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| - | [[Image:Coag_cartoon.jpg | thumb |350px| Schematic representation of the coagulation response]]
| + | ==Symmetry in the Bcl-Xl interface== |
| - | | + | <StructureSection load='2yxj_With_Ligand_Mati_Cohen.pdb' size='500' frame='true' align='right' caption='Bcl-Xl and ABT737 from PDB-ID 2yxj' scene=''>Bcl-Xl is a member of the [http://en.wikipedia.org/wiki/Bcl-2 Bcl-2 family]. This family consists of [http://en.wikipedia.org/wiki/Apoptosis pro-apoptotic] and [http://en.wikipedia.org/wiki/Apoptosis anti-apoptotic] members. Bcl-Xl (in the image) ,an anti-apoptotic protein, binds pro-apoptotic proteins like BAK and BAD thus regularly inhibit program cell death. Many cancer cells overexpress at least one of the anti-apoptotic members of this family ,thus escaping a needed apoptosis . Therefore, these proteins are important targets for the development of new anti-cancer drugs. |
| - | ==Coagulation Factor XIa== | + | The PDB file [[2yxj]] shows the structure of Bcl-Xl and ABT 737. ABT 737 is a potent inhibitor of Bcl-Xl (Kd = 1nM). It binds Bcl-xl in the same position as BAK does as can be seen in [[1bxl]]. |
| - | ===Introduction===
| + | Interestingly the interface of Bcl-Xl is almost symmetric. There are <scene name='43/437742/2yxj_arg/9'>two positively charged residues</scene> Arg 100 and Arg 139. |
| - | Factor XIa is unique protease derived from the activation of the coagulation zymogen, factor XI. Factor XIa partcipates in the procoagulant response via contact activation pathway. Synthesized by the liver similar to most vitamin K-dependent coagulation proteins, the zymogen, factor XI circulates in plasma as a 160 kDa disulfide-linked homodimer in complex with high molecular weight kininogen (HK)<ref>PMID:915004</ref>. Studies show that factor XI is a substrate for various plasma proteins such as factor XIIa, thrombin, meizothrombin and factor XIa (via autoactivation). Proteolysis of the <scene name='Sandbox/Arg369-ile370/1'> Arg369-Ile370</scene> bond generates the active enzyme factor XIa which in turn cleaves its substrate factor factor IX to produce the serine protease factor IXa.
| + | <scene name='43/437742/2yxj_glu/7'>two negatively charged residues</scene> Glu96 and Glu129. |
| - | <Structure load='2f83' size='350' frame='true' align='right' caption=' Crystal structure of factor XI' />
| + | Two <scene name='43/437742/2yxj_hyd/4'>hydrophobic patches</scene> which include Phe191 Val141 and |
| - | | + | Ala93 for one, and the other patch includes Phe146 Val126 and Leu108. A look at the <scene name='43/437742/2yxj_space_fill_color_charged/3'>Overall</scene> picture shows that there are hydrophobic patches (in gray) "above" and "below" the ligand ,negatively charged residues "above-right" and "below-left" of the ligand and positively charges on the "right" and "left" of it. |
| - | ==Protein Structure==
| + | This symmetry can be exploited, a symmetric molecule can bind the same interface in two different ways thus increasing the "chance" of binding which means better binding affinity. |
| - | Factor XIa is a <scene name='Sandbox/Disulfides/1'>disulfide</scene> linked-dimer of similar amino acid composition of approximately 625 residues. The first 18 amino acid residues constitute the signal peptide whereas residues 19-387 and 388-625 represents the heavy- and light- chains of the factor XIa molecule respectively. The protein forms five main distinct domains. Beginning from the N-terminus,each dimeric subunit contains 4 apple domains (A1, A2, A3 and A4) which are characterized by approximately 90 or 91 amino acid residues. Protein-protein interactions are thought to be the primary role of the apple domains. The A3 domain is reported to mediate binding to platelet glycoprotein Ib (GPIb)<ref>PMID:15317813</ref> as well as interactions with exosite I of thrombin, and kringle 2 domain of prothrombin. The A1 domain is the main site of factor XI protein-protein interaction when in complex with high molecular weight kininogen<ref>PMID:7686159</ref>. The C-terminus (heavy chain) of factor XIa contain a trypsin-like catalytic domain <ref>PMID:893417</ref>. Together with Prekallikrein (PK) a monomeric homolog of factor XIa, they belong to the PAN (plasminogen, apple, nematode) module family which all have a conserved N-terminal apple domain found in hepatocyte growtth factor and plasminogen <ref>PMID:10561497</ref>.
