Molecular Dynamics Simulation Of Two Complexs:VWF-A3/Collagen And VWF-A1/VWF-A3

As the most common cause of death in the developed countries,acute arterial thrombosis can lead to fatal myocardial infarction(heart attack)and stroke.Platelet adhesion to vascular lesion is the key process of physiological hemostasis and pathological thrombosis,this process under high shear is mediated by the "GPIb?-VWF-Collagen" interaction in the first step.On the one hand,when binding to collagen on the subendothelium,the plasma VWF will be activated to a high affinity conformation,easier to bind to platelet GPIb?;on the other hand,the binding and unbinding of VWF and GPIb? are regulated by shear stress in the blood flow.Mature VWF molecules are linear polymers,consisting of A,B,C,and D domains.The A domains are important domains in VWF,including A1A2A3-tridomain,of which the A1 domain and A3 domain contain the binding sites for platelet GPIb? and Collagen,respectively.Clinical Studies have shown that Mutations occurring in VWF would lead to bleeding disorders.The theoretical bases of Molecular Dynamics simulations are Newton's classical mechanics,statistical mechanics,and quantum mechanics.Molecular Dynamics simulations may facilitate the prediction of druggable binding sites on protein–protein interfaces by detecting binding hot spots and transient pockets.MD allows for a detailed analysis of structural and functional aspects of PPIs and thus provides valuable insights into protein–protein interactions mechanisms and supports the design of PPI modulators.Previous studies have shown that A1 domain could bind to A3 domain,resulting decreased binding affinity between A1 and platelet GPIb?.Since both the A1/A3 complex and the A3/Collagen complex are involved in the activation of VWF,we constructed two molecule systems for each of them and ran equilibrium simulations and steered molecular dynamics simulations,aiming to further reveal the activation mechanisms of VWF.To date,the X-ray diffraction experiments have resolved the crystal structure of A3/Collagen,while not one for A1/A3.So we manually docked the complex,using the SwarmDock server.Through the residue interaction index(RII)and salt-bridges formed during equilibrium simulations we found 8 key residues(4 in A3,4 in Collagen)in A3/Collagen and 21 key redidues(10 in A1,11 in A3)in A1/A3,furthermore the A1-GLN1367,A1-LYS1335 and A1-GLU1359 are key residues in GPIb?/A1.In addition we found that dissociation force of A3/Collagen was significantly higher than that of A1/A3,so shear stress will first open the cyclic A1A2A3-tridomain,thereby exposing the binding sites of A1/ GPIb?,our simulation results not only show the process,but also illuminate how VWF is transferred from low affinity conformation to the high affinity conformation at the atomic level.