Protonation State-Induced Unfolding of Protein Secondary Structure in the Gas Phase.

The combination of infrared spectroscopy (IR) and ion mobility mass spectrometry (IM-MS) has revealed that protein secondary structures are retained upon transformation from aqueous solution to the gas phase under gentle conditions. Yet the details about where and how these structural elements are embedded in the gas phase remain elusive. In this study, we employ long time scale molecular dynamics (MD) simulations to examine the extent to which proteins retain their solution structures and the impact of protonation state on the stability of secondary structures in the gas phase. Our investigation focuses on two well-studied proteins, myoglobin and ß-lactoglobulin, representing typical helical and ß-sheet proteins, respectively. Our simulations accurately reproduce the experimental collision cross section (CCS) data measured by IM-MS. Based on accurately reproducing previous experimental collision cross section data and dominant secondary structural species obtained from IM-MS and IR, we confirm that both proteins largely retain their native secondary structural components upon passing from aqueous solution to the gas phase. However, we observe significant reductions in secondary structure contents (19.2 ± 1.2% for myoglobin and 7.3 ± 0.6% for ß-lactoglobulin) in specific regions predominantly composed of ionizable residues. Further mechanistic analysis suggests that alterations in protonation states of these residues after phase transition induce changes in their local interaction networks and backbone dihedral angles, which potentially promote the unfolding of secondary structures in the gas phase. We anticipate that similar protonation state induced unfolding may be observed in other proteins possessing distinct secondary structures. Further studies on a broader array of proteins will be essential to refine our understanding of protein structural behavior during the transition to the gas phase.

In silico screening of natural products as uPAR inhibitors via multiple structure-based docking and molecular dynamics simulations.

Cancer remains one of the most pressing challenges to global healthcare, exerting a significant impact on patient life expectancy. Cancer metastasis is a critical determinant of the lethality and treatment resistance of cancer. The urokinase-type plasminogen activator receptor (uPAR) shows great potential as a target for anticancer and antimetastatic therapies. In this work, we aimed to identify potential uPAR inhibitors by structural dynamics-based virtual screenings against a natural product library on four representative apo-uPAR structural models recently derived from long-timescale molecular dynamics (MD) simulations. Fifteen potential inhibitors (NP1-NP15) were initially identified through molecular docking, consensus scoring, and visual inspection. Subsequently, we employed MD-based molecular mechanics-generalized Born surface area (MM-GBSA) calculations to evaluate their binding affinities to uPAR. Structural dynamics analyses further indicated that all of the top 6 compounds exhibited stable binding to uPAR and interacted with the critical residues in the binding interface between uPAR and its endogenous ligand uPA, suggesting their potential as uPAR inhibitors by interrupting the uPAR-uPA interaction. We finally predicted the ADMET properties of these compounds. The natural products NP5, NP12, and NP14 with better binding affinities to uPAR than the uPAR inhibitors previously discovered by us were proven to be potentially orally active in humans. This work offers potential uPAR inhibitors that may contribute to the development of novel effective anticancer and antimetastatic therapeutics.Communicated by Ramaswamy H. Sarma.

Permafrost degradation is accelerating beneath the bottom of Yanhu Lake in the Hoh Xil, Qinghai-Tibet Plateau.

