User:Anat Levit/Sandbox 2: Difference between revisions

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PKs exert their biological function through activation of two homologous G-protein coupled receptors (see Wikipedia: [http://en.wikipedia.org/wiki/G_protein_coupled_receptors G protein-coupled receptors]),

termed Prokineticin receptor 1 (PROKR1) and Prokineticin receptor 2 (PROKR2).

The receptors are made of seven transmembrane α-helices of approximately 30 residues in length (rainbow colored from N to C terminal), which are connected by intra and extracellular loops. The helices are placed in a lipidic environment, while the loop regions are surrounded by aqueous medium. ~~Although progress~~ has been ~~achieved~~ in ~~recent~~ years, GPCR ~~crystallization is still an unresolved issue~~. ~~An alternative approach for visualizing a protein's 3D structure is~~ the homology modeling approach, ~~where~~ the target protein is built starting from the experimentally known 3D structure of a related protein.

The receptors are made of seven transmembrane α-helices of approximately 30 residues in length (rainbow colored from N to C terminal), which are connected by intra and extracellular loops. The helices are placed in a lipidic environment, while the loop regions are surrounded by aqueous medium.

Until recently, our atomic-level understanding of GPCRs has been based on rhodopsin in its inactive state ([[1f88]]). In the past couple of years, the field of GPCR structural biology has enjoyed a renaissance, with the publication of three new members: human A2A-Adenosine receptor ([[3eml]]), the turkey β1-Adrenergic receptor ([[2vt4]]) and the human β2-Adrenergic receptor ([[2rh1]]), as well as resolution of the activated state of bovine rhodopsin ([[3dqb]] and [[3cap]]) (for review of all avilable structures see Hanson and Stevens 2009).

The amount of structural information available now makes the homology modeling approach, in which the target protein is built starting from the experimentally known 3D structure of a related protein, much more applicable to GPCRs.

The structural models of human PROKRs presented here were generated using the I-TASSER server, based on the templates [[1l9h]], [[3eml]], [[2rh1]] for human PROKR1 and [[1l9h]], [[3eml]], [[1f88]], [[2rh1]] for PROKR2.

The human Prokineticin receptors share

The human Prokineticin receptors share

<scene name='User:Anat_Levit/Sandbox_1/Pkr1_consurf/1'>85% sequence homology</scene>, which is a high value among known GPCRs. The proteins diverse mainly in their extra and intra-cellular tails.

The prokineticin and their receptors are expressed in various tissues, including the cardiovascular, gastrointestinal, immune, reproductive, endocrine and nervous systems. The receptors have been shown to couple to Gq, Gi and Gs, thereafter mediating intracellular calcium mobilization, phosphorylation of p42/p44 MAPK, AKT and cAMP accumulation, respectively. Receptor activation has been shown to mediate proliferation, anti-apoptosis, differentiation and mobilization of target cells.

[[Image:ColorKey_ConSurf_NoYellow_NoGray.gif|right|200 px]]

The prokineticin receptors have been found to be involved in various pathologies involving the cardiovascular, reproductive, endocrine and nervous systems. Notably, PROKR2 has been found to be <scene name='User:Anat_Levit/~~Sandbox_1~~/Pkr1_ks_mutations/1'>mutated in Kallmann syndrome</scene> with dilated cardiomyopathy, a hypogonadism caused by a deficiency of gonadotropin-releasing hormone (GnRH) (see Wikipedia:

The prokineticin receptors have been found to be involved in various pathologies involving the cardiovascular, reproductive, endocrine and nervous systems. Notably, PROKR2 has been found to be

[http://en.wikipedia.org/wiki/Kallmann_syndrome Kallmann syndrome]). Except for V331M and R357W ('''colored ~~red~~''') which are Leu and Asn in PROKR1, respectively, all other residues mutated in PROKR2 are identical in PROKR1 ('''colored ~~blue~~'''). Interestingly, two of the mutated residues, W178 (4.50) and P290 (6.50), are two of the most conserved residues in family A GPCRs (<scene name='User:Anat_Levit/Sandbox_1/Pkr1_consurf/1'>restore previous scene</scene>).

