**************** The 18th., Lab Seminar *****************

Date: Mon, November 28, 2005  PM 1:30-

Place: No.616 Seminar room
　　　　　　 Graduate School of Information Science

Speaker: Isseki Yu

Title: Molecular Dynamics Simulation of Sucrose-and Trehalose-Coated
Carboxy-Myoglobin PROTEINS:Structure,Function,and Bioinformatics 59:291
‐302 (2005)

G.Cottone,1 S.Giuffrida,1 G.Ciccotti,2 and L.Cordone 1 *
1 INFM and Dipartimento di Scienze Fisiche ed Astronomiche,Universita`di
Palermo,Palermo,Italy
2 INFM and Dipartimento di Fisica,Universita`di Roma La Sapienza,Roma,Italy

ABSTRUCT
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).

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