Sandbox 121: Difference between revisions

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Teacher: Allison Granberry, Hostos-Lincoln Academy of Science
Teacher: Allison Granberry, Hostos-Lincoln Academy of Science


Mentors: Haregewein Assefa,Touro College of Pharmacy, Thijs Beuming, Schrodinger
Mentors: Thijs Beuming, Schrodinger, Haregewein Assefa,Touro College of Pharmacy


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When B2AR is activated, the G-protein disassociates. A surrogate nanobody, <scene name='Sandbox_121/B2ar_struc/13'>Nb80</scene>, that is a camelid antibody produced to mimic the G-protein needed for an active state of the  B2AR.
When B2AR is activated, the G-protein disassociates. A surrogate nanobody, <scene name='Sandbox_121/B2ar_struc/13'>Nb80</scene>, that is a camelid antibody produced to mimic the G-protein needed for an active state of the  B2AR.


Active B₂AR in complex with BI-167107: <scene name='Sandbox_121/B2ar_struc/7'>Polar</scene> and <scene name='Sandbox_121/B2ar_struc/8'>Hydrophobic</scene> Interactions


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! scope="col" width="250" | Photo
! scope="col" width="250" | Photo
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| Isoproterenol || Isoproterenol is an agonist that is structurally similar to NE and readily binds to β₂AR with high affinity. Isoproterenol contains an isopropyl amino group and a catechol group. || [[Image:B2AR-Isoproterenol-Structure-2.JPG|thumb|center|alt= Alt text| |300px]]  || [[Image:Isoproterenol-Picture.JPG|thumb|center|alt= Alt text| |250px]]  
| Isoproterenol || Isoproterenol is an agonist that is structurally similar to NE and readily binds to β₂AR with high affinity. Isoproterenol contains an isopropyl amino group and a catechol group. || [[Image:B2AR-Isoproterenol-edited-structure.jpg|thumb|center|alt= Alt text| |300px]]  || [[Image:Isoproterenol-Picture.JPG|thumb|center|alt= Alt text| |250px]]  
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| BI-167107 || The active state of β₂AR was crystallized using BI-1671071 . Although it is not a catecholamine, it is a full agonist. || [[Image:B2AR-BI-167107-Structure.JPG|thumb|center|alt= Alt text| |300px]] || [[Image:B2AR-BI-167107-Picture.JPG|thumb|center|alt= Alt text| |250px]]
| BI-167107 || The active state of β₂AR was crystallized using BI-1671071 . Although it is not a catecholamine, it is a full agonist. || [[Image:B2AR-BI-167107-Structure.JPG|thumb|center|alt= Alt text| |300px]] || [[Image:B2AR-BI-167107-Picture.JPG|thumb|center|alt= Alt text| |250px]]
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Notable differences between carazolol and both isoproterenol and the natural agonist norepinephrine are that:  
Notable differences between carazolol and both isoproterenol and the natural agonist norepinephrine are that:  
(i) Carazolol lacks the hydroxyl groups thought to be necessary for the activation of β₂AR.  
(i) Carazolol lacks the hydroxyl groups thought to be necessary for the activation of β₂AR.  
(ii) Carazolol is one carbon longer in length from the amino group to the carbazole.  
(ii)The side chain of carazolol is two atoms (one carbon and one oxygen) longer in length from the amino group to the carbazole moiety.  
These are common characteristics of β₂AR antagonists.  
These are common characteristics of β₂AR antagonists.  


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[[Image:B2AR_Binding_Pocket_PolarInt_Act_In.JPG|right|thumb|alt= Alt text| The binding mode of isoproterenol and carazolol in B2AR. Hydrophobic residues are displayed in yellow. Polar interactions are displayed with residues in cyan, oxygen in red, and hydrogen in white. (a) A model of B2AR in its active state in complex with isoproterenol.
(b) B2AR in its inactive state in complex with carazolol. |450px]]
==='''Ligand Binding'''===


==='''Ligand Binding'''===
[[Image:B2AR_Binding_Pocket_PolarInt_Act_In.JPG|right|thumb|alt= Alt text| The binding mode of isoproterenol and carazolol in B2AR. Hydrophobic residues are displayed in yellow. Polar interactions are displayed with residues in cyan, oxygen in red, and hydrogen in white. (a) A model of B2AR in its active state in complex with isoproterenol.
(b) B2AR in its inactive state in complex with carazolol. |425px]]
Ligands share several key interactions in the binding pocket including:
Ligands share several key interactions in the binding pocket including:


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(ii) Hydrophobic interaction between ligand and Val117 in TM3, Phe193  
(ii) Hydrophobic interaction between ligand and Val117 in TM3, Phe193  
in ECL2, Phe289 in TM6, and Phe290 inTM6.  
in ECL2, Phe289 in TM6, and Phe290 inTM6.  
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<applet load='2RH1' size='500' frame='true' align='left' scene='Sandbox_121/2rh1/1' caption='B₂AR inactive state in complex with Carazolol'/>
Inactive B₂AR in complex with Carazolol: <scene name='Sandbox_121/2rh1/6'>Polar</scene> and <scene name='Sandbox_121/2rh1/7'>Hydrophobic</scene> Interactions
<applet load='3P0G' size='500' frame='true' align='right' scene='Sandbox_121/B2ar_struc/1' caption='B₂AR active state in complex with BI-167107'/>
Active B₂AR in complex with BI-167107: <scene name='Sandbox_121/B2ar_struc/7'>Polar</scene> and <scene name='Sandbox_121/B2ar_struc/8'>Hydrophobic</scene> Interactions




