Computational protocol: Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies

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Protocol publication

[…] Three-dimensional models of KYP bound to different DNA sequences were generated using the crystal structure of KYP in complex with mCpHpH DNA and the H3 (1-15) peptide [PDB:4QEO] () as a starting model. Changes in the DNA sequence were made using the FOLDX software (,). Models were energy minimized and equilibrated using the GROMACS package () with the CHARMM36 force fields (–). The initial shortest distance between the protein and the box boundaries was set to 1.2 nm. The energy of the system was minimized in vacuum when maximum force on any atom was less than 100 kJ/mol/nm with a maximum of 10 000 steps. The system was then equilibrated with a short MD run of 25 000 steps with a 2-fs time-step (a total of 50 ps). The system was simulated in the NVT ensemble by keeping the temperature (300K) constant; a weak coupling (performed using the Berendsen method) () to external heat baths was applied (relaxation times 0.1 ps). Protein and non-protein were coupled to separate baths in order to ensure even distribution of velocities (and therefore temperature) across the system. All covalent bonds were constrained using the LINCS algorithm and non-bonded interactions were computed using the PME method () with a grid spacing of 0.12 nm for electrostatic contribution. Interaction energies between KYP and DNA were calculated using the FOLDX software (,). […]

Pipeline specifications

Software tools FoldX, GROMACS, P-LINCS
Application Protein structure analysis
Chemicals Cytosine