Homology Modeling and Molecular Dynamics Simulations of the Gla Domains of Human Coagulation Factor IX and Its G[12]A Mutant

Li, Leping; Darden, Tom; Hiskey, Richard G.; Pedersen, Lee G.

doi:10.1021/jp952190j

Cited by 9 publications

(5 citation statements)

References 52 publications

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“…Smaller fluctuations in the values of RMSDs of protein S and Gas6 indicate the achievement of stability of the structures upon solvation. The RMSD values are comparable in magnitude with the values of previously studied coagulation proteins for which long-range forces were accommodated (Li et al, 1995(Li et al, , 1996Wolberg et al, 1996). Although the Gla domains of both protein S and Gas6 were constructed by introducing the appropriate mutations to the corresponding domain of BF1, we find that the RMSDs remain similar for this domain in all three proteins.…”

Section: Global Aspects Of the Simulations Of Protein S And Gas6supporting

confidence: 76%

Prediction of solution structures of the Ca2+-bound gamma-carboxyglutamic acid domains of protein S and homolog growth arrest specific protein 6: use of the particle mesh Ewald method

Perera¹,

Li²,

Darden³

et al. 1997

Biophysical Journal

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The solution structures of the N-terminal domains of protein S, a plasma vitamin K-dependent glycoprotein, and its homolog growth arrest specific protein 6 (Gas6) were predicted by molecular dynamics computer simulations. The initial structures were based on the x-ray crystallographic structure of the corresponding region of bovine prothrombin fragment 1. The subsequent molecular dynamics trajectories were calculated using the second-generation AMBER force field. The long-range electrostatic forces were evaluated by the particle mesh Ewald method. The structures that stabilized over a 400-ps time interval were compared with the corresponding region of the simulated solution structure of bovine prothrombin fragment 1. Structural properties of the gamma-carboxyglutamic acid (Gla) domains obtained from simulations and calcium binding were found to be conserved for all three proteins. Analysis of the predicted solution structure of the Gla domain of Gas6 suggests that this domain should bind with negatively charged phospholipid surfaces analogous to bovine prothrombin fragment 1 and protein S.

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Section: Global Aspects Of the Simulations Of Protein S And Gas6supporting

confidence: 76%

Prediction of solution structures of the Ca2+-bound gamma-carboxyglutamic acid domains of protein S and homolog growth arrest specific protein 6: use of the particle mesh Ewald method

Perera¹,

Li²,

Darden³

et al. 1997

Biophysical Journal

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“…The AMBER 4.0 force field was used (Pearlman et al, 1995). The simulation was performed according to the procedures reported previously (Li et al, , 1996. In brief, the protein was solvated in a large box of Monte Carlo TIP3P water with each side at least 12.5 Å from the nearest protein atom.…”

Section: Methodsmentioning

confidence: 99%

“…The Gla domain of factor IX can be said to bind nine calcium ions (Li et al, 1996) with high-and low-affinity calcium binding sites. These calcium binding sites are not defined by proton-proton NMR spectroscopy.…”

mentioning

confidence: 99%

Refinement of the NMR Solution Structure of the γ-Carboxyglutamic Acid Domain of Coagulation Factor IX Using Molecular Dynamics Simulation with Initial Ca²⁺ Positions Determined by a Genetic Algorithm

Darden

Freedman

et al. 1997

Biochemistry

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A genetic algorithm (GA) successfully identified the calcium positions in the crystal structure of bovine prothrombin fragment 1 bound with calcium ions (bf1/Ca). The same protocol was then used to determine the calcium positions in a closely related fragment, the Gla domain of coagulation factor IX, the structure of which had previously been determined by NMR spectroscopy in the presence of calcium ions. The most frequently occurring low-energy structure found by GA was used as the starting structure for a molecular dynamics refinement. The molecular dynamics simulation was performed using explicit water and the Particle-Mesh Ewald method to accommodate the long-range electrostatic forces. While the overall conformation of the NMR structure was preserved, significant refinement is apparent when comparing the simulation average structure with its NMR precursor in terms of the N-terminal (Tyr1-N) network, the total number of hydrogen bonds, the calcium ion coordinations, and the compactness of the structure. It is likely that the placement of calcium ions in the protein is critical for refinement. The calcium ions apparently induce structural changes during the course of the simulation that result in a more compact structure.

