caa a22 4500 477135870 CHVBK 20180405111717.0 cr unu---uuuuu 170330e19971001xx s 000 0 eng 10.1023/A:1018383102870 doi (NATIONALLICENCE)springer-10.1023/A:1018383102870 Protein solution structure calculations in solution: Solvated molecular dynamics refinement of calbindin D9k [Elektronische Daten] [Johan Kördel, David Pearlman, Walter Chazin] 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. Kluwer Academic Publishers, 1997 Calcium-binding proteins nationallicence Protein structure nationallicence Restrained molecular dynamics nationallicence Solvated refinement nationallicence Structure refinement nationallicence Kördel Johan Pharmacia & Upjohn, N62:6, S-112 87, Stockholm, Sweden aut Pearlman David Vertex Pharmaceuticals Inc., 02139-4242, Cambridge, MA, U.S.A aut Chazin Walter The Scripps Research Institute, 92037, La Jolla, CA, U.S.A aut Journal of Biomolecular NMR Kluwer Academic Publishers 10/3(1997-10-01), 231-243 0925-2738 10:3<231 1997 10 10858 https://doi.org/10.1023/A:1018383102870 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1023/A:1018383102870 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Kördel Johan Pharmacia & Upjohn, N62:6, S-112 87, Stockholm, Sweden aut NATIONALLICENCE 700 1- Pearlman David Vertex Pharmaceuticals Inc., 02139-4242, Cambridge, MA, U.S.A aut NATIONALLICENCE 700 1- Chazin Walter The Scripps Research Institute, 92037, La Jolla, CA, U.S.A aut NATIONALLICENCE 773 0- Journal of Biomolecular NMR Kluwer Academic Publishers 10/3(1997-10-01), 231-243 0925-2738 10:3<231 1997 10 10858 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer