Sandbox 32

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<Structure load='1ake' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /><!-- PLEASE DO NOT DELETE THIS TEMPLATE -->
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=Trypsin=
 
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Trypsin is a medium size globular protein that functions as a pancreatic serine protease. This enzyme hydrolyzes bonds by cleaving peptides on the C-terminal side of the amino acid residues lysine and arginine. It has also been shown that cleavage will not occur if there is a proline residue on the carboxyl side of the cleavage site. Trypsin was first discovered in 1876 by Kuhne, who investigated the proteolytic activity of the enzyme. In 1931 the enzyme was purified by crystallization by Norothrop and Kunitz and later in 1974 the three dimensional structure of trypsin was determined. Throughout the 1990's the role of trypsin in hereditary pancreatitis and the mutation that causes it was discovered. Today trypsin is used in the development of cell and tissue protocols, as well as in the medical field to determine the role of trypsin in pancreatic diseases<ref>Trypsin. 2010. 30 October 2010 <http://www.worthington-biochem.com/tyr/default.html></ref>.
 
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==Structure==
 
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The <scene name='Sandbox_32/N-c_rainbow/2'>pathway</scene> of the protein can be followed from N-terminus of the protein (blue) to the C-terminus of the protein (red).
 
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Trypsin has many important structural aspects. The <applet scene='Sandbox_32/Secondary_structure/1' size='350' frame='true' align='true' align='right' caption='Trypsin protein with structural aspects shown.'/>secondary structures are shown this figure <scene name='Sandbox_32/Secondary_structure/1'>(Secondary Structure)</scene>. The main backbone of the trypsin protein is shown in yellow <scene name='Sandbox_32/Secondary_structure_main_chain/1'>(main backbone)</scene>. Trypsin has two alpha helices shown in blue <scene name='Sandbox_32/Secondary_structure_alpha/1'>(alpha helices)</scene> and two beta sheets shown in green <scene name='Sandbox_32/Secondary_structure_beta/1'>(beta Sheets)</scene>. The beta sheets in the Trypsin protein are antiparallel to each other and connected by a Beta-hairpin turn.
 
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==Polar vs. Nonpolar Residues==
 
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This image shows the <scene name='Sandbox_32/Polar_versus_nonpolar/2'>polarity</scene> of the residues in the protein. The polar areas of the protein are shown in pink, while the non-polar areas of the molecule are shown in light blue. The polarity of the individual amino acid residues can be seen better in the <scene name='Sandbox_32/Polar_vs_non_stick/1'>stick model</scene> or the <scene name='Sandbox_32/Spacefill_polar_vs_nonpolar/2'>spacefill model</scene>. The polar amino acid residues are again shown in pink, while the non-polar amino acid residues are shown in blue. By rotating the three representations of the polar versus non-polar areas of the protein to an aerial view, it can be seen that the polar (hydrophilic) areas are located toward the outside of the protein, while the non-polar (hydrophobic) areas are located toward the inside of the protein.
 
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==Contacts Between Structural Components and Remainder of the Protein==
 
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===Charge===
 
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The charge of the different components of Trypsin are shown in this figure <scene name='Sandbox_32/Charge/1'>(charge figure)</scene>. The cationic (+) atoms are shown in blue, while the anionic (-) are shown in red. These charged aspects of the protein face the outside environment surrounding the protein. The light purple parts of the protein are uncharged and the gray portions of the protein are hydrophobic. These portions of the protein make up the hydrophobic core of the protein. The charged and uncharged portions of the protein directly relate to the hydrophilic and hydrophobic character of the protein.
 
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===Side Chains===
 
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The <scene name='Sandbox_32/Side_chains/1'>side chains</scene> are attached to the amino acids residues that make up the protein. In this figure the side chains of the protein are shown in pink and the rest of the protein is shown in grey. There are numerous different side chains represented on the protein. Some of the side chains are aromatic, while others are not. Some side chains are <scene name='Sandbox_32/Side_chains_charged/1'>charged</scene>, while others are uncharged. The type of side chain it is and therefore the corresponding amino acid can be determined by the charge on the side chain.
 
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===Disulfide Bonds===
 
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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.
 
