Factor IX: Difference between revisions

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Bovine <scene name='Factor_IX/Gladomain/2'>Factor IX -(1-46)</scene> bound to a snake venom protein (Factor IX-bp), is crystallized in the presence of calcium and magnesium ions and in the presence of calcium alone<ref>PMID:12695512</ref>.

This structure emphasizes the possible role of magnesium in Gla domain binding to membrane surfaces. However upon examination of the calcium bound Factor IX-(1-46) complex revealed that the calcium coordination within this FIX Gla domain structure differs from other vitamin K-dependent proteins (prothrombin, Factor VII, and Factor X). This deviation may be explained by the interaction of the snake venom FIX-bp interaction.

To further probe into the structure of FIX Gla domain, [[conformation-specific anti-Factor IX antibodies]] were utilized. Using an

<scene name='Factor_IX/Antifactor/1'>anti-Factor IX antibody</scene>, 10C12, which is then reformatted into a F(ab')2 form (two Fab fragments connected by a leucine zipper)<ref>PMID:14722079</ref>. This antibody is a calcium specific antibody for factor IX and provides information on the inhibition of membrane binding. The antibody interacts with the loop (Leu-6, Phe-9, and Val-10) of the ''γ''-carboxyglutamic acids residues bound to calcium ions in the Gla domain.

<scene name='Factor_IX/Antifactor/2'>anti-Factor IX antibody</scene>, 10C12, which is then reformatted into a F(ab')2 form (two Fab fragments connected by a leucine zipper)<ref>PMID:14722079</ref>. This antibody is a calcium specific antibody for factor IX and provides information on the inhibition of membrane binding. The antibody interacts with the loop (Leu-6, Phe-9, and Val-10) of the ''γ''-carboxyglutamic acids residues bound to calcium ions in the Gla domain.

The Gla domain of Factor IX consists of an N-terminal loop and three short ''ω''-<scene name='Factor_IX/Antifactor_2/2'>helixes</scene>(helix A: residues 14-19; helix B: residues 24-32; helix C: residues 35-45). The calcium ions are positioned between the loop and the A and B helices with calcium liganding providing the folding energy to align the loop properly. Helices A and B are connected by a tight turn and further stabilized by a conserved disulfide bond between residues 18 and 23 of the Gla domain. The two cysteine residues also form two hydrogen bonds (Tyr-45 to Cys-18, 3.10 Å; Tyr-45 to Cys-23, 2.88 Å) to the side chain of a conserved Tyr-45 of helix C, providing an anchor to bundle three helices together. This tyrosine residue and the disulfide bond are part of the hydrophobic core between helix C and helix A/B that includes Phe-25, Ala-28, Phe-41, and Trp-42, a cluster that provides further hydrophobic energy to bind helix C to helix A/B. All of these residues are conserved among Gla domains of vitamin K-dependent proteins.

The Gla domain of Factor IX consists of an N-terminal loop and three short ''ω''-<scene name='Factor_IX/Antifactor_2/3'>helixes</scene>(helix A: residues 14-19; helix B: residues 24-32; helix C: residues 35-45). The calcium ions are positioned between the loop and the A and B helices with calcium liganding providing the folding energy to align the loop properly. Helices A and B are connected by a tight turn and further stabilized by a conserved disulfide bond between residues 18 and 23 of the Gla domain. The two cysteine residues also form two hydrogen bonds (Tyr-45 to Cys-18, 3.10 Å; Tyr-45 to Cys-23, 2.88 Å) to the side chain of a conserved Tyr-45 of helix C, providing an anchor to bundle three helices together. This tyrosine residue and the disulfide bond are part of the hydrophobic core between helix C and helix A/B that includes Phe-25, Ala-28, Phe-41, and Trp-42, a cluster that provides further hydrophobic energy to bind helix C to helix A/B. All of these residues are conserved among Gla domains of vitamin K-dependent proteins.

The binding of FIX to the phospholipid membrane is carried out by the loop, in the N terminus of the Gla domain. Four Ca2+ ions from Ca-2 to Ca-5 are essential to stabilize the ''ω''-loop region for membrane-binding <ref>PMID:8069632</ref> because these Ca2+ ions bind to conserved Gla7 and Gla8 residues in this region. The replacement by Mg2+ ions may lead to destabilization of the structure of the Gla domain, particularly in this region because of significant differences that exist with Ca2+ ion in both coordination distance and coordination sphere (Mg2+ ion takes generally a typical bipyramidal configuration and six coordination). This may explain why the Ca2+ ions are not replaced by Mg2+ ions in the present structure.

