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Author Name: Gräter, Frauke

1 to 7 of 7 Results

Substituting density functional theory in reaction barrier calculations for hydrogen atom transfer in proteins [data] Dec 7, 2023 - HITS MBM Riedmiller, Kai; Reiser, Patrick; Bobkova, Elizaveta; Maltsev, Kiril; Gryn’ova, Ganna; Friederich, Pascal; Gräter, Frauke, 2023, "Substituting density functional theory in reaction barrier calculations for hydrogen atom transfer in proteins [data]", https://doi.org/10.11588/data/TGDD4Y, heiDATA, V2 Hydrogen atom transfer (HAT) reactions are important in many biological systems. As these reactions are hard to observe experimentally, it is of high interest to shed light on them using simulations. Here, we present a machine learning model based on graph neural networks for the...
Mechanical forces control the valency of the malaria adhesin VAR2CSA by exposing cryptic glycan binding sites [data] Dec 4, 2023 - HITS MBM Roessner Rita; Michelarakis, Nicholas; Gräter, Frauke; Aponte-Santamaría, Camilo, 2023, "Mechanical forces control the valency of the malaria adhesin VAR2CSA by exposing cryptic glycan binding sites [data]", https://doi.org/10.11588/data/EZHMDU, heiDATA, V1 Plasmodium falciparum (Pf) is responsible for the most lethal form of malaria. VAR2CSA is an adhesin protein expressed by this parasite at the membrane of infected erythrocytes for attachment to the placenta, leading to pregnancy-associated malaria. VAR2CSA is a large 355 kDa mul...
Intrinsically disordered region of talin’s FERM domain functions as an initial PIP2 recognition site [research data] Feb 15, 2023 - HITS MBM Buhr, Jannik; Franz, Florian; Gräter, Frauke, 2023, "Intrinsically disordered region of talin’s FERM domain functions as an initial PIP2 recognition site [research data]", https://doi.org/10.11588/data/BQTQUN, heiDATA, V1 Focal adhesions (FAs) mediate the interaction of the cytoskeleton with the extracellular matrix (ECM) in a highly dynamic fashion. talin is a central regulator, adaptor protein and mechano-sensor of focal adhesion complexes. For recruitment and firm attachment at FAs, talin’s N-t...
Dual kinetic and structural role for the surface in guiding SAS-6 self-assembly to direct centriole architecture [Data] Sep 23, 2021 - 3D Matter Made to Order (3DMM2O) de Buhr, Svenja; Gräter, Frauke, 2021, "Dual kinetic and structural role for the surface in guiding SAS-6 self-assembly to direct centriole architecture [Data]", https://doi.org/10.11588/data/3NKHAY, heiDATA, V1 This dataset contains input structures and parameters for coarse-grained molecular dynamics simulation of SAS-6 protein oligomers as well as post-processing files and analysis scripts. Abstract of related publication: Discovering mechanisms governing organelle assembly is a funda...
Collagen breaks at weak sacrificial bonds taming its mechanoradicals [Data] Mar 24, 2023 - HITS MBM Rennekamp, Benedikt; Gräter, Frauke, 2023, "Collagen breaks at weak sacrificial bonds taming its mechanoradicals [Data]", https://doi.org/10.11588/data/HJ6SVM, heiDATA, V1, UNF:6:Da6omTKjrSvNcDwyJxuHOg== [fileUNF] This dataset contains input files for MD simulations, derived breakage counts from these simulations that are used to generate the figures in the publication, and the experimental, uncropped SDS-PAGE gels of the presented results in the related publication. Abstract of related pu...
Bond dissociation energies of X−H bonds in proteins [data] Feb 14, 2023 - HITS MBM Riedmiller, Kai; Treyde, Wojtek; Gräter, Frauke, 2022, "Bond dissociation energies of X−H bonds in proteins [data]", https://doi.org/10.11588/data/AA3UAQ, heiDATA, V2 Knowledge of reliable X−H bond dissociation energies (X = C, N, O, S) for amino acids in proteins is key for studying the radical chemistry of proteins. X−H bond dissociation energies of model dipeptides were computed using the isodesmic reaction method at the BMK/6-31+G(2df,p) a...
Allosteric Activation of Vinculin by Talin [data] Jun 1, 2023 - HITS MBM Gräter, Frauke; Franz, Florian; Winograd-Katz, Sabina; Tapia-Rojo, Rafael; Boujemaa-Paterski, Rajaa; Li, Wenhong; Unger, Tamar; Albeck, Shira; Aponte-Santamaria, Camilo; Garcia-Manyes, Sergi; Medalia, Ohad; Geiger, Benny, 2023, "Allosteric Activation of Vinculin by Talin [data]", https://doi.org/10.11588/data/WZDKT6, heiDATA, V1, UNF:6:32j0OWUdxRAbsyCMzwdFcQ== [fileUNF] The talin-vinculin axis is a key mechanosensing component of cellular focal adhesions. How talin and vinculin respond to forces and regulate one another remains unclear. By combining single molecule magnetic tweezer experiments, Molecular Dynamics simulations, actin bundling assa...

