Sandbox 51: Difference between revisions

1hpl is the horse pancreatic lipase enzyme that is thought to have a similar structure and function to the human pancreatic lipase.  The  <scene name='Sandbox_51/Lipase_crystal_structure/1'> Crystal Structure</scene> of the human pancreatic lipase has not yet been published.  Lipase is a dimer of two <scene name='Sandbox_51/Lipase_crystal_structure/3'>monomers</scene> with 449 amino acid residues interacting with one <scene name='Sandbox_51/Ligand_position/2'>Calcium Ligand</scene> each.  The calcium ion <scene name='Sandbox_51/Calcium_orientation/2'>orientation</scene> shows that the molecule is located between acidic residues Arg, Asp and Glu.  The enzyme has 13 alpha helices (pink) and 22 beta sheets (yellow) per subunit, as displayed in the <scene name='Sandbox_51/Secondary_structure/2'>secondary structure</scene> <ref>Egloff, M.P., etc. "The 2.46 angstroms resolution structure of the pancreatic lipase colipase complex inhibited by a C11 alkyl phosphonate."(1995) J. Biochemistry 34: 2751-2762 [http://www.pdb.org/pdb/explore/explore.do?structureId=1lpb]</ref>.  At the <scene name='Sandbox_51/Monomer_interface/1'>interface</scene> of the two monomers, interactions include 4 hydrogen bonds and 4 salt bridges that stabilize the dimer <ref>"HORSE PANCREATIC LIPASE. THE CRYSTAL STRUCTURE AT 2.3 ANGSTROMS RESOLUTION." http://bisc.cse.ucsc.edu/pages/BiscHom/1hpl_AB.html</ref>.  The molecule has a varying degree of <scene name='Sandbox_51/Polar_structure/3'>polar and hydrophobic residues</scene> interspersed within the molecules (polar are shown in purple and hydrophobic in white) <ref>Bourne, Y., etc. "Horse pancreatic lipase..."(1994) J.Mol.Biol. 238: 709-732 [http://www.pdb.org/pdb/explore/explore.do?structureId=1HPL]</ref>.  This is important because the enzyme actively digests at the lipid-water interface of the fatty micelles, requiring stability in both polar and non polar environments <ref>Fundamentals of Biochemistry...</ref>. Within each monomer and dimer structures, the molecules are held together by disulfide bonds, hydrogen bonding, and electrostatic interactions (salt bridges).  The enzyme has six covalent <scene name='Sandbox_51/Disulfide_bons/1'>disulfide bonds</scene> per monomer.  Also, the <scene name='Sandbox_51/Salt_bridges/3'>salt bridges</scene> stabilize the monomers and dimer of the enzyme at positively charged nitrogens (blue) in Arg and Lys, and negative oxygens (red) in Asp and Glu residues.  <scene name='Sandbox_51/Hydrogen_bonds/2'>Hydrogen bonds</scene> are present within each monomer, as shown by the hydrogen bond forming residues (light gray), and the oxygen (red) and nitrogen (blue) atoms involved in the hydrogen bonding. Lipase is water soluble due to the polar residues on the surface, and hydrophobic sequences on the interior.  At enzyme activation and interaction with colipase, a confirmation change occurs to expose the more hydrophobic regions to the nonpolar lipid micelle.

The enzyme has <scene name='Sandbox_51/Nc_terminal/1'>two domains</scene> of various composition specific for certain interactions, an N-terminal (blue) and a C-terminal (red).  In the <scene name='Sandbox_51/Secondary_structure/2'>secondary structure</scene>, the N-terminal domain has the hydrolase alpha/beta folding structure, consisting of an alpha-beta sheet consisting of 8 strands connected by helices. The C-terminal domain (enzyme colipase binds) has a beta-sheet sandwich folding pattern <ref>Horse pancreatic lipase...</ref>. The <scene name='Sandbox_51/Active_site/3'>active site</scene> of the lipase molecule is found in the N-terminal domain (residues 1-336) and contains a <scene name='Sandbox_51/Catalytic_tria/1'>catalytic triad</scene> consisting of a Ser-His-Arg for the ester hydrolysis reaction (similar to that of a serine protease). The active site is covered by a 25-residue helical 'lid' blocking the binding site, unless appropriate conditions <ref>Fundamentals of Biochemistry...</ref>.

In addition to the effects of bile salts, Lipase is activated by the coenzyme colipase, which binds to the C-terminal non-catalytic domain.  Upon binding, active lipase is stabilized for the hydrophobic interaction with the triacylglycerides <ref>Fundamentals of Biochemistry...</ref>.  Colipase must be present for activation of lipase.  Lipase activation at the lipid-water interface of triacylglycerides, in the presence of colipase and bile salts, is known as interfacial activation. Colipase is also secreted in the pancreas, but in its inactive form, which must be activated by trypsin before interacting with lipase <ref>"Colipase". Wikipedia: The Free Encyclopedia. 5 July 2011 [http://en.wikipedia.org/wiki/Colipase]</ref>.  Colipase and lipase <scene name='Sandbox_51/Contacts/3'>contacts</scene> are at opposite of the active site on the C-terminal, including polar interactions such as <scene name='Sandbox_51/Salt_bridges/2'>salt bridges</scene> and van der waals forces which stabilize the interaction <ref>van Tilbeurgh H, etc."Structure of the pancreatic lipase-procolipase complex",  1992 Sep 10;359(6391):159-62. PMID:1522902.[http://www.proteopedia.org/wiki/index.php/1n8s]</ref>. <scene name='Sandbox_51/Lipase_and_colipase/1'>Colipase and lipase in complex with a triacylglyceride</scene> shows a unique feature of lipase is the lid over the active sight.  Once colipase has anchored lipase to the lipid-water membrane, a surface change occurs.  The lid of lipase is known to be essential to lipase action.  The 10 residue beta-5 loop changes confirmation exposing lipase's oxyanion hole and hydrophobic surface.  Before colipase binding, lipase is in the <scene name='Sandbox_51/Closed_lid/2'>closed confirmation</scene> where the beta-5 loop(residues 76-84, in pink) and lid (residues 237-261, yellow) protect the oxyanion hole from solvent interaction.  The <scene name='Sandbox_51/Mutated_open_ring/4'>open lid</scene> structure is accompanied by peptide shifts which increase hydrophobic surface area initiating the reaction with the lipid.  One such important shift is part of the lid at residues 240-252 (in yellow), very close to the active site.  Also, it is evident from the image that part of the beta-5 loop interacts with colipase in the open state.  The lid opening is accompanied by a change in secondary structure from a mostly beta-extended confirmation to a structure where more than half the active site is formed from alpha helices <ref>Thomas, A.etc. "Role of the Lid Hydrophobicity Pattern in Pancreatic

Lipase Activity*", The Journal of Biological Chemistry, 2005 September 22; 280(48):40074–40083.</ref>.  Colipase hydrophobic loops interact with the hydrophobic atmosphere of the triacylglyceride initiating lipase active site binding to the lipid, and lid opening. Once colipase is bound, lipase initiates a serine-like hydrolysis involving His, Asp, Ser residues in the catalytic triad <ref>Fundamentals of Biochemistry...</ref>. In the reaction, serine attacks the ester, forming an acyl-enzyme intermediate.  The His and Asp residues help to stabilize the oxyanion intermediate through hydrogen bonding.  Water enters the active site and reacts to release lipase and free the fatty acid. This acylation and deacylation reaction is usually completely reversible.