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)

View:

Part 1: Document Description
Part 2: Study Description
Part 5: Other Study-Related Materials
Entire Codebook

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, Biochemistry

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

Label:

Movie 1 - NSD2 T1150A SAM sMD.mp4

Text:

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

video/mp4

Label:

NSD2 MD Data 2.xlsx

Text:

Source data of the results of the MD analysis.

application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

Label:

H3K36me0.pdb

application/vnd.palm

Label:

H3K36me1.pdb

application/vnd.palm

Label:

H3K36me2.pdb

application/vnd.palm

Label:

model_NSD2-T1150A.pdb

application/vnd.palm

Label:

model_NSD2-WT.pdb

application/vnd.palm

Label:

SAM-sMD.pdb

application/vnd.palm

Label:

SAM.pdb

application/vnd.palm

Label:

Set up and PDBs.pse

Text:

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

application/octet-stream

Label:

Zinc.pdb

application/vnd.palm

Label:

Analysis_RMSD.py

Text:

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

text/x-python

Label:

Analysis_SN2-Transistion_States.py

Text:

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

text/x-python

Label:

contact_map_explorer.py

Text:

Python script to analyse the contacts of a trajectory

text/x-python

Label:

Production_NSD2-T1150A_sMD.py

Text:

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

text/x-python

Label:

Production_NSD2-T1150_complexed_SAM.py

Text:

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

text/x-python

Label:

README.pdf

Text:

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

application/pdf

Label:

K36me0_deprot.xml

Text:

Parameters for unmethylated, deprotonated lysine 36

text/xml

Label:

K36me1_deprot.xml

Text:

Parameters for monomethylated, deprotonated lysine 36

text/xml

Label:

K36me2_deprot.xml

Text:

Parameters for dimethylated, deprotonated lysine 36

text/xml

Label:

POVME3_input.ini

Text:

Input parameters for POVME3 volume calculation

application/octet-stream

Label:

SAM.xml

Text:

Parameters for the cofactor SAM (AdoMet).

text/xml

Label:

ZNB.xml

Text:

Parameters for the Zink-Dummy model.

text/xml

Label:

Suppl. Table 3.xlsx

Text:

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