Comparison between Generalized-Born and Poisson–Boltzmann methods in physics-based scoring functions for protein structure prediction

Continuum solvent models such as Generalized-Born and Poisson–Boltzmann methods hold the promise to treat solvation effect efficiently and to enable rapid scoring of protein structures when they are combined with physics-based energy functions. Yet, direct comparison of these two approaches on large protein data set is lacking. Building on our previous work with a scoring function based on a Generalized-Born (GB) solvation model, and short molecular-dynamics simulations, we further extended the scoring function to compare with the MM-PBSA method to treat the solvent effect. We benchmarked this scoring function against seven publicly available decoy sets. We found that, somewhat surprisingly, the results of MM-PBSA approach are comparable to the previous GB-based scoring function. We also discussed the effect to the scoring function accuracy due to presence of large ligands and ions in some native structures of the decoy sets.     

In vivo chondrogenesis of adult bone-marrow-derived autologous mesenchymal stem cells

The purpose of this study has been to investigate the possible effects of the normal joint cavity environment on chondrocytic differentiation of bone-marrow-derived mesenchymal stem cells (MSCs). Autologous bone marrow was aspirated from the iliac crest of male sheep. MSCs were purified, expanded, and labeled with the fluorescent dye PKH26. Labeled MSCs were then grown on a three-dimensional porous scaffold of poly (L-lactic-co-glycolic acid) in vitro and implanted into the joint cavity by a surgical procedure. At 4 or 8 weeks after implantation, the implants were removed for histochemical and immunohistochemical analysis. The cells labeled with red fluorescent PKH26 in the implants expressed type II collagen and synthesized sulfated proteoglycans. However, the osteoblast-specific marker, osteocalcin, was not detected by immunohistochemistry indicating that the implanted MSCs had not differentiated into osteoblasts by being directly exposed to the normal joint cavity. To investigate the possible factors involved in chondrocytic differentiation of MSCs further, we co-cultured sheep MSCs with the main components of the normal joint cavity, viz., synovial fluid or synovial cells, in vitro. After 1 or 2 weeks of co-culture, the MSCs in both co-culture systems expressed markers of chondrogenesis. These results suggest that synovial fluid and synovium from normal joint cavity are important for the chondrocytic differentiation of adult bone-marrow-derived MSCs.This work was supported by the National Natural Science Foundation of China (nos. 39900036, 20174006, and 20221402), the National Advanced Technology Programs of China (nos. 2003AA744051, 2003AA205041), the Award Foundation for Young Teachers from the Ministry of Education, 973 project (no. G1999054306-03), and the 248 key innovative project of Beijing (no. H010210190123).     

Luminescent pH sensing and DNA binding properties of a novel ruthenium(II) complex

A new Ru(II) complex, [Ru(bpy)(2)(dhipH3)](ClO4)(2) (in which bpy=2,2'-bipyridine, dhipH(3)=3,4-dihydroxy-imidado[4,5-f][1,10]-phenanthroline), was synthesized and characterized, and the pH effect on the emission spectra of the complex was studied. The interaction of the complex with calf thymus DNA was investigated by UV-visible and emission spectroscopy, and viscosity measurements. The results suggest that the complex acted as a sensitive luminescent pH sensor and a strong ct-DNA intercalator with an intrinsic binding constant of (4.0+/-0.7) x 10(5) M(-1) in buffered 50 mM NaCl.     