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==='''Conformational Change'''===
==='''Conformational Change'''===
[[Image:B2AR-Binding_Pocket_OH.JPG|thumb|left|alt= Alt text| Models of  isoproternol binding to two B2AR structures. (a) Inactive B2AR: 4.78Å distance between the catechol-OH of the ligand and Ser207 of TM5  is too large for a H-bond. (b)  Active B2AR: A hydrogen bond distance of 2.17Å  between the catechol-OH of the ligand and Ser207 on TM5 is shown. |300px]]
<Structure load='Morph_2rh1_on_3p0g_all_atoms.pdb' size='500' frame='true' align='left' caption='Conformational Changes in B2AR from Inactive State(2rh1) to Active State(3p0g)' scene='Sandbox_254/B2ar_morph_ser_glu_arg/32'/>‎
[[Image:B2AR-Binding_Pocket_clash.JPG|thumb|right|alt= Alt text| Model of carazolol binding to B2AR structure. (a) Active B2AR: there is a steric clash between the ligand and Ser207 of TM5.  (b)Inactive B2AR: carazolol in B2AR fits perfectly and blocks the agonist from entering  the binding pocket. |300px]]
When an agonist is in the <scene name='Sandbox_254/B2ar_morph_ser_glu_arg/23'>binding pocket</scene> a 2.1Å inward movement of TM5 at Ser207 is observed. This bulge at ser207 allows for a hydrogen bond between the ligand and the receptor. This interaction appears to be a key event in activation.


When an agonist is in the binding pocket a 2.1Å inward movement of TM5 at Ser207 is observed. This bulge at ser207 allows for a hydrogen bond between the ligand and the receptor. This interaction appears to be a key event in activation.  
[[Image:B2AR-Binding_Pocket_OH.JPG|thumb|right|alt= Alt text| Models of  isoproternol binding to two B2AR structures. (a) Inactive B2AR: 4.78Å distance between the catechol-OH of the ligand and Ser207 of TM5 is too large for a H-bond. (b)  Active B2AR: A hydrogen bond distance of 2.17Å  between the catechol-OH of the ligand and Ser207  on TM5 is shown. |450px]]
After the agonist binds, there is a rearrangement of interactions between residues located beneath the binding pocket that contributes to a rotation and outward movement of TM6 at Phe282. This change is associated with the breaking of the ionic lock between Glu268 in TM6 and Arg131 in TM3, resulting in an 11.4Å outward movement of the helix at the cytoplasmic face.  
[[Image:B2AR-Binding_Pocket_clash.JPG|thumb|right|alt= Alt text| Model of carazolol binding to B2AR structure. (a) Active B2AR: there is a steric clash between the ligand and Ser207 of TM5. (b)Inactive B2AR: carazolol in B2AR fits perfectly and blocks the agonist from entering  the binding pocket. |450px]]
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After the agonist binds, there is a rearrangement of interactions between residues located beneath the binding pocket that contributes to a rotation and outward movement of TM6 at Phe282. This change is associated with the breaking of the ionic lock between Glu268 in TM6 and Arg131 in TM3, resulting in an 11.4Å outward movement of the helix at the cytoplasmic face.


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==='''Molecular Morph'''===
==='''Molecular Morph'''===
The coordinates for molecular morphs between inactive state of B2AR (2rh1) and active state (3p0g) were generated using iPyMOL and eMovie (http://www.weizmann.ac.il/ISPC/eMovie.html). Morphs, a series of 10 linear interpolations between a starting and finishing model, are useful when viewing the transition of a conformational change. This model of B2AR using morphs should not be thought of as precise animation of conformational changes upon activation but rather as a comparison of the inactive state to the active state.
The coordinates for molecular morphs between inactive state of B2AR (2rh1) and active state (3p0g) were generated using iPyMOL and eMovie (http://www.weizmann.ac.il/ISPC/eMovie.html). Morphs, a series of 10 linear interpolations between a starting and finishing model, are useful when viewing the transition of a conformational change. This model of B2AR using morphs should not be thought of as precise animation of conformational changes upon activation but rather as a comparison of the inactive state to the active state.
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==='''Reference'''===
1. Vadim Cherezov, Daniel M. Rosenbaum, Michael A. Hanson, Søren G. F. Rasmussen, Foon Sun Thian, Tong Sun Kobilka, Hee-Jung Choi, Peter Kuhn, William I. Weis, Brian K. Kobilka, Raymond C. Stevens (2007). High Resolution Crystal Structure of an Engineered Human B2-Adrenergic G Protein- Coupled Receptor Science 318, 1258-1265.
2.Søren G. F. Rasmussen, Hee-Jung Choi, Juan Jose Fung, Els Pardon, Paola Casarosa, Pil Seok Chae, Brian T. DeVree, Daniel M. Rosenbaum, Foon Sun Thian, Tong Sun Kobilka, Andreas Schnapp, Ingo Konetzki, Roger K. Sunahara,Samuel H. Gellman, Alexander Pautsch, Jan Steyaert, William I. Weis & Brian K. Kobilka (2011). Structure of a nanobody-stabilized active state of the B2 adrenoceptor Nature 469, 175-180.
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==='''Acknowledgements'''===
Camille and Henry Dreyfus Foundation,
The Rockefeller University Center for Clinical and Translational Science,
The Rockefeller University Science Outreach Program,
Howard Hughes Medical Institute Pre-college Program,
Center for BioMolecular Modeling, Milwaukee School of Engineering,
The David A. Cofrin Center for Biomedical Information,
in the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College,
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