Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer

Pavšič, Miha (author)

The data provided and described here give insight into the solution dynamics of the dimer of human EpCAM ectodomain (EpEX). As the starting point, crystal structure of EpEX non-covalent dimer was used (PDB ID 4MZV). The coordinates of solvent-embedded dimer were used to generate a topology file, which was in turn used for all-atom molecular dynamics (MD) simulation run of 20 ns length using full-system periodic electrostatics at a constant temperature of 310 K and a constant pressure of 1 atm. The MD trajectory file (part of this dataset) contains 4000 frames corresponding to recording/sampling atom positions every 5 ps. The simulation run was then analyzed in terms of root mean square deviations (RMSD) of protein atoms, and non-covalent inter-subunit interactions. The MD trajectory and analyzed data enable—in contrast to the static crystal structure—detailed analysis of solution-like protein structural dynamics and support design of EpCAM-targetting binders and structure-based analysis of EpCAM interactome.

• Language: English
• Keywords: EpCAM, tumor marker, molecular dynamics simulation, structure, residue-residue contact network
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Publication status: Published
• Publication version: Version of Record
• Year: 2021
• Number of pages: 7 str.
• Numbering: Vol. 38, art. 107403
• PID: 20.500.12556/RUL-138861
• UDC: 577
• ISSN on article: 2352-3409
• DOI: 10.1016/j.dib.2021.107403
• COBISS.SI-ID: 86882563
• Publication date in RUL: 24.08.2022

Record is a part of a journal

• Title: Data in brief
• Publisher: Elsevier
• ISSN: 2352-3409
• COBISS.SI-ID: 32117977

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: EpCAM, tumorski označevalec, simulacija molekulske dinamike, struktura, mreža stikov med aminokislinskimi ostanki

Projects

• Funder: ARRS - Slovenian Research Agency
• Project number: J1-7119
• Name: Biologija EpCAM na strukturnem nivoju kot osnova za učinkovito tumorsko ciljanje

• Funder: ARRS - Slovenian Research Agency
• Project number: P1-0207
• Name: Toksini in biomembrane