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“…The modeling of the Gla domain of human coagulation factor IX was reported previously (Li et al, 1996). The wild-type model of factor IX (1-47) was based on the crystal structure of calcium-bound bovine prothrombin fragment 1 (SorianoGarcia et al, 1992).…”

Section: Materials Amd Methodsmentioning

confidence: 99%

Characterization of γ-Carboxyglutamic Acid Residue 21 of Human Factor IX

Cheung

Hamaguchi

et al. 1996

Biochemistry

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We investigated the functional role of gamma-carboxyglutamic acid (Gla) residue 21 of human factor IX, using site-directed mutagenesis to change the glutamic acid residue to aspartic acid (FIX21D). FIX21D had reduced activity in an activated partial thromboplastin time (aPTT) assay and was activated by factor XIa more slowly than wild-type factor IX (FIXwt). FIX21D underwent normal, two-stage calcium-dependent intrinsic fluorescence quenching, indicating that a folding event similar to that seen in FIXwt occurred upon the addition of calcium ions. Antibody A-7, which recognizes factor IX-specific residues at positions 33-40, bound FIX21D as well as FIXwt; however, the calcium-specific monoclonal antibody, JK-IX-2, whose epitope includes residues 1 and 22, did not recognize FIX21D. FIX21D bound phosphatidylserine/phosphatidylcholine (PS/PC) vesicles with Kd approximately 10-fold greater than FIXwt, as measured by a fluorescence light scattering assay. Finally, although FIXwt binds endothelial cells with a Kd of 2.8 nM, FIX21D did not bind endothelial cells. Molecular modeling simulations of FIXwt and FIX21D indicate that mutating Gla 21 to Asp causes structural changes in residues 3-5 and 8-10, as well as in two exposed calcium ions, consistent with the reduced function of FIX21D. Immunological and intrinsic fluorescence quenching assays and the molecular dynamics simulations suggest normal folding in the C-terminal region of the Gla domain. Thus we hypothesize the FIX21D has reduced JK-IX-2 and phospholipid and endothelial cell binding due to localized structural changes in residues 3-10 and the exposed calcium ions. Our study suggests that the Gla 21 to Asp mutation disrupts function in the N-terminal region of the Gla domain without affecting structure in the C-terminal Gla domain region.

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Homology Modeling and Molecular Dynamics Simulations of the Gla Domains of Human Coagulation Factor IX and Its G[12]A Mutant

Cited by 9 publications

References 52 publications

Prediction of solution structures of the Ca2+-bound gamma-carboxyglutamic acid domains of protein S and homolog growth arrest specific protein 6: use of the particle mesh Ewald method

Prediction of solution structures of the Ca2+-bound gamma-carboxyglutamic acid domains of protein S and homolog growth arrest specific protein 6: use of the particle mesh Ewald method

Refinement of the NMR Solution Structure of the γ-Carboxyglutamic Acid Domain of Coagulation Factor IX Using Molecular Dynamics Simulation with Initial Ca²⁺ Positions Determined by a Genetic Algorithm

Characterization of γ-Carboxyglutamic Acid Residue 21 of Human Factor IX

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Homology Modeling and Molecular Dynamics Simulations of the Gla Domains of Human Coagulation Factor IX and Its G[12]A Mutant

Cited by 9 publications

References 52 publications

Prediction of solution structures of the Ca2+-bound gamma-carboxyglutamic acid domains of protein S and homolog growth arrest specific protein 6: use of the particle mesh Ewald method

Prediction of solution structures of the Ca2+-bound gamma-carboxyglutamic acid domains of protein S and homolog growth arrest specific protein 6: use of the particle mesh Ewald method

Refinement of the NMR Solution Structure of the γ-Carboxyglutamic Acid Domain of Coagulation Factor IX Using Molecular Dynamics Simulation with Initial Ca2+ Positions Determined by a Genetic Algorithm

Characterization of γ-Carboxyglutamic Acid Residue 21 of Human Factor IX

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Refinement of the NMR Solution Structure of the γ-Carboxyglutamic Acid Domain of Coagulation Factor IX Using Molecular Dynamics Simulation with Initial Ca²⁺ Positions Determined by a Genetic Algorithm