Enhancing the stability of a novel D-allulose 3-epimerase from Ruminococcus sp. CAG55 by interface interaction engineering and terminally attached a self-assembling peptide.

D-allulose, a highly desirable sugar substitute, is primarily produced using the D-allulose 3-epimerase (DAE). However, the availability of usable DAE enzymes is limited. In this study, we discovered and engineered a novel DAE Rum55, derived from a human gut bacterium Ruminococcus sp. CAG55. The activity of Rum55 was strictly dependent on the presence of Co2+, and it exhibited an equilibrium conversion rate of 30.6 % and a half-life of 4.5 h at 50 °C. To enhance its performance, we engineered the interface interaction of Rum55 to stabilize its tetramer structure, and the best variant E268R was then attached with a self-assembling peptide to form active enzyme aggregates as carrier-free immobilization. The half-life of the best variant E268R-EKL16 at 50 °C was dramatically increased 30-fold to 135.3 h, and it maintained 90 % of its activity after 13 consecutive reaction cycles. Additionally, we identified that metal ions played a key role in stabilizing the tetramer structure of Rum55, and the dependence on metal ions for E268R-EKL16 was significantly reduced. This study provides a useful route for improving the thermostability of DAEs, opening up new possibilities for the industrial production of D-allulose.

LncRNA-XIST Promotes Lung Adenocarcinoma Growth and Inhibits Ferroptosis by Regulating GPX4.

This study aimed to explore the regulatory effects and molecular mechanisms of long non-coding RNA X-inactive-specific transcript (LncRNA-XIST) in lung adenocarcinoma. si-XIST or glutathione peroxidase 4 (GPX4) plasmids were transfected in PC-9 cells to suppress LncRNA-XIST expression or over-express GPX4, respectively. The mRNA expression levels of LncRNA-XIST and GPX4 in lung adenocarcinoma tissues or cells were assessed using RT-qPCR. CCK-8 assay was performed to examine cell activity, and corresponding biochemical kits were used to measure the levels of Fe2+, reactive oxygen species (ROS), malondialdehyde (MDA) in cells. Western blot is used to examine relative protein expression of FANCD2, SLC7A11, and GPX4 in lung adenocarcinoma cells. The mRNA and protein expression levels of LncRNA-XIST in clinical tissues and cells of lung adenocarcinoma were significantly higher than those in adjacent tissues and normal cells. Functional analysis showed that knockdown of LncRNA-XIST notably weakened the viability of lung adenocarcinoma cells and promoted ferroptosis (manifested by significantly up-regulated levels of ROS, MDA, and Fe2+ and down-regulated the expression of SLC7A11 and FANCD2, P < 0.05). Further mechanism analysis revealed that knockdown of LncRNA-XIST markedly inhibited the expression of GPX4 in lung adenocarcinoma cells and that GPX4 was significantly over-expressed in clinical tissues and cells of lung adenocarcinoma. Notably, the expression of GPX4 was positively correlated with that of LncRNA-XIST. Over-expression of GPX4 remarkably promoted cell proliferation and inhibited ferroptosis in lung adenocarcinoma. Besides, the GPX4 over-expression reversed the LncRNA-XIST knockdown-induced ferroptosis and decrease in lung adenocarcinoma cell viability. LncRNA-XIST increases the activity of lung adenocarcinoma cells and inhibits ferroptosis by up-regulating GPX4. Knocking down LncRNA-XIST may be an effective treatment for lung adenocarcinoma.

SOX9 promotes the invasion and migration of lung adenocarcinoma cells by activating the RAP1 signaling pathway.

OBJECTIVE: SOX9 has been shown to be related to the metastasis of various cancers. Recently, it has been reported that SOX9 plays a regulatory role in lung adenocarcinoma (LUAD) cell metastasis, but the specific mechanism remains to be explored. Therefore, the objective of this study was to observe the effect and mechanism of SOX9 on the invasion and migration of LUAD cells. METHODS: RT-qPCR was applied to observe the expression of SOX9 and RAP1 in tumor tissues and corresponding normal lung tissues collected from LUAD patients. Co-immunoprecipitation and Pearson correlation to analyze the expression correlation of SOX9 with RAP1. To observe the role of SOX9, the invasion and migration levels of LUAD A549 cells in each group were observed by Transwell invasion assay and Scratch migration assay after knocking down or overexpressing SOX9. Besides, the expression levels of RAP1 pathway-related proteins (RAP1, RAP1GAP and RasGRP33) were observed by RT-qCPR or western blot. Subsequently, RAP1 was overexpressed and SOX9 was knocked down in A549 cells, and then the cell invasion/migration level and RAP1 pathway activity were assessed. RESULTS: The expression levels of SOX9 and RAP1 in tumor tissues and A549 cells of LUAD patients were significantly increased and positively correlated. Overexpression of SOX9 or RAP1 alone in A549 cells enhanced the invasion and migration ability of cells, as well as up-regulated the expression levels of RAP1, RAP1GAP and RasGRP33. However, knocking down SOX9 decreased cell invasion and migration levels and weakened the activity of RAP1 pathway. Notably, overexpressing RAP1 while knocking down SOX9 significantly activated RAP1 pathway and promoted cell invasion and migration. CONCLUSION: Overexpression of SOX9 in LUAD can significantly activate the RAP1 signaling pathway and promote cell invasion and migration.

Molecular Dynamics Simulation of Protein Cages.

Molecular dynamics (MD) simulations enable the description of the physical movement of the system over time based on classical mechanics at various scales depending on the models. Protein cages are a particular group of different-size proteins with hollow, spherical structures and are widely found in nature, which have vast applications in numerous fields. The MD simulation of cage proteins is particularly important as a powerful tool to unveil their structures and dynamics for various properties, assembly behavior, and molecular transport mechanisms. Here, we describe how to conduct MD simulations for cage proteins, especially technical details, and analyze some of the properties of interest using GROMACS/NAMD packages.

