QM/MM structure refined from NMR-structure of a single chain diiron protein
Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.
Computational design and characterization of a monomeric helical dinuclear metalloprotein.
Artificial diiron proteins: from structure to function.
MDELRELLKAEQQAIKIYKEVLKKAKEGDEQELARLIQEIVKAEKQAVKVYKEAAEKARNPEKRQVIDKILEDEEKHIEW LKAASKQGNAEQFASLVQQILQDEQRHVEEIEKKN
Solution structure of four helix-bundle model
Crystal structure of four-helix bundle model
Crystal structure of four-helix bundle model: Due Ferri (II) turn mutant
Sequence No suitable database references were found at time of processing
The structure was first determined using triple-resonance spectrscopy. The structure was then further refined using classical MD followed by 5 ps of Car Parrinello hybrid QM/MM dynamics.
Average over last ps of 5ps QM/MM trajectory. Two metal-site water molecules are included in the average. Other solvent molecules and counter ions are excluded. Atoms included in the QM-part are indicated with a value of 1 in the beta-factor column, whereas atoms in the MM-part are indicated with a value of 0 in the beta-factor column.
1. Step: Classical Molecular dynamics simulation starting from NMR-structure, using non-bonded model for metal-site. 2. step: QM/MM MD for relaxation of local frustrations at the metal site.
2 mM DUE FERRI SINGLE CHAIN U-15N, 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O
2 mM DUE FERRI SINGLE CHAIN U-15N, 10% 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O
2 mM DUE FERRI SINGLE CHAIN U-15N, 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O DIHEXANOYLPHOSPHATIDYLCHOLINE, DIMYRISTOYLPHOSPHATIDYLCHOLINE
A. Brunger, P. Adams, M. Clore, P.Gros, M. Nilges, and R. Reed
F. Delaglio, S. Grzesiek, A. Bax, Geerten, and W. Vuister
P. Nicholas, D. Fushman, V. Ruchinsky, and D. Cowburn
Laxmikant, K, Skeel, R, Bhandarkar, M, Brunner, R, Gursoy, A, Krawetz, N, Phillips, J, Shinozaki, A, Varadarajan, K,Schulten, K
Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., Onufriev, A., Simmerling, C., Wang, B., Woods, R. J.
CPMD: Hutter, J, Alavi, A, Deutsch, T, Ballone, P, Bernasconi, M, Focher, P, Goedecker, S; GROMOS Scott WRP, Huhnenberger, PH, Tironi, TG, Mark, AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF: Laio, A., VandeVondele, J., Rothlisberger, U.
(Version 3.10), based on CPMD and GROMOS