Exploring the Distinct Binding and Activation Mechanisms for Different CagA Oncoproteins and SHP2 by Molecular Dynamics Simulations.

CagA is a major virulence factor of Helicobacter pylori. H. pylori CagA is geographically subclassified into East Asian CagA and Western CagA, which are characterized by the presence of a EPIYA-D or EPIYA-C segment. The East Asian CagA is more closely associated with gastric cancer than the Western CagA. In this study, molecular dynamic (MD) simulations were performed to investigate the binding details of SHP2 and EPIYA segments, and to explore the allosteric regulation mechanism of SHP2. Our results show that the EPIYA-D has a stronger binding affinity to the N-SH2 domain of SHP2 than EPIYA-C. In addition, a single EPIYA-D binding to N-SH2 domain of SHP2 can cause a deflection of the key helix B, and the deflected helix B could squeeze the N-SH2 and PTP domains to break the autoinhibition pocket of SHP2. However, a single EPIYA-C binding to the N-SH2 domain of SHP2 cannot break the autoinhibition of SHP2 because the secondary structure of the key helix B is destroyed. However, the tandem EPIYA-C not only increases its binding affinity to SHP2, but also does not significantly break the secondary structure of the key helix B. Our study can help us better understand the mechanism of gastric cancer caused by Helicobacter pylori infection.

Exploring the Allosteric Mechanism of Src Homology-2 Domain-Containing Protein Tyrosine Phosphatase 2 (SHP2) by Molecular Dynamics Simulations.

The Src homology-2 (SH2) domain-containing protein tyrosine phosphatase 2 (SHP2, encoded by PTPN11) is a critical allosteric phosphatase for many signaling pathways. Programmed cell death 1 (PD-1) could be phosphorylated at its immunoreceptor tyrosine-based inhibitory motif (ITIM) and immunoreceptor tyrosine-based switch motif (ITSM) and can bind to SHP2 to initiate T cell inactivation. Although the interaction of SHP2-PD-1 plays an important role in the immune process, the complex structure and the allosteric regulation mechanism remain unknown. In this study, molecular dynamics (MD) simulations were performed to study the binding details of SHP2 and PD-1, and explore the allosteric regulation mechanism of SHP2. The results show that ITIM has a preference to bind to the N-SH2 domain and ITSM has almost the same binding affinity to the N-SH2 and C-SH2 domain. Only when ITIM binds to the N-SH2 domain and ITSM binds to the C-SH2 domain can the full activation of SHP2 be obtained. The binding of ITIM and ITSM could change the motion mode of SHP2 and switch it to the activated state.

Triptolide suppresses paraquat induced idiopathic pulmonary fibrosis by inhibiting TGFB1-dependent epithelial mesenchymal transition.

Idiopathic pulmonary fibrosis (IPF) and tumor are highly similar to abnormal cell proliferation that damages the body. This malignant cell evolution in a stressful environment closely resembles that of epithelial-mesenchymal transition (EMT). As a popular EMT-inducing factor, TGFß plays an important role in the progression of multiple diseases. However, the drugs that target TGFB1 are limited. In this study, we found that triptolide (TPL), a Chinese medicine extract, exerts an anti-lung fibrosis effect by inhibiting the EMT of lung epithelial cells. In addition, triptolide directly binds to TGFß and subsequently increase E-cadherin expression and decrease vimentin expression. In in vivo studies, TPL improves the survival state and inhibits lung fibrosis in mice. In summary, this study revealed the potential therapeutic effect of paraquat induced TPL in lung fibrosis by regulating TGFß-dependent EMT progression.

The Laser Rangefinder System in Quadrature Modem and Ambiguity Resolution.

We propose a laser rangefinder system based on the quadrature modem to achieve amplitude modulation, the method improves the accuracy of the phase measuring and simplifies the hardware design compared to the system with the secondary mixing methods, and to solve the range ambiguity caused by the measuring process, the ranging ambiguity resolving algorithm based on the over-determined equation is proposed, which avoids the searching of the optimal solution, finally the two K60 laser rangefinders and three proposed rangefinders were experimented on the national standard baseline with the precision of 0.18 mm. the measuring time of the proposed system is less than 1.8 s, the average measuring error of those three prototypes is less than 2 mm, and the standard deviation is less than 1 mm within the measuring range 0~60 m. The experimental results show that the proposed design system of the rangefinder has higher measurement accuracy and speed in comparison with the traditional ones, which indicates the high reliability of the proposed design system.

Lens proteomics: analysis of rat crystallins when lenses are exposed to dexamethasone.

To identify glucocorticoid induced cataract (GIC)-specific modified crystallins and related changes, we analyzed rat crystallins and related changes in lenses exposed to dexamethasone (Dex). To carry out proteomics analyses, we separated soluble lens proteins with two-dimensional electrophoresis (2-DE) and modified crystallins were analyzed with matrix assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF-MS/MS). Related changes in mRNA, protein levels and morphological and functional changes of modified crystallins were also determined. Measured masses (except for γD-crystallin as the larger and cross-link form), the isoelectric points (PIs; except for ßB3-crystallin as the alkalinization form) and amino acid sequences of all known rat crystallins matched previously reported data. Analysis by 2-DE indicated that αA, αB, ßB3 and γD increased when lenses were exposed to 5 µM Dex; ßA4 increased when lenses were exposed to 1 µM Dex and the five proteins that had the highest expressional trend were identical with the results of Q-PCR. ßA3/A1 crystallin (expressional trend identical with results of Q-PCR) and the serum albumin precursor gradually disappeared when exposed to 1-50 µM Dex. Results of Western blotting, immunohistochemistry or fluorescence analysis showed that αA and αB increased most when exposed to 5 µM Dex and ßA1/A3 and KI-67 decreased obviously when exposed to 1-50 µM Dex. Electron microscopy showed that the condition of the lens was better when lenses were exposed to 5 µM Dex than at other levels and cracks between the fiber cells became larger when lenses were exposed to 1-50 µM Dex. A chaperone role of α-crystallin protecting heated catalase (CAT) and the activity of superoxide dismutase (SOD), glutathione (GSH), and caspase-3 were highest when exposed to 5 µM Dex. Moreover, αA-crystallins were associated with increased phosphorylation (PI decreased). In conclusion, the proteomics analysis and related changes of rat crystallins when lenses were exposed to Dex in this study will be useful for comparison with normal lens proteins and GIC. We also provided a mechanism for GIC from a proteomics aspect based on the in vitro model.