Extrapolating non-target risk of Bt crops from laboratory to field

The tiered approach to assessing ecological risk of insect-resistant transgenic crops assumes that lower tier laboratory studies, which expose surrogate non-target organisms to high doses of insecticidal proteins, can detect harmful effects that might be manifested in the field. To test this assumption, we performed meta-analyses comparing results for non-target invertebrates exposed to Bacillus thuringiensis (Bt) Cry proteins in laboratory studies with results derived from independent field studies examining effects on the abundance of non-target invertebrates. For Lepidopteran-active Cry proteins, laboratory studies correctly predicted the reduced field abundance of non-target Lepidoptera. However, laboratory studies incorporating tri-trophic interactions of Bt plants, herbivores and parasitoids were better correlated with the decreased field abundance of parasitoids than were direct-exposure assays. For predators, laboratory tri-trophic studies predicted reduced abundances that were not realized in field studies and thus overestimated ecological risk. Exposure to Coleopteran-active Cry proteins did not significantly reduce the laboratory survival or field abundance of any functional group examined. Our findings support the assumption that laboratory studies of transgenic insecticidal crops show effects that are either consistent with, or more conservative than, those found in field studies, with the important caveat that laboratory studies should explore all ecologically relevant routes of exposure.     

The diagnostic potential of MPT63‐derived HLA‐A*0201‐restricted CD8+T‐cell epitopes for active pulmonary tuberculosis

MPT63 protein is found only in Mycobacterium tuberculosis complex, including M. tuberculosis and M. bovis. Detection of MPT63‐specific IFN‐γ‐secreting T cells could be useful for the diagnosis of tuberculosis (TB) diseases. In the present study, the HLA‐A*0201 restriction of ten predicted MPT63‐derived CD8 ⁺ T‐cell epitopes was assessed on the basis of T2 cell line and HLA‐A*0201 transgenic mice. The diagnostic potential of immunogenic peptides in active pulmonary TB patients was evaluated using an IFN‐γ enzyme‐linked immunospot assay. It was found that five peptides bound to HLA‐A*0201 with high affinity, whereas the remaining peptides exhibited low affinity for HLA‐A*0201. Five immunogenic peptides (MPT63_18–26, MPT63_29–37, MPT63_20–28, MPT63_5–14 and MPT63_10–19) elicited large numbers of cytotoxic IFN‐γ‐secreting T cells in HLA‐A*0201 transgenic mice. Each of the five immunogenic peptides was recognized by peripheral blood mononuclear cells from 45% to 73% of 40 HLA‐A*0201 positive TB patients. The total diagnostic sensitivity of the five immunogenic peptides was higher than that of a T‐SPOT.TB assay (based on ESAT‐6 and CFP‐10) (93% versus 90%). It is noticeable that the diagnostic sensitivity of the combination of five immunogenic peptides and T‐SPOT.TB assay reached 100%. These MPT63‐derived HLA‐A*0201‐restricted CD8 ⁺ T‐cell epitopes would likely contribute to the immunological diagnosis of M. tuberculosis infection and may provide the components for designing an effective TB vaccine.     

The Mechanism of CeCl<Subscript>3</Subscript> on the Activiation of Alanine Aminotransferase from Mice

The activity of alanine aminotransferase (ALT; E.C. 2.6.1.2) is often changed upon inflammatory responses in animals. Rare earths was shown to provoke various inflammatory responses both in rats and mice; however, the molecular mechanism by which rare earths exert its toxicity has not been completely understood, especially, we know little about the mechanism of the interaction between CeCl₃ and ALT. In this report, we investigated the mechanisms of CeCl₃ on ALT activity in vivo and in vitro. Our results showed that Ce³⁺ could significantly activate ALT in vivo and in vitro; the kinetics constant (Km) and Vmax were 0.018 μM and 1,380 unit mg⁻¹ protein min⁻¹, respectively, at a low concentration of Ce³⁺, and 0.027 μM and 624 unit mg⁻¹ protein min⁻¹, respectively, at a high concentration of Ce³⁺. By UV absorption and fluorescence spectroscopy assays, the Ce³⁺ was determined to be directly bound to ALT; the binding site of Ce³⁺ to ALT was 1.72, and the binding constants of the binding site were 4.82 × 10⁸ and 9.05 × 10⁷ L mol⁻¹. Based on the analysis of the circular dichroism spectra, it was concluded that the binding of Ce³⁺ altered the secondary structure of ALT, suggesting that the observed enhancement of ALT activity was caused by a subtle structural change in the active site through the formation of the complex with Ce³⁺.