Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor
We here give information for a deeper understanding of single molecule force spectroscopy (SMFS) data through the example of the blood protein von Willebrand factor (VWF). It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD) loading-rate range c...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2016-09-01
|
| Series: | Data in Brief |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S235234091630467X |
| _version_ | 1819049652853407744 |
|---|---|
| author | Sandra Posch Camilo Aponte-Santamaría Richard Schwarzl Andreas Karner Matthias Radtke Frauke Gräter Tobias Obser Gesa König Maria A. Brehm Hermann J. Gruber Roland R. Netz Carsten Baldauf Reinhard Schneppenheim Robert Tampé Peter Hinterdorfer |
| author_facet | Sandra Posch Camilo Aponte-Santamaría Richard Schwarzl Andreas Karner Matthias Radtke Frauke Gräter Tobias Obser Gesa König Maria A. Brehm Hermann J. Gruber Roland R. Netz Carsten Baldauf Reinhard Schneppenheim Robert Tampé Peter Hinterdorfer |
| author_sort | Sandra Posch |
| collection | DOAJ |
| description | We here give information for a deeper understanding of single molecule force spectroscopy (SMFS) data through the example of the blood protein von Willebrand factor (VWF). It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD) loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently developed model by Bullerjahn, Sturm, and Kroy (BSK) was used for this demonstration. Further, Brownian dynamics (BD) simulations, which can be utilized to estimate the lifetimes of intramolecular VWF interactions under physiological shear, are described. For interpretation and discussion of the methods and data presented here, we would like to directly point the reader to the related research paper, “Mutual A domain interactions in the force sensing protein von Willebrand Factor” (Posch et al., 2016) [1]. Keywords: Atomic force microscopy, Single molecule force spectroscopy, Molecular dynamics simulation, Brownian dynamics simulation, von Willebrand factor |
| first_indexed | 2024-12-21T11:35:34Z |
| format | Article |
| id | doaj.art-a6af907a1b04473db79970e4cbf3d20c |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-12-21T11:35:34Z |
| publishDate | 2016-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-a6af907a1b04473db79970e4cbf3d20c2022-12-21T19:05:27ZengElsevierData in Brief2352-34092016-09-01810801087Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factorSandra Posch0Camilo Aponte-Santamaría1Richard Schwarzl2Andreas Karner3Matthias Radtke4Frauke Gräter5Tobias Obser6Gesa König7Maria A. Brehm8Hermann J. Gruber9Roland R. Netz10Carsten Baldauf11Reinhard Schneppenheim12Robert Tampé13Peter Hinterdorfer14Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University, Linz, AustriaMolecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, GermanyDepartment of Physics, FU Berlin, Berlin, GermanyCenter for Advanced Bioanalysis GmbH (CBL), Linz, AustriaDepartment of Physics, FU Berlin, Berlin, GermanyMolecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, GermanyDepartment of Pediatric Hematology and Oncology, University Medical Center Hamburg -Eppendorf, Hamburg, GermanyDepartment of Pediatric Hematology and Oncology, University Medical Center Hamburg -Eppendorf, Hamburg, GermanyDepartment of Pediatric Hematology and Oncology, University Medical Center Hamburg -Eppendorf, Hamburg, GermanyDepartment of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University, Linz, AustriaDepartment of Physics, FU Berlin, Berlin, GermanyTheory Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, GermanyDepartment of Pediatric Hematology and Oncology, University Medical Center Hamburg -Eppendorf, Hamburg, GermanyInstitute of Biochemistry, Biocenter, Goethe-University Frankfurt, Frankfurt/Main, GermanyDepartment of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University, Linz, Austria; Center for Advanced Bioanalysis GmbH (CBL), Linz, Austria; Corresponding author at: Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University, Linz, Austria.We here give information for a deeper understanding of single molecule force spectroscopy (SMFS) data through the example of the blood protein von Willebrand factor (VWF). It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD) loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently developed model by Bullerjahn, Sturm, and Kroy (BSK) was used for this demonstration. Further, Brownian dynamics (BD) simulations, which can be utilized to estimate the lifetimes of intramolecular VWF interactions under physiological shear, are described. For interpretation and discussion of the methods and data presented here, we would like to directly point the reader to the related research paper, “Mutual A domain interactions in the force sensing protein von Willebrand Factor” (Posch et al., 2016) [1]. Keywords: Atomic force microscopy, Single molecule force spectroscopy, Molecular dynamics simulation, Brownian dynamics simulation, von Willebrand factorhttp://www.sciencedirect.com/science/article/pii/S235234091630467X |
| spellingShingle | Sandra Posch Camilo Aponte-Santamaría Richard Schwarzl Andreas Karner Matthias Radtke Frauke Gräter Tobias Obser Gesa König Maria A. Brehm Hermann J. Gruber Roland R. Netz Carsten Baldauf Reinhard Schneppenheim Robert Tampé Peter Hinterdorfer Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor Data in Brief |
| title | Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor |
| title_full | Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor |
| title_fullStr | Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor |
| title_full_unstemmed | Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor |
| title_short | Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor |
| title_sort | single molecule force spectroscopy data and bd and md simulations on the blood protein von willebrand factor |
| url | http://www.sciencedirect.com/science/article/pii/S235234091630467X |
| work_keys_str_mv | AT sandraposch singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT camiloapontesantamaria singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT richardschwarzl singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT andreaskarner singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT matthiasradtke singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT fraukegrater singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT tobiasobser singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT gesakonig singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT mariaabrehm singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT hermannjgruber singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT rolandrnetz singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT carstenbaldauf singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT reinhardschneppenheim singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT roberttampe singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor AT peterhinterdorfer singlemoleculeforcespectroscopydataandbdandmdsimulationsonthebloodproteinvonwillebrandfactor |