Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation (doi:10.18419/darus-3263)

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Part 2: Study Description
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Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

doi:10.18419/darus-3263

DaRUS

2023-03-14

1

Jeltsch, Albert; Schnee, Philipp; Saad, Mina; Weirich, Sara; Pleiss, Jürgen; Bashtrykov, Pavel, 2023, "Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation", https://doi.org/10.18419/darus-3263, DaRUS, V1

Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

doi:10.18419/darus-3263

Jeltsch, Albert (Universität Stuttgart)

Schnee, Philipp (Universität Stuttgart)

Saad, Mina (Universität Stuttgart, Ain Shams University)

Weirich, Sara (Universität Stuttgart)

Pleiss, Jürgen (Universität Stuttgart)

Bashtrykov, Pavel (Universität Stuttgart)

EXC 2075 - 390740016

DaRUS

Jeltsch, Albert

Jeltsch, Albert

2022-11-09

https://doi.org/10.18419/darus-3263

Chemistry, Computer and Information Science, Medicine, Health and Life Sciences, Protein Methyltransferases, Enzyme Specificity

Biochemistry, Molecular Dynamics Simulation

This data collection contains additional data related to Khella et al.: "The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation". This includes <BR><ul> <li>Movie 1: Example of a successful docking of AdoMet to the NSD2 T1150A - H3K36me2 peptide complex</li> <li>Modelled structures of NSD2 bound to different peptides and cofactors <li>Source data of the results of the MD analysis</li> <li>MD simulations codes and analysis scripts</li> <li>Supplementary Tables</li> </ul>

Videos

Molecular models of protein structures

Primary data tables

MD simulations Python scripts

MD simulations analysis Python scripts

Mina S. Khella, Philipp Schnee, Sara Weirich, Tan Bui, Alexander Bröhm, Pavel Bashtrykov, Jürgen Pleiss, Albert Jeltsch: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation. J Biol Chem, 2023, 5, 104796

10.1016/j.jbc.2023.104796

Mina S. Khella, Philipp Schnee, Sara Weirich, Tan Bui, Alexander Bröhm, Pavel Bashtrykov, Jürgen Pleiss, Albert Jeltsch: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation. J Biol Chem, 2023, 5, 104796

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Movie 1 - NSD2 T1150A SAM sMD.mp4

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Example of a successful docking of AdoMet to the NSD2 T1150A – H3K36me2 peptide complex.

video/mp4

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NSD2 MD Data 2.xlsx

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Source data of the results of the MD analysis.

application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

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H3K36me0.pdb

application/vnd.palm

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H3K36me1.pdb

application/vnd.palm

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H3K36me2.pdb

application/vnd.palm

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model_NSD2-T1150A.pdb

application/vnd.palm

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model_NSD2-WT.pdb

application/vnd.palm

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SAM-sMD.pdb

application/vnd.palm

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SAM.pdb

application/vnd.palm

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Set up and PDBs.pse

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PDB files used to start the (s)MD simulations.

application/octet-stream

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Zinc.pdb

application/vnd.palm

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Analysis_RMSD.py

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Python script to analyse the RMSD of a trajectory to a reference frame. Intentionally used for sMD.

text/x-python

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Analysis_SN2-Transistion_States.py

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Python script to analyse the SN2 transition states in a sMD trajectory.

text/x-python

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contact_map_explorer.py

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Python script to analyse the contacts of a trajectory

text/x-python

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Production_NSD2-T1150A_sMD.py

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Python script for the production of SAM-enzyme association sMD simulation trajectories.

text/x-python

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Production_NSD2-T1150_complexed_SAM.py

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Python script for the production of enzyme-SAM complex MD simulation trajectories.

text/x-python

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README.pdf

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Description of the python scripts provided in this repository. Instructions for use, installation and outcome.

application/pdf

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K36me0_deprot.xml

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Parameters for unmethylated, deprotonated lysine 36

text/xml

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K36me1_deprot.xml

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Parameters for monomethylated, deprotonated lysine 36

text/xml

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K36me2_deprot.xml

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Parameters for dimethylated, deprotonated lysine 36

text/xml

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POVME3_input.ini

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Input parameters for POVME3 volume calculation

application/octet-stream

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SAM.xml

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Parameters for the cofactor SAM (AdoMet).

text/xml

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ZNB.xml

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Parameters for the Zink-Dummy model.

text/xml

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Suppl. Table 3.xlsx

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List of differentially expressed genes between OCILY18 (NSD2 T1150A) vs (OCILY1, OCILY7, OCILY10 and DOHH2) (NSD2 WT) with their corresponding Log2 FC and –log10 p-value.

application/vnd.openxmlformats-officedocument.spreadsheetml.sheet