User:Gary A. Toumas/Sandbox 1
From Proteopedia
< User:Gary A. Toumas(Difference between revisions)
| (14 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
=Cobra Venom Factor= | =Cobra Venom Factor= | ||
| - | + | Cobra Venom factor is a stable functional co-factor of C3 and C5 convertases present in the venom of various rattle snake species. As part of the alternative pathway of immunological response to pathogens, C3 and C5 convertases are upregulated to induce the formation of membrane attack protein. CVF provides a functional and stable co-factor for convertase formation that can survive much longer than native co-factors and drastically increase the concentration of membrane attack protein which kills self cells and causes necrosis common to snake bites. | |
<StructureSection load='3frp' scene='User:Gary_A._Toumas/Sandbox_1/Changing_colors/1' size='500' side='left' caption='Cobra Venom Factor (PDB entry [[3frp]])'> | <StructureSection load='3frp' scene='User:Gary_A._Toumas/Sandbox_1/Changing_colors/1' size='500' side='left' caption='Cobra Venom Factor (PDB entry [[3frp]])'> | ||
===Structure=== | ===Structure=== | ||
| - | Let's look at <scene name='User:Gary_A._Toumas/Sandbox_1/Practice_scene/1'>Another animation</scene>. But what if we wanted to look at the <scene name='User:Gary_A._Toumas/Sandbox_1/Looking_at_ca_ion/1'>calcium ion</scene>? The alpha chain forms <scene name='User:Gary_A._Toumas/Sandbox_1/Alpha_chain_domains/1'>domains MG1-5, MG6 alpha and LNK</scene> regions shown here in white, red purple, green, yellow, blue and cyan respectively. | ||
| - | |||
| - | Cobra Venom Factor binds factor B, and forms structurally stable C3 and C5 convertases. CVF consists of three chains forming 10 domains: MG1-8 domains, CUB domain and C345c domain. Chains alpha, beta and gamma are shown in blue, red and green respectively. The macroglobular domains MG1-8 of CVF form a ring structure that is similar to C3b and C3c structure, and is termed the key beta-ring. CVF contains 8 stabilizing disulfide bonds; three located within C345c, one linking C345c and MG 7, two within MG8, one within LNK and one in the MG5/MG6 interface. A calcium binding site exists within the MG5/MG6 interface, and binds calcium with six ligands: Asp517, Asp520, Val518, Pro494, Glu581 through a water molecule. The function of this binding site has not yet been thoroughly defined. | ||
| - | |||
| - | Both the CUB and C345c domains have been implicated in factor B binding and are also structurally similar to C3b and C3c, but are slightly rotated towards each other . The CUB domain is formed by segments of the gamma and beta chains γ- (896-945) and β- (1252-1311). The C345c domain is covalently linked via the ANK region. The catalytic activity of CVFBb comes from a serine protease, and is located within factor Bb. | ||
| - | Residues 730DE and 736EE at the α'NT region of C3b have been indicated as the major binding sites for factor B binding. Similarly, residues 714-723 of the gamma chain have been indicated as the corresponding binding sites of factor B. These residues may be responsible for the added stability of CVF, as well as the relative positioning of the CUB and C345c domains. | ||
| - | |||
| - | Convertase formation is upregulated by CVF and is enhanced by the added stability of CVF when compared to native convertases. The absence of binding sites for factor H, factor I, complement receptor 1, decay-accelerating factor (DAF), and membrane co-factor protein in CVF may also contribute to its increased half-life. The factor H and CR1 binding sites in C3b depend on the presence of two glutamic acid residues E744 and E747 located in the MG6 domain. CVF, however, has aspartic acid and lysine residues in these corresponding locations: 728D and 731K. Similarly, segments of the TED domain are absent from CVF and contribute to the lack of binding ability by factor H. Additionally a binding site for properdin, a stabilizing protein, has been proposed at 1381-1414 of the beta chain. | ||
| - | |||
| - | </ | + | <scene name='User:Gary_A._Toumas/Sandbox_1/Cobra_venom_factor/1'>Cobra Venom Factor</scene> binds factor B, and forms structurally stable C3 and C5 convertases. CVF consists of <scene name='User:Gary_A._Toumas/Sandbox_1/Three_chains/1'>three chains</scene> forming 10 domains: MG1-8 domains, CUB domain and C345c domain. The alpha chain forms <scene name='User:Gary_A._Toumas/Sandbox_1/Alpha_chain_domains/1'>domains MG1-5, MG6 alpha and LNK</scene> regions shown here in white, red purple, green, yellow, blue and cyan respectively. The macroglobular domains MG1-8 of CVF form a ring structure that is similar to C3b and C3c structure, and is termed the <scene name='User:Gary_A._Toumas/Sandbox_1/Key_beta_ring/1'>key beta ring</scene>. CVF contains eight stabilizing <scene name='User:Gary_A._Toumas/Sandbox_1/Disulfide_bonds/1'>disulfide bonds</scene>; three located within C345c, one linking C345c and MG 7, two within MG8, one within LNK and one in the MG5/MG6 interface. A <scene name='User:Gary_A._Toumas/Sandbox_1/Show_calcium_binding/1'>calcium binding site</scene> exists within the MG5/MG6 interface, and binds Ca+ with six ligands: Asp517, Asp520, Val518, Pro494, Glu581 through a water molecule. The function of this binding site has not yet been thoroughly defined. |
