Sandbox 50

From Proteopedia

(Difference between revisions)

Revision as of 20:52, 14 November 2011

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.

1 Horse Pancreatic Lipase

Horse Pancreatic Lipase

Introduction

Lipase, which is produced primarily in the pancreas, functions as a catalyst in the hydrolysis of ester bonds in lipid substrates. This makes lipases an essential molecule for fat digestion. Horse pancreatic lipase’s (EC 3.1.1.3) function is to convert triacylglycerols into 2-monoacylglycerols and free fatty acids. These monomers are then able to be shuttled into the small intestine to be absorbed into the lymphatic system.^[1]

Structure

Horse pancreatic lipase contains two identical peptide chains containing 449 amino acid residues. The N to C terminal order is shown where the N terminus is in blue and can be followed to the C terminus in red. Each chain contains . The N-terminal domain is shown in blue and the C terminal domain is shown in green. The N terminal domain is characterized by an expected alpha/beta hydrolase fold, while the C terminal domain contains a beta sheet sandwich that is involved in colipase binding.^[2] The active site of HPL is highlighted in red to show its location in the N terminal domain of the A chain. Additionally, the can be seen here where negatively charged amino acid residues are seen in red, and positively charged amino acids are seen in blue.

The of HPL contains 13 alpha helices and 28 strands of beta sheets, representing 22% and 30%, respectively, of the protein's residues. Hydrophic collapse contributes to much of the secondary and tertiary structures, as the shown in grey are mostly facing towards the interior of the protein. Conversely, the in pink point congregate more on the exterior and point outwards. ^[3]

Disulfide Bonds

Additional tertiary stability is provided by between cysteine residues shown in yellow linkages. Cysteine residues not involved in disulfide bonds are shown as spheres.

Chain Contacts

The two chains of HPL are connected through , , , and . In the last scene, water molecules are shown as pink spheres.

Calcium Ions

Two calcium ions are also present in the protein to further the structure of HPL. Each chain contains one calcium ion, each bound by the same residues. While the calcium ligands are no involved in the manipulating the substrate in the active site, enzymatic activity has been shown to be related to free calcium concentration. At lower calcium concentrations, lipases show reduced activity.^[4] This is most likely due to reduced structural coordination. A more detailed view of the calcium coordination can be seen here:

Image:Calcium binding.PNG

Calcium Ion Coordination^[5]

Colipase Binding

When bile salts accumulate at the lid/water interface, adsoprtion of the enzyme on its substrates is prohibited. In order to overcome this inhibitory effect, colipase binds to HPL and anchors lipase at the interface coated with bile salts.^[6] When bound to colipase,HPL exists in its active, .^[7] Here chains A and C (blue and pink) are the chians from the original HPL protein, and chains B and D (green and yellow) are colipase peptides.

Rate studies show that the disassociation constant of the lipase-colipase complex is 101.1x10^−9 M. When the substrate is absent, the disassociation constant increases by several orders, indicating that disassociation of colipase from lipase increases when no substrates are present. These studies confirm that pancreatic lipase has many highly , as horse, ox, pig, rat, dog, and chicken colipases all can activate HPL and have similar disassociation constants. ^[8]

In the presence of colipase, the enzyme is activated which moves the (shown in red) which is composed of amino acids 216-239. The N-terminal flap moves in a concerted fashion along with the C-terminal domain to reveal the active site (green), allowing it to bind with a substrate. It is hypothesized that this flexibility may have significance in binding the colipase-lipase complex with the water-lipid interface.^[9] The reorganization of the flap also induces a second conformational change that creates the oxyanion hole.^[10]

Active Site and Mechanism

Image:Mech..PNG

HPL hydrolysis reaction^[11]

The of HPL is characterized by side chain residues Ser 152, His 263, and Asp 176 shown in red. Additionally, the main chain amides of Phe 77 (blue) and Leu 153 (green) are shown, as both are also involved with enzymatic activity.^[12]

This active site in HPL is used to hydrolyze triacylglycerol into carboxylate and diacylglycerol.

