Institute of Biochemistry

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1,021 to 1,030 of 1,292 Results

no enzyme control PB_955.txt Sep 27, 2022 - NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation Plain Text - 9.3 MB - MD5: 8a550e97f117c08732d08b76217ea681
no enzyme control PB_956.txt Sep 27, 2022 - NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation Plain Text - 7.7 MB - MD5: 0001bb40f5c9c9a817db0900fad68482
readme.pdf Sep 27, 2022 - NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation Adobe PDF - 119.2 KB - MD5: fee216cf25110a60a46f76ebb5aba084
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.
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").

no enzyme control PB_955.txt

Sep 27, 2022 - NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation

Plain Text - 9.3 MB -

no enzyme control PB_956.txt

Sep 27, 2022 - NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation

Plain Text - 7.7 MB -

readme.pdf

Sep 27, 2022 - NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation

Adobe PDF - 119.2 KB -

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.

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").

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