Homology modeling and molecular dynamics simulation of human prothrombin fragment 1. |
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Authors: | L. Li T. Darden C. Foley R. Hiskey L. Pedersen |
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Abstract: | The crystallographic structure of bovine prothrombin fragment 1 bound with calcium ions was used to construct the corresponding human prothrombin structure (hf1/Ca). The model structure was refined by molecular dynamics to estimate the average solution structure. Accommodation of long-range ionic forces was essential to reach a stable solution structure. The gamma-carboxyglutamic acid (Gla) domain and the kringle domain of hf1/Ca independently equilibrated. Likewise, the hydrogen bond network and the calcium ion coordinations were well preserved. A discussion of the phospholipid binding of the vitamin K-dependent coagulation proteins in the context of the structure and mutational data of the Gla domain is presented. |
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Keywords: | Gla domain kringle domain phospholipid binding prothrombin vitamin K-dependent proteins |
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