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| - | ===''Secondary structure''===
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| - | About 36 β-strands have been observed in the crystal structure of factor XI with twice as much found in the heavy chain (25 β-strands) compared to the light chain (11 β-strands). The topology of the apple domain reveals 7 antiparallel β-sheets and an α-helix which fold into a compact structure as oppose to an extended structure found in the vitamin K-dependent serine proteases. This core PAN topology is also found in leech antiplatelet protein and hepatocyte growth factor)<ref>PMID:10561497</ref>. A single disulfide linkage connects the C- and N-terminals of the dimer whereas two disulfide bond join the helix to the 4β- and 5β-sheets. The apple domains of factor XIa are tightly linked to each other forming a disk-like structure close to the base of the C-terminal catalytic domain. This observation is consistent with the high surface area measurements for the side interfaces between apple domains A1 and A2 (441ÅxÅ) and between A3 and A4 (444ÅxÅ) in contrast to smaller end interfaces between A1 and A4(380ÅxÅ) and between A2 and A3(284ÅxÅ).
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| - | '''β-turn'''
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| - | [[Image:Beta_turn.jpg | thumb |250px| β-turn in factor XIa]] | + | |
| - | The globular and compact nature of factor XIa as opposed to an elongated form (prevalent in vitamin K-dependent serine proteases) could in part be attributed to the abundance of β-turns in the protein. β-turns are characterized by a hydrogen bond involving carbonyl oxygen (C=O) of residue (i) and amide hydrogen (NH) of residue (i+3). The heavy chain has ~4 β-turns and one such β-turn (residues 566-568) is found in the light chain of factor XIa (see figure on the right). This β-turn based on distance between Cαi-Cαi+3 (5.4Å) and the measured dihedral angles: φ(i+1)=50.5°, ψ(i+1)=47.2° and φ(i+2)=90° and ψ(i+2)=15.8°could be classified as '''Type I′''' according to Hutchinson and Thornton (1994)<ref>PMID:7756980</ref>.
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| - | '''Helix Capping Motif'''
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| - | === Factor FXIa dimer===
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| - | The β-sheets form a tight packing against each other with two A4 domains forming a large interface between the dimer subunits. Found in the central position is the main interchain disulfide bond contributed by Cys-321 located on the finger-like loop of the A4 domain. The apple domains form a V-shape in which two A2 domains are distanced ~50Å apart whiles the A1 and A3 domains from adjacent monomers are in close proximity of 5Å apart <ref>PMID:16699514</ref>. The <scene name='Sandbox/Hydrophobic_core/1'>hydrophobic core</scene> interface made up of Leu-284, Ile-290 and Tyr-329 and the <scene name='Sandbox/Salt_bridge/1'>salt bridge</scene> between Lys-331 of one monomer and Glu-287 of the other monomer are absolutely required for dimer formation<ref>PMID:11092900</ref>. Most of the complex protein-protein interactions involving factor XIa are mediated by the apple domains of the dimeric subunits.
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| - | ===Posttranslational Modification===
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| - | Unlike most serine proteases which contain a[http://en.wikipedia.org/wiki/Gla_domain γ-carboxyglutamic acid (Gla)]domain, which facilitates the binding of vitamin-K dependent coagulation proteases to phospholipid vesicles, plasma factor XIa lacks the Gla domain. Meanwhile the protease undergoes considerable posttranslational retailing following it synthesis. Approximately <scene name='Sandbox/19_disulfide_bonds/1'>19 disulfide bonds</scene>: 15 of which are confirmed and 4 potential disulfide linkages are reported to be present in factor XIa molecule. The homodimers are linked by a single disulfide bond at Cys-321 connecting the A4 domains of each subunit <ref>PMID:1998667</ref>. Ser-17 and Thr-22 are phosphorylated <ref>PMID:18187866</ref> whereas 5 N-linked glycosylations (GlcNAc) sites were also reported following glycoproteome analysis <ref>PMID:19159218</ref>.
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| - | ==Formation of Factor XIa==
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| - | Factor XI is partially proteolyzed ''in vitro'' by thrombin and factor XIIa generating the active serine-protease, factor XIa. Similar to other chymotrypsin-like proteases, its topology consist of two β-barrels linked through a central loop. Next to the C-terminal Cys-356 of the factor XI heavy chain, the polypeptide forms a 3-10 helix conformation and again turn sharply 90 degrees at Cys-362 forming a disulfide bond with Cys-482 within the active site region.
