aspartate receptor (NMDAR) plays a critical role in the pathophysiology of depression and is considered a potential target for the structure-based discovery of new antidepressants. However, the 3D structures of C-terminus residues 1290–1310 of GluN2B (GluN2B-CT1290-1310) remain elusive and the interaction between GluN2B-CT1290-1310 and DAPK1 is unknown. In this study, the mechanism of interaction between DAPK1 and GluN2B-CT1290-1310 was predicted by computational simulation methods including protein–peptide docking and molecular dynamics (MD) simulation. Based on the equilibrated MD trajectory, the total binding free energy between GluN2B-CT1290-1310 and DAPK1 was computed by the mechanics generalized born surface area (MM/GBSA) approach. The simulation results showed that hydrophobic, van der Waals, and electrostatic interactions are responsible for the binding of GluN2B-CT1290–1310/DAPK1. Moreover, through per-residue free energy decomposition and in silico alanine scanning analysis, hotspot residues between GluN2B-CT1290-1310 and DAPK1 interface were identified. In conclusion, this work predicted the binding mode and quantitatively characterized the protein–peptide interface, which will aid in the discovery of novel drugs targeting the GluN2B-CT1290-1310 and DAPK1 interface. View Full-Text
Keywords: DAPK1-GluN2B peptide; protein–peptide docking; MD simulation; binding free energy; hotspot DAPK1-GluN2B peptide; protein–peptide docking; MD simulation; binding free energy; hotspot
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MDPI and ACS Style

Tu, G.; Fu, T.; Yang, F.; Yao, L.; Xue, W.; Zhu, F. Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation. Molecules 2018, 23, 3018. https://doi.org/10.3390/molecules23113018

AMA Style

Tu G, Fu T, Yang F, Yao L, Xue W, Zhu F. Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation. Molecules. 2018; 23(11):3018. https://doi.org/10.3390/molecules23113018

Chicago/Turabian Style

Tu, Gao; Fu, Tingting; Yang, Fengyuan; Yao, Lixia; Xue, Weiwei; Zhu, Feng. 2018. "Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation" Molecules 23, no. 11: 3018. https://doi.org/10.3390/molecules23113018

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