Protein–Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study
Ontology highlight
ABSTRACT:
SUBMITTER: Pan Z
PROVIDER: S-EPMC8549111 | biostudies-literature | 2021 Sep
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:We report on the design and performance of an echelon-based single shot visible/near-infrared spectrometer with adequate sensitivity to measure the nonlinear optical and terahertz Kerr effects in neat molecular liquids at room temperature. Useful molecular information spanning tens of picoseconds can be measured in just a few milliseconds, and the signal-to-noise performance scales favorably with respect to the standard stage scan technique. These results demonstrate the viability of stage-free nonlinear Kerr effect measurements and provide a route for improvements to the speed of future multidimensional Kerr effect studies.
| S-EPMC6842322 | biostudies-literature
Project description:Electrodynamic responses from three-dimensional topological insulators are characterized by the universal magnetoelectric term constituent of the Lagrangian formalism. The quantized magnetoelectric coupling, which is generally referred to as topological magnetoelectric effect, has been predicted to induce exotic phenomena including the universal low-energy magneto-optical effects. Here we report the experimental indication of the topological magnetoelectric effect, which is exemplified by magneto-optical Faraday and Kerr rotations in the quantum anomalous Hall states of magnetic topological insulator surfaces by terahertz magneto-optics. The universal relation composed of the observed Faraday and Kerr rotation angles but not of any material parameters (for example, dielectric constant and magnetic susceptibility) well exhibits the trajectory towards the fine structure constant in the quantized limit.
| S-EPMC4961790 | biostudies-literature
Project description:Elastomers are one of the most important materials in modern society because of the inherent viscoelastic properties due to their cross-linked polymer chains. Their vibration-absorbing and adhesive properties are especially useful and thus utilized in various applications, for example, tires in automobiles and bicycles, seismic dampers in buildings, and seals in a space shuttle. Thus, the nondestructive inspection of their internal states such as the internal deformation is essential in safety. Generally, industrial elastomers include various kinds of additives, such as carbon blacks for reinforcing them. The additives make most of them opaque in a wide spectral range from visible to mid-infrared, resulting in that the nondestructive inspection of the internal deformation is quite difficult. Here, we demonstrate transmission terahertz polarization spectroscopy as a powerful technique for investigating the internal optical anisotropy in optically opaque elastomers with conductive additives, which are transparent only in the terahertz frequency region. The internal deformation can be probed through the polarization changes inside the material due to the anisotropic dielectric response of the conductive additives. Our study about the polarization-dependent terahertz response of elastomers with conductive additives provides novel knowledge for in situ, nondestructive evaluation of their internal deformation.
| S-EPMC5180234 | biostudies-literature
Project description:Waste polyesters are a potential feedstock for recycled and upcycled products. These polymers are generally semicrystalline, which presents a challenge for chemical and biological recycling to monomers, and thus the thermodynamic work associated with polyester decrystallization is an important consideration in some depolymerization strategies. Here, we use molecular dynamics simulations to calculate the free energy required to decrystallize a single chain from the crystal surface of five commercially and scientifically important, semiaromatic polyesters (PET, PTT, PBT, PEN, and PEF) in water. Our results indicate the decrystallization work ranges from approximately 15 kcal/mol (PEN) to 8 kcal/mol (PEF) per repeat unit for chains in the middle of a crystal surface. The insight gained into the molecular interactions that form the structural basis of semicrystalline synthetic polyesters can guide the pursuit of more efficient plastic processing, which could include catalyst development, optimizing recycling conditions including pretreatment, enzyme and solvent selections, and design of new materials.
| S-EPMC11866931 | biostudies-literature
Project description:Terahertz waves are nondestructive and non-ionizing to synthetic and natural materials, including polymeric and biological materials. As a result, terahertz-based spectroscopy has emerged as a suitable technique to uncover fundamental molecular mechanisms and material properties in this electromagnetic spectrum regime. In terahertz time-domain spectroscopy (THz-TDS), the material's optical properties are resolved using the raw time-domain signals collected from the sample and air reference data depending on accurate prior knowledge of the sample geometry. Alternatively, different spectral analysis algorithms can extract the complex index of refraction of optically thick or optically thin samples without specific thickness knowledge. A THz-TDS signal without apparent Fabry-Pérot oscillations is commonly associated with optically thin samples, whereas the terahertz signal of optically thick samples exhibits distinct Fabry-Pérot oscillations. While several extraction algorithms have been reported a priori, the steps from reducing the time-domain signal to calculating the complex index of refraction and resolving the correct thickness can be daunting and intimidating while obscuring important steps. Therefore, the objective is to decipher, demystify, and demonstrate the extraction algorithms for Fabry-Pérot-absent and -present terahertz signals for various polymers with different molecular structure classifications and nonlinear optical crystal zinc telluride. The experimental results were in good agreement with previously published values while elucidating the contributions of the molecular structure to the stability of the algorithms. Finally, the necessary condition for manifesting Fabry-Pérot oscillations was delineated.
