Do hydration dynamics follow the structural perturbation during thermal denaturation of a protein: a terahertz absorption study

We investigate the thermal denaturation of human serum albumin and the associated solvation using terahertz (THz) spectroscopy in aqueous buffer solution. Far- and near-ultraviolet circular dichroism spectroscopy reveal that the protein undergoes a native (N) to extended (E) state transition at temperature ≤55°C with a marginal change in the secondary and tertiary structure. At 70°C, the protein transforms into an unfolded (U) state with significant irreversible disruption of its structures. We measure the concentration- and temperature-dependent THz absorption coefficient (α) of the protein solution using a p-Ge THz difference spectrometer (2.1–2.8 THz frequency range), thereby probing the collective protein-water network dynamics. When the solvated protein is heated up to 55°C and cooled down again, a reversible change in THz absorption is observed. When increasing the temperature up to 70°C, we find a dramatic irreversible change of THz absorption. The increase in THz absorption compared to bulk water is attributed to a blue shift in the spectrum of the solvated protein compared to bulk water. This is supported by measurements of THz absorption coefficients using THz time-domain spectroscopy (0.1–1.2 THz frequency range). We also use picosecond-resolved fluorescence spectroscopy of the tryptophan 214 moiety of human serum albumin. All experimental observations can be explained by a change in the hydration dynamics of the solvated protein due to the additional exposure of hydrophobic residues upon unfolding.     

Evidence of protein collective motions on the picosecond timescale

We investigate the presence of structural collective motions on a picosecond timescale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time domain spectroscopy and molecular dynamics simulations. The THz response dramatically increases with oxidation, with the largest increase for lowest hydrations, and highest frequencies. For both oxidation states the THz response rapidly increases with hydration saturating above ∼25% (g H₂O/g protein). Quasiharmonic vibrational modes and dipole-dipole correlation functions were calculated from molecular dynamics trajectories. The collective mode density of states alone reproduces the measured hydration dependence, providing strong evidence of the existence of these motions. The large oxidation dependence is reproduced only by the dipole-dipole correlation function, indicating the contrast arises from diffusive motions consistent with structural changes occurring in the vicinity of buried internal water molecules. This source for the observed oxidation dependence is consistent with the lack of an oxidation dependence in nuclear resonant vibrational spectroscopy measurements.     

Terahertz Time-Domain Spectroscopy of Four Hydroxycinnamic Acid Derivatives

The well-resolved absorption spectra of the hydroxycinnamic acid (HCA) derivatives, caffeic acid, ferulic acid, sinapic acid and chlorogenic acid, were measured over the frequency region from 0.3 to 2.0 THz at 294 K with terahertz time-domain spectroscopy (THz-TDS). Theoretical calculation was applied to assist the analysis and assignment of the individual THz absorption spectra of the HCA derivatives with density functional theory (DFT). The distinctive spectral features were originated from the collective motion of molecules held together by hydrogen bonds. The real and imaginary parts of dielectric function of the four HCA derivatives were also obtained.     

First principles investigation of L-alanine in terahertz region

Terahertz absorption spectrum (0.5–4.0 THz) of L-alanine in the solid phase was measured by terahertz time-domain spectroscopy at room temperature. Simulations utilizing gaseous-state and solid-state theory were performed to determine the origins of the observed vibrational features. Our calculations showed that the measured features in solid-state materials could be well understood by considering the crystal packing interactions in a solid-state density functional theory calculation. Furthermore, intermolecular vibrations of L-alanine are found to be the dominating contributions to these measured spectral features in the range of 0.5–4.0 THz, except that located at 3.11 THz.     

褪黑素的太赫兹时域光谱

太赫兹时域光谱技术是一种新兴的无损探测技术。利用太赫兹波的低能性以及大部分生物分子的振动跃迁和旋转在该频段表现出的强色散和吸收作用等特点,可以对生物分子及生命体的活动进行无损探测和研究。本文分别采用透射式和反射式太赫兹时域光谱系统,对不同质量比的褪黑素压片进行测试,分析它在太赫兹波段的光学性质,发现它在0.29、0.50、0.70、0.91、1.20、2.17和2.55 THz处存在特征吸收峰;频域谱的强度随样品浓度的变化呈线性关系。利用Gaussian 09及Gaussian VIEW软件进行模拟分析,得到褪黑素在0.46、0.91、1.15、2.01、2.23和2.61 THz处存在特征吸收峰,为实验结果提供了有力地支持。这些工作为褪黑素等生化样品的检测和鉴定提供了依据和参考。     

