A novel strategy regarding geometric product for liquids discrimination based on THz reflection spectroscopy

A novel expression of geometric product that associated with the geometric relationship from geometric algebra constructed by the vectorized refractive index and absorption coefficient in THz region is proposed, which could provide a new insight into the THz properties of materials. From the novel expression, the candidate characteristic parameters are extracted for liquids discrimination and present the abundant second order correlation information of optical parameters with the consideration of dimension rising. Three groups of liquids, containing C-reactive protein calibrators and alpha fetoprotein calibrators, were selected as examples to validate the feasibility of the proposed strategy. Comparing with the traditional THz parameters, including refractive index, absorption coefficient, and complex permittivity, the novel approach exhibits notable superiority for differentiation with the evaluation of statistical differences and effect sizes. The proposed geometric product expression could have a large potential on promoting the substance identification in some applications of THz technology.

Photo-Switching of Protein Dynamical Collectivity

We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins (RFP) mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy show in all cases an increase in the turn-on temperature in the bleached state. The result is surprising given that there is little change in the protein surface, and thus, the solvent dynamics held responsible for the transition should not change. A spectral analysis of the measurements guided by quasiharmonic calculations of the protein absorbance reveals that indeed the solvent dynamical turn-on temperature is independent of the thermal stability/photostate however the protein dynamical turn-on temperature shifts to higher temperatures. This is the first demonstration of switching the protein dynamical turn-on temperature with protein functional state. The observed shift in protein dynamical turn-on temperature relative to the solvent indicates an increase in the required mobile waters necessary for the protein picosecond motions, that is, these motions are more collective. Melting-point measurements reveal that the photobleached state is more thermally stable, and structural analysis of related RFP’s shows that there is an increase in internal water channels as well as a more uniform atomic root mean squared displacement. These observations are consistent with previous suggestions that water channels form with extended light excitation providing O2 access to the chromophore and subsequent fluorescence loss. We report that these same channels increase internal coupling enhancing thermal stability and collectivity of the picosecond protein motions. The terahertz spectroscopic characterization of the protein and solvent dynamical onsets can be applied generally to measure changes in collectivity of protein motions.

Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra

Terahertz time-domain spectra (THz-TDS) were investigated using the results of molecular dynamics (MD) simulations of Staphylococcal nuclease at two hydration states in the temperature range between 100 and 300 K. The temperature dependence of THz-TDS was found to differ significantly from that of the incoherent neutron scattering spectra (INSS) calculated from the same MD simulation results. We further examined contributions of the mutual and auto-correlations of the atomic fluctuations to THz-TDS and found that the negative value of the former contribution nearly canceled out the positive value of the latter, resulting in a monotonic increase of the reduced absorption cross section. Because of this cancellation, no distinct broad peak was observed in the absorption lineshape function of THz-TDS, whereas the protein boson peak was observed in INSS. The contribution of water molecules to THz-TDS was extremely large for the hydrated protein at temperatures above 200 K, in which large-amplitude motions of water were excited. The combination of THz-TDS, INSS and MD simulations has the potential to extract function-relevant protein dynamics occurring on the picosecond to nanosecond timescale.

Effect of Temperature and Hydration Level on Purple Membrane Dynamics Studied Using Broadband Dielectric Spectroscopy from Sub-GHz to THz Regions

To investigate the effects of temperature and hydration on the dynamics of purple membrane (PM), we measured the broadband complex dielectric spectra from 0.5 GHz to 2.3 THz using a vector network analyzer and terahertz time-domain spectroscopy from 233 to 293 K. In the lower temperature region down to 83 K, the complex dielectric spectra in the THz region were also obtained. The complex dielectric spectra were analyzed through curve fitting using several model functions. We found that the hydrated states of one relaxational mode, which was assigned as the coupled motion of water molecules with the PM surface, began to overlap with the THz region at approximately 230 K. On the other hand, the relaxational mode was not observed for the dehydrated state. On the basis of this result, we conclude that the protein-dynamical-transition-like behavior in the THz region is due to the onset of the overlap of the relaxational mode with the THz region. Temperature hysteresis was observed in the dielectric spectrum at 263 K when the hydration level was high. It is suggested that the hydration water behaves similarly to supercooled liquid at that temperature. The third hydration layer may be partly formed to observe such a phenomenon. We also found that the relaxation time is slower than that of a globular protein, lysozyme, and the microscopic environment in the vicinity of the PM surface is suggested to be more heterogeneous than lysozyme. It is proposed that the spectral overlap of the relaxational mode and the low-frequency vibrational mode is necessary for the large conformational change of protein.

