1B1G

SOLVATED REFINEMENT OF CA-LOADED CALBINDIN D9K

Summary for 1B1G

• Entry DOI: 10.2210/pdb1b1g/pdb
• Descriptor: PROTEIN (CALBINDIN D9K), CALCIUM ION (2 entities in total)
• Functional Keywords: calcium-binding protein, metal binding protein
• Biological source: Bos taurus (cattle)
• Total number of polymer chains: 1
• Total formula weight: 8550.65

Authors

Kordel, J.,Pearlman, D.A.,Chazin, W.J. (deposition date: 1998-11-20, release date: 1998-11-25, Last modification date: 2023-12-27)

Primary citation

Kordel, J.,Pearlman, D.A.,Chazin, W.J.
Protein solution structure calculations in solution: solvated molecular dynamics refinement of calbindin D9k.
J.Biomol.NMR, 10:231-243, 1997

PubMed Abstract: 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.

PubMed: 9390401
DOI: 10.1023/A:1018383102870

Experimental method

SOLUTION NMR