1b1g: Difference between revisions

Revision as of 12:50, 21 February 2008

SOLVATED REFINEMENT OF CA-LOADED CALBINDIN D9K

OverviewOverview

The three-dimensional solution structures of proteins determined with NMR-derived constraints are almost always calculated in vacuo. The solution structure of (Ca2+)2-calbindin D9k has been redetermined by new restrained molecular dynamics (MD) calculations that include Ca2+ ions and explicit solvent molecules. Four parallel sets of MD refinements were run to provide accurate comparisons of structures produced in vacuo, in vacuo with Ca2+ ions, and with two different protocols in a solvent bath with Ca2+ ions. The structural ensembles were analyzed in terms of structural definition, molecular energies, packing density, solvent-accessible surface, hydrogen bonds, and the coordination of calcium ions in the two binding loops. Refinement including Ca2+ ions and explicit solvent results in significant improvements in the precision and accuracy of the structure, particularly in the binding loops. These results are consistent with results previously obtained in free MD simulations of proteins in solution and show that the rMD refined NMR-derived solution structures of proteins, especially metalloproteins, can be significantly improved by these strategies.

About this StructureAbout this Structure

1B1G is a Single protein structure of sequence from Bos taurus with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

Protein solution structure calculations in solution: solvated molecular dynamics refinement of calbindin D9k., Kordel J, Pearlman DA, Chazin WJ, J Biomol NMR. 1997 Oct;10(3):231-43. PMID:9390401

Page seeded by OCA on Thu Feb 21 11:50:33 2008

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OCA

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-[[Image:1b1g.gif|left|200px]]<br /><applet load="1b1g" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1b1g.gif|left|200px]]<br /><applet load="1b1g" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1b1g" />
 '''SOLVATED REFINEMENT OF CA-LOADED CALBINDIN D9K'''<br />
 ==Overview==
-The three-dimensional solution structures of proteins determined with, NMR-derived constraints are almost always calculated in vacuo. The, solution structure of (Ca2+)2-calbindin D9k has been redetermined by new, restrained molecular dynamics (MD) calculations that include Ca2+ ions and, explicit solvent molecules. Four parallel sets of MD refinements were run, to provide accurate comparisons of structures produced in vacuo, in vacuo, with Ca2+ ions, and with two different protocols in a solvent bath with, Ca2+ ions. The structural ensembles were analyzed in terms of structural, definition, molecular energies, packing density, solvent-accessible, surface, hydrogen bonds, and the coordination of calcium ions in the two, binding loops. Refinement including Ca2+ ions and explicit solvent results, in significant improvements in the precision and accuracy of the, structure, particularly in the binding loops. These results are consistent, with results previously obtained in free MD simulations of proteins in, solution and show that the rMD refined NMR-derived solution structures of, proteins, especially metalloproteins, can be significantly improved by, these strategies.
+The three-dimensional solution structures of proteins determined with NMR-derived constraints are almost always calculated in vacuo. The solution structure of (Ca2+)2-calbindin D9k has been redetermined by new restrained molecular dynamics (MD) calculations that include Ca2+ ions and explicit solvent molecules. Four parallel sets of MD refinements were run to provide accurate comparisons of structures produced in vacuo, in vacuo with Ca2+ ions, and with two different protocols in a solvent bath with Ca2+ ions. The structural ensembles were analyzed in terms of structural definition, molecular energies, packing density, solvent-accessible surface, hydrogen bonds, and the coordination of calcium ions in the two binding loops. Refinement including Ca2+ ions and explicit solvent results in significant improvements in the precision and accuracy of the structure, particularly in the binding loops. These results are consistent with results previously obtained in free MD simulations of proteins in solution and show that the rMD refined NMR-derived solution structures of proteins, especially metalloproteins, can be significantly improved by these strategies.
 ==About this Structure==
-B1G is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1B1G OCA].
+B1G is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B1G OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Bos taurus]]
 [[Category: Single protein]]
-[[Category: Chazin, W.J.]]
+[[Category: Chazin, W J.]]
 [[Category: Kordel, J.]]
-[[Category: Pearlman, D.A.]]
+[[Category: Pearlman, D A.]]
 [[Category: CA]]
 [[Category: calcium-binding protein]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:16:50 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:50:33 2008''