NanoFAST: structure-based design of a small fluorogen-activating protein with only 98 amino acids

One of the essential characteristics of any tag used in bioscience and medical applications is its size. The larger the label, the more it may affect the studied object, and the more it may distort its behavior. In this paper, using NMR spectroscopy and X-ray crystallography, we have studied the structure of fluorogen-activating protein FAST both in the apo form and in complex with the fluorogen. We showed that significant change in the protein occurs upon interaction with the ligand. While the protein is completely ordered in the complex, its apo form is characterized by higher mobility and disordering of its N-terminus. We used structural information to design the shortened FAST (which we named nanoFAST) by truncating 26 N-terminal residues. Thus, we created the shortest genetically encoded tag among all known fluorescent and fluorogen-activating proteins, which is composed of only 98 amino acids.

We solved the structure of a fluorogen-activating protein FAST and synthesized the library of potential fluorogens. Using these data, we designed the shortest genetically encoded fluorescent tag among all known.     

Cationic methyl complexes of rhodium(III): synthesis, structure, and some reactions

Cationic methyl complex of rhodium(III), trans-[Rh(Acac)(PPh₃)₂(CH₃)(CH₃CN)][BPh₄] (1) is prepared by interaction of trans-[Rh(Acac)(PPh₃)₂(CH₃)I] with AgBPh₄ in acetonitrile. Cationic methyl complexes of rhodium(III), cis-[Rh(Acac)(PPh₃)₂ (CH₃)(CH₃CN)][BPh₄] (2) and cis-[Rh(BA)(PPh₃)₂(CH₃)(CH₃CN)][BPh₄] (3) (Acac, BA are acetylacetonate and benzoylacetonate, respectively), are obtained by CH₃I oxidative addition to rhodium(I) complexes [Rh(Acac)(PPh₃)₂] and [Rh(BA)(PPh₃)₂] in acetonitrile in the presence of NaBPh₄. Complexes 2 and 3 react readily with NH₃ at room temperature to form cis-[Rh(Acac)(PPh₃)₂(CH₃)(NH₃)][BPh₄] (4) and cis-[Rh(BA)(PPh₃)₂(CH₃)(NH₃)][BPh₄] (5), respectively. Complexes 1-5 were characterized by elemental analysis, ¹H and ³¹P{¹H} NMR spectra. Complexes 1, 2, 3 and 4 were characterized by X-ray diffraction analysis. Complexes 2 and 3 in solutions (CH₂Cl₂, CHCl₃) are presented as mixtures of cis-(PPh₃)₂ isomers involved into a fluxional process. Complex 2 on heating in acetonitrile is converted into trans-isomer 1. In parallel with that isomerization, reductive elimination of methyl group with formation of [CH₃PPh₃][BPh₄] takes place. Replacement of CH₃CN in complexes 1 and 2 by anion I⁻ yields in both cases the neutral complex trans-[Rh(Acac)(PPh₃)₂(CH₃)I]. Strong trans influence of CH₃ ligand manifests itself in the elongation (in solid) and labilization (in solution) of rhodium-acetonitrile nitrogen bond.     

Comparative analysis of the quality of membrane protein bacteriorhodopsin crystals during crystallization in octylglucoside and octylthioglucoside

Crystallization of bacteriorhodopsin (bR) in the lipidic cubic phase using n-octyl-β-D-glucoside (OG) and its more stable and inexpensive analogue n-octyl-β-D-thioglucoside (OTG) was comparatively analyzed [1]. It was shown that bacteriorhodopsin is efficiently crystallized in OTG in the same detergent concentration range as in OG. However, x-ray diffraction analysis shows that bR crystals in OG are characterized by a better resolution (1.35 Å) than bR crystals in OTG (1.45 Å).     

Transient thermal stresses in a medium with a circular cavity with surface effects

A two-dimensional, transient, uncoupled thermoelastic problem of an infinite medium with a circular nano-scale cavity is considered. The analysis is based on the generalized Gurtin and Murdoch model [Murdoch, A.I., 2005. Some fundamental aspects of surface modelling. Journal of Elasticity 80, 33–52.] where the surface of the cavity possesses its own surface tension and thermomechanical properties. A semi-analytical solution for the problem is obtained using a complex variable boundary integral equation method and the Laplace transform. Several examples are presented to study the significance of surface thermomechanical properties and surface tension, and to compare the results obtained using the generalized Gurtin and Murdoch model and a thin interphase layer model.     

Unexpected photochemical transformation of imidazole derivatives containing the 5-hydroxy-2-methyl-4H-pyran-4-one moiety. Environmentally friendly method for the synthesis of substituted imidazo[1,5-a]pyridine-5,8-diones

An unexpected photochemical transformation of imidazole derivatives containing the 5-hydroxy-2-methyl-4H-pyran-4-one moiety was discovered, which led to the synthesis of previously unknown imidazo[1,5-a]pyridine-5,8-dione derivatives. The structures of imidazole and imidazo[1,5-a]pyridine-5,8-dione derivatives were unambiguously determined by X-ray diffraction analysis.     

Chemical modification of a porous silicon surface induced by nitrogen dioxide adsorption

The effect of gaseous and liquid nitrogen dioxide on the composition and electronic properties of porous silicon (PS) is investigated by means of optical spectroscopy and electron paramagnetic resonance. It is detected that the interaction process is weak and strong forms of chemisorption on the PS surface, and the process may be regarded as an actual chemical reaction between PS and NO(2). It is found that NO(2) adsorption consists in forming different surface nitrogen-containing molecular groups and dangling bonds of Si atoms (P(b)-centers) as well as in oxidizing and hydrating the PS surface. Also observed are the formation of ionic complexes of P(b)-centers with NO(2) molecules and the generation of free charge carriers (holes) in the volume of silicon nanocrystals forming PS.     

A study of the reactions of 2-aryl-4-hydroxy-6H-1,3-thiazin-6-ones with chromone-3-carboxaldehydes

Reaction of 3-formylchromones with 2-aryl-4-hydroxy-6H-1,3-thiazin-6-ones in the presence of pyridine leads to formation of a mixture of novel N-thioaroyl-5-hydroxy-2H,5H-pyrano[3,2-с]chromen-2-one-3-carboxamides and 2-aryl-5-(4′-oxochromen-3′-yl)-6,7-dihydro-4H,5H-pyrano[2,3-d][1,3]thiazine-4,7-diones. The yields of these compounds clearly depend on the nature of the substituent on the 3-formylchromone and on the reaction conditions.     

Partial estimation of covariance matrices

A classical approach to accurately estimating the covariance matrix Σ of a p-variate normal distribution is to draw a sample of size n > p and form a sample covariance matrix. However, many modern applications operate with much smaller sample sizes, thus calling for estimation guarantees in the regime ${n \ll p}$ . We show that a sample of size n = O(m log⁶ p) is sufficient to accurately estimate in operator norm an arbitrary symmetric part of Σ consisting of m ≤ n nonzero entries per row. This follows from a general result on estimating Hadamard products M · Σ, where M is an arbitrary symmetric matrix.