User:Cody Couperus/Sandbox 1: Difference between revisions

(4 intermediate revisions by the same user not shown)

Line 1:

==Introduction==

<scene name='58/583418/Thombin_main_secondary/2'>Thrombin</scene> is the serine protease that catalyzes the penultimate step in blood coagulation. It is activated from its [http://en.wikipedia.org/wiki/Zymogen zymogen], prothrombin, at the site of tissue injury by [[Factor_Xa | FXa]] and its cofactor [http://en.wikipedia.org/wiki/Factor_V FVa] in the presence of phospholipid membrane and calcium. Thrombin is then able to catalyze the cleavage of [[Fibrinogen | fibrinogen]] to insoluable fibrin which spontaneously polymerizes to form a stable clot.<ref name="zero">PMID: 7023326</ref><ref name="one">PMID: 11001069</ref> Thrombin also acts as a procoagulant by:

<scene name='58/583418/Thombin_main_secondary/2'>Thrombin</scene> is the serine protease that catalyzes the penultimate step in blood coagulation. It is activated from its [http://en.wikipedia.org/wiki/Zymogen zymogen], prothrombin, at the site of tissue injury by [[Factor_Xa | Factor Xa (FXa)]] and its cofactor [http://en.wikipedia.org/wiki/Factor_V FVa] in the presence of phospholipid membrane and calcium. Thrombin is then able to catalyze the cleavage of [[Fibrinogen | fibrinogen]] to insoluable fibrin which spontaneously polymerizes to form a stable clot.<ref name="zero">PMID: 7023326</ref><ref name="one">PMID: 11001069</ref> Thrombin also acts as a procoagulant by:

* Activating platelets through their [http://en.wikipedia.org/wiki/Protease-activated_receptor protease activated receptors (PARs)]<ref name="one"/>

Line 15:

* [http://www.sciencedirect.com/science/article/pii/0968000484900744 Protease nexin 1]<ref name="three"/><ref name='four'/><ref name='five'/>

Generation of thrombin is decreased when thrombin reaches endothelial lining and interacts with [[1fge |thrombomodulin]] which significantly increases activity of thrombin in activating [http://en.wikipedia.org/wiki/Protein_C protein C (APC)].<ref>PMID: 3029867</ref> This enzyme will go on to inactivate FVa<ref>PMID: 7989361</ref><ref name='six'>PMID: 8639840</ref> and [[Factor_VIII | FVIIIa]]<ref name='six'/> , cofactors for activation of prothrombin<ref>PMID: 15147718</ref> and [[Factor_Xa | FXa]]<ref>PMID: 10881749</ref>, respectively.

Generation of thrombin is decreased when thrombin reaches endothelial lining and interacts with [[1fge |thrombomodulin]] which significantly increases activity of thrombin in activating [http://en.wikipedia.org/wiki/Protein_C protein C (PC -> APC)].<ref>PMID: 3029867</ref> This enzyme will go on to inactivate FVa<ref>PMID: 7989361</ref><ref name='six'>PMID: 8639840</ref> and [[Factor_VIII | FVIIIa]]<ref name='six'/> , cofactors for activation of prothrombin<ref>PMID: 15147718</ref> and [[Factor_Xa | FXa]]<ref>PMID: 10881749</ref>, respectively.

By balancing substrate specificity, activity, and inhibition thrombin plays a central role in the blood coagulation cascade. <ref name="three"/>

Line 22:

==The Thrombin Life Cycle==

Upon tissue damage [http://en.wikipedia.org/wiki/Tissue_factor tissue factor (TF)] is released by subendothelial cells. This interacts with circulating [[Factor_VII| FVIIa]], a zymogen-like serine protease, significantly increasing its activity. '''The FVIIa-TF complex activates FVII, FIX, and FX'''. The now active '''FXa cleaves prothrombin''' bound to membranes through its [http://en.wikipedia.org/wiki/Gla_domain gamma-carboxyglutamyl (Gla) domain], activating it to thrombin.

