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 language | English (US) |
|---|---|
| Pages (from-to) | 994-997 |
| Number of pages | 4 |
| Journal | Data in Brief |
| Volume | 17 |
| DOIs | |
| State | Published - 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.
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© 2018 The Authors