Sandbox 30: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 16: | Line 16: | ||
* <scene name='Sandbox_30/Backbone/1'>Backbone</scene> | * <scene name='Sandbox_30/Backbone/1'>Backbone</scene> | ||
* <scene name='Sandbox_30/Side_chains/1'>Side Chains (orange)</scene> | * <scene name='Sandbox_30/Side_chains/1'>Side Chains (orange)</scene> | ||
* <scene name='Sandbox_30/Polar_and_nonpolar/1'>Polar (blue), and Nonpolar (Crimson)</scene> | * <scene name='Sandbox_30/Polar_and_nonpolar/1'>Polar (blue), and Nonpolar (Crimson)</scene> - Ball and stick | ||
* <scene name='Sandbox_30/Polar_and_nonpolar/2'>Polar (blue), and Nonpolar (Crimson)</scene> - Space filling model | |||
* <scene name='Sandbox_30/Ball_and_stick_with_water/1'>Water (blue) around Trypsin (orange)</scene> | * <scene name='Sandbox_30/Ball_and_stick_with_water/1'>Water (blue) around Trypsin (orange)</scene> | ||
* <scene name='Sandbox_30/Hydrophobic_red/1'>Hydrophobic Portion of Trypsin (red)</scene> | * <scene name='Sandbox_30/Hydrophobic_red/1'>Hydrophobic Portion of Trypsin (red)</scene> | ||
| Line 27: | Line 28: | ||
===Polar and Nonpolar Residues=== | ===Polar and Nonpolar Residues=== | ||
Polar residues are typically hydrophobic, and seek to be sheltered from the aqueous environments that proteins typically inhibit. The polarity of an amino acid is determined by its <scene name='Sandbox_30/Side_chains/1'>side chain (orange)</scene>. When considering the <scene name='Sandbox_30/Polar_and_nonpolar/1'>ball and stick model</scene> it may look like the polar (blue) and nonpolar(crimson) residues are not organized in a specific manner, but when you consider the <scene name='Sandbox_30/Polar_and_nonpolar/2'>space filling model,</scene> it is evident that the majority of the polar residues are shielded by they nonpolar residues. | |||
Another way to show this principle is by looking at the location of the <scene name='Sandbox_30/Hydrophobic_red/1'>hydrophobic sections</scene> of Trypsin (red). The hydrophobic portions desire to be shielded from the water in the smallest area possible in order to minimize its interaction with water, thereby maximizing the entropy of the water. It is evident that basically all water molecules are kept outside the protein when viewing a <scene name='Sandbox_30/Ball_and_stick_with_water/1'>rendering with water</scene> (water-blue, trypsin-orange). | |||
===Ligand Interactions=== | ===Ligand Interactions=== | ||
