Molecular Dynamics Study on Docking of A3/A1 and Interdomain Interactions / 医用生物力学

Objective To investigate the interaction between von Willebrand factor (vWF) A1 and A3 domain, and type 2 M mutant W1745C-A3 effect on thermal stability and mechanical stability of A3/A1. Methods The crystal structures of A1 and A3 were downloaded from Protein Data Base (PDB). The wild-type (WT) A3/A1 structure was obtained by using SwarmDock Server, then W1745C-A3/A1 mutant was constructed by replacing the Trp1745 with Cys1745 in A3/A1. Through steered molecular dynamics simulation, formation and evolution of hydrogen bond and salt bridge between A1 and A3 interfaces were observed, and the differences in conformation, disrupted force and dissociation time between WT-A3/A1 and W1745C-A3/A1 were compared. Results There were 5 pairs of hydrogen bonds with survival rate > 0-2 and 1 pair of salt bridge with survival rate > 0-5 between A1 and A2. The W1745C-A3/A1 complex could withstand greater disrupted force and longer dissociation time compared with WT-A3/A1, by improving the stability of hydrogen bonds and increasing 1 pair of stable salt bridge. Conclusions The interaction between A1 and A3 would hinder the binding sites of A1 to GPIbα, and the W1745C-A3 mutation would further reduce the affinity of A1 to platelets. These results provide references for revealing the molecular mechanism of von Willebrand diseases in the clinic and developing the corresponding drugs targeted to hemostasis disorders.

What in silico molecular docking can do for the ‘bench-working biologists’.

Required by an increasing amount of scientists, the in silico docking field is in full expansion, new algorithms and methods appearing at an exponential rate. The sheer range of available programs is overwhelming for the benchworking biologist, which is often discouraging by the lack of a graphical user interface, good user manual or literature to validate a given program. This mini-review attempts to present the docking problem and available solutions from a non-bioinformatician point of view and makes a selection of the available servers and programs. These tools are evaluated from several points of view, as numbers of citations, ease of usage and computer requirements. Finally, the capabilities and limitations as well as specific applications of in silico docking techniques are presented.