Optomechanical interaction between single-walled carbon nanotubes of various structures

We consider optomechanical interaction in an asymmetric structure of a carbon nanotubes dimer of different orientations and/or different atomic structures in the field of a plane wave or a focused Gaussian beam. Here we show that optical coupling in such the system can lead to nonreciprocal interactions between the constituents. We demonstrate that a non-conservative force is applied to the center of mass of an optically coupled nanotube dimer, resulting in an unexpected lateral action. The sign and magnitude of this force depend on abrupt phase transitions in the properties of the asymmetric dimer.

SERS Amplification in Au/Si Asymmetric Dimer Array Coupled to Efficient Adsorption of Thiophenol Molecules

Maximizing the surface-enhanced Raman scattering (SERS) is a significant effort focused on the substrate design. In this paper, we are reporting on an important enhancement in the SERS signal that has been reached with a hybrid asymmetric dimer array on gold film coupled to the efficient adsorption of thiophenol molecules on this array. Indeed, the key factor for the SERS effect is the adsorption efficiency of chemical molecules on the surface of plasmonic nanostructures, which is measured by the value of the adsorption constant usually named K. In addition, this approach can be applied to several SERS substrates allowing a prescriptive estimate of their relative performance as sensor and to probe the affinity of substrates for a target analyte. Moreover, this prescriptive estimate leads to higher predictability of SERS activity of molecules, which is also a key point for the development of sensors for a broad spectrum of analytes. We experimentally investigated the sensitivity of the Au/Si asymmetric dimer array on the gold film for SERS sensing of thiophenol molecules, which are well-known for their excellent adsorption on noble metals and serving as a proof-of-concept in our study. For this sensing, a detection limit of 10 pM was achieved as well as an adsorption constant K of 6 × 106 M−1. The enhancement factor of 5.2 × 1010 was found at the detection limit of 10 pM for thiophenol molecules.

Plasmons Coupling and Anti-Crossing of Nanometal Asymmetric Dimer

In this paper, by defining a new physical quantity called as the frequency offset in the harmonic oscillator model and combining with the established plasmon coupling model, we successfully explain the anti-crossing property caused by plasmon coupling of dimer composed of a silver nanoring and a silver nanorod. In the plasmons coupling model, we reasonably reveal that the physical mechanism of the coupling between bright mode and dark mode of the plasmons is mainly represented by the coulomb potential and the electrostatic potential. With this model, we explain also the asymmetric feature the variation of frequency offset and coupling coefficient with coupling distance.

Discovery of a New Asymmetric Dimer Nenestatin B and Implications of Dimerizing Enzyme in a Deep Sea Actinomycete

Benzofluorene-containing atypical angucyclines are an important family of natural products with a broad spectrum of antibacterial and cytotoxic properties. Interestingly, symmetric and asymmetric dimer showed better activity than the monomer...

Conformational flexibility and ligand binding properties of ovine β-lactoglobulin

Ovine β‑lactoglobulin was characterized by spectroscopic (CD), calorimetric (ITC) and X-ray structural studies. The structure of ovine β‑lactoglobulin complex with decanol showed that tight packing of molecules in the crystalline phase enforces a distortion of protein flexible loops resulting in the formation of an asymmetric dimer. The loops surrounding β-barrel in ovine lactoglobulin possessed the same conformational flexibility as observed previously in other lactoglobulins and the change of their conformation regulates the access to the binding pocket. The structure of asymmetric dimer revealed a new region in β-barrel where ligand polar group can be located. These findings indicated protein adaptability to ligand dimensions and inter- and intramolecular interactions in the crystalline phase. Calorimetric and crystallographic studies provided the experimental evidence that ovine lactoglobulin is able to bind aliphatic ligands. Thermodynamic parameters of sodium dodecyl sulfate binding determined by ITC at pH 7.5 had Ka, ΔH, TΔS and ΔG values similar to those observed for bovine and caprine protein indicating the same mechanism of ligand binding.

Structural basis for activation of a diguanylate cyclase required for bacterial predation in Bdellovibrio

The bacterial second messenger cyclic-di-GMP is a widespread, prominent effector of lifestyle change. An example of this occurs in the predatory bacterium Bdellovibrio bacteriovorus, which cycles between free-living and intraperiplasmic phases after entering (and killing) another bacterium. The initiation of prey invasion is governed by DgcB (GGDEF enzyme) that produces cyclic-di-GMP in response to an unknown stimulus. Here, we report the structure of DgcB, and demonstrate that the GGDEF and sensory forkhead-associated (FHA) domains form an asymmetric dimer. Our structures indicate that the FHA domain is a consensus phosphopeptide sensor, and that the ligand for activation is surprisingly derived from the N-terminal region of DgcB itself. We confirm this hypothesis by determining the structure of a FHA:phosphopeptide complex, from which we design a constitutively-active mutant (confirmed via enzyme assays). Our results provide an understanding of the stimulus driving DgcB-mediated prey invasion and detail a unique mechanism of GGDEF enzyme regulation.

Structure of the N-terminal domain of Euprosthenops australis dragline silk suggests that conversion of spidroin dope to spider silk involves a conserved asymmetric dimer intermediate

Spider silk is a biomaterial with exceptional mechanical toughness, and there is great interest in developing biomimetic methods to produce engineered spider silk-based materials. However, the mechanisms that regulate the conversion of spider silk proteins (spidroins) from highly soluble dope into silk are not completely understood. The N-terminal domain (NT) of Euprosthenops australis dragline silk protein undergoes conformational and quaternary-structure changes from a monomer at a pH above 7 to a homodimer at lower pH values. Conversion from the monomer to the dimer requires the protonation of three conserved glutamic acid residues, resulting in a low-pH `locked' dimer stabilized by symmetric electrostatic interactions at the poles of the dimer. The detailed molecular events during this transition are still unresolved. Here, a 2.1 Å resolution crystal structure of an NT T61A mutant in an alternative, asymmetric, dimer form in which the electrostatic interactions at one of the poles are dramatically different from those in symmetrical dimers is presented. A similar asymmetric dimer structure from dragline silk of Nephila clavipes has previously been described. It is suggested that asymmetric dimers represent a conserved intermediate state in spider silk formation, and a revised `lock-and-trigger' mechanism for spider silk formation is presented.