Lee C J, Lin P, Chandrasekaran V, Duke R E, Everse S J, Perera L, Pedersen L G
Department of Chemistry, UNC-CH, Chapel Hill, NC, USA.
J Thromb Haemost. 2008 Jan;6(1):83-9. doi: 10.1111/j.1538-7836.2007.02821.x. Epub 2007 Oct 29.
The prothrombinase complex consists of factor Xa, FVa, calcium ions, and phospholipid membrane. The prothrombinase complex plays a key role in the blood coagulation process.
To derive solvent-equilibrated models of human FVa and the prothrombinase complex.
Several modeling techniques have been employed, including homology modeling, protein-protein docking, and molecular dynamics simulation methods, to build the structural models.
We found, upon simulation, a possibly significant shift towards planarity of the five FVa domains. To estimate a prothrombinase structure, we docked an FXa model to the equilibrated FVa model using experimental data as docking filters. We found that simulation of the docked complex led to some changes in the protein-protein contacts, but not buried surface area, as compared to the initial docking model. Possible locations of prothrombin binding to prothrombinase are indicated.
凝血酶原酶复合物由因子Xa、FVa、钙离子和磷脂膜组成。凝血酶原酶复合物在血液凝固过程中起关键作用。
推导人FVa和凝血酶原酶复合物的溶剂平衡模型。
采用了多种建模技术，包括同源建模、蛋白质-蛋白质对接和分子动力学模拟方法来构建结构模型。
我们发现，在模拟过程中，五个FVa结构域可能会显著向平面化转变。为了估计凝血酶原酶结构，我们使用实验数据作为对接过滤器，将FXa模型对接至平衡后的FVa模型。我们发现，与初始对接模型相比，对接复合物的模拟导致蛋白质-蛋白质接触发生了一些变化，但掩埋表面积未变。文中指出了凝血酶与凝血酶原酶结合的可能位置。
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