Long-range DNA-water interactions

DNA functions only in aqueous environments and adopts different conformations depending on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating and oscillating dipoles that, in turn, give rise to a strong megahertz to terahertz absorption. Investigating the impact of hydration on DNA dynamics and the spectral features of water molecules influenced by DNA, however, is extremely challenging because of the strong absorption of water in the megahertz to terahertz frequency range. In response, we have employed a high-precision megahertz to terahertz dielectric spectrometer, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within the hydration shells of DNA as well as the collective vibrational motions of hydrated DNA, which are vital to DNA conformation and functionality. Our results reveal that the dynamics of water molecules in a DNA solution is heterogeneous, exhibiting a hierarchy of four distinct relaxation times ranging from ∼8 ps to 1 ns, and the hydration structure of a DNA chain can extend to as far as ∼18 Å from its surface. The low-frequency collective vibrational modes of hydrated DNA have been identified and found to be sensitive to environmental conditions including temperature and hydration level. The results reveal critical information on hydrated DNA dynamics and DNA-water interfaces, which impact the biochemical functions and reactivity of DNA.     

The Influence of Element Deformation on Terahertz Mode Interaction in Split-Ring Resonator-Based Meta-Atoms

The interaction between terahertz (THz) resonance modes and element deformation in rectangular split-ring resonator (RSRR)-based meta-atoms (MAs) is investigated experimentally. Two types of RSRR-based MAs are presented: lateral-varied SRR (LV-SRR) and arm-twisted SRR (AT-SRR). When the distances from the gaps to the opposite sides of above meta-atoms increase from 10 to 40 μm, the inductive-capacitive (LC) resonance modes and dipole oscillation modes exhibit redshift behavior. The quality factor (Q factor) of LC resonance decreases while that of dipole oscillation modes increases. The THz mode interaction is subject to the distance between the gap and opposite side. An extension of lateral side contributes much more to the enhancement of Q factor of dipole oscillation mode than the twisted arms. The relationship between the near-field coupling effect and THz modes is revealed by the analysis of surface currents as well as the electric energy density distribution, as is in agreement with the experimental results.     

Surface Plasmon Resonant THz Wave Transmission on Carbon Nanotube Film

The properties of the terahertz resonant surface plasmons wave on the carbon nanotube film and dielectric interface have been investigated. As a first step towards engineering terahertz SPPs-like surface modes, we present a computer experiment to demonstrate that the carbon nanotube film surface can also be employed to concentrate and guide the terahertz SPPs wave. The carbon nanotube film is modeled in an experimentally realizable geometry. It is shown that a unique electromagnetic surface mode in terahertz region can be supported along the carbon nanotube film/dielectric interface when the free-space broadband terahertz pulse is incident on the carbon nanotube film with subwavelength gratings. Comparing with noble metals, plasmonic nano-structure materials based on carbon nanotube film offer a potentially more versatile approach to engineering tightly confined surface modes in the THz regime.     

Collective vibrational modes in biological molecules investigated by terahertz time-domain spectroscopy

We present well-resolved absorption spectra of biological molecules in the far-IR (FIR) spectral region recorded by terahertz time-domain spectroscopy (THz-TDS). As an illustrative example we discuss the absorption spectra of benzoic acid, its monosubstitutes salicylic acid (2-hydroxy-benzoic acid), 3- and 4-hydroxybenzoic acid, and aspirin (acetylsalicylic acid) in the spectral region between 18 and 150 cm(-1). The spectra exhibit distinct features originating from low-frequency vibrational modes caused by intra- or intermolecular collective motion and lattice modes. Due to the collective origin of the observed modes the absorption spectra are highly sensitive to the overall structure and configuration of the molecules, as well as their environment. The THz-TDS procedure can provide a direct fingerprint of the molecular structure or conformational state of a compound.     

Function of terahertz spectra in monitoring the decomposing process of biological macromolecules and in investigating the causes of photoinhibition

Chlorophyll α and β-carotene play an important role in harvesting light energy, which is used to drive photosynthesis in plants. In this study, terahertz(THz) and visible range spectra of chlorophyll α and β-carotene and their changes under light treatment were investigated. The results show that the all THz transmission and absorption spectra of chlorophyll α and β-carotene changed upon light treatment, with the maximum changes at 15 min of illumination indicating the greatest changes of the collective vibrational mode of chlorophyll α and β-carotene. The absorption spectra of chlorophyll α in the visible light region decreased upon light treatment, signifying the degradation of chlorophyll a molecules. It can be inferred from these results that the THz spectra are very sensitive in monitoring the changes of the collective vibrational mode, despite the absence of changes in molecular configuration. The THz spectra can therefore be used to monitor the decomposing process of biological macromolecules; however, visible absorption spectra can only be used to monitor the breakdown extent of biological macromolecules.     

