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Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor.

Abstract (Expand)

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"

Authors: 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

Date Published: 21st Jul 2016

Publication Type: Journal

Macromolecular Entropy Can Be Accurately Computed from Force

Abstract (Expand)

A method is presented to evaluate a molecule’s entropy from the atomic forces calculated in a molecular dynamics simulation. Specifically, diagonalization of the mass-weighted force covariance matrix … produces eigenvalues which in the harmonic approximation can be related to vibrational frequencies. The harmonic oscillator entropies of each vibrational mode may be summed to give the total entropy. The results for a series of hydrocarbons, dialanine and a β hairpin are found to agree much better with values derived from thermodynamic integration than results calculated using quasiharmonic analysis. Forces are found to follow a harmonic distribution more closely than coordinate displacements and better capture the underlying potential energy surface. The method’s accuracy, simplicity, and computational similarity to quasiharmonic analysis, requiring as input force trajectories instead of coordinate trajectories, makes it readily applicable to a wide range of problems.

Authors: Ulf Hensen, Frauke Gräter, Richard H. Henchman

Date Published: 15th Oct 2014

Publication Type: Journal

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