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. 1995 Nov;4(11):2341–2348. doi: 10.1002/pro.5560041112

Homology modeling and molecular dynamics simulation of human prothrombin fragment 1.

L Li 1, T Darden 1, C Foley 1, R Hiskey 1, L Pedersen 1
PMCID: PMC2143007  PMID: 8563631

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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Selected References

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