Sandbox 30: Difference between revisions
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==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</scene> (orange). 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 nonpolar residues are shielded by the polar 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</scene> (orange). 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 nonpolar residues are shielded by the polar 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). This form of trypsin (PDB 1QLQ), has been modified to help enable its crystalization, and thus has four water molecules inside of it instead of the normal three which is present in the wild-type trpsin<ref> Czapinska, Honorata et al. "High-resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence." ''Journal of Molecular Biology.'' Volume 295, Issue 5, 4 February 2000, Pages 1237-1249 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45F4TXM-2W&_user=4187488&_coverDate=02/04/2000&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000062504&_version=1&_urlVersion=0&_userid=4187488&md5=221a9d3b8b66f6f908a8d93c6b10f18f&searchtype=a#secx12 doi:10.1006/jmbi.1999.3445] </ref>. | 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). Alternatively, for a more in depth analysis of trypsin, you can view | ||
<scene name='Sandbox_30/Space_fill_charge_and_polar/1'>charged (Blue +)(Red -), uncharged polar (purple), and hydrophobic (gray) space filling rendering</scene> which can be even more informing. 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). This form of trypsin (PDB 1QLQ), has been modified to help enable its crystalization, and thus has four water molecules inside of it instead of the normal three which is present in the wild-type trpsin<ref> Czapinska, Honorata et al. "High-resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence." ''Journal of Molecular Biology.'' Volume 295, Issue 5, 4 February 2000, Pages 1237-1249 [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45F4TXM-2W&_user=4187488&_coverDate=02/04/2000&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_acct=C000062504&_version=1&_urlVersion=0&_userid=4187488&md5=221a9d3b8b66f6f908a8d93c6b10f18f&searchtype=a#secx12 doi:10.1006/jmbi.1999.3445] </ref>. | |||
==Intramolecular and Intermolecular Forces== | ==Intramolecular and Intermolecular Forces== | ||
The structure of trypsin is stabilized by a variety of intramolecular and intermolecular forces. Trypsin has three <scene name='Sandbox_30/Disulfied_bonds/ | The structure of trypsin is stabilized by a variety of intramolecular and intermolecular forces. Trypsin has three <scene name='Sandbox_30/Disulfied_bonds/2'>disulfide bonds,</scene> which form between the cysteine amino acids. The cysteine amino acids are shown as pink, and you can see how they are placed in the proper 3-dimensional space to bond with each other. The bond they form is represented by the yellow bar in between them, as each of their sulfurs bind to one another. Disulfide bonds are especially important for structural stability in extracellular environments, where conditions are more prone to fluctuation. Secondary structures are stabilized via interactions that compliment their specific side chains. For example, the first α helix in trypsin's structure is stabilized by several other | ||
<scene name='Sandbox_30/A_helix_hydrophobic/1'>hydrophobic residues</scene> in the molecule itself. The ball and stick amino acids marked with an * are part of α helix while the space filling molecules stabilize the α helix. the The α helix is also stabilized by <scene name='Sandbox_30/A_helix_hydrogen_bonds/1'>intramolecular hydrogen bonding,</scene> as well as | <scene name='Sandbox_30/A_helix_hydrophobic/1'>hydrophobic residues</scene> in the molecule itself. The ball and stick amino acids marked with an * are part of α helix while the space filling molecules stabilize the α helix. the The α helix is also stabilized by <scene name='Sandbox_30/A_helix_hydrogen_bonds/1'>intramolecular hydrogen bonding,</scene> as well as | ||
<scene name='Sandbox_30/A_helix_hydrogen_bonds/2'>the addition of hydrogen bonding to water molecules</scene> (water is dark blue). | <scene name='Sandbox_30/A_helix_hydrogen_bonds/2'>the addition of hydrogen bonding to water molecules</scene> (water is dark blue). | ||
