Near-field enhanced ultraviolet resonance Raman spectroscopy using aluminum bow-tie nano-antenna.
Ontology highlight
ABSTRACT:
SUBMITTER: Li L
PROVIDER: S-EPMC3460951 | biostudies-other | 2012 Sep
REPOSITORIES: biostudies-other
Similar Datasets
Project description:A printed Bow-Tie slot antenna with loaded stub is proposed and the effects of changing the dimensions of the slot area, the stub and load sizes are considered in this paper. These parameters have a considerable effect on the antenna characteristics as well as its performance. An in-depth parametric study of these dimensions is presented. This paper proposes the necessary conditions for initial approximation of dimensions needed to design this antenna. In order to achieve the desired performance of the antenna fine tuning of all sizes of these parameters is required. The parametric studies used in this paper provide proper trends for initiation and tuning the design. A prototype of the antenna for 1.7GHz to 2.6GHz band is fabricated. Measurements conducted verify that the designed antenna has wideband characteristics with 50% bandwidth around the center frequency of 2.1GHz. Conducted measurements for reflection coefficient (S11) and radiation pattern also validate our simulation results.
| S-EPMC5256992 | biostudies-literature
Project description:Calmodulin (CaM) is a ubiquitous moderator protein for calcium signaling in all eukaryotic cells. This small calcium-binding protein exhibits a broad range of structural transitions, including domain opening and folding-unfolding, that allow it to recognize a wide variety of binding partners in vivo. While the static structures of CaM associated with its various binding activities are fairly well-known, it has been challenging to examine the dynamics of transition between these structures in real-time, due to a lack of suitable spectroscopic probes of CaM structure. In this article, we examine the potential of ultraviolet resonance Raman (UVRR) spectroscopy for clarifying the nature of structural transitions in CaM. We find that the UVRR spectral change (with 229 nm excitation) due to thermal unfolding of CaM is qualitatively different from that associated with opening of the C-terminal domain in response to Ca(2+) binding. This spectral difference is entirely due to differences in tertiary contacts at the interdomain tyrosine residue Tyr138, toward which other spectroscopic methods are not sensitive. We conclude that UVRR is ideally suited to identifying the different types of structural transitions in CaM and other proteins with conformation-sensitive tyrosine residues, opening a path to time-resolved studies of CaM dynamics using Raman spectroscopy.
| S-EPMC4116657 | biostudies-literature
Project description:Raman spectroscopy is a form of vibrational spectroscopy based on inelastic scattering of light. In resonance Raman spectroscopy, the wavelength of the incident light falls within an absorption band of a chromophore, and this overlap of excitation and absorption energy greatly enhances the Raman scattering efficiency of the absorbing species. The ability to probe vibrational spectra of select chromophores within a complex mixture of molecules makes resonance Raman spectroscopy an excellent tool for studies of biomolecules. In this Current Topic, we discuss the type of molecular insights obtained from steady-state and time-resolved resonance Raman studies of a prototypical photoactive protein, rhodopsin. We also review recent efforts in ultraviolet resonance Raman investigations of soluble and membrane-associated biomolecules, including integral membrane proteins and antimicrobial peptides. These examples illustrate that resonance Raman is a sensitive, selective, and practical method for studying the structures of biological molecules, and the molecular bonding, geometry, and environments of protein cofactors, the backbone, and side chains.
