Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor
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
Affiliations
Sandra Posch
Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University, Linz, Austria
Camilo Aponte-Santamaría
Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
Richard Schwarzl
Department of Physics, FU Berlin, Berlin, Germany
Andreas Karner
Center for Advanced Bioanalysis GmbH (CBL), Linz, Austria
Matthias Radtke
Department of Physics, FU Berlin, Berlin, Germany
Frauke Gräter
Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
Tobias Obser
Department of Pediatric Hematology and Oncology, University Medical Center Hamburg -Eppendorf, Hamburg, Germany
Gesa König
Department of Pediatric Hematology and Oncology, University Medical Center Hamburg -Eppendorf, Hamburg, Germany
Maria A. Brehm
Department of Pediatric Hematology and Oncology, University Medical Center Hamburg -Eppendorf, Hamburg, Germany
Hermann J. Gruber
Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University, Linz, Austria
Roland R. Netz
Department of Physics, FU Berlin, Berlin, Germany
Carsten Baldauf
Theory Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
Reinhard Schneppenheim
Department of Pediatric Hematology and Oncology, University Medical Center Hamburg -Eppendorf, Hamburg, Germany
Robert Tampé
Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Frankfurt/Main, Germany
Peter Hinterdorfer
Department 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 factor
