Data on the mode of binding between avenanthramides and IKKβ domains in a docking model

Choung-Hun Kang, Woo Shik Shin, Dongwook Yeo, Wonchung Lim, Li Li Ji

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

The data presented in this article are related to the research paper entitled “Anti-inflammatory effect of avenanthramides via NF-κB pathways in C2C12 skeletal muscle cells.” (Kang et al., in press) [1] This article includes experimental procedures used to analyze the mode of binding between and IkB kinase (IKKβ) and avenanthramides which are a group of phenolic alkaloids found in oats. The protein-ligand docking and the computer simulation method of molecular dynamics (MD) for studying the physical interactions of molecules were performed.

Original languageEnglish (US)
Pages (from-to)994-997
Number of pages4
JournalData in Brief
Volume17
DOIs
StatePublished - Apr 2018

Bibliographical note

Funding Information:
MD simulations were performed for IKKβ in complex with the structurally solved inhibitors. Each system was solvated in a cubic box with positive TIP3P water [7] and nutrient ions composed of a solvent buffer zone at the 10 Å edge of the composite. A 100 ns simulation was performed on the docking model using the OPLS-AA 2005 force field under isoelectric isothermal (NPT) conditions at 300 K using DESMOND ver 3.1 (Research DES, Desmond Molecular Dynamics System, NY, USA 2008). The stability of the simulation was evaluated by monitoring the CαRMSD (Root-mean-square deviation of α-carbon) with respect to the minimized starting structure. For IKKβ consisting of the kinase domain (KD), ubiquitin-like domain (ULD) and scaffold/dimerization domain (SDD), CαRMSD was evaluated for the ligand binding KD domain [1] . This work was supported by INHA UNIVERSITY Research Grant.

Publisher Copyright:
© 2018 The Authors

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