| S-EPMC5092233 | biostudies-literature
Project description:Archaerhodopsin 3 (AR3) is a light driven proton pump from Halorubrum sodomense that has been used as a genetically targetable neuronal silencer and an effective fluorescent sensor of transmembrane potential. Unlike the more extensively studied bacteriorhodopsin (BR) from Halobacterium salinarum, AR3 readily incorporates into the plasma membrane of both E. coli and mammalian cells. Here, we used near-IR resonance Raman confocal microscopy to study the effects of pH and membrane potential on the AR3 retinal chromophore structure. Measurements were performed both on AR3 reconstituted into E. coli polar lipids and in vivo in E. coli expressing AR3 in the absence and presence of a negative transmembrane potential. The retinal chromophore structure of AR3 is in an all-trans configuration almost identical to BR over the entire pH range from 3 to 11. Small changes are detected in the retinal ethylenic stretching frequency and Schiff Base (SB) hydrogen bonding strength relative to BR which may be related to a different water structure near the SB. In the case of the AR3 mutant D95N, at neutral pH an all-trans retinal O-like species (O(all-trans)) is found. At higher pH a second 13-cis retinal N-like species (N(13-cis)) is detected which is attributed to a slowly decaying intermediate in the red-light photocycle of D95N. However, the amount of N(13-cis) detected is less in E. coli cells but is restored upon addition of carbonyl cyanide m-chlorophenyl hydrazone (CCCP) or sonication, both of which dissipate the normal negative membrane potential. We postulate that these changes are due to the effect of membrane potential on the N(13-cis) to M(13-cis) levels accumulated in the D95N red-light photocycle and on a molecular level by the effects of the electric field on the protonation/deprotonation of the cytoplasmic accessible SB. This mechanism also provides a possible explanation for the observed fluorescence dependence of AR3 and other microbial rhodopsins on transmembrane potential.
| S-EPMC3568500 | biostudies-literature
Project description:Aromatic amino acids of membrane proteins are enriched at the lipid-water interface. The role of tryptophan on the folding and stability of an integral membrane protein is investigated with ultraviolet resonance Raman and fluorescence spectroscopy. We investigate a model system, the ?-barrel outer membrane protein A (OmpA), and focus on interfacial tryptophan residues oriented toward the lipid bilayer (trp-7, trp-170, or trp-15) or the interior of the ?-barrel pore (trp-102). OmpA mutants with a single tryptophan residue at a nonnative position 170 (Trp-170) or a native position 7 (Trp-7) exhibit the greatest stability, with Gibbs free energies of unfolding in the absence of denaturant of 9.4 and 6.7 kcal/mol, respectively. These mutants are more stable than the tryptophan-free OmpA mutant, which exhibits a free energy of unfolding of 2.6 kcal/mol. Ultraviolet resonance Raman spectra of Trp-170 and Trp-7 reveal evolution of a hydrogen bond in a nonpolar environment during the folding reaction, evidenced by systematic shifts in hydrophobicity and hydrogen bond markers. These observations suggest that the hydrogen bond acceptor is the lipid acyl carbonyl group, and this interaction contributes significantly to membrane protein stabilization. Other spectral changes are observed for a tryptophan residue at position 15, and these modifications are attributed to development of a tryptophan-lipid cation-? interaction that is more stabilizing than an intraprotein hydrogen bond by ?2 kcal/mol. As expected, there is no evidence for lipid-protein interactions for the tryptophan residue oriented toward the interior of the ?-barrel pore. These results highlight the significance of lipid-protein interactions, and indicate that the bilayer provides more than a hydrophobic environment for membrane protein folding. Instead, a paradigm of lipid-assisted membrane protein folding and stabilization must be adopted.
| S-EPMC3149241 | biostudies-literature
Project description:Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network-that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.
| S-EPMC4370773 | biostudies-literature
Project description:Understanding factors associated with tie strength in social networks is essential in a wide variety of settings. With the internet and cellular phones providing additional avenues of communication, measuring and inferring tie strength has become much more complex. We introduce the social bow tie framework, which consists of a focal tie and all actors connected to either or both of the two focal nodes on either side of the focal tie. We also define several intuitive and interpretable metrics that quantify properties of the bow tie which enable us to investigate associations between the strength of the "central" tie and properties of the bow tie. We combine the bow tie framework with machine learning to investigate what aspects of the bow tie are most predictive of tie strength in two very different types of social networks, a collection of medium-sized social networks from 75 rural villages in India and a nationwide call network of European mobile phone users. Our results show that tie strength depends not only on the properties of shared friends, but also on non-shared friends, those observable to only one person in the tie, hence introducing a fundamental asymmetry to social interaction.