Broadband Dielectric Spectroscopy on Lysozyme in the Sub-Gigahertz to Terahertz Frequency Regions: Effects of Hydration and Thermal Excitation

We have performed dielectric spectral measurements of lysozyme in a solid state to understand the effects of hydration and thermal excitation on the low-frequency dynamics of protein. Dielectric measurements were performed under changing hydration conditions at room temperature in the frequency region of 0.5 GHz to 1.8 THz. We also studied the temperature dependence (83 to 293 K) of the complex dielectric spectra in the THz frequency region (0.3 THz to 1.8 THz). Spectral analyses were performed using model functions for the complex dielectric constant. To reproduce the spectra, we found that two relaxational modes and two underdamped modes are necessary together with an ionic conductivity term in the model function. At room temperature, the two relaxational modes have relaxation times of ∼20 ps and ∼100 ps. The faster component has a major spectral intensity and is suggested to be due to coupled water-protein motion. The two underdamped modes are necessary to reproduce the temperature dependence of the spectra in the THz region satisfactorily. The protein dynamical transition is a well-known behavior in the neutron-scattering experiment for proteins, where the atomic mean-square displacement shows a sudden change in the temperature dependence at approximately 200 K, when the samples are hydrated. A similar behavior has also been observed in the temperature dependence of the absorption spectra of protein in the THz frequency region. From our broadband dielectric spectroscopic measurements, we conclude that the increase in the spectral intensities in the THz region at approximately 200 K is due to a spectral blue-shift of the fast relaxational mode.

Structure and collective dynamics of hydrated anti-freeze protein type III from 180 K to 298 K by X-ray diffraction and inelastic X-ray scattering

We investigated hydrated antifreeze protein type III (AFP III) powder with a hydration level h (=mass of water/mass of protein) of 0.4 in the temperature range between 180 K and 298 K using X-ray diffraction and inelastic X-ray scattering (IXS). The X-ray diffraction data showed smooth, largely monotonic changes between 180 K and 298 K without freezing water. Meanwhile, the collective dynamics observed by IXS showed a strong change in the sound velocity at 180 K, after being largely temperature independent at higher temperatures (298-220 K). We interpret this change in terms of the dynamic transition previously discussed using other probes including THz IR absorption spectroscopy and incoherent elastic and quasi-elastic neutron scattering. This finding suggests that the dynamic transition of hydrated proteins is observable on the subpicosecond time scale as well as nano- and pico-second scales, both in collective dynamics from IXS and single particle dynamics from neutron scattering. Moreover, it is most likely that the dynamic transition of hydrated AFP III is not directly correlated with its hydration structure.

Temperature and Hydration Dependence of Low-Frequency Spectra of Lipid Bilayers Studied by Terahertz Time-Domain Spectroscopy

We have studied temperature and hydration dependent low-frequency spectra of lipid bilayers of 1,2-dimyristoyl-sn-glycero-3-phosphoryl-3'-rac-glycerol (DMPG) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) by terahertz time-domain spectroscopy (THz-TDS). We measured X-ray diffraction patterns and mid-infrared spectra of these lipid bilayers and found that the lipid bilayers have two different types of phases, i.e., the gel phase and the crystalline phase, depending on the preparation methods of the samples. In both phases, a few distinct bands were observed in the THz region. For DMPG, the peak wavenumbers of the absorption bands did not change upon hydration, while the bandwidth in the crystalline phase was smaller than that in the gel phase. We performed spectral analyses for the complex dielectric spectra for DMPG and DMPC with a model function, mainly to determine the peak wavenumbers of the absorption bands. In contrast to the case of the DMPG bilayers, the peak wavenumber of the absorption band of the DMPC bilayer shifts upon hydration. In the hydrated DMPC bilayer, it was suggested fast reorienting water molecules exist with a relaxation time of sub-picoseconds. It is suggested that the THz absorption patterns reflect the lipid packing pattern in the bilayers. The temperature dependence of the absorption band was analyzed by an empirical equation, and the anharmonicity of the vibrational potential of the low-frequency mode was quantitatively evaluated.

Systematic study on G-protein couple receptor prototypes: did they really evolve from prokaryotic genes?

G‐protein couple receptor (GPCR) is one of the most striking examples of signalling proteins and it is only observed in eukaryotes. Based on various GPCR identification methods and classification systems, several evolutionary presumptions of different GPCR families have been reported. However, the prototype of GPCR still limits our knowledge. By investigating its structure and domain variance, the authors propose that GPCR might be evolved from prokaryotic world. The results given by the authors indicate that metabotropic glutamate receptor family would be the ancestor of GPCR. Phylogenetic analysis hints that one of metabotropic glutamate receptor GABA is possibly formed and evolved from the ancient chemical union of bacteriorhodopsin and periplasmic binding protein. The results obtained by the authors also unprecedentedly demonstrate that specific domains and identical structures are shown in each type of GPCR, which provides unique opportunities for future strategies on GPCR orphans’ prediction and classification.