Substituting density functional theory in reaction barrier calculations for hydrogen atom transfer in proteins [data]

Dec 7, 2023 - HITS MBM

Riedmiller, Kai; Reiser, Patrick; Bobkova, Elizaveta; Maltsev, Kiril; Gryn’ova, Ganna; Friederich, Pascal; Gräter, Frauke, 2023, "Substituting density functional theory in reaction barrier calculations for hydrogen atom transfer in proteins [data]", https://doi.org/10.11588/data/TGDD4Y, heiDATA, V2

Hydrogen atom transfer (HAT) reactions are important in many biological systems. As these reactions are hard to observe experimentally, it is of high interest to shed light on them using simulations. Here, we present a machine learning model based on graph neural networks for the...

Mechanical forces control the valency of the malaria adhesin VAR2CSA by exposing cryptic glycan binding sites [data]

Dec 4, 2023 - HITS MBM

Roessner Rita; Michelarakis, Nicholas; Gräter, Frauke; Aponte-Santamaría, Camilo, 2023, "Mechanical forces control the valency of the malaria adhesin VAR2CSA by exposing cryptic glycan binding sites [data]", https://doi.org/10.11588/data/EZHMDU, heiDATA, V1

Plasmodium falciparum (Pf) is responsible for the most lethal form of malaria. VAR2CSA is an adhesin protein expressed by this parasite at the membrane of infected erythrocytes for attachment to the placenta, leading to pregnancy-associated malaria. VAR2CSA is a large 355 kDa mul...

Intrinsically disordered region of talin’s FERM domain functions as an initial PIP2 recognition site [research data]

Feb 15, 2023 - HITS MBM

Buhr, Jannik; Franz, Florian; Gräter, Frauke, 2023, "Intrinsically disordered region of talin’s FERM domain functions as an initial PIP2 recognition site [research data]", https://doi.org/10.11588/data/BQTQUN, heiDATA, V1

Focal adhesions (FAs) mediate the interaction of the cytoskeleton with the extracellular matrix (ECM) in a highly dynamic fashion. talin is a central regulator, adaptor protein and mechano-sensor of focal adhesion complexes. For recruitment and firm attachment at FAs, talin’s N-t...

Dual kinetic and structural role for the surface in guiding SAS-6 self-assembly to direct centriole architecture [Data]

Sep 23, 2021 - 3D Matter Made to Order (3DMM2O)

de Buhr, Svenja; Gräter, Frauke, 2021, "Dual kinetic and structural role for the surface in guiding SAS-6 self-assembly to direct centriole architecture [Data]", https://doi.org/10.11588/data/3NKHAY, heiDATA, V1

This dataset contains input structures and parameters for coarse-grained molecular dynamics simulation of SAS-6 protein oligomers as well as post-processing files and analysis scripts. Abstract of related publication: Discovering mechanisms governing organelle assembly is a funda...

Collagen breaks at weak sacrificial bonds taming its mechanoradicals [Data]

Mar 24, 2023 - HITS MBM

Rennekamp, Benedikt; Gräter, Frauke, 2023, "Collagen breaks at weak sacrificial bonds taming its mechanoradicals [Data]", https://doi.org/10.11588/data/HJ6SVM, heiDATA, V1, UNF:6:Da6omTKjrSvNcDwyJxuHOg== [fileUNF]

This dataset contains input files for MD simulations, derived breakage counts from these simulations that are used to generate the figures in the publication, and the experimental, uncropped SDS-PAGE gels of the presented results in the related publication. Abstract of related pu...

Bond dissociation energies of X−H bonds in proteins [data]

Feb 14, 2023 - HITS MBM

Riedmiller, Kai; Treyde, Wojtek; Gräter, Frauke, 2022, "Bond dissociation energies of X−H bonds in proteins [data]", https://doi.org/10.11588/data/AA3UAQ, heiDATA, V2

Knowledge of reliable X−H bond dissociation energies (X = C, N, O, S) for amino acids in proteins is key for studying the radical chemistry of proteins. X−H bond dissociation energies of model dipeptides were computed using the isodesmic reaction method at the BMK/6-31+G(2df,p) a...

Allosteric Activation of Vinculin by Talin [data]

Jun 1, 2023 - HITS MBM

Gräter, Frauke; Franz, Florian; Winograd-Katz, Sabina; Tapia-Rojo, Rafael; Boujemaa-Paterski, Rajaa; Li, Wenhong; Unger, Tamar; Albeck, Shira; Aponte-Santamaria, Camilo; Garcia-Manyes, Sergi; Medalia, Ohad; Geiger, Benny, 2023, "Allosteric Activation of Vinculin by Talin [data]", https://doi.org/10.11588/data/WZDKT6, heiDATA, V1, UNF:6:32j0OWUdxRAbsyCMzwdFcQ== [fileUNF]

The talin-vinculin axis is a key mechanosensing component of cellular focal adhesions. How talin and vinculin respond to forces and regulate one another remains unclear. By combining single molecule magnetic tweezer experiments, Molecular Dynamics simulations, actin bundling assa...

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