Sandbox 43

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<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' />
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==Introduction==
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<scene name='Sandbox_43/Samaniego_scene/1'>Adenylate kinase</scene> is an enzyme that catalyzes the reversible reaction in which a molecule of ATP and a molecule of AMP are converted into two molecules of ADP through the following reaction scheme:
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== '''Pancreatic Lipase''' ==
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ATP + AMP ⇔ 2 ADP
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Adenylate kinase is integral in maintaining cellular energy homeostasis by providing ADP, which is later utilized in oxidative phosphorylation in metabolic pathways for energy production. This enzyme also possesses a unique flexibility to bind to ligands, pictured as the space filling region.
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== '''Introduction''' ==
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==Structural Elements==
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<StructureSection load='1hpl' size='500' side='right' caption='Structure of Horse Pancreatic Lipase (PDB entry [[1hpl]])' scene=''>A subclass of esterases, pancreatic lipase (EC 3.1.1.3) is an enzyme that catalyzes the hydrolysis and formation of lipids. While produced in the pancreas, it is also present in the stomach and mouth. Due to its effective ester bond hydrolysis of lipids, lipase is essential for fat digestion, breaking lipids into monoglycerides and single fatty acids. If one is lipase deficient, it is hard to obtain adequate nutrition from food. This results in diseases such as cystic fibrosis, Crohn's disease, and celiac disease.
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The <scene name='Sandbox_43/Samaniego_scene_bg/2'>secondary structural elements</scene> of adenylate kinase show alpha helices (black) and beta sheets (blue) surrounding the non-hydrolysable substrate analogue (orange). <scene name='Sandbox_43/Samaniego_scene_hbonds/1'>Hydrogen bonds</scene> should be visible in green but may not load. These hydrogen bonds connect amino acids of alpha helices and beta sheets, which comprise the backbone of the protein. The anti-parallel configuration of the hydrogen bonds on beta sheets provides stability for the protein.
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== '''Structure''' ==
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The <scene name='Sandbox_43/Samaniego_scene_stickswires/1'>hydrophobic residues</scene> of adenylate kinase are depicted in the black and blue ball and stick representation. These are buried on the interior of the enzyme to avoid contact with the solvent, demonstrating the hydrophobic effect. The protein is surround by <scene name='Sandbox_43/Samaniego_scene_hydrophobic/1'>hydrophilic residues</scene> depicted in the yellow portions. These hydrophilic portions can include polar and charged amino acids, which have a high affinity for the intermolecular solvent interactions in terms of hydrogen bonding and solubility.
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The quaternary structure of horse pancreatic lipase (as featured right) contains two molecules which each contain 449 amino acid residues, 705 water molecules, and 1 calcium ion. These two identical molecules are connected by a two-fold symmetry axis. The <scene name='Sandbox_43/Interactions_between_chains/1'>interactions between the a chain and the b chain</scene> include <scene name='Sandbox_43/Hydogen_bonds/1'>hydrogen bonds</scene> and salt bridges. The secondary structure of lipase is composed of 102 residues that constitute 13 <scene name='Sandbox_43/Alpha_helixes/1'>alpha helices</scene> (22% helical) and 139 residues that constitute 28 <scene name='Sandbox_43/Beta_sheets/3'>beta sheet</scene> strands (30% beta sheets). Lipase is essentially composed of two domains, the <scene name='Sandbox_43/N_terminal/1'>N-terminal domain</scene>, which contains the <scene name='Sandbox_43/Active_site/4'>active site</scene> of lipase (consisting of three residues: Ser-152, Asp-176, and His-263). The N-terminal domain also contains the <scene name='Sandbox_43/Active_site/3'>lid region</scene> (residues 216-239) which serves to block the active site, which is nestled in the <scene name='Sandbox_43/Hydrophobic/2'>hydrophobic regions</scene>, from the solvent. Additionally, the <scene name='Sandbox_43/C_terminal/1'>C-terminal domain</scene> is essential to the binding of lipase with colipase, an important cofactor for the catalysis of lipids. This forms the <scene name='Sandbox_43/Complex_with_colipase/1'>lipase-colipase complex</scene>.
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==Solvent Accessibility==
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When dissolved in <scene name='Sandbox_43/Samaniego_scene_water2/1'>water</scene> (light blue), the hydrophilic residues of adenylate kinase interact with this polar solvent to fold the protein into its most stable conformation through hydrogen bonding. It can be seen that water interacts with the ligand (green) at its center, where catalysis occurs. However, water mostly surrounds the hydrophilic exterior of the molecule, where the majority of hydrogen bonding occurs.
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== '''Calcium Ligand''' ==
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The most prominent ligand involved in the structure of lipase is the <scene name='Sandbox_43/Calcium_ligand/3'>calcium ion</scene>. This ion has been shown to promote the folding of lipase into its active dimer state. As such, the calcium ion is extremely important in forming the lipase-fat complex, necessary for the breakdown of lipids. Studies have shown that an increase in calcium concentration in a lipase catalyzed reaction resulted in an increase in the rate of the reaction.
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==Ligand Interactions==
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Portions of adenylate kinase which interact with the ligand are shown here in purple. These are called the <scene name='Sandbox_43/Samaniego_scene_ligand2/1'>ligand contacts</scene> and have polar-charged side chains, which help to stabilize the ligand as it binds to the protein's active site. The catalytic resides (unable to be pictured) are able to directly interact/bind to the ligand.
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== '''Colipase Cofactor''' ==
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==Sources==
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Library CHEM410 page: http://libguides.messiah.edu/content.php?pid=279182&sid=2407875
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<scene name='Sandbox_43/Colipase/1'>Colipase</scene> is a small protein that is necessary for efficient lipid catalysis by lipase. It is secreted by the pancreas in its inactive form as procolipase which is converted into the active colipase by trypsin. It binds to the non-catalytic C-terminal domain of lipase and in so doing stabilizes its active conformation as it hydrolyzes lipids. Furthermore, it also binds to the lipid interface, increasing the affinity between lipase and the lipid.
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Wikipedia: http://en.wikipedia.org/wiki/Adenylate_kinase
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European Bioinformatics Institute: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000850

