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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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Calculated spectral densities, G(ω), for protein (a) and that for solvent (b) calculated from MD of FHS (solid line) and MHS (broken line) in the frequency range 0 < ω < 10 meV. (c) Scaled solvent spectral densities, G(ω)/Nsolv, where Nsolv is the number of degrees of freedom in solvent, are also shown. The results at 100 K (thin line) and 300 K (thick line) are shown. The spectra were broadened by assuming a frequency resolution of 20 μeV.
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fig3: Calculated spectral densities, G(ω), for protein (a) and that for solvent (b) calculated from MD of FHS (solid line) and MHS (broken line) in the frequency range 0 < ω < 10 meV. (c) Scaled solvent spectral densities, G(ω)/Nsolv, where Nsolv is the number of degrees of freedom in solvent, are also shown. The results at 100 K (thin line) and 300 K (thick line) are shown. The spectra were broadened by assuming a frequency resolution of 20 μeV.

Mentions: Compared with the results in MHS, both Sinc(Q,ω) (Fig. 1, a and b) and X(ω) (Fig. 1 c) in FHS are in good agreement in the frequency range ω > 4 meV at both temperatures. On the other hand, the shape of G(ω) in MHS differs entirely from that in FHS at both temperatures. This is due to the fact that the contribution of water to the spectra is negligibly small in the high frequency region of Sinc(Q,ω) and X(ω), whereas it is significantly large in G(ω). Fig. 3, a and b, shows the contribution of protein in G(ω) and that of solvent. Here, it should be noted that G(ω) satisfies the normalization given by Eq. 9. Let us first compare the spectral densities between the two models at the same temperature. For protein G(ω) (Fig. 3 a), there is good agreement between FHS and MHS above 4 meV, indicating that the effect of the difference in the hydration levels on protein dynamics does not appear in the frequency range ω > 4 meV. However, solvent G(ω) in FHS is much larger than in MHS at all temperatures, as the number of solvent degrees of freedom in FHS is about six times larger than that in MHS (Fig. 3 b). Next, we compare the temperature change in each model. Protein G(ω) in FHS at 100 K significantly drops compared to the results in FHS at 300 K, indicating the density shift to higher frequency. Interestingly, solvent G(ω) in FHS decreases drastically in low temperature in the frequency range shown in this figure, corresponding to that of water in FHS at 100 K (0.14 Å2) is much smaller than that at 300 K (556.6 Å2). In Fig. 3 c, scaled solvent spectral densities, G(ω)/Nsolv, where Nsolv is the number of degrees of freedom for the solvent, are also shown. G(ω)/Nsolv is comparable at 100 K but considerably different at 300 K between FHS and MHS. It is noted that of water in FHS at 100 K (0.14 Å2) is close to that in MHS (0.19 Å2). At 300 K, the scaled density in MHS has higher frequency components than FHS, indicating that a higher fraction of water molecules in MHS tends to be restricted in their dynamics. This result is confirmed by the fact that of water in FHS (556.6 Å2) is one order larger than that in MHS (25.8 Å2) at 300 K.


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

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

Calculated spectral densities, G(ω), for protein (a) and that for solvent (b) calculated from MD of FHS (solid line) and MHS (broken line) in the frequency range 0 < ω < 10 meV. (c) Scaled solvent spectral densities, G(ω)/Nsolv, where Nsolv is the number of degrees of freedom in solvent, are also shown. The results at 100 K (thin line) and 300 K (thick line) are shown. The spectra were broadened by assuming a frequency resolution of 20 μeV.
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Related In: Results  -  Collection

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fig3: Calculated spectral densities, G(ω), for protein (a) and that for solvent (b) calculated from MD of FHS (solid line) and MHS (broken line) in the frequency range 0 < ω < 10 meV. (c) Scaled solvent spectral densities, G(ω)/Nsolv, where Nsolv is the number of degrees of freedom in solvent, are also shown. The results at 100 K (thin line) and 300 K (thick line) are shown. The spectra were broadened by assuming a frequency resolution of 20 μeV.
Mentions: Compared with the results in MHS, both Sinc(Q,ω) (Fig. 1, a and b) and X(ω) (Fig. 1 c) in FHS are in good agreement in the frequency range ω > 4 meV at both temperatures. On the other hand, the shape of G(ω) in MHS differs entirely from that in FHS at both temperatures. This is due to the fact that the contribution of water to the spectra is negligibly small in the high frequency region of Sinc(Q,ω) and X(ω), whereas it is significantly large in G(ω). Fig. 3, a and b, shows the contribution of protein in G(ω) and that of solvent. Here, it should be noted that G(ω) satisfies the normalization given by Eq. 9. Let us first compare the spectral densities between the two models at the same temperature. For protein G(ω) (Fig. 3 a), there is good agreement between FHS and MHS above 4 meV, indicating that the effect of the difference in the hydration levels on protein dynamics does not appear in the frequency range ω > 4 meV. However, solvent G(ω) in FHS is much larger than in MHS at all temperatures, as the number of solvent degrees of freedom in FHS is about six times larger than that in MHS (Fig. 3 b). Next, we compare the temperature change in each model. Protein G(ω) in FHS at 100 K significantly drops compared to the results in FHS at 300 K, indicating the density shift to higher frequency. Interestingly, solvent G(ω) in FHS decreases drastically in low temperature in the frequency range shown in this figure, corresponding to that of water in FHS at 100 K (0.14 Å2) is much smaller than that at 300 K (556.6 Å2). In Fig. 3 c, scaled solvent spectral densities, G(ω)/Nsolv, where Nsolv is the number of degrees of freedom for the solvent, are also shown. G(ω)/Nsolv is comparable at 100 K but considerably different at 300 K between FHS and MHS. It is noted that of water in FHS at 100 K (0.14 Å2) is close to that in MHS (0.19 Å2). At 300 K, the scaled density in MHS has higher frequency components than FHS, indicating that a higher fraction of water molecules in MHS tends to be restricted in their dynamics. This result is confirmed by the fact that of water in FHS (556.6 Å2) is one order larger than that in MHS (25.8 Å2) at 300 K.

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