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Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer.

ABSTRACT: 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.

SUBMITTER: Pavsic M

PROVIDER: S-EPMC8477132 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer.

Pavšič Miha M

Data in brief 20210920

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. T ...[more]

PMID: 34611538

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