Alpha thrombin of serine protease is a kind of protein, can be used as the blood coagulation cascade. Thrombinprocoagulant itself is a differences, fibrinogen make fibrin clot, but thrombin - thrombomodulin (TM) complicated start anticoagulation path, through the crack protein c. TM fragment of only the fifth and sixth egf like domain (TM56) enough to bind thrombin, but there are also the fourth egf like domain (TM456) induced vital anticoagulant activity of thrombin. Crystallography of thrombin - TM456 complex and not found in the thrombin bring significant structural change, this shows that TM4 may only provide a scaffold best calibration of protein C for the cleavage, thrombin. However, all kinds of experimental data show that exist TM4 may affect the dynamic properties of the active site cycle. In the present work, we use two traditional and accelerate the molecular dynamics simulation method is used to study the dynamic characteristics of the structure, thrombin of thrombin: TM56, thrombin: TM456 in a wide range of time scales. Two different but related allosteric way, while determining mediation pro - and anticoagulant blood clotting enzyme activity. A allosteric way, at the same time, present in the thrombin: TM56 and blood coagulation enzyme: TM456, direct connection TM5 domain of thrombin active site. Other allosteric path, which only appears in the slow time scale exist TM4 domain, including prolong the network related action connection TM4 and TM5 domain and active site cycle of thrombin.

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