FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe.

Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose FoldPAthreader, a protein folding pathway prediction method that uses a novel folding force field model by exploring the intrinsic relationship between protein evolution and folding from the known protein universe. Further, the folding force field is used to guide Monte Carlo conformational sampling, driving the protein chain fold into its native state by exploring potential intermediates. On 30 example targets, FoldPAthreader successfully predicts 70% of the proteins whose folding pathway is consistent with biological experimental data.

Model-Based Practically Precise Fabrication of HgSe Quantum Dots toward Their Application in a Long-Wave Infrared Micro Spectrometer.

Quantum dot (QD) passive filters present a simple and low-cost strategy for the micromation of spectrometers. In this field, the consistency between ultranarrow band gap QD fabrication and the precise control of its absorption characteristics is the key-challenge to extend QD spectrometers into the long-wave infrared (LWIR) region. Here, we show the model-based, practically precise fabrication of HgSe QDs as well as their specific spectral responses. Both the theoretical and experimental models of the HgSe QDs r-λ are formulated, which reveals the variation of transmission spectrum with the size of HgSe QDs. Then, the HgSe QDs synthesis parameter-spectral response hyperplane model and neural network model were obtained by using traditional polynomial fitting and machine learning, respectively. We also demonstrate the model-based precise fabrication of HgSe QDs with transmission characteristic peaks within 14 µm. The further simulation also shows that the 255─element QD filter array has the signal-to-noise ratio up to 14.57 dB with detection resolution about 5 cm-1.

The Influence of Synthetic Parameters on HgSe QDs.

HgSe quantum dots (QDs) were synthesized by a thermal injection method. The effects of material ratio, growth time, and reaction temperature on the growth and spectral properties of the QDs have been studied. The experimental results show that the QDs had the highest yield of 53.04% when the molar ratio of Se source to Hg source was 1.5. Also, the excess source of SeS2 was reduced to Se. In addition, the critical radius and spectral red-shift rate of QDs can be increased with the reaction temperature. When the reaction temperature was increased to 100 °C, the spectrum reached far-infrared and the growth rate was increased to 10 times and reached 0.63 nm/min. Differing particle morphologies can be obtained by increasing the growth time to 40 min. Moreover, the growth rate reached the minimum at 30 min and the maximum at 80 min of the growth time. This study can provide guidance for the synthesis of long-wave infrared QD materials.

Influence of Ink Properties on the Morphology of Long-Wave Infrared HgSe Quantum Dot Films.

As the core device of the miniature quantum dot (QD) spectrometer, the morphology control of the filter film array cannot be ignored. We eliminated strong interference from additives on the spectrum of a long-wave infrared (LWIR) QD filter film by selecting volatile additives. This work is significant for detecting targets by spectroscopic methods. In this work, a filter film with characteristic spectral bands located in the LWIR was obtained by the natural evaporation of QD ink, which was prepared by mixing various volatile organic solvents with HgSe QD-toluene solution. The factors affecting the morphology of HgSe LWIR films, including ink surface tension, particle size, and solute volume fraction, were the main focus of the analysis. The experimental results suggested that the film slipped in the evaporation process, and the multilayer annular deposition formed when the surface tension of the ink was no more than 24.86 mN/m. The "coffee ring" and the multilayer annular deposition essentially disappeared when the solute particles were larger than 188.11 nm. QDs in the film were accumulated, and a "gully" morphology appeared when the solute volume fraction was greater than 0.1. In addition, both the increase rate of the film height and the decrease rate of the transmission slowed down. The relationship between film height and transmission was obtained by fitting, and the curve conformed to the Lambert-Beer law. Therefore, a uniform and flat film without "coffee rings" can be prepared by adjusting the surface tension, particle size, and volume fraction. This method could provide an empirical method for the preparation of LWIR QD filter film arrays.

12-Benzoyl-2-methyl-naphtho-[2,3-b]indolizine-6,11-dione.

In the title compound, C(24)H(15)NO(3), the fused naphthaquin-one-pyrrole unit is approximately planar, the naphthaquinone ring system making a dihedral angle of 2.91 (10)° with the pyrrole ring. The plane of the pyrrole ring makes a dihedral angle 61.64 (14)° with that of the benzene ring of the benzoyl-methyl-ene group. The crystal structure is stablized by intra-molecular C-H⋯O inter-actions.

Anti-ultraviolet radiation effects of Coptis chinensis and Phellodendron amurense glycans by immunomodulating and inhibiting oxidative injury.