Upon tissue damage [http://en.wikipedia.org/wiki/Tissue_factor tissue factor (TF)] is released by subendothelial cells. This interacts with circulating [[Factor_VII| FVIIa]], a zymogen-like serine protease, significantly increasing its activity. '''The FVIIa-TF complex (extrinsic Xase) activates FVII, FIX, and FX'''. The now active '''FXa cleaves prothrombin''' bound to membranes through its [http://en.wikipedia.org/wiki/Gla_domain gamma-carboxyglutamyl (Gla) domain], activating it to thrombin.

Thrombin interacts with platelet membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/14720584 GpIbα] and subsequently '''cleaves protease activated receptor-1 (PAR1)''' causing a signaling cascade which leads to platelet [http://en.wikipedia.org/wiki/Platelet_alpha-granule α-granule] release and membrane flipping exposing the negatively charged [http://en.wikipedia.org/wiki/Phosphatidylserine phosphatidylserine]. The platelet alpha granules contain the physiologically relevant pool of FVa. <ref>Camire, R. M. (2010). Platelet factor V to the rescue. Blood, 115(4), 753-754. [http://bloodjournal.hematologylibrary.org/content/115/4/753.full DOI: 10.1182/blood-2009-11-252619]</ref>

Line 60:

The serine protease <scene name='58/583418/Catalytic_triad/1'>catalytic triad</scene> ([http://en.wikipedia.org/wiki/Catalytic_triad wiki]) residues, based on chymotrypsin numbering, are Ser195, His57, and Asp102. As is common with serine proteases, an <scene name='58/583418/Oxyanion_hole/2'>oxyanion hole</scene> hole is formed by backbone amides of Ser195 and Gly193.<ref name='seven'/> This has the functional role of stabilizing the oxyanion intermediate involved in the serine protease mechanism by hydrogen bonding to the oxygen of the P1 residue (standard substrate-protease nomeclature <ref>PMID: 22925665</ref>. In addition, since thrombin cleaves after Arg/Lys the <scene name='58/583418/S1/3'>S1 specificity site</scene>, formed by the 180s- and 220s- loops, has Asp189 at the base to form a salt bridge with the incoming substrate. Furthermore, the S4 binding pocket accommodates hydrophobic substrate residues.

The <scene name='58/583418/Loops/3'>active site</scene> cleft rims are formed by the hydrophobic and rigid <scene name='58/583418/Loops/3'>60-~~loops~~</scene> (residues L60, Y60a, P60b, P60c, W60d, D60e, K60f, N60g, F60h, T60i, and N60g) and the <scene name='58/583418/Loops/3'>γ-loop</scene> (residues T147, W147a, T147b, A147c, N147d, and V147f) while the base is mostly hydrophilic negatively charged amino acids. The cleft is deep compared to more promiscuous serine proteases, consequently substrates must either have a large loop that is cleaved or have favorable interactions with the insertion loops <ref>PMID: 16102053</ref>.

The <scene name='58/583418/Loops/3'>active site</scene> cleft rims are formed by the hydrophobic and rigid <scene name='58/583418/Loops/3'>60-loop</scene> (residues L60, Y60a, P60b, P60c, W60d, D60e, K60f, N60g, F60h, T60i, and N60g) and the <scene name='58/583418/Loops/3'>γ-loop</scene> (residues T147, W147a, T147b, A147c, N147d, and V147f) while the base is mostly hydrophilic negatively charged amino acids. The cleft is deep compared to more promiscuous serine proteases, consequently substrates must either have a large loop that is cleaved or have favorable interactions with the insertion loops <ref>PMID: 16102053</ref>.

Many other loops project out of the B chain but most are rigid due to proline and tryptophan residues.

Line 66:

'''Exosite I''' is located on the B chain and had both basic and hydrophobic character. It is important in binding <scene name='58/583418/Fibrinogen/1'>fibrinogen</scene>, platelet activated receptors, and <scene name='58/583418/Thrombomodulin/1'>thrombomodulin</scene>.

'''Exosite II''' is also part of the B chain, and derived from numerous basic amino acids, this is the site of <scene name='58/583418/Antithrombin/1'>heparin binding</scene> through the sulfate groups on the glycosaminoglycan. It is also the site of ~~GpIα~~ binding on the platelet surface.