| S-EPMC11642474 | biostudies-literature
Project description:BackgroundMembers of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively.ResultsA molecular level understanding of binding pocket adaptation mechanisms that simultaneously allow both ligand specificity at subsite one and promiscuity at subsite two has potentially important implications in ligand binding and drug design studies. We sought to investigate the determinants of ligand binding selectivity in tmCBP through biophysical characterization of tmCBP in the presence of varying β-glucan oligosaccharides. Crystal structures show that whilst the amino acids that comprise both the tmCBP subsite one and subsite two binding sites remain fixed in conformation regardless of which ligands are present, the rich hydrogen bonding potential of water molecules may facilitate the ordering and the plasticity of this unique PBP binding site.ConclusionsThe identification of the roles these water molecules play in ligand recognition suggests potential mechanisms that can be utilized to adapt a single ligand binding site to recognize multiple distinct ligands.
| S-EPMC3850815 | biostudies-literature
Project description:The cohesin-dockerin receptor-ligand family is the key element in the formation of multi-enzyme lignocellulose-digesting extracellular complexes called cellulosomes. Changes in a receptor protein upon binding of a ligand - commonly referred to as allostery - are not just essential for signalling, but may also alter the overall mechanical stability of a protein receptor. Here, we measured the change in mechanical stability of a library of cohesin receptor domains upon binding of their dockerin ligands in a multiplexed atomic force microscopy-based single-molecule force spectroscopy experiment. A parallelized, cell-free protein expression and immobilization protocol enables rapid mechanical phenotyping of an entire library of constructs with a single cantilever and thus ensures high throughput and precision. Our results show that dockerin binding increases the mechanical stability of every probed cohesin independently of its original folding strength. Furthermore, our results indicate that certain cohesins undergo a transition from a multitude of different folds or unfolding pathways to a single stable fold upon binding their ligand.
| S-EPMC6018229 | biostudies-literature
Project description:Terahertz (THz) spectroscopy is a promising method for analysing polar gas molecules mixed with unwanted aerosols due to its ability to obtain spectral fingerprints of rotational transition and immunity to aerosol scattering. In this article, dynamic THz spectroscopy of acetonitrile (CH3CN) gas was performed in the presence of smoke under the atmospheric pressure using a fibre-based, asynchronous-optical-sampling THz time-domain spectrometer. To match THz spectral signatures of gas molecules at atmospheric pressure, the spectral resolution was optimized to 1 GHz with a measurement rate of 1 Hz. The spectral overlapping of closely packed absorption lines significantly boosted the detection limit to 200 ppm when considering all the spectral contributions of the numerous absorption lines from 0.2 THz to 1 THz. Temporal changes of the CH3CN gas concentration were monitored under the smoky condition at the atmospheric pressure during volatilization of CH3CN droplets and the following diffusion of the volatilized CH3CN gas without the influence of scattering or absorption by the smoke. This system will be a powerful tool for real-time monitoring of target gases in practical applications of gas analysis in the atmospheric pressure, such as combustion processes or fire accident.
| S-EPMC4908425 | biostudies-literature
Project description:Understanding the transfer of spin angular momentum is essential in modern magnetism research. A model case is the generation of magnons in magnetic insulators by heating an adjacent metal film. Here, we reveal the initial steps of this spin Seebeck effect with <27 fs time resolution using terahertz spectroscopy on bilayers of ferrimagnetic yttrium iron garnet and platinum. Upon exciting the metal with an infrared laser pulse, a spin Seebeck current js arises on the same ~100 fs time scale on which the metal electrons thermalize. This observation highlights that efficient spin transfer critically relies on carrier multiplication and is driven by conduction electrons scattering off the metal-insulator interface. Analytical modeling shows that the electrons' dynamics are almost instantaneously imprinted onto js because their spins have a correlation time of only ~4 fs and deflect the ferrimagnetic moments without inertia. Applications in material characterization, interface probing, spin-noise spectroscopy and terahertz spin pumping emerge.
| S-EPMC6057952 | biostudies-literature
Project description:Terahertz spectroscopy is one of the most suitable methods for the analysis of electron transport in solids, and has been applied to various materials. Here, we demonstrate that terahertz spectroscopy is the technique of choice to characterize solid electrolytes. We measure the terahertz conductivity of stabilized zirconia, a widely used solid electrolyte material, by terahertz time-domain spectroscopy at high temperatures, providing a wealth of information unavailable from conventional techniques. It is found that the conductivity reflects the microscopic motion of the ion just before hopping to an unoccupied site. Our results suggest a powerful approach in probing the ionic conduction mechanism and could help us explore other solid electrolytes for fuel cells and all-solid-state batteries.
| S-EPMC6572842 | biostudies-literature