Molecular dynamics simulation of sucrose- and trehalose-coated carboxy-myoglobin.
We performed a room temperature molecular dynamics (MD) simulation on a system containing 1 carboxy-myoglobin (MbCO) molecule in a sucrose-water matrix of identical composition (89% [sucrose/(sucrose + water)] w/w) as for a previous trehalose-water-MbCO simulation (Cottone et al., Biophys J 2001;80:931-938). Results show that, as for trehalose, the amplitude of protein atomic mean-square fluctuations, on the nanosecond timescale, is reduced with respect to aqueous solutions also in sucrose. A detailed comparison as a function of residue number evidences mobility differences along the protein backbone, which can be related to a different efficacy in bioprotection. Different heme pocket structures are observed in the 2 systems. The joint distribution of the magnitude of the electric field at the CO oxygen atom and of the angle between the field and the CO unit vector shows a secondary maximum in sucrose, absent in trehalose. This can explain the CO stretching band profile (A substates distribution) differences evidenced by infrared spectroscopy in sucrose- and trehalose-coated MbCO (Giuffrida et al., J Phys Chem B 2004;108:15415-15421), and in particular the appearance of a further substate in sucrose. Analysis of hydrogen bonds at the protein-solvent interface shows that the fraction of water molecules shared between the protein and the sugar is lower in sucrose than in trehalose, in spite of a larger number of water molecules bound to the protein in the former system, thus indicating a lower protein-matrix coupling, as recently observed by Fourier transform infrared (FTIR) experiments (Giuffrida et al., J Phys Chem B 2004;108:15415-15421).
Cottone
G
G
INFM and Dipartimento di Scienze Fisiche ed Astronomiche, Università di Palermo, Palermo, Italy.
Giuffrida
S
S
Ciccotti
G
G
Cordone
L
L
D001665:Binding Sites; D002236:Carbohydrate Conformation; D003198:Computer Simulation; D004187:Disaccharides / Q000737:chemistry; D007700:Kinetics; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry*; D013395:Sucrose / Q000737:chemistry*; D014199:Trehalose / Q000737:chemistry*
D004187:Disaccharides; D009211:Myoglobin; C018013:carboxymyoglobin; D013395:Sucrose; D014199:Trehalose