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==Ions and Their Intermolecular Forces Between them and the Protein==
 
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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.
 
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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.
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== '''Adenylate Kinase''' (PDB ID #: 1ake)==
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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.
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The <scene name='Sandbox_32/Chain_a/2'>A Chain</scene> by itself may be in a slightly different conformation than when it is <scene name='Sandbox_32/Both_chains/1'>attached</scene> to the B chain (as found in nature).
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==Other Structural Features==
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===Composition===
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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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==Function and Catalytic Mechanism==
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===Catalytic Mechanism===
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[[Image:503-3a-2serineprotease.jpg |thumb]]
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[[Image:Triad_1.jpg|thumb]]
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The function of Trypsin is to break down peptides using a hydrolysis reaction into amino acid building blocks. This mechanism is a general catalytic mechanism that all Serine proteases use. The active site where this mechanism occurs in Trypsin is composed of three amino acids and called a <scene name='Sandbox_45/Ctriadd102h57s195/4'>catalytic triad</scene>. The three catalytic residues are Serine 195, Histidine 57, and Aspartate 102 <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. The structure of the catalytic triad and the mechanism are shown in the figures to the right. In the mechanism, serine is bonded to the imidazole ring of the histidine. When histidine accepts a proton from serine an alkoxide nucleophile is formed. This nucleophile attacks the substrate when the substrate is present. The role of the aspartate residue is hold histidine in the proper position to make it a good proton acceptor. What makes this mechanism works is that a pocket if formed from the three residues and the three residues function to hold each other in proper position for nucleophilic attack.
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The steps of the mechanism involve two tetrahedral intermediates and an Acyl-enzyme intermediate <ref>Structural Biochemistry. 10 June 2010. 30 October 2010.<http://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Catalytic_Triad>.</ref>. The mechanism can be followed in more detail in the figure on the right <ref>Image From: http://www.bmolchem.wisc.edu/courses/spring503/503-sec1/DRAWINGS/503-3a-2serineprotease.jpg</ref>.
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===Oxyanion Hole===
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An important motif that is formed in this reaction is an oxyanion hole. This is also shown in the figure to the right <ref> Williams, Loren. Georgia Tech. http://www2.chemistry.gatech.edu/~1W26/bcourse_information/6521/protein/serine_protease/triad_1/html.</ref>. This oxyanion hole is specifically formed between the amide hydrogen atoms of Serine 195 and Glycine 193. This oxyanion hole stabilizes the tetrahedral intermediate through the distribution of negative charge to the cleaved amide <ref>Structural Biochemistry. 10 June 2010. 30 October 2010.<http://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Catalytic_Triad>.</ref>.
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==Trypsin Proenzyme: Zymogen==
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===Trypsinogen===
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[[Image:Tryogen.gif |thumb]]
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Trypsinogen is the precursor form or zymogen of Trypsin. Zymogens are enzyme precursors that are made and secreted in the lysosome of the cell. Zymogens are not active until they go through a chemical process such as hydrolysis, cleavage, or other cleavages that reveal the active site. The zymogen precursor is necessary in order to prevent the destruction of cellular proteins and to allow the enzyme to be in it's active state only when in appropriate conditions. Trypsinogen is specifically produced in the exocrine cells of the pancreas. There are three isoforms of Trypsinogen that are secreted by the pancreas. The precursor is only activated when it reaches the lumen of the small intestine. This activation occurs through the help of an enteropeptidase and once activated trypsin stimulates the formation of more trypsinogen<ref>Trypsin. 30 October 2010 <http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzyme/trypsin.html>.</ref>. The structure of Bovine Trypsinogen is shown in the figure to the right <ref> Image From: http://chemistry.umeche.maine.edu/MAT500/Peptidase1.html</ref>.
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==Comparison to Chymotrypsin and Elastase==
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<applet scene='Sandbox_32/Chymotrypsin/1' size='275' frame='true' align='true' align='left' caption='Structure of Chymotrypsin and Elastase.'/>