'''Exosite II''' is also part of the B chain, and derived from numerous basic amino acids, this is the site of <scene name='58/583418/Antithrombin/1'>heparin binding</scene> through the sulfate groups on the glycosaminoglycan. It is also the site of GpIbα binding on the platelet surface.

The <scene name='58/583418/Sodium_binding_loop/1'>sodium binding site</scene> is formed by the 180s- and 220s- loops. Na+ is bound by the backbone oxygens of Arg221a and Lys224 in addition to four water molecules in a classic [http://chemwiki.ucdavis.edu/Inorganic_Chemistry/Crystal_Field_Theory/High_Spin_and_Low_Spin_Complexes#Octahedral_Geometry octahedral geometry]<ref>PMID: 9108691</ref>. Through the covelent disulfide linkage between Cys220 and Cys 191 the sodium binding site is linked to Ser195 and the oxyanion hole.

Line 89:

==Secondary Structure Features==

Thrombin has a <scene name='58/583418/Cis_proline/1'>cis peptide bond</scene> in a loop containing proline 37. The dihedral (~~Cα-~~C'-N-Cα) angle omega is ~~142~~.7 degrees.

Thrombin has a <scene name='58/583418/Cis_proline/1'>cis peptide bond</scene> in a loop containing proline 37. The dihedral (C'-Cα-N-C') angle omega is -69.4 degrees.

[[Image:Capping.png|450px|center|thumb| “Capping box” motif in alpha thrombin (PDB: 1PPB) represented by His230 (Ncap) side chain and main chain hydrogen bonded with the backbone nitrogen of Arg233 (N3). An additional feature is a weak hydrophobic interaction between Thr229 (N’) and Val234 (N4) termed the “hydrophobic staple.” This motif derives it’s name from the box shaped hydrogen bonding pattern.]]