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| - | Thrombin-catalyzed proteolysis of factor XI involves crucial interations with Glu-66, Lys-83 and Gln-84 of the A1 domain (this ensures maximum proximity to the <scene name='Sandbox/Activation_loop/1'>activation loop</scene> of factor XI) of the factor XI molecule through its exosites I and II regions <ref>PMID:16699514</ref>. Thus binding of thrombin to one subunit of the zymogen dimer promotes cleavage of the bond between <scene name='Sandbox/Arg369-ile370/1'> Arg369-Ile370</scene> contained in the <scene name='Sandbox/Activation_loop/1'>activation loop</scene> of factor XI. The <scene name='Sandbox/Activation_loop/1'>activation loop</scene> (residues 370-376) consequently undergoes the greatest conformational change as Ile-370 is displaced ~20Å from its position in factor XI and inserts into the activation pocket of factor XIa producing the oxyanion hole in the active site of the protease <ref>PMID:14523451</ref>.
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| - | ==Active Site Residues==
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| - | <Structure load='3bg8' size='350' frame='true' align='right' caption='Factor XIa light chain'/>
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| - | Similar to other serine proteases, the [http://en.wikipedia.org/wiki/Catalytic_triad catalytic triad] residues Ser-557, Asp-462 and His-413 constitute the <scene name='Sandbox/Active_site/2'>active site</scene> of factor XIa. A [http://en.wikipedia.org/wiki/Low-barrier_hydrogen_bond low barrier hydrogen bond (LBHB)] formed between the carboxyl group of Asp-462 and imidazole nitrogen of His 413 causes the deprotonation Ser-557 (enhacing its nucleophilicity). Thus catalysis involves a nucleophilic attack by Ser-557 on the carbonyl carbon of the target amino acid at the C-terminal of the substrate producing an intermediate which is stablized by the oxyanion hole. Rearrangement of the resulting tetrahedral intermediate and a second nucleophilic attack by water yields a cleaved peptide with a free carboxyl end <ref>PMID:14523451</ref>.
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| - | ==Substrate Recognition and Cleavage==
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| - | The primary substrate of factor XIa is another zymogen, factor IX which is cleavage sequentially at the peptides bonds between Arg145-Ala146 and Arg180-Val181 of factor IX to release an activation peptide <ref>PMID:17676929</ref>. Recognition of the substrate (factor IX) involves residues different from the <scene name='Sandbox/Active_site/2'>active site</scene> residues. In the inactive zymogen (factor XI), the highly conserved <scene name='Sandbox/Arg_184/1'>Arg-184</scene> is buried in the interface between the apple domains and the catalytic domain where it interacts with <scene name='Sandbox/3_residues/1'>three residues</scene>: Ser-268 from the A3 domain and Asp-488 and Asn-566 in the catalytic domain. Thus following activation, <scene name='Sandbox/Arg_184/1'>Arg-184</scene> is believed to constitute a switch which undegoes a conformational change breaking its interaction with Ser-268, Asp-488 and Asn 566 facilitating the protease interaction with factor IX <ref>PMID:16699514</ref>.
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| - | ==Evolutionary relationship==
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| - | ==Factor XIa Deficiency==
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| - | In contrast to a dysfunctional protein often reported in patients with defects in the vitamin K-dependent proteases, most cases of factor XIa deficiency are associated with low circulating amounts of the protein in the plasma <ref>PMID:4067382</ref>. Studies of the structural features of factor XI/FXIa has hightened in recent times due its implication both venous<ref>10706899</ref> and arterial<ref>PMID:15733058</ref> thrombosis, pathology od sepsis and ischemia-reperfusion damage in the central nervous system. Mutations in the A4 domain of factor XIa often interfere with the ability of the protein to dimerize.
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| - | Amino acid substitutions such as Phe283Leu<ref>PMID:17257616</ref> and Gly350Glu<ref>PMID:15026311 </ref> in the heavy chain results in an increased dimer dissociation and absence of dimer formation respectively. Some mutations in the factor XI A4 domain and catalytic domains are inherited as autosomal recessive bleeding diathesis however, other amino acid substitutions are exert a dominant negative effect on the normal monomer subunit affecting protein secretion. Studies suggest that dimerization is not affected under dominant negative mutations but the mutant subunit traps the normal subunit in the cell preventing its secretion. Majority of these missense mutations:Ser225Phe, Cys398Tyr, Gly400Val and Trp569Ser which produce a dominant negative effect involves residues found in the catalytic domain<ref>PMID:15026311 </ref>.
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| - | ==References==
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| - | <references />
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