| + | Both the CUB and C345c domains have been implicated in factor B binding and are also structurally similar to C3b and C3c, but are slightly rotated towards each other . The CUB domain is formed by segments of the gamma and beta chains γ- (896-945) and β- (1252-1311). The C345c domain is covalently linked via the <scene name='User:Gary_A._Toumas/Sandbox_1/Ank_region/1'>ANK region</scene> The catalytic activity of CVFBb comes from a serine protease, and is located within factor Bb. | ||
| + | Residues 730DE and 736EE at the α'NT region of C3b have been indicated as the major binding sites for factor B binding. Similarly, <scene name='User:Gary_A._Toumas/Sandbox_1/Potential_factor_b_bindingsite/1'>residues 714-723 of the gamma chain</scene> have been indicated as the corresponding binding sites of factor B. These residues may be responsible for the added stability of CVF, as well as the relative positioning of the CUB and C345c domains.<ref>PMID: 19368894</ref> | ||
| + | Convertase formation is upregulated by CVF and is enhanced by the added stability of CVF when compared to native convertases. The absence of binding sites for factor H, factor I, complement receptor 1, decay-accelerating factor (DAF), and membrane co-factor protein in CVF may also contribute to its increased half-life. Factor H and CR1 binding sites in C3b depend on the presence of two glutamic acid residues E744 and E747 located in the MG6 domain. CVF, however, has aspartic acid and lysine residues in these corresponding locations: 728D and 731K. Similarly, segments of the TED domain are absent from CVF and contribute to the lack of binding ability by factor H. Additionally a binding site for properdin, a stabilizing protein, has been proposed at 1381-1414 of the beta chain. | ||
| - | <StructureSection load='2q66' scene='Proteopedia:Main_page_develop/2q66_initial/3' size='500' side='right' caption='Structure of Yeast Poly(A) Polymerase with ATP and oligo(A) (PDB entry [[2q66]])'> | ||
| - | ===Practice Mini Title=== | ||
| - | Poly(A) Polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains an oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The enzyme is an inactive mutant with the catalytic aspartate 154 changed to alanine. Poly(A) polymerase normally has a second magnesium ion, but that second magnesium ion is absent from this structure due to the inactivating mutation D154A. In the <scene name='2q66/2q66_summary/1'>summary picture</scene>, the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for ATP. The magnesium is coordinated by <scene name='2q66/2q66_asp/2'>ASP100 and ASP102</scene>, and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the <scene name='2q66/2q66_stacking/2'>terminal base of the RNA (in yellow) and VAL234 (in cyan)</scene>. Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. <scene name='2q66/2q66_asn/1'>ASN 226</scene> may form a [[hydrogen bond]] to adenine in the active enzyme, but the distance is a bit too long in this mutant structure. Instead of forming specific hydrogen bonds with the enzyme, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of <scene name='Goodsell_Sandbox/2q66_water/2'>buried water molecules</scene>. Discrimination between ATP and GTP is achieved through a close steric contact between the <scene name='2q66/2q66_c2/2'>adenine C2 (in white) and the sidechains of THR 304 and MET310 (shown in cyan)</scene>. Guanine bases have an extra amino group at this position that would be too bulky to fit against these amino acids. | ||
</StructureSection> | </StructureSection> | ||
Current revision
Cobra Venom Factor
Cobra Venom factor is a stable functional co-factor of C3 and C5 convertases present in the venom of various rattle snake species. As part of the alternative pathway of immunological response to pathogens, C3 and C5 convertases are upregulated to induce the formation of membrane attack protein. CVF provides a functional and stable co-factor for convertase formation that can survive much longer than native co-factors and drastically increase the concentration of membrane attack protein which kills self cells and causes necrosis common to snake bites.
| |||||||||||
