Sandbox 32: Difference between revisions

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There are three <scene name='Sandbox_32/Disulfide_bonds/1'>disulfide bonds</scene> in the Trypsin protein. These bonds occur between Cysteine residues and are shown in yellow in this image of the protein. The remainder of the protein is shown in grey. Disulfide bonds in a protein act as stabilizing forces that occur within and between polypeptide chains.
There are three <scene name='Sandbox_32/Disulfide_bonds/1'>disulfide bonds</scene> in the Trypsin protein. These bonds occur between Cysteine residues and are shown in yellow in this image of the protein. The remainder of the protein is shown in grey. Disulfide bonds in a protein act as stabilizing forces that occur within and between polypeptide chains.
==Ions and Their Intermolecular Forces Between them and the Protein==
==Ions and Their Intermolecular Forces Between them and the Protein==
The Trypsin protein has <scene name='Sandbox_32/Ions_in_protein/1'>ions</scene> that interact with other aspects of the protein. These ions are shown in the figure as the red and yellow compounds, while the remainder of the protein is white in color. Three of the four ions contain four oxygen molecules (red) and one Sulfur molecule (yellow). The final ion contains two Oxygen molecules and one Sulfur molecule. <applet scene='Sandbox_32/Secondary_structure/1' size='350' frame='true' align='true' align='right' caption='Trypsin protein with structural aspects shown.'/>
The Trypsin protein has <scene name='Sandbox_32/Ions_in_protein/1'>ligands</scene> that interact with other aspects of the protein. These ligands are shown in the figure as the red and yellow compounds, while the remainder of the protein is white in color. Three of the four ligands contain four oxygen atoms (red) and one Sulfur atom (yellow). The final ligand contains two Oxygen atoms and one Sulfur atom. <applet scene='Sandbox_32/Secondary_structure/1' size='350' frame='true' align='true' align='right' caption='Trypsin protein with structural aspects shown.'/>


The interactions between the <scene name='Sandbox_32/Sulfur_ion_interactions/1'>Sulfur molecules and the remainder of the protein</scene> are shown in this figure. The Sulfur molecules are shown in green and the ball and stick model shows the parts of the protein that are interacting with the corresponding Sulfur molecules. The remaining parts of the protein interacting with the green Sulfur molecules are the certain parts of the nearby amino acid residues. The Sulfur molecules shown in white in this figure can be ignored since they are related to the Sulfur molecules in the disulfide bonds.
The interactions between the <scene name='Sandbox_32/Sulfur_ion_interactions/1'>Sulfur atoms</scene> are shown in this figure. The Sulfur atoms are shown in green and the ball and stick model shows the parts of the protein that are interacting with the corresponding Sulfur atoms. The remaining parts of the protein interacting with the green Sulfur atoms are the certain parts of the nearby amino acid residues. The Sulfur atoms shown in white in this figure can be ignored since they are related to the Sulfur atoms in the disulfide bonds.


The interactions between the <scene name='Sandbox_32/Oxygen_ion_interactions/2'>Oxygen molecules and the remainder of the protein</scene> are shown in this figure. The Oxygen molecules are shown in red and the ball and stick model shows the parts of the protein that are interacting with the corresponding Oxygen molecules.
The interactions between the <scene name='Sandbox_32/Oxygen_ion_interactions/2'>Oxygen atoms</scene> are shown in this figure. The Oxygen atoms are shown in red and the ball and stick model shows the parts of the protein that are interacting with the corresponding Oxygen atoms.


The composition of the Trypsin protein can be seen when surrounded <scene name='Sandbox_32/Compostion/2'>water molecules</scene>. This image shows where and how water molecules bond to the protein. The water molecules are blue, while the protein is an off-white color. These interactions are important when it comes to how the protein interacts with its environment.
The composition of the Trypsin protein can be seen when surrounded <scene name='Sandbox_32/Compostion/2'>water molecules</scene>. This image shows where and how water molecules bond to the protein. The water molecules are blue, while the protein is an off-white color. These interactions are important when it comes to how the protein interacts with its environment.
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