ISSN:
1573-5001
Keywords:
Calcium-binding proteins
;
Protein structure
;
Restrained molecular dynamics
;
Solvated refinement
;
Structure refinement
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
,
Chemistry and Pharmacology
Notes:
Abstract The three-dimensional solution structures of proteins determinedwith NMR-derived constraints are almost always calculated in vacuo. Thesolution structure of (Ca2+)_2-calbindinD9k has been redetermined by new restrained molecular dynamics(MD) calculations that include Ca2+ ions and explicit solventmolecules. Four parallel sets of MD refinements were run to provide accuratecomparisons of structures produced in vacuo, in vacuo withCa2+ ions, and with two different protocols in a solvent bathwith Ca2+ ions. The structural ensembles were analyzed interms of structural definition, molecular energies, packing density,solvent-accessible surface, hydrogen bonds, and the coordination of calciumions in the two binding loops. Refinement including Ca2+ ionsand explicit solvent results in significant improvements in the precisionand accuracy of the structure, particularly in the binding loops. Theseresults are consistent with results previously obtained in free MDsimulations of proteins in solution and show that the rMD refinedNMR-derived solution structures of proteins, especially metalloproteins, canbe significantly improved by these strategies.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1023/A:1018383102870
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