| S-EPMC6008360 | biostudies-literature
Project description:The flavin-adenine-dinucleotide-binding BLUF domain constitutes a new class of blue-light receptors, and the N-terminal domain of AppA is a representative of this family. The BLUF domain is of special interest because it uses a rigid flavin rather than an isomerizable chromophore, such as a rhodopsin or phytochrome, for its light-activation process. Crystal and solution structures of several BLUF domains were recently obtained, and their overall structures are consistent. However, there is a key ambiguity regarding the position of a conserved tryptophan (Trp-104 in AppA), in that this residue was found either close to flavin (Trp(in) conformation) or exposed to the solvent (Trp(out) conformation). The location of Trp-104 is a crucial factor in understanding the photocycle mechanism of BLUF domains, because this residue has been shown to play an essential role in the activation of AppA. In this study, we demonstrated a Trp(in) conformation for the BLUF domain of AppA through direct observation of the vibrational spectrum of Trp-104 by ultraviolet resonance Raman spectroscopy, and also observed light-induced conformational and environmental changes in Trp-104. This study provides a structural basis for future investigations of the photocycle mechanism of BLUF proteins.
| S-EPMC2862157 | biostudies-literature
Project description:In classical electrodynamics, nanostructured graphene is commonly modeled by the computationally demanding problem of a three-dimensional conducting film of atomic-scale thickness. Here, we propose an efficient alternative two-dimensional electrostatic approach where all calculation procedures are restricted to the graphene sheet. Furthermore, to explore possible quantum effects, we perform tight-binding calculations, adopting a random-phase approximation. We investigate multiple plasmon modes in 20 nm equilateral triangles of graphene, treating the optical response classically as well as quantum mechanically. Compared to the classical plasmonic spectrum which is "blind" to the edge termination, we find that the quantum plasmon frequencies exhibit blueshifts in the case of armchair edge termination of the underlying atomic lattice, while redshifts are found for zigzag edges. Furthermore, we find spectral features in the zigzag case which are associated with electronic edge states not present for armchair termination. Merging pairs of triangles into dimers, plasmon hybridization leads to energy splitting that appears strongest in classical calculations while splitting is lower for armchair edges and even more reduced for zigzag edges. Our various results illustrate a surprising phenomenon: Even 20 nm large graphene structures clearly exhibit quantum plasmonic features due to atomic-scale details in the edge termination.
| S-EPMC5396075 | biostudies-literature
Project description:Infrared nano-spectroscopy based on scattering-type scanning near-field optical microscopy (s-SNOM) is commonly employed to probe the vibrational fingerprints of materials at the nanometer length scale. However, due to the elongated and axisymmetric tip shank, s-SNOM is less sensitive to the in-plane sample anisotropy in general. In this article, we report an easy-to-implement method to probe the in-plane dielectric responses of materials with the assistance of a metallic disk micro-antenna. As a proof-of-concept demonstration, we investigate here the in-plane phonon responses of two prototypical samples, i.e. in (100) sapphire and x-cut lithium niobate (LiNbO3). In particular, the sapphire in-plane vibrations between 350 cm-1 to 800 cm-1 that correspond to LO phonon modes along the crystal b- and c-axis are determined with a spatial resolution of < λ/10, without needing any fitting parameters. In LiNbO3, we identify the in-plane orientation of its optical axis via the phonon modes, demonstrating that our method can be applied without prior knowledge of the crystal orientation. Our method can be elegantly adapted to retrieve the in-plane anisotropic response of a broad range of materials, i.e. subwavelength microcrystals, van-der-Waals materials, or topological insulators.
| S-EPMC8113487 | biostudies-literature