The crystallographic structure of bovine prothrombin fragment 1 bound with calcium ions was used to construct the corresponding human prothrombin structure (hfl/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 y-carboxyglutamic acid (Gla) domain and the kringle domain of hfl/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.Keywords: Gla domain; kringle domain; phospholipid binding; prothrombin; vitamin K-dependent proteins Prothrombin is a vitamin K-dependent coagulation protein that consists of a y-carboxyglutamic acid (G1a)-rich domain, two kringle domains, and a catalytic serine protease domain. Upon activation by prothrombinase complex, a membrane-bound complex of factor Xa and factor Va converts prothrombin to the active serine protease a-thrombin. The prothrombin structure can be divided into three components designated fragments 1 and 2 and prethrombin 2 . Fragment 1 is defined as the Gla domain (1-33, human numbering), the connecting region (34-a), and the first kringle domain (65-144) of prothrombin. Like other vitamin K-dependent proteins, the Gla domain of prothrombin is rich in y-carboxyglutamic acids (10 Gla residues). It is widely accepted that these y-carboxyglutamic acids are essential in calcium-mediated phospholipid binding, in maintaining the integrity of the Gla domain, and in calcium-dependent activities of these proteins (Borowski et al., 1985;Astermark et al., 1992;Kotkow et al., 1993;Colpitts & Castellino, 1994). Using site-specific mutagenesis techniques, it was proposed that while some y-carboxyglutamic acids are important for maintaining the basic structure of the Gla domain, others are involved in membrane binding and interdomain interaction (Ratcliffe et al., 1993). A similar conclusion was reached in a mutagenesis study of the Gla domain of human protein C . Because the Gla domain may be involved in several different interactions, the specific role(s) of the individual Gla residues remain unclear. A reliable model for the solution structure would clearly be useful.The crystal structure of bovine prothrombin fragment 1 bound with calcium ions (bfl/Ca) has been determined to 2.2 A resolution (Soriano-Garcia et al., 1992). The human and bovine proteins differ distinctly in the number of calcium ions bound (Deerfield et al., 1987) and in details of their Ca2+-induced fluorescence quench (Prendergast & Mann, 1977;Marsh et al., 1979). The crystal structure of bfl/Ca was used by our lab to develop a simulation model for the solution structure. The special challenge to model the highly ionic Gla domain was solved by establishing a careful simulation preparation protocol and by accommodating lo...