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Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra.

Joti Y, Nakagawa H, Kataoka M, Kitao A - Biophys. J. (2008)

Bottom Line: The peak frequency in the minimal hydration state shifts to lower than that in the full hydration state.Protein motions, which contribute to the boson peak, are distributed throughout the whole protein.The fine structure of the dynamics structure factor is expected to be detected by the experiment if a high resolution instrument (< approximately 20 microeV) is developed in the near future.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

ABSTRACT
Hydration effects on protein dynamics were investigated by comparing the frequency dependence of the calculated neutron scattering spectra between full and minimal hydration states at temperatures between 100 and 300 K. The protein boson peak is observed in the frequency range 1-4 meV at 100 K in both states. The peak frequency in the minimal hydration state shifts to lower than that in the full hydration state. Protein motions with a frequency higher than 4 meV were shown to undergo almost harmonic motion in both states at all temperatures simulated, whereas those with a frequency lower than 1 meV dominate the total fluctuations above 220 K and contribute to the origin of the glass-like transition. At 300 K, the boson peak becomes buried in the quasielastic contributions in the full hydration state but is still observed in the minimal hydration state. The boson peak is observed when protein dynamics are trapped within a local minimum of its energy surface. Protein motions, which contribute to the boson peak, are distributed throughout the whole protein. The fine structure of the dynamics structure factor is expected to be detected by the experiment if a high resolution instrument (< approximately 20 microeV) is developed in the near future.

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(a−d) The frequency dependence of the mean-square fluctuations of the Hα atoms, χa(ω), in Eq. 4 are drawn as two-dimensional contour plots. The results in FHS at (a) 100 K and (c) 300 K and those in MHS (b) 100 K and (d) 300 K are shown. (e−h) Residue dependence of  of these atoms calculated by Eq. 10 at (e) 100 K (thin line) and (f) 300 K (thick line) are shown. The sums of χa(ω) over the hydrogen atoms connected to α-carbons in (g) FHS (solid line) and (h) MHS (broken line) are shown as a function of frequency. Here, the values at 300 K are scaled by 1/3 for comparison with the results at 100 K. A diagram of the secondary structure of SNase is shown in e and f, with boxes for α-helices and triangles for β-sheets.
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fig5: (a−d) The frequency dependence of the mean-square fluctuations of the Hα atoms, χa(ω), in Eq. 4 are drawn as two-dimensional contour plots. The results in FHS at (a) 100 K and (c) 300 K and those in MHS (b) 100 K and (d) 300 K are shown. (e−h) Residue dependence of of these atoms calculated by Eq. 10 at (e) 100 K (thin line) and (f) 300 K (thick line) are shown. The sums of χa(ω) over the hydrogen atoms connected to α-carbons in (g) FHS (solid line) and (h) MHS (broken line) are shown as a function of frequency. Here, the values at 300 K are scaled by 1/3 for comparison with the results at 100 K. A diagram of the secondary structure of SNase is shown in e and f, with boxes for α-helices and triangles for β-sheets.

Mentions: As mentioned, we defined 1 < ω < 4 meV as the frequency range of the protein boson peak. The contribution of to total is smaller than the other two components in both FHS and MHS at temperatures above 180 K. Fig. 5, a–d, shows the frequency dependence of χa(ω) (Eq. 4) for the hydrogen atoms connected to α-carbons. It should be noted that the magnitude at 300 K is scaled by the temperature ratio of 100 K to 300 K, 1:3. Here, χa(ω) is smoothed by a 20-μeV resolution function. The sum of χa(ω) over the hydrogen atoms connected to α-carbons (Hα) are plotted in Fig. 5, g and h, and the frequency dependence is similar to that over all atoms (X(ω) in Fig. 1 c). Sharp peaks between 1 and 2 meV are observed, except in FHS at 300 K. As seen in Fig. 5, b and d, χa(ω) in MHS at 300 K is significantly larger than that in MHS at 100 K below 2 meV. Jumping-among-minima motions are expected to take place partly at 300 K. In the results in FHS at 300 K, peaks between 1 and 2 meV disappear and quasielastic contributions dominate χa(ω) (Fig. 5 c) since anharmonic motions are supposed to occur frequently.


Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra.

