1b7m: Difference between revisions

Revision as of 11:10, 2 May 2008

VERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES

OverviewOverview

The stability profile of mutant protein (SPMP) (Ota,M., Kanaya,S. and Nishikawa,K., 1995, J. Mol. Biol., 248, 733-738) estimates the changes in conformational stability due to single amino acid substitutions using a pseudo-energy potential developed for evaluating structure-sequence compatibility in the structure prediction method, the 3D-1D compatibility evaluation. Nine mutant human lysozymes expected to significantly increase in stability from SPMP were constructed, in order to experimentally verify the reliability of SPMP. The thermodynamic parameters for denaturation and crystal structures of these mutant proteins were determined. One mutant protein was stabilized as expected, compared with the wild-type protein. However, the others were not stabilized even though the structural changes were subtle, indicating that SPMP overestimates the increase in stability or underestimates negative effects due to substitution. The stability changes in the other mutant human lysozymes previously reported were also analyzed by SPMP. The correlation of the stability changes between the experiment and prediction depended on the types of substitution: there were some correlations for proline mutants and cavity-creating mutants, but no correlation for mutants related to side-chain hydrogen bonds. The present results may indicate some additional factors that should be considered in the calculation of SPMP, suggesting that SPMP can be refined further.

About this StructureAbout this Structure

1B7M is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.

ReferenceReference

Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes., Takano K, Ota M, Ogasahara K, Yamagata Y, Nishikawa K, Yutani K, Protein Eng. 1999 Aug;12(8):663-72. PMID:10469827 Page seeded by OCA on Fri May 2 11:10:30 2008

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

OCA

@@ Line 1: / Line 1: @@
 [[Image:1b7m.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1b7m |SIZE=350|CAPTION= <scene name='initialview01'>1b7m</scene>, resolution 2.2&Aring;
+The line below this paragraph, containing "STRUCTURE_1b7m", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1b7m|  PDB=1b7m  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b7m OCA], [http://www.ebi.ac.uk/pdbsum/1b7m PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1b7m RCSB]</span>
-}}
 '''VERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES'''
@@ Line 32: / Line 29: @@
 [[Category: Yamagata, Y.]]
 [[Category: Yutani, K.]]
-[[Category: human lysozyme]]
+[[Category: Human lysozyme]]
-[[Category: mutant stability]]
+[[Category: Mutant stability]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 11:10:30 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:55:19 2008''