Image:Lipase mech.gif

lipase-catalyzed hydrolysis of esters^[13]

In the first step, His263 deprotonates Ser152. Ser152 is then free to attack the carboxy carbon of triacylglycerol through a nucleophilic addition reaction. Next, the diacylglycerol product is eliminated when the oxyaninion collapses. This deprotonates His263. In the third step, His263 deprotonates water, which can then attack the carboxyl carbon of Ser152 through a nucleophilic addition reaction. Finally, the carboxylate product and Ser152 are eliminated with the collapse of the oxyanion, and His263 is deprotonated.^[14]

References

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_50"

@@ Line 11: / Line 11: @@
 Horse pancreatic lipase contains two identical peptide chains containing 449 amino acid residues. The N to C terminal order is shown <scene name='Sandbox_50/5-3_rainbow/1'>here</scene> where the N terminus is in blue and can be followed to the C terminus in red. Each chain contains
-<scene name='Sandbox_50/N_and_c_terminus/1'>two well defined domains</scene>. The N-terminal domain is shown in blue and the C terminal domain is shown in green. The N terminal domain is characterized by an expected alpha/beta hydrolase fold, while the C terminal domain contains a beta sheet sandwich that is involved in colipase binding.  The active site of HPL is highlighted in red to show its location in the N terminal domain of the A chain. Additionally, the <scene name='Sandbox_50/Aa_types/1'>charge distribution</scene> can be seen here where negatively charged amino acid residues are seen in red, and positively charged amino acids are seen in blue.
+<scene name='Sandbox_50/N_and_c_terminus/1'>two well defined domains</scene>. The N-terminal domain is shown in blue and the C terminal domain is shown in green. The N terminal domain is characterized by an expected alpha/beta hydrolase fold, while the C terminal domain contains a beta sheet sandwich that is involved in colipase binding.<ref>http://www.pdb.org/pdb/explore/explore.do?structureId=1HPL</ref> The active site of HPL is highlighted in red to show its location in the N terminal domain of the A chain. Additionally, the <scene name='Sandbox_50/Aa_types/1'>charge distribution</scene> can be seen here where negatively charged amino acid residues are seen in red, and positively charged amino acids are seen in blue.
-The <scene name='Sandbox_50/Helix/2'>secondary structure</scene> of HPL contains 13 alpha helices and 28 strands of beta sheets, representing 22% and 30%, respectively, of the protein's residues. Hydrophic collapse contributes to much of the secondary and tertiary structures, as the <scene name='Sandbox_50/Hphobic_residues/2'>hydrophobic residues</scene> shown in grey are mostly facing towards the interior of the protein. Conversely, the <scene name='Sandbox_50/Polar_residues/2'>polar residues</scene> in pink point congregate more on the exterior and point outwards.
+The <scene name='Sandbox_50/Helix/2'>secondary structure</scene> of HPL contains 13 alpha helices and 28 strands of beta sheets, representing 22% and 30%, respectively, of the protein's residues. Hydrophic collapse contributes to much of the secondary and tertiary structures, as the <scene name='Sandbox_50/Hphobic_residues/2'>hydrophobic residues</scene> shown in grey are mostly facing towards the interior of the protein. Conversely, the <scene name='Sandbox_50/Polar_residues/2'>polar residues</scene> in pink point congregate more on the exterior and point outwards. <ref>http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1HPL</ref>
 === Disulfide Bonds ===

Sandbox 50

From Proteopedia

Revision as of 20:52, 14 November 2011

Contents

Horse Pancreatic Lipase

Introduction

Structure

Disulfide Bonds

Chain Contacts

Calcium Ions

Colipase Binding

Active Site and Mechanism

References

Views

Personal tools

Navigation

Search

Toolbox