THz time domain spectroscopy of biomolecular conformational modes

Applications of terahertz spectroscopy in biosystems

Terahertz (THz) spectroscopic investigations of condensed-phase biological samples are reviewed ranging from the simple crystalline forms of amino acids, carbohydrates and polypeptides to the more complex aqueous forms of small proteins, DNA and RNA. Vibrationally resolved studies of crystalline samples have revealed the exquisite sensitivity of THz modes to crystalline order, temperature, conformational form, peptide sequence and local solvate environment and have given unprecedented measures of the binding force constants and anharmonic character of the force fields, properties necessary to improve predictability but not readily obtainable using any other method. These studies have provided benchmark vibrational data on extended periodic structures for direct comparisons with classical (CHARMm) and quantum chemical (density functional theory) theories. For the larger amorphous and/or aqueous phase samples, the THz modes form a continuum-like absorption that arises because of the full accessibility to conformational space and/or the rapid time scale for inter-conversion in these environments. Despite severe absorption by liquid water, detailed investigations have uncovered the photo- and hydration-induced conformational flexibility of proteins, the solvent shell depth of the water/biomolecule boundary layers and the solvent reorientation dynamics occurring in these interfacial layers that occur on sub-picosecond time scales. As such, THz spectroscopy has enhanced and extended the accessibility to intermolecular forces, length- and timescales important in biological structure and activity.

Terahertz spectroscopy of bacteriorhodopsin and rhodopsin: similarities and differences

We studied the low-frequency terahertz spectroscopy of two photoactive protein systems, rhodopsin and bacteriorhodopsin, as a means to characterize collective low-frequency motions in helical transmembrane proteins. From this work, we found that the nature of the vibrational motions activated by terahertz radiation is surprisingly similar between these two structurally similar proteins. Specifically, at the lowest frequencies probed, the cytoplasmic loop regions of the proteins are highly active; and at the higher terahertz frequencies studied, the extracellular loop regions of the protein systems become vibrationally activated. In the case of bacteriorhodopsin, the calculated terahertz spectra are compared with the experimental terahertz signature. This work illustrates the importance of terahertz spectroscopy to identify vibrational degrees of freedom which correlate to known conformational changes in these proteins.

Terahertz absorption spectra of some saccharides and their metal complexes

In this work, THz absorption spectra of some saccharides and their metal complexes were measured. The main purpose of this work is to investigate the M-O vibrations, intermolecular and intramolecular hydrogen bonds and other vibrations in the FIR region using powerful spectroscopic techniques adopting the metal-sugar complexes prepared in our laboratory. The M-O vibrations in the FIR spectra of metal-sugar complexes indicate the formation of metal complexes. The THz spectrum of glucose below 100cm(-1) was measured at first to confirm the THz experimental method. Characteristic absorption bands in the spectra of various samples are observed. THz spectra of saccharides below 100cm(-1) often have several absorption bands, and different saccharides have various absorption peaks in the THz region, which may be used to distinguish different saccharides. The differences in the number of bands observed are related to different structures of the samples, and these absorption bands are related to the collective motion of molecules. But the THz spectra of their metal complexes are different from the ligands, and no band appears in the region below 50cm(-1) at the present experimental condition, which indicates that THz spectroscopy may also be helpful to identify the formation of metal-sugar complexes, and the changes after complexation in the THz spectra below 100cm(-1) may be related to different metal ions. The metal-sugar complexes with similar crystal structures resemble mid-IR spectra, but their THz spectra may have some differences.

High-resolution waveguide THz spectroscopy of biological molecules

Low-frequency vibrational modes of biological molecules consist of intramolecular modes, which are dependent on the molecule as a whole, as well as intermolecular modes, which arise from hydrogen-bonding interactions and van der Waals forces. Vibrational modes thus contain important information about conformation dynamics of biological molecules, and can also be used for identification purposes. However, conventional Fourier transform infrared spectroscopy and terahertz time-domain spectroscopy (THz-TDS) often result in broad, overlapping features that are difficult to distinguish. The technique of waveguide THz-TDS has been recently developed, resulting in sharper features. For this technique, an ordered polycrystalline film of the molecule is formed on a metal sample plate. This plate is incorporated into a metal parallel-plate waveguide and probed via waveguide THz-TDS. The planar order of the film reduces the inhomogeneous broadening, and cooling of the samples to 77K reduces the homogenous broadening. This combination results in the line-narrowing of THz vibrational modes, in some cases to an unprecedented degree. Here, this technique has been demonstrated with seven small biological molecules, thymine, deoxycytidine, adenosine, D-glucose, tryptophan, glycine, and L-alanine. The successful demonstration of this technique shows the possibilities and promise for future studies of internal vibrational modes of large biological molecules.