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Trypsin, chymotrypsin, and elastase are all digestive enzymes that are produced in the pancreas and catalyze the hydrolysis of peptide bonds. Each of these enzymes has different specificities in regards to the side chains next to the peptide bond. Chymotrypsin prefers a large hydrophobic residue, trypsin is specific for a positively charged residue, and elastase prefers a small neutral residue. Chymotrypsin, trypsin and elastase are all proteins that contain a catalytic mechanism and hydrolyze peptides using the serine protease mechanism. Chymotrypsin and elastase are both homologs of Trypsin since they are 40% alike in structure and composition <ref> Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008. </ref>. In the <scene name='Sandbox_32/Chymotrypsin/2'>Chymotrypsin</scene> structure shown the alpha helices are blue, the beta sheets are green, and the remainder of the protein is red. In the <scene name='Sandbox_32/Elastase/2'>Elastase</scene> structure shown the alpha helices are in red, the beta sheets are yellow, and the remainder of the protein is orange.
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==Applications and Uses of Trypsin==
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Trypsin has many applications due to fact that it is easily purified in high quantities. The trypsin enzyme is often used in the research setting to digest proteins and then identify the resulting peptides using mass spectrometry. Trypsin has many uses in the medical field such as dissolving blood clots and treating inflammation. Other applications include its use in pre-digesting of baby food, fingerprinting and sequencing work, and environmental monitoring <ref> Trypsin. 2010. 30 October 2010 <http://www.worthington-biochem.com/tyr/default.html></ref>.
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Adenylate Kinase contains both types of secondary structure, <scene name='Sandbox_32/Helices_sheets/2'>alpha helices and beta sheets</scene>. In this scene, alpha helices are in light blue and beta sheets are in yellow.
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The <scene name='Sandbox_32/H_bonds_2/1'>hydrogen bonding</scene> highlighted in this scene shows us that the secondary structure (helices and sheets) is held together by hydrogen bonds. The beta sheets appear to be parallel, as the H-bonds are not all aligned in one direction.
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<scene name='Sandbox_32/Hydrophobic_stickandwireframe/1'>Hydrophobic side chains</scene>, highlighted here in pink, tend to point towards the inside of the molecule where they do not have to interact with the polar water molecules.
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==References==
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The <scene name='Sandbox_32/Hydrophilic/1'>hydrophilic side chains</scene>, highlighted here in blue along with the transparent pink hydrophobic residues, tend to be pointed towards the outside of the protein, where it will interact with the cytosol.
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<references/>
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<scene name='Sandbox_32/Water_ligand/3'>Water molecules</scene> (shown in blue) surround and solvate the protein. The ligand is highlighted in green. The waters seem to congregated on one side than the other, possibly to make room for chain B to bind.
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Sidechain and ligand <scene name='Sandbox_32/Sidechain_ligand_interaction/2'>interactions</scene> are shown in this scene. The ligand is in orange, and the interacting side chains are in dark blue and red. Of these contacting residues, only some actually catalyze the reaction on the substrate. These <scene name='Sandbox_32/Active_site_2/1'>active site</scene> residues are highlighted in red. These are the residues which interact chemically with the substrate to turn it into product. The non-active site residues are important in substrate (or ligand) binding.

Current revision

Adenylate Kinase

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Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013.


Adenylate Kinase (PDB ID #: 1ake)

The by itself may be in a slightly different conformation than when it is to the B chain (as found in nature).

Adenylate Kinase contains both types of secondary structure, . In this scene, alpha helices are in light blue and beta sheets are in yellow.

The highlighted in this scene shows us that the secondary structure (helices and sheets) is held together by hydrogen bonds. The beta sheets appear to be parallel, as the H-bonds are not all aligned in one direction.

, highlighted here in pink, tend to point towards the inside of the molecule where they do not have to interact with the polar water molecules.

The , highlighted here in blue along with the transparent pink hydrophobic residues, tend to be pointed towards the outside of the protein, where it will interact with the cytosol.

(shown in blue) surround and solvate the protein. The ligand is highlighted in green. The waters seem to congregated on one side than the other, possibly to make room for chain B to bind.

Sidechain and ligand are shown in this scene. The ligand is in orange, and the interacting side chains are in dark blue and red. Of these contacting residues, only some actually catalyze the reaction on the substrate. These residues are highlighted in red. These are the residues which interact chemically with the substrate to turn it into product. The non-active site residues are important in substrate (or ligand) binding.

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