Department of Molecular Biochemistry

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861 to 870 of 1,049 Results

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.
SETD2 MD Data.xlsx 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 MS Excel Spreadsheet - 572.3 KB - MD5: b0809a96189ad4f9d583abeffe0955f4 Data presented in the manuscript.
Analysis_Contact_Maps_Analysis.py Mar 2, 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 Plain Text - 2.0 KB - MD5: b0a2caadbfb0c6ae3e16e468810d8c2e Follow-up python script for "Analysis_Contact_Maps.py"
Analysis_Contact_Maps.py Mar 2, 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 Plain Text - 8.1 KB - MD5: 7bf709c86e3e19e740e6f74ca723efa6 Python script to analyse the contacts of a trajectory (needs follow up script "Analysis_Contact_Maps_Analysis.py").
Analysis_Peptide_Unfolding.py Mar 2, 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 Plain Text - 6.0 KB - MD5: 083105216742702a9cd08fca114b8106 Python script to analyse the unfolding behavior of a peptide in a sMD simulation.
Analysis_RMSD-C_N_Distance_Correlation.py Mar 2, 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 Plain Text - 7.1 KB - MD5: be9e0a85075a865bc8c8b9fab8f9f8bb Python script to analyse the correlation of RMSD and C-to-N-terminal distance of a trajectory. Intentionally used for sMD. (optional script)
Analysis_SN2-Transistion_States.py Mar 2, 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 Plain Text - 3.6 KB - MD5: 56825bb781e96d9e4ac27d37222b7931 Python script to analyse the SN2 transition states in a trajectory.
Enspara_Clustering_Analysis.py Mar 2, 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 Plain Text - 1.4 KB - MD5: 52c57eb9028afc94ccc2504c680e1ef6 Python script to analyse the output of the enspara output files (generated with "Enspara_Command.txt")
Enspara_Command.txt Mar 2, 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 Plain Text - 642 B - MD5: 25782c1c72742bed83986eab713de328 Command line input for the enspara python library. Needs follow up from "Enspara_Clustering_Analysis.py".

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 -

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.

SETD2 MD Data.xlsx

MS Excel Spreadsheet - 572.3 KB -

Data presented in the manuscript.

Analysis_Contact_Maps_Analysis.py

Mar 2, 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

Plain Text - 2.0 KB -

Follow-up python script for "Analysis_Contact_Maps.py"

Analysis_Contact_Maps.py

Plain Text - 8.1 KB -

Python script to analyse the contacts of a trajectory (needs follow up script "Analysis_Contact_Maps_Analysis.py").

Analysis_Peptide_Unfolding.py

Plain Text - 6.0 KB -

Python script to analyse the unfolding behavior of a peptide in a sMD simulation.

Analysis_RMSD-C_N_Distance_Correlation.py

Plain Text - 7.1 KB -

Python script to analyse the correlation of RMSD and C-to-N-terminal distance of a trajectory. Intentionally used for sMD. (optional script)

Analysis_SN2-Transistion_States.py

Plain Text - 3.6 KB -

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

Enspara_Clustering_Analysis.py

Plain Text - 1.4 KB -

Python script to analyse the output of the enspara output files (generated with "Enspara_Command.txt")

Enspara_Command.txt

Plain Text - 642 B -

Command line input for the enspara python library. Needs follow up from "Enspara_Clustering_Analysis.py".

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