Protein solution structure calculations in solution: solvated molecular dynamics refinement of calbindin D9k.Kordel, J., Pearlman, D.A., Chazin, W.J.
(1997) J.Biomol.NMR 10: 231-243
- PubMed: 9390401
- PubMed Abstract:
- High-Resolution Solution Structure of Calcium-Loaded Calbindin D9k
Kordel, J.,Skelton, N.J.,Akke, M.,Chazin, W.J.
(1993) J.Mol.Biol. 231: 711
- 1H NMR Sequential Resonance Assignments, Secondary Structure, and Global Fold in Solution of the Major (Trans-Pro43) Form of Bovine Calbindin D9k
Kordel, J.,Forsen, S.,Chazin, W.J.
(1989) Biochemistry 28: 7065
- The Rate and Structural Consequences of Proline Cis-Trans Isomerization in Calbindin D9k: NMR Studies of the Minor (Cis-Pro43) Isoform and the Pro43Gly Mutant
Kordel, J.,Forsen, S.,Drakenberg, T.,Chazin, W.J.
(1990) Biochemistry 29: 4400
- The Refined Structure of Vitamin D-Dependent Calcium-Binding Protein from Bovine Intestine. Molecular Details, Ion Binding, and Implications for the Structure of Other Calcium-Binding Proteins
Szebenyi, D.M.E.,Moffat, K.
(1986) J.Biol.Chem. 261: 8761
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) calcu ...
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.
Pharmacia & Upjohn, Stockholm, Sweden.