Niobium direct detectors for fast and sensitive terahertz spectroscopy

We report the performance of a niobium hot-electron bolometer designed for laboratory terahertz spectroscopy. The antenna-coupled detector can operate above 4.2 K and has fast (subnanosecond) response. Detailed microwave measurements of performance over a wide range of operating conditions were correlated with quantitative terahertz measurements. The maximum responsivity is 4 x 10(4) VW with a noise equivalent power at the detector of 2 x 10(-14) W/Hz(12), approaching the intrinsic thermal fluctuation limit for the device. This detector enables a variety of novel laboratory spectroscopy measurements.

The guanidine hydrochloride-induced denaturation of CP43 and CP47 studied by terahertz time-domain spectroscopy

Terahertz time-domain spectroscopy (THz-TDS) is a new technique in studying the conformational state of a molecule in recent years. In this work, we reported the first use of THz-TDS to examine the denaturation of two photosynthesis membrane proteins: CP43 and CP47. THz-TDS was proven to be useful in discriminating the different conformational states of given proteins with similar structure and in monitoring the denaturation process of proteins. Upon treatment with guanidine hydrochloride (GuHCl), a 1.8 THz peak appeared for CP47 and free chlorophyll a (Chl a). This peak was deemed to originate from the interaction between Chl a and GuHCl molecules. The Chl a molecules in CP47 interacted with GuHCl more easily than those in CP43.

Medical applications of terahertz imaging: a review of current technology and potential applications in biomedical engineering

Terahertz (THz) imaging is in its early stages of development but already the potential clinical impact of this new imaging modality is clear. From cancer research to DNA analysis THz technology is improving or even making possible imaging of hitherto inaccessible phenomena. In this paper we present a short review of THz imaging from the point of view of biomedical engineering. We discuss the current state of the art in terms of THz imaging systems; describe current applications, future potential and our own approaches to harnessing this novel technology. We draw attention to open problems in the area with respect to the limitations of the technology before concluding with descriptions of our future work in the area.

Sensing minute changes in biological cell monolayers with THz differential time-domain spectroscopy

We used terahertz differential time-domain spectroscopy (THz-DTDS) to measure minute changes of bovine lung microvessel endothelial cells (BLMVEC) in response to vascular endothelial growth factor (VEGF). These changes were reflected by alterations in THz wave attenuations and THz dielectric properties of the treated cells. The VEGF-induced THz attenuations of cell monolayers correlated well with changes in transendothelial resistance, as measured using electric cell-substrate impedance sensing (ECIS). However, the morphological differences that gave rise to these changes were not observed with standard optical phase contrast microscopy. We conclude that THz-DTDS is a highly sensitive, non-invasive, powerful new tool to measure minute changes in the morphology of live, cultured cell monolayers. This method enables spectroscopic investigations of cells in the THz band, providing information unavailable through other conventional methods such as optical phase contrast microscopy and ECIS.

Collective Dynamics of Lysozyme in Water: Terahertz Absorption Spectroscopy and Comparison with Theory

To directly measure the low-frequency vibrational modes of proteins in biologically relevant water environment rather than previously explored dry or slightly hydrated phase, we have developed a broadband terahertz spectrometer suitable for strongly attenuating protein solutions. Radiation is provided by harmonic multipliers (up to 0.21 THz), a Gunn oscillator (at 0.139 THz), and the UCSB free-electron lasers (up to 4.8 THz). Our spectrometer combines these intense sources with a sensitive cryogenic detector and a variable path length sample cell to detect radiation after it is attenuated by more than 7 orders of magnitudes by the aqueous sample. Using this spectrometer, we have measured the molar extinction of solvated lysozyme between 0.075 and 3.72 THz (2.5-124 cm(-1)), and we made direct comparison to several published theoretical models based on molecular dynamics simulations and normal-mode analysis. We confirm the existence of dense, overlapping normal modes in the terahertz frequency range. Our observed spectrum, while in rough qualitative agreement with these models, differs in detail. Further, we observe a low-frequency cutoff in terahertz dynamics between 0.2 and 0.3 THz, and we see no evidence of a predicted normal mode at approximately 0.09 THz for the protein.

Hydration-Induced Far-Infrared Absorption Increase in Myoglobin

The interaction of proteins with an aqueous environment leads to a thin region of "biological water", the molecules of which have properties that differ from those of bulk water, in particular, reduced absorption of far-infrared radiation caused by protein-induced hindrance of the water rotational and vibrational degrees of freedom. New results at terahertz (THz) frequencies, however, show that absorption per protein molecule is increased by the presence of biological water. Absorption measurements were made of the heme protein myoglobin mixed with water from 3.6 to 98 wt % in the frequency range of 0.1-1.2 THz, using THz time-domain spectroscopy. Analysis shows greater THz absorption when compared to a non-interacting protein-water model. Including the suppressed absorption of biological water leads to a substantial hydration-dependent increase in absorption per protein molecule over a wide range of concentration and frequencies, meaning that water increases the protein's polarizability.

Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy

Biological polymers are expected to exhibit functionally relevant, global, and subglobal collective modes in the terahertz (THz) frequency range (i.e., picosecond timescale). In an effort to monitor these collective motions, we have experimentally determined the absorption spectrum of solvated bovine serum albumin (BSA) from 0.3 to 3.72 THz (10-124 cm(-1)). We successfully extract the terahertz molar absorption of the solvated BSA from the much stronger attenuation of water and observe in the solvated protein a dense, overlapping spectrum of vibrational modes that increases monotonically with increasing frequency. We see no evidence of distinct, strong, spectral features, suggesting that no specific collective vibrations dominate the protein's spectrum of motions, consistent with the predictions of molecular dynamics simulations and normal mode analyses of a range of small proteins. The shape of the observed spectrum resembles the ideal quadratic spectral density expected for a disordered ionic solid, indicating that the terahertz normal mode density of the solvated BSA may be modeled, to first order, as that of a three-dimensional elastic nanoparticle with an aperiodic charge distribution. Nevertheless, there are important detailed departures from that of a disordered inorganic solid or the normal mode densities predicted for several smaller proteins. These departures are presumably the spectral features arising from the unique molecular details of the solvated BSA. The techniques used here and measurements have the potential to experimentally confront theoretical calculations on a frequency scale that is important for macromolecular motions in a biologically relevant water environment.

Hydration dependence of conformational dielectric relaxation of lysozyme

Dielectric response of hen egg white lysozyme is measured in the far infrared (5-65 cm-1, 0.15-1.95 THz, 0.6-8.1 meV) as a function of hydration. The frequency range is associated with collective vibrational modes of protein tertiary structure. The observed frequency dependence of the absorbance is broad and glass-like. For the entire frequency range, there is a slight increase in both the absorbance and index of refraction with increasing hydration for <0.27 h (mass of H2O per unit mass protein). At 0.27 h, the absorbance and index begin to increase more rapidly. This transition corresponds to the point where the first hydration shell is filled. The abrupt increase in dielectric response cannot be fully accounted for by the additional contribution to the dielectric response due to bulk water, suggesting that the protein has not yet achieved its fully hydrated state. The broad, glass-like response suggests that at low hydrations, the low frequency conformational hen egg white lysozyme dynamics can be described by a dielectric relaxation model where the protein relaxes to different local minima in the conformational energy landscape. However, the low frequency complex permittivity does not allow for a pure relaxational mechanism. The data can best be modeled with a single low frequency resonance (nu approximately 120 GHz=4 cm-1) and a single Debye relaxation process (tau approximately .03-.04 ps). Terahertz dielectric response is currently being considered as a possible biosensing technique and the results demonstrate the required hydration control necessary for reliable biosensor applications.

Protein flexibility using constraints from molecular dynamics simulations

Proteins are held together in the native state by hydrophobic interactions, hydrogen bonds and interactions with the surrounding water, whose strength as well as spatial and temporal distribution affects protein flexibility and hence function. We study these effects using 10 ns molecular dynamics simulations of pure water and of two proteins, the glutamate receptor ligand binding domain and barnase. We find that most of the noncovalent interactions flicker on and off over typically nanoseconds, and so we can obtain good statistics from the molecular dynamics simulations. Based on this information, a topological network of rigid bonds corresponding to a protein structure with covalent and noncovalent bonds is constructed, with account being taken of the influence of the flickering hydrogen bonds. We define the duty cycle for the noncovalent interactions as the percentage of time a given interaction is present, which we use as an input to investigate flexibility/rigidity patterns, in the algorithm FIRST which constructs and analyses topological networks.

Using terahertz pulsed spectroscopy to quantify pharmaceutical polymorphism and crystallinity

Terahertz pulsed spectroscopy (TPS) is a new technique that is capable of eliciting rich information when investigating pharmaceutical materials. In solids, it probes long-range crystalline lattice vibrations and low energy torsion and hydrogen bonding vibrations. These properties make TPS potentially an ideal tool to investigate crystallinity and polymorphism. In this study four drugs with different solid-state properties were analyzed using TPS and levels of polymorphism and crystallinity were quantified. Carbamazepine and enalapril maleate polymorphs, amorphous, and crystalline indomethacin, and thermotropic liquid crystalline and crystalline fenoprofen calcium mixtures were quantified using partial least-squares analysis. Root-mean-squared errors of cross validation as low as 0.349% and limits of detection as low as approximately 1% were obtained, demonstrating that TPS is an analytical technique of potential in quantifying solid-state properties of pharmaceutical compounds.

Dynamic range in terahertz time-domain transmission and reflection spectroscopy

We present a quantitative method for identification of the dynamic range of the detectable absorption coefficient in the analysis of transmission terahertz (THz) time-domain spectroscopy data. In transmission measurements the largest detectable absorption coefficient is determined by the dynamic range of the THz signals, whereas in reflection measurements the largest detectable absorption coefficient is determined by the scan-to-scan reproducibility of the signal.