2foc: Difference between revisions

Revision as of 18:23, 21 February 2008

Structure of porcine pancreatic elastase in 55% dimethylformamide

OverviewOverview

Multiple solvent crystal structures (MSCS) of porcine pancreatic elastase were used to map the binding surface the enzyme. Crystal structures of elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80% 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40% cyclohexane in 50% isopropanol and 10% water showed no bound benzene or cyclohexane molecules, but did reveal bound isopropanol. The clusters of organic solvent probe molecules coincide with pockets occupied by known inhibitors. MSCS also reveal the areas of plasticity within the elastase binding site and allow for the visualization of a nearly complete first hydration shell. The pattern of organic solvent clusters determined by MSCS for elastase is consistent with patterns for hot spots in protein-ligand interactions determined from database analysis in general. The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design.

About this StructureAbout this Structure

2FOC is a Single protein structure of sequence from Sus scrofa with , and as ligands. Active as Pancreatic elastase, with EC number 3.4.21.36 Full crystallographic information is available from OCA.

ReferenceReference

Multiple solvent crystal structures: probing binding sites, plasticity and hydration., Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D, J Mol Biol. 2006 Apr 14;357(5):1471-82. Epub 2006 Jan 30. PMID:16488429

Page seeded by OCA on Thu Feb 21 17:23:26 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2foc.gif|left|200px]]<br /><applet load="2foc" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2foc.gif|left|200px]]<br /><applet load="2foc" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2foc, resolution 2.000&Aring;" />
 '''Structure of porcine pancreatic elastase in 55% dimethylformamide'''<br />
 ==Overview==
-Multiple solvent crystal structures (MSCS) of porcine pancreatic elastase, were used to map the binding surface the enzyme. Crystal structures of, elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80%, 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol, showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not, bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40%, cyclohexane in 50% isopropanol and 10% water showed no bound benzene or, cyclohexane molecules, but did reveal bound isopropanol. The clusters of, organic solvent probe molecules coincide with pockets occupied by known, inhibitors. MSCS also reveal the areas of plasticity within the elastase, binding site and allow for the visualization of a nearly complete first, hydration shell. The pattern of organic solvent clusters determined by, MSCS for elastase is consistent with patterns for hot spots in, protein-ligand interactions determined from database analysis in general., The MSCS method allows probing of hot spots, plasticity and hydration, simultaneously, providing a powerful complementary strategy to guide, computational methods currently in development for binding site, determination, ligand docking and design.
+Multiple solvent crystal structures (MSCS) of porcine pancreatic elastase were used to map the binding surface the enzyme. Crystal structures of elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80% 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40% cyclohexane in 50% isopropanol and 10% water showed no bound benzene or cyclohexane molecules, but did reveal bound isopropanol. The clusters of organic solvent probe molecules coincide with pockets occupied by known inhibitors. MSCS also reveal the areas of plasticity within the elastase binding site and allow for the visualization of a nearly complete first hydration shell. The pattern of organic solvent clusters determined by MSCS for elastase is consistent with patterns for hot spots in protein-ligand interactions determined from database analysis in general. The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design.
 ==About this Structure==
-FOC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with CA, SO4 and DMF as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Pancreatic_elastase Pancreatic elastase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.36 3.4.21.36] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FOC OCA].
+FOC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=DMF:'>DMF</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Pancreatic_elastase Pancreatic elastase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.36 3.4.21.36] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FOC OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: Sus scrofa]]
-[[Category: Bellamacina, C.R.]]
+[[Category: Bellamacina, C R.]]
 [[Category: Mattos, C.]]
 [[Category: Peisach, E.]]
 [[Category: Pereira, A.]]
-[[Category: Petsko, G.A.]]
+[[Category: Petsko, G A.]]
 [[Category: Ringe, D.]]
 [[Category: Vitkup, D.]]
@@ Line 26: / Line 26: @@
 [[Category: elastase; solvent mapping; organic solvents; protein binding sites; multiple solvent crystal structures]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:39:28 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:23:26 2008''