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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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The spectra, X(ω), defined as Eq. 6, as a function of frequency, ω (0 < ω < 10 meV) calculated (a) for all atoms in the system and (b) for only protein atoms using the results in FHS (solid line) and MHS (broken line) at 100 (thin line) and 300 K (thick line) in log-log plots. The regression line using the values between 0.002 and 0.1 meV is drawn for each spectrum.
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fig6: The spectra, X(ω), defined as Eq. 6, as a function of frequency, ω (0 < ω < 10 meV) calculated (a) for all atoms in the system and (b) for only protein atoms using the results in FHS (solid line) and MHS (broken line) at 100 (thin line) and 300 K (thick line) in log-log plots. The regression line using the values between 0.002 and 0.1 meV is drawn for each spectrum.

Mentions: Finally, we discuss the frequency dependence of X(ω) of protein at frequencies lower than 1 meV. Interestingly, a linear relationship between the logarithm of X(ω) and that of ω is seen in the frequency range between 0.002 meV and 0.1 meV for all simulation conditions in Fig. 6. Here, no resolution function is applied to the spectra. Thus, X(ω) in this frequency range can be approximated as(15)\documentclass[10pt]{article}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{pmc}\usepackage[Euler]{upgreek}\pagestyle{empty}\oddsidemargin -1.0in\begin{document}\begin{equation*}X({\omega})=\frac{A}{{\omega}^{{\alpha}}},\end{equation*}\end{document}where A and α depend on the simulation conditions. When only the protein contribution was considered (Fig. 6 b), differences in α values are not particularly large. However, the contribution of water molecules is significantly large as seen in the α value difference between 100 and 300 K in FHS. As mentioned, the contribution from a proton () to X(ω) is much larger than that of a deuterium (). The total numbers of protons and deutriums in the system are comparable (3688 and 4824, respectively). The significant contribution from water is due to the bulk-like water at 300 K in FHS. A total of 95% of water molecules have mean-square fluctuations two orders greater than the average value of the proton in the protein. In the very low frequency region, these bulk-like water molecules contribute to X(ω) significantly. In other cases, the protein contribution mostly determines the A and α values. A trend was also found for the Fourier transformed autocorrelation function of the potential energy functions of plastocyanin at frequencies between ∼0.4 and ∼4 meV (44) and for Sinc(Q,ω) of lysozyme at frequencies between ∼0.01 and ∼0.4 meV (45). The fractional Brownian dynamics model is discussed in both cases (44,45), considering the fractality of the energy landscape. Here, we found a trend in the lower frequency range ω < ∼0.01 meV. Protein dynamics, which occur on a much longer than nanosecond timescale, are related to function and are expected to be investigated from the combination of simulations and experiment.


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

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

The spectra, X(ω), defined as Eq. 6, as a function of frequency, ω (0 < ω < 10 meV) calculated (a) for all atoms in the system and (b) for only protein atoms using the results in FHS (solid line) and MHS (broken line) at 100 (thin line) and 300 K (thick line) in log-log plots. The regression line using the values between 0.002 and 0.1 meV is drawn for each spectrum.
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Related In: Results  -  Collection

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

fig6: The spectra, X(ω), defined as Eq. 6, as a function of frequency, ω (0 < ω < 10 meV) calculated (a) for all atoms in the system and (b) for only protein atoms using the results in FHS (solid line) and MHS (broken line) at 100 (thin line) and 300 K (thick line) in log-log plots. The regression line using the values between 0.002 and 0.1 meV is drawn for each spectrum.
Mentions: Finally, we discuss the frequency dependence of X(ω) of protein at frequencies lower than 1 meV. Interestingly, a linear relationship between the logarithm of X(ω) and that of ω is seen in the frequency range between 0.002 meV and 0.1 meV for all simulation conditions in Fig. 6. Here, no resolution function is applied to the spectra. Thus, X(ω) in this frequency range can be approximated as(15)\documentclass[10pt]{article}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{pmc}\usepackage[Euler]{upgreek}\pagestyle{empty}\oddsidemargin -1.0in\begin{document}\begin{equation*}X({\omega})=\frac{A}{{\omega}^{{\alpha}}},\end{equation*}\end{document}where A and α depend on the simulation conditions. When only the protein contribution was considered (Fig. 6 b), differences in α values are not particularly large. However, the contribution of water molecules is significantly large as seen in the α value difference between 100 and 300 K in FHS. As mentioned, the contribution from a proton () to X(ω) is much larger than that of a deuterium (). The total numbers of protons and deutriums in the system are comparable (3688 and 4824, respectively). The significant contribution from water is due to the bulk-like water at 300 K in FHS. A total of 95% of water molecules have mean-square fluctuations two orders greater than the average value of the proton in the protein. In the very low frequency region, these bulk-like water molecules contribute to X(ω) significantly. In other cases, the protein contribution mostly determines the A and α values. A trend was also found for the Fourier transformed autocorrelation function of the potential energy functions of plastocyanin at frequencies between ∼0.4 and ∼4 meV (44) and for Sinc(Q,ω) of lysozyme at frequencies between ∼0.01 and ∼0.4 meV (45). The fractional Brownian dynamics model is discussed in both cases (44,45), considering the fractality of the energy landscape. Here, we found a trend in the lower frequency range ω < ∼0.01 meV. Protein dynamics, which occur on a much longer than nanosecond timescale, are related to function and are expected to be investigated from the combination of simulations and experiment.

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