HPLC analysis proved that Coptis chinensis glycan contained Ara, Man, and Gal. The monosaccharide constituents of Phellodendron amurense glycan were determined by HPLC analysis. HPLC analysis proved that P. amurense glycan contained Ara, Xyl, Glu, and Gal. FT-IR spectrum of C. chinensis glycan and P. amurense glycan showed the characteristic absorption peaks of carbohydrate polymers. Exposure of the human skin to ultraviolet radiation (UVR) leads to depletion of cutaneous antioxidants, regulation of gene expression and ultimately to the development of skin diseases. In the present study, free radical scavenging activity of C. chinensis and P. amurense glycan were evaluated. The photoprotective effect of C. chinensis and P. amurense glycan against UV-induced oxidative damage was also investigated in skin. At the concentration range employed, the two glycans showed strong free radical scavenging activity. Ultraviolet radiation reduced skin antioxidant enzyme and immunity activities in animals. Administration of C. chinensis and P. amurense glycans dose-dependently significantly increased skin antioxidant enzyme and immunity activities in animals. In conclusion, C. chinensis and P. amurense glycans present photoprotective properties, which can be attributed to molecules, such as flavonoids and carotenoids, which act as UV-absorbing molecules and as antioxidants, as well as stimulate immunity activities in animals.

Chlorinated briarane diterpenoids from the sea whip gorgonian corals Junceella fragilis and Ellisella robusta (Ellisellidae).

A new chlorinated briarane, fragilide J (1), has been isolated from the sea whip gorgonian coral Junceella fragilis. In addition, the sea whip gorgonian coral Ellisella robusta yielded two chlorinated briaranes, including a new compound, robustolide L (2), and a known metabolite, robustolide H (3). The structures of these compounds were determined using spectroscopic methods. The structure, including the absolute configuration of 3, was further confirmed by X-ray data analysis for the first time.

Targeted delivery of tumor antigens to activated dendritic cells via CD11c molecules induces potent antitumor immunity in mice.

PURPOSE: CD11c is an antigen receptor predominantly expressed on dendritic cells (DC), to which antigen targeting has been shown to induce robust antigen-specific immune responses. To facilitate targeted delivery of tumor antigens to DCs, we generated fusion proteins consisting of the extracellular domain of human HER or its rat homologue neu, fused to the single-chain fragment variable specific for CD11c (scFv(CD11c)-HER2/neu). EXPERIMENTAL DESIGN: Induction of cellular and humoral immune responses and antitumoral activity of the fusion proteins admixed with DC-activating CpG oligonucleotides (scFv(CD11c)-HER2/neu(CpG)) were tested in transplantable HER2/neu-expressing murine tumor models and in transgenic BALB-neuT mice developing spontaneous neu-driven mammary carcinomas. RESULTS: Vaccination of BALB/c mice with scFv(CD11c)-HER2(CpG) protected mice from subsequent challenge with HER2-positive, but not HER2-negative, murine breast tumor cells, accompanied by induction of strong HER2-specific T-cell and antibody responses. In a therapeutic setting, injection of scFv(CD11c)-HER2(CpG) caused rejection of established HER2-positive tumors. Importantly, antitumoral activity of such a fusion protein vaccine could be reproduced in immunotolerant BALB-neuT mice, where scFv(CD11c)-neu(CpG) vaccination significantly protected against a subsequent challenge with neu-expressing murine breast tumor cells and markedly delayed the onset of spontaneous mammary carcinomas. CONCLUSIONS: CD11c-targeted protein vaccines for in vivo delivery of tumor antigens to DCs induce potent immune responses and antitumoral activities and provide a rationale for further development of this approach for cancer immunotherapy.

Crotonkinins A and B and related diterpenoids from Croton tonkinensis as anti-inflammatory and antitumor agents.

Cytotoxicity-guided phytochemical investigation of a methanolic extract of Croton tonkinensis afforded two new kaurane diterpenoids (1, 2) and 10 known ent-kaurane-type diterpenoids (3- 12). The structures of 1 and 2 were based on analysis of spectroscopic and mass spectral data. Compounds 3- 12 were identified by comparison of their spectroscopic and physical data with those reported in the literature. Selected compounds from this plant were examined for cytotoxic and anti-inflammatory activities. Compounds 4 and 9 showed the highest cytotoxic activity against the tested tumor cell lines. Compounds 3, 4, 6, 8, 9, and 11 had IC 50 values less than 5 microM and were more potent than the nonspecific NOS inhibitor L-NAME in inhibiting LPS-induced NO production.