1b1g
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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 CA 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
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