<scene name='User:Anat_Levit/Sandbox_2/Pkr1_ks_mutations/1'>mutated in Kallmann syndrome</scene> with dilated cardiomyopathy, a hypogonadism caused by a deficiency of gonadotropin-releasing hormone (GnRH) (see Wikipedia:

[http://en.wikipedia.org/wiki/Kallmann_syndrome Kallmann syndrome]). Except for V331M and R357W ('''colored cyan''') which are Leu and Asn in PROKR1, respectively, all other residues mutated in PROKR2 are '''identical''' in PROKR1 ('''colored magenta'''). Interestingly, two of the mutated residues, W178 (4.50) and P290 (6.50), are two of the most conserved residues in family A GPCRs (<scene name='User:Anat_Levit/Sandbox_1/Pkr1_consurf/1'>restore previous scene</scene>).

~~[[Image:ColorKey_ConSurf_NoYellow_NoGray.gif|right|200 px]]~~

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== Phosphorylation site variations ==

Almost all GPCRs are regulated by [http://en.wikipedia.org/wiki/Phosphorylation phosphorylation ] and this is a key process in determining the signaling properties of these receptors. Receptors are multiply phosphorylated at sites that can occur throughout the intracellular regions of the receptor. It is well established that GPCR phosphorylation is a complex process involving a range of different protein kinases able to phosphorylate the same receptor at different sites and that this results in differential signaling outcomes, which can be tailored in a tissue specific manner to regulate biological processes.

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The phosphovariants can now be identified when the phosphorylation sites or interacting kinases were altered between subtype sequences.

The identified sites were classified according to one of the following types, defined by Ryu et al. 2009:

# In <scene name='User:Anat_Levit/~~Sandbox_1~~/~~Type_i~~/2'>type I</scene> the phosphorylation site is in the same location as the variation, and can either create a new phosphorylation site (Type I+) or eliminate an existing site (Type I-) ('''colored green''').

# In <scene name='User:Anat_Levit/Sandbox_2/Type_i_variants/1' target='Phospho'>type I</scene> the phosphorylation site is in the same location as the variation, and can either create a new phosphorylation site (Type I+) or eliminate an existing site (Type I-) ('''colored green''').

# In <scene name='User:Anat_Levit/~~Sandbox_1~~/~~Type_ii~~/2'>type II</scene> the variation is not in the same location as the phosphorylation site, and can either create a new phosphorylation site (Type II+) or eliminate an existing site (Type II-) ('''colored blue''').

# In <scene name='User:Anat_Levit/Sandbox_2/Type_ii_variants/1' target='Phospho'>type II</scene> the variation is not in the same location as the phosphorylation site, and can either create a new phosphorylation site (Type II+) or eliminate an existing site (Type II-) ('''colored blue''').

# <scene name='User:Anat_Levit/~~Sandbox_1~~/~~Type_iii~~/1'>Type III</scene> are variations that change only the type of kinase involved, without affecting the phosphorylation site itself ('''colored red''').

# <scene name='User:Anat_Levit/Sandbox_2/Type_iii_variants/1' target='Phospho'>Type III</scene> are variations that change only the type of kinase involved, without affecting the phosphorylation site itself ('''colored red''').

<scene name='User:Anat_Levit/~~Sandbox_1~~/~~Type_i~~/3'>Identical</scene> phosphor-acceptor residues predicted to be phosphorylated by the same kinases are '''colored yellow''' (<scene name='User:Anat_Levit/~~Sandbox_1~~/~~All_phosphosites~~/1'>view all predictions</scene>).

<scene name='User:Anat_Levit/Sandbox_2/Type_iii_variants/2' target='Phospho'>Identical</scene> phosphor-acceptor residues predicted to be phosphorylated by the same kinases are '''colored yellow''' (<scene name='User:Anat_Levit/Sandbox_2/Type_iii_variants/3' target='Phospho'>view all predictions</scene>).

As seen from the results, homologues residues in the receptors are predicted to be phosphorylated by different kinases, and some of the predicted phospho-sites are receptor unique.

