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Low-frequency vibrational properties of lysozyme in sugar aqueous solutions: A Raman scattering and molecular dynamics simulation study
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10.1063/1.3273218
/content/aip/journal/jcp/131/24/10.1063/1.3273218
http://aip.metastore.ingenta.com/content/aip/journal/jcp/131/24/10.1063/1.3273218

Figures

Image of FIG. 1.
FIG. 1.

(a) Raman susceptibility of lysozyme/water and lysozyme/sugar/water solutions at a concentration of 40 wt %. The susceptibility of dry lysozyme (D) is also shown for comparison. The averaged VDOS of lysozyme obtained from MD simulations are represented below for lysozyme: (b) in the lysozyme/water (W) and the 60 wt % lysozyme/trehalose/water (T) solutions, (c) in the different trehalose solutions, and (d) in the different 60 wt % sugar solutions. The curves in (a)–(d) have been smoothed with the Savitzky–Golay algorithm (Ref. 90) to make easier the comparison of results. Moreover, the scale is logarithmic in (c) and (d) to underline these effects in the frequency range. Their statistical significance was confirmed by a detailed analysis of the standard deviations on the VDOS (data not shown).

Image of FIG. 2.
FIG. 2.

VDOS of different parts of lysozyme determined from MD simulations of the lysozyme/water (W) and the 60 wt % lysozyme/trehalose/water (T) solutions (maltose and sucrose solutions behave similarly and are thus not shown for clarity reasons). The averaged VDOS of some fragments of the most and the least solvent exposed lysozyme residues are shown in the left [(a)–(d)] and right [(e)–(h)] panels of the figure, respectively. [(a) and (b)]: side chain atoms and methyl hydrogens of the 30 most exposed residues, respectively, (c): groups of the most exposed arginine residues, (d): carboxylate groups of the most exposed aspartic and glutamic acids residues. [(e) and (f)]: side chains and methyl hydrogens of the 30 most buried residues, respectively, (g): ring atoms of aromatic residues (phe, trp, tyr), and (h): backbone carbonyl groups of the 30 most buried residues. An example of the atoms considered in the calculations (represented as purple spheres) is given for each subset of atoms. Curves have been smoothed with the Savitzky–Golay algorithm (Ref. 90) to simplify the comparison of results. Furthermore, a careful analysis of the standard deviations, not shown for clarity reasons, confirmed that the effects of sugars on lysozyme were statistically meaningful.

Image of FIG. 3.
FIG. 3.

(a) Raman susceptibility of the lysozyme/water solution at 295 and 368 K, at which lysozyme was shown to be denatured in Refs. 32–34. (b) VDOS of native and denatured lysozyme obtained from MD simulations in water at 300 and 400 K, respectively. The starting conformations for the five simulations of denatured lysozyme were obtained from simulations of lysozyme in implicit solvent at 1000 K (see Sec. II B). Curves in (a) and (b) have been smoothed with the Savitzky–Golay algorithm (Ref. 90). (c) Examples of the conformations used to compute the VDOS in (b).

Image of FIG. 4.
FIG. 4.

(a) Raman susceptibility of water and sugar/water solutions at a concentration of 40 wt %. (b) VDOS of water calculated from MD simulations of the lysozyme/water and the different lysozyme/trehalose/water solutions. Curves in (a) and (b) have been smoothed with the Savitzky–Golay algorithm (Ref. 90) to simplify the comparison of results. The low-frequency VDOS of water have been fitted with a log-normal (LGN) and a Gaussian (G) curves. The dependences on the sugar concentration of the frequency positions and of these two functions are displayed in (c) and (d), respectively.

Tables

Generic image for table
Table I.

System compositions (where , , and denote the number of lysozyme, sugar, and water molecules, respectively), densities, and equilibration/total simulation times for the different sugar concentrations (on a protein-free basis). Data corresponding to result from only one simulation of the lysozyme/pure water solution. T, M, and S denote trehalose, maltose, and sucrose, respectively.

Generic image for table
Table II.

Structural parameters describing the five unfolded conformations used to compute the average VDOS of lysozyme in its denatured state: (i) RMSD from the crystallographic structure of the carbon atoms, (ii) radius of gyration , (iii) solvent accessible surface area (SASA), and (iv) hydration number , defined here as the number of water molecules whose oxygen atom is within 3.4 or 4.5 Å from polar (O, N, S) or apolar (C) heavy atoms of lysozyme, respectively. For comparison, the values for the native lysozyme are given in the last line of the table. Standard deviations from mean values are given in parentheses.

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/content/aip/journal/jcp/131/24/10.1063/1.3273218
2009-12-23
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Low-frequency vibrational properties of lysozyme in sugar aqueous solutions: A Raman scattering and molecular dynamics simulation study
http://aip.metastore.ingenta.com/content/aip/journal/jcp/131/24/10.1063/1.3273218
10.1063/1.3273218
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