@@ Line 1: / Line 1: @@
 <StructureSection load='1PPB' size='350' side='right' caption='Thrombin (1PPB) viewed in cartoon representation colored by secondary structure. Active site residues Ser195, Asp102, and His57 are viewed in ball and stick form.' scene='58/583418/Thombin_main_secondary/2'>
 ==Introduction==
-<scene name='58/583418/Thombin_main_secondary/2'>Thrombin</scene> is the serine protease that catalyzes the penultimate step in blood coagulation. It is activated from its [http://en.wikipedia.org/wiki/Zymogen zymogen], prothrombin, at the site of tissue injury by [[Factor_Xa | FXa]] and its cofactor [http://en.wikipedia.org/wiki/Factor_V FVa] in the presence of phospholipid membrane and calcium. Thrombin is then able to catalyze the cleavage of [[Fibrinogen | fibrinogen]] to insoluable fibrin which spontaneously polymerizes to form a stable clot.<ref name="zero">PMID: 7023326</ref><ref name="one">PMID: 11001069</ref> Thrombin also acts as a procoagulant by:
+<scene name='58/583418/Thombin_main_secondary/2'>Thrombin</scene> is the serine protease that catalyzes the penultimate step in blood coagulation. It is activated from its [http://en.wikipedia.org/wiki/Zymogen zymogen], prothrombin, at the site of tissue injury by [[Factor_Xa | Factor Xa (FXa)]] and its cofactor [http://en.wikipedia.org/wiki/Factor_V FVa] in the presence of phospholipid membrane and calcium. Thrombin is then able to catalyze the cleavage of [[Fibrinogen | fibrinogen]] to insoluable fibrin which spontaneously polymerizes to form a stable clot.<ref name="zero">PMID: 7023326</ref><ref name="one">PMID: 11001069</ref> Thrombin also acts as a procoagulant by:
 * Activating platelets through their [http://en.wikipedia.org/wiki/Protease-activated_receptor protease activated receptors (PARs)]<ref name="one"/>
@@ Line 15: / Line 15: @@
 * [http://www.sciencedirect.com/science/article/pii/0968000484900744 Protease nexin 1]<ref name="three"/><ref name='four'/><ref name='five'/>
-Generation of thrombin is decreased when thrombin reaches endothelial lining and interacts with [[1fge |thrombomodulin]] which significantly increases activity of thrombin in activating [http://en.wikipedia.org/wiki/Protein_C protein C (APC)].<ref>PMID: 3029867</ref> This enzyme will go on to inactivate FVa<ref>PMID: 7989361</ref><ref name='six'>PMID: 8639840</ref> and [[Factor_VIII | FVIIIa]]<ref name='six'/> , cofactors for activation of prothrombin<ref>PMID: 15147718</ref> and [[Factor_Xa | FXa]]<ref>PMID: 10881749</ref>, respectively.
+Generation of thrombin is decreased when thrombin reaches endothelial lining and interacts with [[1fge |thrombomodulin]] which significantly increases activity of thrombin in activating [http://en.wikipedia.org/wiki/Protein_C protein C (PC -> APC)].<ref>PMID: 3029867</ref> This enzyme will go on to inactivate FVa<ref>PMID: 7989361</ref><ref name='six'>PMID: 8639840</ref> and [[Factor_VIII | FVIIIa]]<ref name='six'/> , cofactors for activation of prothrombin<ref>PMID: 15147718</ref> and [[Factor_Xa | FXa]]<ref>PMID: 10881749</ref>, respectively.
 By balancing substrate specificity, activity, and inhibition thrombin plays a central role in the blood coagulation cascade. <ref name="three"/>
@@ Line 22: / Line 22: @@
 ==The Thrombin Life Cycle==
-Upon tissue damage [http://en.wikipedia.org/wiki/Tissue_factor tissue factor (TF)] is released by subendothelial cells. This interacts with circulating [[Factor_VII| FVIIa]], a zymogen-like serine protease, significantly increasing its activity. '''The FVIIa-TF complex activates FVII, FIX, and FX'''. The now active '''FXa cleaves prothrombin''' bound to membranes through its [http://en.wikipedia.org/wiki/Gla_domain gamma-carboxyglutamyl (Gla) domain], activating it to thrombin.
+Upon tissue damage [http://en.wikipedia.org/wiki/Tissue_factor tissue factor (TF)] is released by subendothelial cells. This interacts with circulating [[Factor_VII| FVIIa]], a zymogen-like serine protease, significantly increasing its activity. '''The FVIIa-TF complex (extrinsic Xase) activates FVII, FIX, and FX'''. The now active '''FXa cleaves prothrombin''' bound to membranes through its [http://en.wikipedia.org/wiki/Gla_domain gamma-carboxyglutamyl (Gla) domain], activating it to thrombin.
 Thrombin interacts with platelet membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/14720584 GpIbα] and subsequently '''cleaves protease activated receptor-1 (PAR1)''' causing a signaling cascade which leads to platelet [http://en.wikipedia.org/wiki/Platelet_alpha-granule α-granule] release and membrane flipping exposing the negatively charged [http://en.wikipedia.org/wiki/Phosphatidylserine phosphatidylserine]. The platelet alpha granules contain the physiologically relevant pool of FVa. <ref>Camire, R. M. (2010). Platelet factor V to the rescue. Blood, 115(4), 753-754. [http://bloodjournal.hematologylibrary.org/content/115/4/753.full DOI: 10.1182/blood-2009-11-252619]</ref>