Current revision

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

Drag the structure with the mouse to rotate

Contents

Introduction

is an enzyme that catalyzes the reversible reaction in which a molecule of ATP and a molecule of AMP are converted into two molecules of ADP through the following reaction scheme:

ATP + AMP ⇔ 2 ADP

Adenylate kinase is integral in maintaining cellular energy homeostasis by providing ADP, which is later utilized in oxidative phosphorylation in metabolic pathways for energy production. This enzyme also possesses a unique flexibility to bind to ligands, pictured as the space filling region.

Structural Elements

The of adenylate kinase show alpha helices (black) and beta sheets (blue) surrounding the non-hydrolysable substrate analogue (orange). should be visible in green but may not load. These hydrogen bonds connect amino acids of alpha helices and beta sheets, which comprise the backbone of the protein. The anti-parallel configuration of the hydrogen bonds on beta sheets provides stability for the protein.

The of adenylate kinase are depicted in the black and blue ball and stick representation. These are buried on the interior of the enzyme to avoid contact with the solvent, demonstrating the hydrophobic effect. The protein is surround by depicted in the yellow portions. These hydrophilic portions can include polar and charged amino acids, which have a high affinity for the intermolecular solvent interactions in terms of hydrogen bonding and solubility.

Solvent Accessibility

When dissolved in (light blue), the hydrophilic residues of adenylate kinase interact with this polar solvent to fold the protein into its most stable conformation through hydrogen bonding. It can be seen that water interacts with the ligand (green) at its center, where catalysis occurs. However, water mostly surrounds the hydrophilic exterior of the molecule, where the majority of hydrogen bonding occurs.

Ligand Interactions

Portions of adenylate kinase which interact with the ligand are shown here in purple. These are called the and have polar-charged side chains, which help to stabilize the ligand as it binds to the protein's active site. The catalytic resides (unable to be pictured) are able to directly interact/bind to the ligand.

Sources

Library CHEM410 page: http://libguides.messiah.edu/content.php?pid=279182&sid=2407875 Wikipedia: http://en.wikipedia.org/wiki/Adenylate_kinase European Bioinformatics Institute: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000850

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