Lakes on the Qinghai-Tibet Plateau (QTP) have notably expanded over the past 20 years. Due to lake water level rise and lake area expansion, the permafrost surrounding these lakes is increasingly becoming submerged by lake water. However, the change process of submerged permafrost remains unclear, which is not conducive to further analyzing the environmental effects of permafrost change. Yanhu Lake, a tectonic lake on the QTP, has experienced significant expansion and water level rise. Field measurement results indicate that the water level of Yanhu Lake increased by 2.87 m per year on average from 2016 to 2019. Cold permafrost, developed in the lake basin, was partially submerged by lake water at the end of 2017. Based on the water level change and permafrost thermal regime, a numerical heat conduction permafrost model was employed to predict future changes in permafrost beneath the lake bottom. The simulated results indicate that the submerged permafrost would continuously degrade because of the significant thermal impact of lake water. By 2100, the maximum talik thicknesses could reach approximately 7, 12, 16, and 19 m under lake-bottom temperatures of +2.0, +4.0, +6.0, and +8.0 °C, respectively. Approximately 291 years would be required to completely melt 47 m of submerged permafrost under the lake-bottom temperature of +4 °C. Note that the permafrost table begins to melt earlier than does the permafrost base, and the decline in the permafrost table occurs relatively fast at first, but then the process is attenuated, after which the permafrost table again rapidly declines. Compared to climate warming, the degradation of the submerged permafrost beneath the lake bottom occurred more rapidly and notably.

Protective Effect and Potential Mechanism of the Traditional Chinese Medicine Shaoyao-Gancao Decoction on Ethanol-Induced Gastric Ulcers in Rats.

Background: Shaoyao-Gancao decoction (SGD) is a classic prescription in traditional Chinese medicine. SGD is effective in the treatment of gastric and duodenal ulcers. However, the biological activity and possible mechanisms of SGD in the treatment of gastric ulcers have not been fully elucidated. The purpose of this study was to scientifically evaluate the protective effect and potential mechanism of SGD against ethanol-induced gastric ulcers in rats. Methods: A single gavage of 10 mL/kg of 75% ethanol was used to establish a rat gastric ulcer model. A histopathological examination of the gastric tissue was performed. The levels of TNF-α, EGF, PGE2, SOD, and TBARS in gastric tissue were measured by ELISA. Cellular apoptosis in gastric tissues was assessed by TUNEL assay. The expression levels of caspase-3 and Bcl-2 were determined by immunohistochemistry. The potential mechanism of SGD in treating gastric ulcers was further studied using a network pharmacology research method. Results: The gastric tissue of rats with ethanol-induced gastric ulcers had obvious injury throughout the mucosal layer, which was significantly weakened in rats treated with SGD. Furthermore, treatment with SGD significantly increased the levels of EGF, PGE2, SOD, and Bcl-2 and decreased the levels of TNF-α, TBARS, and caspase-3 in the gastric tissue of rats with ethanol-induced gastric ulcers. SGD reduced ethanol-induced cell apoptosis in gastric tissue from rats with gastric ulcers. A traditional Chinese medicine-based network pharmacology study revealed that SGD exerts its anti-gastric ulcer effect by acting on multiple pathways. Conclusions: The above results indicate that SGD can improve gastric ulcers induced by ethanol. Moreover, this study demonstrated multicomponent, multitarget, and multipathway characteristics of SGD in the treatment of gastric ulcers and provided a foundation for further drug development research.

New permafrost is forming on the exposed bottom of Zonag Lake on the Qinghai-Tibet Plateau.

Most lakes on the Qinghai-Tibet Plateau have expanded in recent years. Zonag Lake, a critical habitat for Tibetan antelopes in the continuous permafrost zone, burst and overflowed after several years of expansion, resulting in a reduction of approximately 100 km2 in the lake area. Observations have revealed new permafrost is forming on the exposed bottom, accompanied by various periglacial landscapes. The permafrost aggradation on the exposed bottom is rapid, and the permafrost base reached 4.9 m, 5.4 m, and 5.7 m in the first three years, respectively. In this study, the future changes and influencing factors of recently formed permafrost are simulated using a one-dimensional finite element model of heat flow. The simulated results indicate that the permafrost on the exposed bottom is likely to continue to develop, appearing first quick back slow trend. Besides the surface temperature, the annual amplitude is also an important factor in affecting the aggradation of permafrost. The unidirectional permafrost aggradation in the study area is different from the bidirectional permafrost aggradation on the closed taliks around the Arctic. Additionally, snow cover and vegetation are two important factors influencing the future development of permafrost on the exposed lake bottom.