Dataset for dynamics and conformational changes in human NEIL2 protein analyzed by integrative structural biology approach

Polina V Zhdanova; Alexander A Ishchenko; Alexander A Chernonosov; Dmitry O Zharkov; Vladimir V Koval

doi:10.1016/j.dib.2021.107760

Dataset for dynamics and conformational changes in human NEIL2 protein analyzed by integrative structural biology approach

Data Brief. 2021 Dec 25:40:107760. doi: 10.1016/j.dib.2021.107760. eCollection 2022 Feb.

Authors

Polina V Zhdanova^{1

2}, Alexander A Ishchenko^{3

4}, Alexander A Chernonosov¹, Dmitry O Zharkov^{1

2}, Vladimir V Koval^{1

2}

Affiliations

¹ Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibisk, Russia.
² Novosibirsk State University, Novosibisk, Russia.
³ Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif F-94805, France.
⁴ Gustave Roussy, Université Paris-Saclay, Villejuif F-94805, France.

Abstract

This work presents new data on human endonuclease VIII-like 2 protein (hNEIL2), a part of DNA glycosylases of the helix-two-turn-helix structural superfamily. While X-ray structure of oNEIL2 (opossum Monodelphis) was resolved partially [1], the structure of hNEIL2 has not yet been determined. This data article describes a powerful combination of hydrogen-deuterium exchange mass spectrometry, homology modeling, and molecular dynamics simulations for protein conformational dynamics analysis. The data supplied in this work are related to the research article entitled "Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry".

Keywords: Base excision repair; CD, circular dichroism; DNA damage; DNA glycosylases; DNA repair; DTT, (2S,3S)-1,4-Bis(sulfanyl)butane-2,3-diol; ESI, electrospray ionization; HDX-MS; HDX-MS, hydrogen-deuterium exchange mass spectrometry; HEPES, 2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid; IPTG, Propan-2-yl 1-thio-β-D-galactopyranoside; LB, Lysogeny broth; LC-MS, liquid chromatography–mass spectrometry; MD, molecular dynamics; MDTRA, Molecular Dynamics Trajectory Reader & Analyzer; Molecular dynamics; NEIL2; PDB, Protein Data Bank; RMSD, root-mean-square deviation; SDS-PAGE, sodium dodecyl sulphate–polyacrylamide gel electrophoresis; Structural dynamics; TCEP, 3,3’,3’’-Phosphanetriyltripropanoic acid; hNEIL2, human endonuclease VIII-like 2 protein.