@@ Line 6: / Line 6: @@
 PKs exert their biological function through activation of two homologous G-protein coupled receptors (see Wikipedia: [http://en.wikipedia.org/wiki/G_protein_coupled_receptors G protein-coupled receptors]),
 termed Prokineticin receptor 1 (PROKR1) and Prokineticin receptor 2 (PROKR2).
-The receptors are made of seven transmembrane α-helices of approximately 30 residues in length (rainbow colored from N to C terminal), which are connected by intra and extracellular loops. The helices are placed in a lipidic environment, while the loop regions are surrounded by aqueous medium. <br/>Although progress has been achieved in recent years, GPCR crystallization is still an unresolved issue. An alternative approach for visualizing a protein's 3D structure is the homology modeling approach, where the target protein is built starting from the experimentally known 3D structure of a related protein.
+The receptors are made of seven transmembrane α-helices of approximately 30 residues in length (rainbow colored from N to C terminal), which are connected by intra and extracellular loops. The helices are placed in a lipidic environment, while the loop regions are surrounded by aqueous medium.
+<br/>Until recently, our atomic-level understanding of GPCRs has been based on rhodopsin in its inactive state ([[1f88]]). In the past couple of years, the field of GPCR structural biology has enjoyed a renaissance, with the publication of three new members: human A2A-Adenosine receptor ([[3eml]]), the turkey β1-Adrenergic receptor ([[2vt4]]) and the human β2-Adrenergic receptor ([[2rh1]]), as well as resolution of the activated state of bovine rhodopsin ([[3dqb]] and [[3cap]]) (for review of all avilable structures see Hanson and Stevens 2009).
+<br/>The amount of structural information available now makes the homology modeling approach, in which the target protein is built starting from the experimentally known 3D structure of a related protein, much more applicable to GPCRs.
 <br/>The structural models of human PROKRs presented here were generated using the I-TASSER server, based on the templates [[1l9h]], [[3eml]], [[2rh1]] for human PROKR1 and [[1l9h]], [[3eml]], [[1f88]], [[2rh1]] for PROKR2.
-The human Prokineticin receptors share
+<br/>The human Prokineticin receptors share
 <scene name='User:Anat_Levit/Sandbox_1/Pkr1_consurf/1'>85% sequence homology</scene>, which is a high value among known GPCRs. The proteins diverse mainly in their extra and intra-cellular tails.
 The prokineticin and their receptors are expressed in various tissues, including the cardiovascular, gastrointestinal, immune, reproductive, endocrine and nervous systems. The receptors have been shown to couple to Gq, Gi and Gs, thereafter mediating intracellular calcium mobilization, phosphorylation of p42/p44 MAPK, AKT and cAMP accumulation, respectively. Receptor activation has been shown to mediate proliferation, anti-apoptosis, differentiation and mobilization of target cells.
+[[Image:ColorKey_ConSurf_NoYellow_NoGray.gif|right|200 px]]
-The prokineticin receptors have been found to be involved in various pathologies involving the cardiovascular, reproductive, endocrine and nervous systems. Notably, PROKR2 has been found to be <scene name='User:Anat_Levit/Sandbox_1/Pkr1_ks_mutations/1'>mutated in Kallmann syndrome</scene> with dilated cardiomyopathy, a hypogonadism caused by a deficiency of gonadotropin-releasing hormone (GnRH) (see Wikipedia:
+The prokineticin receptors have been found to be involved in various pathologies involving the cardiovascular, reproductive, endocrine and nervous systems. Notably, PROKR2 has been found to be
-[http://en.wikipedia.org/wiki/Kallmann_syndrome Kallmann syndrome]). Except for V331M and R357W (<font color='red'>'''colored red'''</font>) which are Leu and Asn in PROKR1, respectively, all other residues mutated in PROKR2 are identical in PROKR1 (<font color='blue'>'''colored blue'''</font>). Interestingly, two of the mutated residues, W178 (4.50) and P290 (6.50), are two of the most conserved residues in family A GPCRs (<scene name='User:Anat_Levit/Sandbox_1/Pkr1_consurf/1'>restore previous scene</scene>).
+<scene name='User:Anat_Levit/Sandbox_2/Pkr1_ks_mutations/1'>mutated in Kallmann syndrome</scene> with dilated cardiomyopathy, a hypogonadism caused by a deficiency of gonadotropin-releasing hormone (GnRH) (see Wikipedia:
+[http://en.wikipedia.org/wiki/Kallmann_syndrome Kallmann syndrome]). Except for V331M and R357W (<font color='cyan'>'''colored cyan'''</font>) which are Leu and Asn in PROKR1, respectively, all other residues mutated in PROKR2 are <font color='magenta'>'''identical'''</font> in PROKR1 (<font color='magenta'>'''colored magenta'''</font>). Interestingly, two of the mutated residues, W178 (4.50) and P290 (6.50), are two of the most conserved residues in family A GPCRs (<scene name='User:Anat_Levit/Sandbox_1/Pkr1_consurf/1'>restore previous scene</scene>).
-[[Image:ColorKey_ConSurf_NoYellow_NoGray.gif|right|200 px]]
@@ Line 29: / Line 33: @@
 == Phosphorylation site variations ==
+<applet load='FILE_consurf1254065510_pipe.pdb' name='Phospho' size='300' frame='true' align='right' caption='Model of human PROKR1 ' SCENE='User:Anat_Levit/Sandbox_1/Pkr1_colored_n_to_c/4'/>
 Almost all GPCRs are regulated by [http://en.wikipedia.org/wiki/Phosphorylation phosphorylation ] and this is a key process in determining the signaling properties of these receptors. Receptors are multiply phosphorylated at sites that can occur throughout the intracellular regions of the receptor. It is well established that GPCR phosphorylation is a complex process involving a range of different protein kinases able to phosphorylate the same receptor at different sites and that this results in differential signaling outcomes, which can be tailored in a tissue specific manner to regulate biological processes.
@@ Line 38: / Line 42: @@
 The phosphovariants can now be identified when the phosphorylation sites or interacting kinases were altered between subtype sequences.
 The identified sites were classified according to one of the following types, defined by Ryu et al. 2009:
-# In <scene name='User:Anat_Levit/Sandbox_1/Type_i/2'>type I</scene> the phosphorylation site is in the same location as the variation, and can either create a new phosphorylation site (Type I+) or eliminate an existing site (Type I-) (<font color='green'>'''colored green'''</font>).
+# In <scene name='User:Anat_Levit/Sandbox_2/Type_i_variants/1' target='Phospho'>type I</scene> the phosphorylation site is in the same location as the variation, and can either create a new phosphorylation site (Type I+) or eliminate an existing site (Type I-) (<font color='green'>'''colored green'''</font>).
-# In <scene name='User:Anat_Levit/Sandbox_1/Type_ii/2'>type II</scene> the variation is not in the same location as the phosphorylation site, and can either create a new phosphorylation site (Type II+) or eliminate an existing site (Type II-) (<font color='blue'>'''colored blue'''</font>).
+# In <scene name='User:Anat_Levit/Sandbox_2/Type_ii_variants/1' target='Phospho'>type II</scene> the variation is not in the same location as the phosphorylation site, and can either create a new phosphorylation site (Type II+) or eliminate an existing site (Type II-) (<font color='blue'>'''colored blue'''</font>).
-# <scene name='User:Anat_Levit/Sandbox_1/Type_iii/1'>Type III</scene> are variations that change only the type of kinase involved, without affecting the phosphorylation site itself (<font color='red'>'''colored red'''</font>).
+# <scene name='User:Anat_Levit/Sandbox_2/Type_iii_variants/1' target='Phospho'>Type III</scene> are variations that change only the type of kinase involved, without affecting the phosphorylation site itself (<font color='red'>'''colored red'''</font>).
-<scene name='User:Anat_Levit/Sandbox_1/Type_i/3'>Identical</scene> phosphor-acceptor residues predicted to be phosphorylated by the same kinases are <font color='yellow'>'''colored yellow'''</font> (<scene name='User:Anat_Levit/Sandbox_1/All_phosphosites/1'>view all predictions</scene>).
+<scene name='User:Anat_Levit/Sandbox_2/Type_iii_variants/2' target='Phospho'>Identical</scene> phosphor-acceptor residues predicted to be phosphorylated by the same kinases are <font color='yellow'>'''colored yellow'''</font> (<scene name='User:Anat_Levit/Sandbox_2/Type_iii_variants/3' target='Phospho'>view all predictions</scene>).
 As seen from the results, homologues residues in the receptors are predicted to be phosphorylated by different kinases, and some of the predicted phospho-sites are receptor unique.