@@ Line 60: / Line 60: @@
 The serine protease <scene name='58/583418/Catalytic_triad/1'>catalytic triad</scene> ([http://en.wikipedia.org/wiki/Catalytic_triad wiki]) residues, based on chymotrypsin numbering, are Ser195, His57, and Asp102. As is common with serine proteases, an <scene name='58/583418/Oxyanion_hole/2'>oxyanion hole</scene> hole is formed by backbone amides of Ser195 and Gly193.<ref name='seven'/> This has the functional role of stabilizing the oxyanion intermediate involved in the serine protease mechanism by hydrogen bonding to the oxygen of the P1 residue (standard substrate-protease nomeclature <ref>PMID: 22925665</ref>. In addition, since thrombin cleaves after Arg/Lys the <scene name='58/583418/S1/3'>S1 specificity site</scene>, formed by the 180s- and 220s- loops, has Asp189 at the base to form a salt bridge with the incoming substrate. Furthermore, the S4 binding pocket accommodates hydrophobic substrate residues.
-The <scene name='58/583418/Loops/3'>active site</scene> cleft rims are formed by the hydrophobic and rigid <scene name='58/583418/Loops/3'>60-loops</scene> (residues L60, Y60a, P60b, P60c, W60d, D60e, K60f, N60g, F60h, T60i, and N60g) and the <scene name='58/583418/Loops/3'>γ-loop</scene> (residues T147, W147a, T147b, A147c, N147d, and V147f) while the base is mostly hydrophilic negatively charged amino acids. The cleft is deep compared to more promiscuous serine proteases, consequently substrates must either have a large loop that is cleaved or have favorable interactions with the insertion loops <ref>PMID: 16102053</ref>.
+The <scene name='58/583418/Loops/3'>active site</scene> cleft rims are formed by the hydrophobic and rigid <scene name='58/583418/Loops/3'>60-loop</scene> (residues L60, Y60a, P60b, P60c, W60d, D60e, K60f, N60g, F60h, T60i, and N60g) and the <scene name='58/583418/Loops/3'>γ-loop</scene> (residues T147, W147a, T147b, A147c, N147d, and V147f) while the base is mostly hydrophilic negatively charged amino acids. The cleft is deep compared to more promiscuous serine proteases, consequently substrates must either have a large loop that is cleaved or have favorable interactions with the insertion loops <ref>PMID: 16102053</ref>.
 Many other loops project out of the B chain but most are rigid due to proline and tryptophan residues.
@@ Line 66: / Line 66: @@
 '''Exosite I''' is located on the B chain and had both basic and hydrophobic character. It is important in binding <scene name='58/583418/Fibrinogen/1'>fibrinogen</scene>, platelet activated receptors, and <scene name='58/583418/Thrombomodulin/1'>thrombomodulin</scene>.
-'''Exosite II''' is also part of the B chain, and derived from numerous basic amino acids, this is the site of <scene name='58/583418/Antithrombin/1'>heparin binding</scene> through the sulfate groups on the glycosaminoglycan. It is also the site of GpIα binding on the platelet surface.
+'''Exosite II''' is also part of the B chain, and derived from numerous basic amino acids, this is the site of <scene name='58/583418/Antithrombin/1'>heparin binding</scene> through the sulfate groups on the glycosaminoglycan. It is also the site of GpIbα binding on the platelet surface.
 The <scene name='58/583418/Sodium_binding_loop/1'>sodium binding site</scene> is formed by the 180s- and 220s- loops. Na+ is bound by the backbone oxygens of Arg221a and Lys224 in addition to four water molecules in a classic [http://chemwiki.ucdavis.edu/Inorganic_Chemistry/Crystal_Field_Theory/High_Spin_and_Low_Spin_Complexes#Octahedral_Geometry octahedral geometry]<ref>PMID: 9108691</ref>. Through the covelent disulfide linkage between Cys220 and Cys 191 the sodium binding site is linked to Ser195 and the oxyanion hole.
@@ Line 89: / Line 89: @@
 ==Secondary Structure Features==
-Thrombin has a <scene name='58/583418/Cis_proline/1'>cis peptide bond</scene> in a loop containing proline 37. The dihedral (Cα-C'-N-Cα) angle omega is 142.7 degrees.
+Thrombin has a <scene name='58/583418/Cis_proline/1'>cis peptide bond</scene> in a loop containing proline 37. The dihedral (C'-Cα-N-C') angle omega is -69.4 degrees.
 [[Image:Capping.png|450px|center|thumb| “Capping box” motif in alpha thrombin (PDB: 1PPB) represented by His230 (Ncap) side chain and main chain hydrogen bonded with the backbone nitrogen of Arg233 (N3). An additional feature is a weak hydrophobic interaction between Thr229 (N’) and Val234 (N4) termed the “hydrophobic staple.” This motif derives it’s name from the box shaped hydrogen bonding pattern.]]