Search

To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the molecular friction coefficient into the contributions for each site on the macromolecule. The method was applied to several fullerenols in ambient water. The friction coefficients for the hydrophilic part, such as the OH group, were larger than those for the hydrophobic part, such as the C. The hydration effect did not depend only on the kind of functional group but also on the surface roughness. This approach would be useful in explaining the experimentally observed large changes in diffusion coefficients of proteins that were accompanied by conformation changes. [ABSTRACT FROM AUTHOR]

The transient grating (TG) method, which is one of the photothermal techniques, can enable sensitive detection of thermal energy with high temporal resolution based on changes in the refractive index of a material. In addition to thermal energy, the TG method can also detect any changes that affect the refractive index, such as changes in the partial molar volume and in the absorption spectrum far from the probe wavelength. In this Perspective, recent studies on chemical reaction dynamics of proteins using the TG method are reviewed and discussed. To reveal the reaction schemes of proteins, it is particularly important to detect dynamics that cannot be detected by optical spectroscopy (spectrally silent dynamics), such as enthalpy changes, conformational changes, and changes in intermolecular interactions (protein–water, protein–protein, protein–lipids, and protein–DNA). The TG method is appropriate and powerful for such applications. Spectrally silent dynamics have clearly been observed by monitoring time-resolved diffusion and volume changes. Furthermore, the impact of the structural fluctuation of proteins on their reactivity has been successfully demonstrated by monitoring the thermal expansion and compressibility changes of short-lived intermediates. For expansion of the TG application to non-photochemical reactions, one attempt using the stopped flow-TG technique is described. Future possible applications of the TG method are suggested. [ABSTRACT FROM AUTHOR]

To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the molecular friction coefficient into the contributions for each site on the macromolecule. The method was applied to several fullerenols in ambient water. The friction coefficients for the hydrophilic part, such as the OH group, were larger than those for the hydrophobic part, such as the C. The hydration effect did not depend only on the kind of functional group but also on the surface roughness. This approach would be useful in explaining the experimentally observed large changes in diffusion coefficients of proteins that were accompanied by conformation changes. [ABSTRACT FROM AUTHOR]

Heliorhodopsins (HeRs) are a new category of rhodopsins. They exist as a dimer and exhibit a characteristic inverted topology. HeRs bind all-trans-retinal as a chromophore in the dark, and its isomerization to the 13-cis form by light illumination leads to a photocyclic reaction involving several photo-intermediates: K, L, M, and O. In this study, the kinetics of conformational changes of HeR from Thermoplasmatales archaeon SG8-52-1 (TaHeR) were studied by the transient grating (TG) and circular dichroism (CD) methods. The TG method reveals that the diffusion coefficient (D) does not change until the O formation suggesting no significant conformation change at the surface of the protein during the early steps of the reaction. Subsequently, D decreases upon the O formation. Although two time constants (202 ms and 2.6 ms) are observed for the conversion from the M to O by the absorption detection, D decreases only at the first step (202 ms). Lightinduced unfolding of helical structure is detected by the CD method. To examine the contribution of a characteristic helix in the intracellular loop 1 (ICL1 helix), Tyr93 on the ICL1 helix was replaced by Gly (Y93G), and the reaction of this mutant was also investigated. It was found that this replacement partially suppresses the D-change, although the CD-change is almost the same as that of the wild type. These results are interpreted in terms of different sensitivities of TG and CD methods, that is, D is sensitive to the structure of the solvent-exposed surface and selectively observes the conformational change in the ICL1 region. It is suggested that the structure of hydrophilic residues in the ICL1 helix is changed during this process. [ABSTRACT FROM AUTHOR]