Sandbox 121: Difference between revisions
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==='''Conformational Change'''=== | ==='''Conformational Change'''=== | ||
[[Image:B2AR-Binding_Pocket_OH.JPG|thumb| | [[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. |300px]] | ||
[[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]] | [[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]] | ||
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{{clear}} | {{clear}} | ||
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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. | ||