Joti Y, Nakagawa H, Kataoka M, Kitao A - Biophys. J. (2008)

(a−d) The frequency dependence of the mean-square fluctuations of the Hα atoms, χa(ω), in Eq. 4 are drawn as two-dimensional contour plots. The results in FHS at (a) 100 K and (c) 300 K and those in MHS (b) 100 K and (d) 300 K are shown. (e−h) Residue dependence of  of these atoms calculated by Eq. 10 at (e) 100 K (thin line) and (f) 300 K (thick line) are shown. The sums of χa(ω) over the hydrogen atoms connected to α-carbons in (g) FHS (solid line) and (h) MHS (broken line) are shown as a function of frequency. Here, the values at 300 K are scaled by 1/3 for comparison with the results at 100 K. A diagram of the secondary structure of SNase is shown in e and f, with boxes for α-helices and triangles for β-sheets.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC2480692&req=5

fig5: (a−d) The frequency dependence of the mean-square fluctuations of the Hα atoms, χa(ω), in Eq. 4 are drawn as two-dimensional contour plots. The results in FHS at (a) 100 K and (c) 300 K and those in MHS (b) 100 K and (d) 300 K are shown. (e−h) Residue dependence of of these atoms calculated by Eq. 10 at (e) 100 K (thin line) and (f) 300 K (thick line) are shown. The sums of χa(ω) over the hydrogen atoms connected to α-carbons in (g) FHS (solid line) and (h) MHS (broken line) are shown as a function of frequency. Here, the values at 300 K are scaled by 1/3 for comparison with the results at 100 K. A diagram of the secondary structure of SNase is shown in e and f, with boxes for α-helices and triangles for β-sheets.
Mentions: As mentioned, we defined 1 < ω < 4 meV as the frequency range of the protein boson peak. The contribution of to total is smaller than the other two components in both FHS and MHS at temperatures above 180 K. Fig. 5, a–d, shows the frequency dependence of χa(ω) (Eq. 4) for the hydrogen atoms connected to α-carbons. It should be noted that the magnitude at 300 K is scaled by the temperature ratio of 100 K to 300 K, 1:3. Here, χa(ω) is smoothed by a 20-μeV resolution function. The sum of χa(ω) over the hydrogen atoms connected to α-carbons (Hα) are plotted in Fig. 5, g and h, and the frequency dependence is similar to that over all atoms (X(ω) in Fig. 1 c). Sharp peaks between 1 and 2 meV are observed, except in FHS at 300 K. As seen in Fig. 5, b and d, χa(ω) in MHS at 300 K is significantly larger than that in MHS at 100 K below 2 meV. Jumping-among-minima motions are expected to take place partly at 300 K. In the results in FHS at 300 K, peaks between 1 and 2 meV disappear and quasielastic contributions dominate χa(ω) (Fig. 5 c) since anharmonic motions are supposed to occur frequently.

Bottom Line: The peak frequency in the minimal hydration state shifts to lower than that in the full hydration state.Protein motions, which contribute to the boson peak, are distributed throughout the whole protein.The fine structure of the dynamics structure factor is expected to be detected by the experiment if a high resolution instrument (< approximately 20 microeV) is developed in the near future.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

ABSTRACT
Hydration effects on protein dynamics were investigated by comparing the frequency dependence of the calculated neutron scattering spectra between full and minimal hydration states at temperatures between 100 and 300 K. The protein boson peak is observed in the frequency range 1-4 meV at 100 K in both states. The peak frequency in the minimal hydration state shifts to lower than that in the full hydration state. Protein motions with a frequency higher than 4 meV were shown to undergo almost harmonic motion in both states at all temperatures simulated, whereas those with a frequency lower than 1 meV dominate the total fluctuations above 220 K and contribute to the origin of the glass-like transition. At 300 K, the boson peak becomes buried in the quasielastic contributions in the full hydration state but is still observed in the minimal hydration state. The boson peak is observed when protein dynamics are trapped within a local minimum of its energy surface. Protein motions, which contribute to the boson peak, are distributed throughout the whole protein. The fine structure of the dynamics structure factor is expected to be detected by the experiment if a high resolution instrument (< approximately 20 microeV) is developed in the near future.

Show MeSH
Related in: MedlinePlus