Factor IX: Difference between revisions

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@@ Line 136: / Line 136: @@
 Bovine <scene name='Factor_IX/Gladomain/2'>Factor IX -(1-46)</scene> bound to a snake venom protein (Factor IX-bp), is crystallized in the presence of calcium and magnesium ions and in the presence of calcium alone<ref>PMID:12695512</ref>.
 This structure emphasizes the possible role of magnesium in Gla domain binding to membrane surfaces. However upon examination of the calcium bound Factor IX-(1-46) complex revealed that the calcium coordination within this FIX Gla domain structure differs from other vitamin K-dependent proteins (prothrombin, Factor VII, and Factor X). This deviation may be explained by the interaction of the snake venom FIX-bp interaction.
 {{STRUCTURE_1nl0|  PDB=1nl0  |  SCENE=  }}
 To further probe into the structure of FIX Gla domain, [[conformation-specific anti-Factor IX antibodies]] were utilized. Using an
-<scene name='Factor_IX/Antifactor/1'>anti-Factor IX antibody</scene>, 10C12, which is then reformatted into a F(ab')2 form (two Fab fragments connected by a leucine zipper)<ref>PMID:14722079</ref>. This antibody is a calcium specific antibody for factor IX and provides information on the inhibition of membrane binding. The antibody interacts with the  loop (Leu-6, Phe-9, and Val-10)  of the  ''&gamma;''-carboxyglutamic acids residues bound to calcium ions in the  Gla domain.
+<scene name='Factor_IX/Antifactor/2'>anti-Factor IX antibody</scene>, 10C12, which is then reformatted into a F(ab')2 form (two Fab fragments connected by a leucine zipper)<ref>PMID:14722079</ref>. This antibody is a calcium specific antibody for factor IX and provides information on the inhibition of membrane binding. The antibody interacts with the  loop (Leu-6, Phe-9, and Val-10)  of the  ''&gamma;''-carboxyglutamic acids residues bound to calcium ions in the  Gla domain.
-The Gla domain of Factor IX consists of an N-terminal loop and three short ''&omega;''-<scene name='Factor_IX/Antifactor_2/2'>helixes</scene>(helix A: residues 14-19; helix B: residues 24-32; helix C: residues 35-45). The calcium ions are positioned between the loop and the A and B helices with calcium liganding providing the folding energy to align the loop properly. Helices A and B are connected by a tight turn and further stabilized by a conserved disulfide bond between residues 18 and 23 of the Gla domain. The two cysteine residues also form two hydrogen bonds (Tyr-45 to Cys-18, 3.10 Å; Tyr-45 to Cys-23, 2.88 Å) to the side chain of a conserved Tyr-45 of helix C, providing an anchor to bundle three helices together. This tyrosine residue and the disulfide bond are part of the hydrophobic core between helix C and helix A/B that includes Phe-25, Ala-28, Phe-41, and Trp-42, a cluster that provides further hydrophobic energy to bind helix C to helix A/B. All of these residues are conserved among Gla domains of vitamin K-dependent proteins.
+The Gla domain of Factor IX consists of an N-terminal loop and three short ''&omega;''-<scene name='Factor_IX/Antifactor_2/3'>helixes</scene>(helix A: residues 14-19; helix B: residues 24-32; helix C: residues 35-45). The calcium ions are positioned between the loop and the A and B helices with calcium liganding providing the folding energy to align the loop properly. Helices A and B are connected by a tight turn and further stabilized by a conserved disulfide bond between residues 18 and 23 of the Gla domain. The two cysteine residues also form two hydrogen bonds (Tyr-45 to Cys-18, 3.10 Å; Tyr-45 to Cys-23, 2.88 Å) to the side chain of a conserved Tyr-45 of helix C, providing an anchor to bundle three helices together. This tyrosine residue and the disulfide bond are part of the hydrophobic core between helix C and helix A/B that includes Phe-25, Ala-28, Phe-41, and Trp-42, a cluster that provides further hydrophobic energy to bind helix C to helix A/B. All of these residues are conserved among Gla domains of vitamin K-dependent proteins.
 The binding of FIX to the phospholipid membrane is carried out by the loop, in the N terminus of the Gla domain. Four Ca2+ ions from Ca-2 to Ca-5 are essential to stabilize the ''&omega;''-loop region for membrane-binding <ref>PMID:8069632</ref> because these Ca2+ ions bind to conserved Gla7 and Gla8 residues in this region. The replacement by Mg2+ ions may lead to destabilization of the structure of the Gla domain, particularly in this region because of significant differences that exist with Ca2+ ion in both coordination distance and coordination sphere (Mg2+ ion takes generally a typical bipyramidal configuration and six coordination). This may explain why the Ca2+ ions are not replaced by Mg2+ ions in the present structure.