Analysis of tissue condition based on interaction between inorganic and organic matter in cuttlefish bone

The absorption properties of an inner layer of cuttlefish bone were measured using a transmission terahertz time-domain spectrometer in a band from approximately 0.1 to 4 THz. For oriented samples, an absorption peak related to the behavior of calcium carbonate appeared at approximately 2 THz. The peak magnitude and frequency depended on the direction of the incident terahertz electric field, indicating that calcium carbonate crystals constituting the inner layer were oriented in a certain direction. The absorbance of a sample heated to 350 °C for 0 to 2 h to remove organic matter tended to decrease with heating time in the oriented direction, while the peak frequency shifted to higher frequencies. Furthermore, we showed that the peak frequency depended on the interaction area within the unheated sample and we thus obtained a two-dimensional image reflecting crystal regularity inside the cuttlefish bone from the spectral data at each position.     

Manipulating Magnetoinductive Coupling with Graphene-Based Plasmonic Metamaterials in THz Region

Coupling between physical modes can trigger some new physical phenomena such as frequency shift, new mode, and Rabi splitting. Resonant modes in graphene-based metamaterials provide a new platform for the research of coupling. In this work, we demonstrate that the plasmonic coupling of split ring resonator (SRR) dimer in graphene-based metamaterials can be easily manipulated. This magnetoinductive coupling can switch on/off the dark modes easily, which is usually done by symmetry-breaking structure previously. Furthermore, the dark mode can also be activated by Fermi energy as well as carrier concentration changing with either physical or chemical methods conveniently. In addition, different graphene-based SRR dimer configurations present different coupling strengths, which benefits the designing and optimizing of graphene-based metamaterials. The demonstration could enhance the versatility of both coupling studies in terahertz (THz) region and graphene-based metamaterials for THz devices.     

Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach

Normal mode analysis (NMA) has received much attention as a direct approach to extract the collective motions of macromolecules. However, the stringent requirement of computational resources by classical all-atom NMA limits the size of the macromolecules to which the method is normally applied. We implemented a novel coarse-grained normal mode approach based on partitioning the all-atom Hessian matrix into relevant and nonrelevant parts. It is interesting to note that, using classical all-atom NMA results as a reference, we found that this method generates more accurate results than do other coarse-grained approaches, including elastic network model and block normal mode approaches. Moreover, this new method is effective in incorporating the energetic contributions from the nonrelevant atoms, including surface water molecules, into the coarse-grained protein motions. The importance of such improvements is demonstrated by the effect of surface water to shift vibrational modes to higher frequencies and by an increase in overlap of the coarse-grained eigenvector space (the motion directions) with that obtained from molecular dynamics simulations of solvated protein in a water box. These results not only confirm the quality of our method but also point out the importance of incorporating surface structural water in studying protein dynamics.     

Torsional vibrational modes of tryptophan studied by terahertz time-domain spectroscopy

The low-frequency torsional modes, index of refraction, and absorption of a tryptophan film and pressed powders from 0.2 to 2.0 THz (6.6-66 cm(-1)) were measured by terahertz time-domain spectroscopy at room temperature. It was found that there were two dominated torsional vibrational modes at around 1.435 and 1.842 THz. The associated relaxation lifetimes ( approximately 1 ps) for these modes of the tryptophan molecule were measured. Using a density-functional calculation, the origins of the observed torsional vibrations were assigned to the chain and ring of the tryptophan molecule.     

Two Methods for Modelling the Propagation of Terahertz Radiation in a Layered Structure

Modelling the interaction of terahertz(THz) radiation with biological tissueposes many interesting problems. THzradiation is neither obviously described byan electric field distribution or anensemble of photons and biological tissueis an inhomogeneous medium with anelectronic permittivity that is bothspatially and frequency dependent making ita complex system to model.A three-layer system of parallel-sidedslabs has been used as the system throughwhich the passage of THz radiation has beensimulated. Two modelling approaches havebeen developed a thin film matrix model anda Monte Carlo model. The source data foreach of these methods, taken at the sametime as the data recorded to experimentallyverify them, was a THz spectrum that hadpassed though air only.Experimental verification of these twomodels was carried out using athree-layered in vitro phantom. Simulatedtransmission spectrum data was compared toexperimental transmission spectrum datafirst to determine and then to compare theaccuracy of the two methods. Goodagreement was found, with typical resultshaving a correlation coefficient of 0.90for the thin film matrix model and 0.78 forthe Monte Carlo model over the full THzspectrum. Further work is underway toimprove the models above 1 THz.     

Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin

Vibrational excitations of low-frequency collective modes are essential for functionally important conformational transitions in proteins. We carried out an analysis of the low-frequency modes in the G protein coupled receptors (GPCR) family of cone opsins based on both normal-mode analysis and molecular dynamics (MD) simulations. Power spectra obtained by MD can be compared directly with normal modes. In agreement with existing experimental evidence related to transmembrane proteins, cone opsins have functionally important transitions that correspond to approximately 950 modes and are found below 80 cm⁻¹. This is in contrast to bacteriorhodopsin and rhodopsin, where the important low-frequency transition modes are below 50 cm⁻¹. We find that the density of states (DOS) profile of blue opsin in a solvent (e.g. water) has increased populations in the very lowest frequency modes (<15 cm⁻¹); this is indicative of the increased thermostability of blue opsin. From our work we found that, although light absorption behaves differently in blue, green and red opsins, their low-frequency vibrational motions are similar. The similarities and differences in the domain motions of blue, red and green opsins are discussed for several representative modes. In addition, the influence of the presence of a solvent is reported and compared with vacuum spectra. We thus demonstrate that terahertz spectroscopy of low-frequency modes might be relevant for identifying those vibrational degrees of freedom that correlate to known conformational changes in opsins. An erratum to this article can be found at     

Broadband Terahertz Absorption in Graphene-Embedded Photonic Crystals

The absorption in graphene is rather low at terahertz frequencies. Here, we present a graphene-embedded photonic crystal structure to realize broadband terahertz absorption in graphene. The approach provides absorption enhancement in the whole terahertz regime (from 0.1 to 10 THz). It is shown that the average absorption in the graphene-embedded photonic crystal can be enhanced in the multiple propagating bands of the photonic crystals. The absorption efficiency can be further improved by optimizing the characteristic frequency, optical thickness ratio in a unit cell, and the angle of incidence on the photonic crystals. A maximum broadband absorption factor of 28.8% was achieved for fixed alternative dielectric materials. The graphene-embedded photonic crystal is promising for terahertz functional devices with broadband response.     

Normal modes as refinement parameters for the F-actin model.

The slow normal modes of G-actin were used as structural parameters to refine the F-actin model against 8-A resolution x-ray fiber diffraction data. The slowest frequency normal modes of G-actin pertain to collective rearrangements of domains, motions that are characterized by correlation lengths on the order of the resolution of the fiber diffraction data. Using a small number of normal mode degrees of freedom (< or = 12) improved the fit to the data significantly. The refined model of F-actin shows that the nucleotide binding cleft has narrowed and that the DNase I binding loop has twisted to a lower radius, consistent with other refinement techniques and electron microscopy data. The methodology of a normal mode refinement is described, and the results, as applied to actin, are detailed.     

THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions

Predicting the conformational changes in proteins that are relevant for substrate binding is an ongoing challenge in the aim of elucidating the functional states of proteins. The motions that are induced by protein-ligand interactions are governed by the protein global modes. Our measurements indicate that the detected changes in the global backbone motion of the enzyme upon binding reflect a shift from the large-scale collective dominant mode in the unbound state towards a functional twisting deformation that assists in closing the binding cleft. Correlated motion in lysozyme has been implicated in enzyme function in previous studies, but detailed characterization of the internal fluctuations that enable the protein to explore the ensemble of conformations that ultimately foster large-scale conformational change is yet unknown. For this reason, we use THz spectroscopy to investigate the picosecond time scale binding modes and collective structural rearrangements that take place in hen egg white lysozyme (HEWL) when bound by the inhibitor (NAG) ₃. These protein thermal motions correspond to fluctuations that have a role in both selecting and sampling from the available protein intrinsic conformations that communicate function. Hence, investigation of these fast, collective modes may provide knowledge about the mechanism leading to the preferred binding process in HEWL-(NAG) ₃. Specifically, in this work we find that the picosecond time scale hydrogen-bonding rearrangements taking place in the protein hydration shell with binding modify the packing density within the hydrophobic core on a local level. These localized, intramolecular contact variations within the protein core appear to facilitate the large cooperative movements within the interfacial region separating the α- and β- domain that mediate binding. The THz time-scale fluctuations identified in the protein-ligand system may also reveal a molecular mechanism for substrate recognition.     

Excited state charge-transfer dynamics study of poplar plastocyanin by ultrafast pump-probe spectroscopy and molecular dynamics simulation

We have applied ultrafast pump-probe spectroscopy to investigate the excited state dynamics of the blue copper protein poplar plastocyanin, by exciting in the blue side of its 600-nm absorption band. The decay of the charge-transfer excited state occurs exponentially with a time constant of approximately 280 fs and is modulated by well visible oscillations. The Fourier transform of the oscillatory component, besides providing most of the vibrational modes found by conventional resonance Raman, presents additional bands in the low frequency region modes, which are reminiscent of collective motions of biological relevance. Notably, a high frequency mode at approximately 508 cm(-1), whose dynamics are consistent with that of the excited state and already observed for other blue copper proteins, is shown to be present also in poplar plastocyanin. This vibrational mode is reproduced by a molecular dynamics simulation involving the excited state of the copper site.