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Prokineticin 1 (PK1) and its close homologue PK2 are two secreted proteins, which belong to the AVIT protein family (foe example see [[1imt]]). They are small related peptides of 80-90 amino acids in length, sharing 10 conserved cysteins, which create a five disulphide-bridged motif (colipase fold) and an identical amino-termini – AVIT. PK's are expressed in a wide array of peripheral tissues, including the steroidogenic glands (such as the ovary, testis and adrenal gland), but also in the gastrointestinal tract, nervous system, bladder, bone marrow and prostate.
== Introduction ==
<applet load='FILE_consurf1254065510_pipe.pdb' size='400' frame='true' align='right' caption='Human PROKR1' SCENE='User:Anat_Levit/Sandbox_1/Pkr1_colored_n_to_c/4'/> 


Human Prokineticin 1 (PK1) and its close homologue PK2 are two secreted proteins, which belong to the AVIT protein family (for example see [[1imt]], the snake ortologues of human PK1). They are small related peptides of 80-90 amino acids in length, sharing 10 conserved cysteins, which create a five disulphide-bridged motif (colipase fold) and an identical amino-termini – AVIT. PK's are expressed in a wide array of peripheral tissues, including the steroidogenic glands (such as the ovary, testis and adrenal gland), but also in the gastrointestinal tract, nervous system, bladder, bone marrow and prostate.
<applet load='FILE_consurf1254065510_pipe.pdb' size='400' frame='true' align='right' caption='Model of human PROKR1 obtained by I-TASSER' SCENE='User:Anat_Levit/Sandbox_1/Pkr1_colored_n_to_c/4'/> 


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]),
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). These receptors share  
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.
<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  
<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.
<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.


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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 <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:  
[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 initial scene</scene>).  
[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>).  


[[Image:ColorKey_ConSurf_NoYellow_NoGray.gif|right|200 px]]
[[Image:ColorKey_ConSurf_NoYellow_NoGray.gif|right|200 px]]
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Being highly homologues proteins, expressed in the same cell types and having similar nano-molar affinity to common ligands, it is of importance to understand the structural and functional differences between these receptors.
Being highly homologues proteins, expressed in the same cell types and having similar nano-molar affinity to common ligands, it is of importance to understand the structural and functional differences between these receptors.
The models will help us as we examine the possible differences between the receptors, specifically, differences in post-translational modifications such as receptor phosphorylation, and differences in ligand binding, i.e., binding site identification.


The receptors are made of seven transmembrane α-helices of approximately 30 residues in length, 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 structural models 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. These models will help us as we examine the possible differences between the receptors, specifically, differences in post-translational modifications such as receptor phosphorylation, and differences in ligand binding, i.e., binding site identification.




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<applet load='PKR1_model1.pdb' size='300' name='PROKR1' frame='true' align='right' caption='Human PROKR1' SCENE='User:Anat_Levit/Sandbox_1/Initial_pkr1/1'/>   
<applet load='PKR1_model1.pdb' size='300' name='PROKR1' frame='true' align='right' caption='Human PROKR1' SCENE='User:Anat_Levit/Sandbox_1/Initial_pkr1/1'/>   




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<scene name='User:Anat_Levit/Sandbox_1/Pkr1_3eml_based_residues/1' target='PROKR1'>PROKR1</scene> and <scene name='User:Anat_Levit/Sandbox_1/Pkr2_1l9h_residues/2' target='PROKR2'>PROKR2</scene> models.   
<scene name='User:Anat_Levit/Sandbox_1/Pkr1_3eml_based_residues/1' target='PROKR1'>PROKR1</scene> and <scene name='User:Anat_Levit/Sandbox_1/Pkr2_1l9h_residues/2' target='PROKR2'>PROKR2</scene> models.   




Based on this analysis, we defined the core residues which line the <scene name='User:Anat_Levit/Sandbox_1/Pkr1_consensus/2' target='PROKR1'>PROKR1</scene> and <scene name='User:Anat_Levit/Sandbox_1/Pkr2_consensus/2' target='PROKR2'>PROKR2</scene> binding pocket (the selected residues appear in at least two of the superpositions described). The pockets of the two receptors are almost identical, except for the additional Tyr140 and Glu319 residues in PROKR2. Tyr140 is known to be mutated in Kallmann syndrome. The p.Y140X nonsense mutation probably results in a PROKR2 with complete loss of function through the generation of an aberrant transcript that can be unstable or encodes for a truncated protein, lacking the carboxyl terminal domain.  
Based on this analysis, we defined the core residues which line the <scene name='User:Anat_Levit/Sandbox_1/Pkr1_consensus/2' target='PROKR1'>PROKR1</scene> and <scene name='User:Anat_Levit/Sandbox_1/Pkr2_consensus/2' target='PROKR2'>PROKR2</scene> binding pocket (the selected residues appear in at least two of the superpositions described). The pockets of the two receptors are almost identical, except for the additional Tyr140 and Glu319 residues in PROKR2. Tyr140 is known to be mutated in Kallmann syndrome. The p.Y140X nonsense mutation probably results in a PROKR2 with complete loss of function through the generation of an aberrant transcript that can be unstable or encodes for a truncated protein, lacking the carboxyl terminal domain.  


===Conclusion===
 
 
== Conclusion ==


The high conservation of the ligand binding pocket of the prokineticin receptors  may explain the very similar affinity of the receptors to their cognate ligands.  
The high conservation of the ligand binding pocket of the prokineticin receptors  may explain the very similar affinity of the receptors to their cognate ligands.  
This has also been observed in other subfamilies of GPCRs (such as dopamine, serotonin, histamine and the adrenergic receptors) and may probably explain the difficulty in obtaining potent subtype-selective compounds in pharmaceutical discovery programs.
This has also been observed in other subfamilies of GPCRs (such as dopamine, serotonin, histamine and the adrenergic receptors) and may probably explain the difficulty in obtaining potent subtype-selective compounds in pharmaceutical discovery programs.
<applet load='PKR2_model1.pdb' size='300' frame='true' name='PROKR2' align='right' caption='Human PROKR2' SCENE='User:Anat_Levit/Sandbox_1/Pkr2_2rh1_residues/2'>


For more information about our lab, please visit us at [http://departments.agri.huji.ac.il/biochemfoodsci722/teachers/niv_masha/index.htm HUJI].
For more information about our lab, please visit us at [http://departments.agri.huji.ac.il/biochemfoodsci722/teachers/niv_masha/index.htm HUJI].
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<applet load='PKR2_model1.pdb' size='300' frame='true' name='PROKR2' align='right' caption='Human PROKR2' SCENE='User:Anat_Levit/Sandbox_1/Pkr2_2rh1_residues/2'>
 
 
 
 
 
 
 
 
 
 
== Conclusion ==
 
The high conservation of the ligand binding pocket of the prokineticin receptors  may explain the very similar affinity of the receptors to their cognate ligands.
This has also been observed in other subfamilies of GPCRs (such as dopamine, serotonin, histamine and the adrenergic receptors) and may probably explain the difficulty in obtaining potent subtype-selective compounds in pharmaceutical discovery programs.
 
 
For more information about our lab, please visit us at [http://departments.agri.huji.ac.il/biochemfoodsci722/teachers/niv_masha/index.htm HUJI].
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