MD Simulations

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51 to 60 of 77 Results

SAM.xml Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation XML - 20.9 KB - MD5: 8504b192cebc39de3edb5595d94cd0e4 Parameters for the cofactor SAM (AdoMet).
Set up and PDBs.pse Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation Unknown - 9.0 MB - MD5: 03afb74cdbb9a2f89b12077a32a2145b PDB files used to start the (s)MD simulations.
Suppl. Table 3.xlsx Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation MS Excel Spreadsheet - 68.7 KB - MD5: 58613d1330e21907928e58900a55577f 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.
Zinc.pdb Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation application/vnd.palm - 1.5 KB - MD5: d0faeef5a7789400011fa63d86b86947
ZNB.xml Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation XML - 1.6 KB - MD5: a8f183de30b9a05bd6a6515d639ea88c Parameters for the Zink-Dummy model.
Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide Aug 15, 2022 Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen, 2022, "Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide", https://doi.org/10.18419/DARUS-2508, DaRUS, V2 This data collection contains additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide. This includes MD simulations code and analysis scripts. The usage of these Phyton scripts is further explained in the enclosed readm...
Movie1_ssK36_hairpin_formation.mp4 Aug 15, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide MPEG-4 Video - 7.9 MB - MD5: bc370cb514eda10a067eaff28bc80a26 Formation of hairpin conformation of ssK36 peptide. The movie shows an MD simulation of the ssK36 peptide in solution and its formation of a hairpin conformation.
Movie2_sMD_ssK36_successfull_binding.mp4 Aug 15, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide MPEG-4 Video - 15.2 MB - MD5: bc3201d5df0f95885e3c4c14f73bc92a Representative sMD simulation without repulsive force. The movie shows the ssK36 peptide approaching SETD2 in a hairpin conformation and afterwards successfully establishing a TS-like structure.
Movie3_sMD_H3K36_unsuccessfull_binding.mp4 Aug 15, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide MPEG-4 Video - 16.3 MB - MD5: 72b0b55bd9fdecbca087667e52ff69c7 Representative sMD with repulsive force. The movie shows the H3K36 peptide approaching SETD2 in an extended conformation. Afterwards, it fails to establish a transition-state like structure.
Movie4_sMD_ssK36_unfolding.mp4 Aug 15, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide MPEG-4 Video - 20.0 MB - MD5: b86d4c5b5dd1809e83e12116fd8b8b66 Representative sMD without repulsive force showing peptide unfolding during the binding process. The ssK36 peptide enters the SETD2 binding cleft in a hairpin conformation and afterwards unfolds into an extended structure similarly as the structure observed in the crystal structure.

SAM.xml

Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

XML - 20.9 KB -

Parameters for the cofactor SAM (AdoMet).

Set up and PDBs.pse

Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

Unknown - 9.0 MB -

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

Suppl. Table 3.xlsx

Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

MS Excel Spreadsheet - 68.7 KB -

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.

Zinc.pdb

Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

application/vnd.palm - 1.5 KB -

ZNB.xml

Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

XML - 1.6 KB -

Parameters for the Zink-Dummy model.

Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide

Aug 15, 2022

Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen, 2022, "Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide", https://doi.org/10.18419/DARUS-2508, DaRUS, V2

This data collection contains additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide. This includes MD simulations code and analysis scripts. The usage of these Phyton scripts is further explained in the enclosed readm...

Movie1_ssK36_hairpin_formation.mp4

Aug 15, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide

MPEG-4 Video - 7.9 MB -

Formation of hairpin conformation of ssK36 peptide. The movie shows an MD simulation of the ssK36 peptide in solution and its formation of a hairpin conformation.

Movie2_sMD_ssK36_successfull_binding.mp4

MPEG-4 Video - 15.2 MB -

Representative sMD simulation without repulsive force. The movie shows the ssK36 peptide approaching SETD2 in a hairpin conformation and afterwards successfully establishing a TS-like structure.

Movie3_sMD_H3K36_unsuccessfull_binding.mp4

MPEG-4 Video - 16.3 MB -

Representative sMD with repulsive force. The movie shows the H3K36 peptide approaching SETD2 in an extended conformation. Afterwards, it fails to establish a transition-state like structure.

Movie4_sMD_ssK36_unfolding.mp4

MPEG-4 Video - 20.0 MB -

Representative sMD without repulsive force showing peptide unfolding during the binding process. The ssK36 peptide enters the SETD2 binding cleft in a hairpin conformation and afterwards unfolds into an extended structure similarly as the structure observed in the crystal structure.

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