modynamic stability. This is of interest in particular to protein engineers and it highlights the usefulness of MD simulations, when fruitfully combined with experiments, in determining the weaker links in a scaffold. The present work is the first 
study which attempts to explain the increased susceptibility of the A2 domain to ADAMTS13 cleavage caused by type 2A mutations based on the three-dimensional structure. This can be helpful to structure based drug design. For example, a drug targeted at patients suffering of type 2A or acquired von Willebrand disease should be designed in a way that it stabilizes the C-terminal helix of the A2 domain. Conversely, an anti-thrombotic drug molecule should be able to insert itself into a groove between the C-terminal helix and the core of the protein in order to favor the undocked conformation of the helix making the protein more susceptible to proteolysis. Current anti-thrombotic drugs have the disadvantage that they need to be administered in large doses to be effective and a patient needs to be taken off the drugs a few days before a surgery to prevent excessive bleeding. Better anti-thrombotic therapeutics are wishful which are more efficient and can be turned off much more quickly when necessary. Advances in the understanding how VWF works at atomic level of detail is fundamental to guide structure based drug design. Materials and Methods Simulations Initial conformations. The simulations with the wild-type were started from the crystallographic structure with PDB code 3GXB. Mutants were constructed per homology by replacing the corresponding side chain in the wild-type and subsequently performing with the program CHARMM 100 steps of steepest descent minimization in vacuo while the positions of all atoms except the mutated residue were kept fixed. The online VWF database of the University of Sheffield was used to search for type 2A von Willebrand disease mutations. General setup of the systems. The MD simulations were performed with the program NAMD using the CHARMM all-hydrogen force field and the TIP3P model of Structural Basis of Type 2A VWD that if the pulling is performed gently enough the force will propagate through the protein and it will not matter which atom is fixed and which one is pulled. Each pulling simulation was run for 25 ns when the protein extension had reached a length within 20 A from the longest dimension of the water box. In the case of the wild-type the simulation was continued after placing the protein in a water box with dimensions of 250665665 A3 for 15 ns and subsequently into another box of 300665665 A3 side lengths for another 15 PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/2221058 ns, totaling 55 ns of pulling. The pulling simulations with the mutants were not extended beyond 25 ns because the unfolding pathways were qualitatively similar to the wild-type and the salient events happened during this first phase. Native side chain contacts. In order to determine the side RO4929097 site chains contained in the hydrophobic packing buried by the Nterminal part of the C-terminal helix a6, the native side chain contacts of Ala1661 were determined. A side chain contact is defined to occur when the distance between the centers of mass of two side chains is not larger than 6 A. Contacts present in a least 60% of the simulation frames of at least one simulation with no tensile force are defined as native. Experiments Construction of expression plasmids for VWF A2 wildtype and mutants. DNA sequence encoding the wild-type VWF A2 domain was a