Design of a gold clustering site in an engineered apo-ferritin cage.

Water-soluble and biocompatible protein-protected gold nanoclusters (Au NCs) hold great promise for numerous applications. However, design and precise regulation of their structure at an atomic level remain challenging. Herein, we have engineered and constructed a gold clustering site at the 4-fold symmetric axis channel of the apo-ferritin cage. Using a series of X-ray crystal structures, we evaluated the stepwise accumulation process of Au ions into the cage and the formation of a multinuclear Au cluster in our designed cavity. We also disclosed the role of key residues in the metal accumulation process. X-ray crystal structures in combination with quantum chemical (QC) calculation revealed a unique Au clustering site with up to 12 Au atoms positions in the cavity. Moreover, the structure of the gold nanocluster was precisely tuned by the dosage of the Au precursor. As the gold concentration increases, the number of Au atoms position at the clustering site increases from 8 to 12, and a structural rearrangement was observed at a higher Au concentration. Furthermore, the binding affinity order of the four Au binding sites on apo-ferritin was unveiled with a stepwise increase of Au precursor concentration.

A distal regulatory strategy of enzymes: from local to global conformational dynamics.

Modulating the distribution of various states in protein ensembles through distal sites may be promising in the evolution of enzymes in desired directions. However, the prediction of distal mutation hotspots that stabilize the favoured states from a computational perspective remains challenging. Here, we presented a strategy based on molecular dynamics (MD) and Markov state models (MSM) to predict distal mutation sites. Extensive MD combined with MSM was applied to determine the principally distributed metastable states interconverting at a slow timescale. Then, molecular docking was used to classify these states into active states and inactive ones. Distal mutation hotspots were targeted based on comparing the conformational features between active and inactive states, where mutations destabilize the inactive states and show little influence on the active state. The proposed strategy was used to explore the highly dynamic MHETase, which shows a potential application in the biodegradation of poly(ethylene terephthalate) (PET). Seven principally populated interrelated metastable states were identified, and the atomistic picture of their conformational changes was unveiled. Several residues at distal positions were found to adopt more H-bond occupancies in inactive states than active states, making them potential mutation hotspots for stabilizing the favoured conformations. In addition, the detailed mechanism revealed the significance of calcium ions at a distance from the catalytic centre in reshaping the free energy landscape. This study deepens the understanding of the conformational dynamics of α/ß hydrolases containing a lid domain and advances the study of enzymatic plastic degradation.

The synergistic mechanisms of apo-ferritin structural transitions and Au(iii) ion transportation: molecular dynamics simulations with the Markov state model.

Due to its unique structure, recent years have witnessed the use of apo-ferritin to accumulate various non-natural metal ions as a scaffold for nanomaterial synthesis. However, the transport mechanism of metal ions into the cavity of apo-ferritin is still unclear, limiting the rational design and controllable preparation of nanomaterials. Here, we conducted all-atom classical molecular dynamics (MD) simulations combined with Markov state models (MSMs) to explore the transportation behavior of Au(iii) ions. We exhibited the complete transportation paths of Au(iii) from solution into the apo-ferritin cage at the atomic level. We also revealed that the transportation of Au(iii) ions is accompanied by coupled protein structural changes. It is shown that the 3-fold axis channel serves as the only entrance with the longest residence time of Au(iii) ions. Besides, there are eight binding clusters and five 3-fold structural metastable states, which are important during Au(iii) transportation. The conformational changes of His118, Asp127, and Glu130, acting as doors, were observed to highly correlate with the Au(iii) ion's position. The MSM analysis and Potential Mean Force (PMF) calculation suggest a remarkable energy barrier near Glu130, making it the rate-limiting step of the whole process. The dominant transportation pathway is from cluster 3 in the 3-fold channel to the inner cavity to cluster 5 on the inner surface, and then to cluster 6. These findings provide inspiration and theoretical guidance for the further rational design and preparation of new nanomaterials using apo-ferritin.

Comparison of arterial supercharging and venous superdrainage on improvement of survival of the extended perforator flap in rats.

BACKGROUND: Arterial supercharging and venous superdrainage have been the commonly used vascular augmentation techniques for resolving partial loss of flaps in reconstructive surgery. It remains controversial which one of them is more effective in improving flap survival. The purpose of this study was to compare the effect of distal venous superdrainage and arterial supercharging on the survival of an extended dorsal perforator flap in rats. MATERIALS AND METHODS: Sixty Sprague-Dawley rats were randomly divided into three groups (n = 20 in each group). An extended dorsal perforator flap with the size of 3 × 12 cm based on the deep circumflex iliac artery and vein was elevated in each rat. In arterial supercharging group, the thoracodorsal artery was retained as the distal supercharging vessel; In venous superdrainage group, the thoracodorsal vein was retained as the distal superdrainage vessel. In control group, no other arteries and veins were retained except the main vascular pedicle. On the seventh day after operation, the survival area of flap was calculated as a percentage of viable area to the total flap. Vascular changes in the choke zones were assessed by angiography. Microvascular density and diameter were assessed via immunohistochemistry staining of CD31 on the fifth day after operation. RESULTS: The flap survival area in arterial supercharging group was significantly higher than that in venous superdrainage group (98.9 ± 0.8% vs. 81.5 ± 3.5%, p < .001). By gross observation, the extent of dilation of choke zone vessels in venous superdrainage group was smaller compared with that in arterial supercharging group. The density of CD31-positive vessels and the diameter of choke zone vessels in arterial supercharging group were significantly larger than that in venous superdrainage group (23.4 ± 4.6 mm-2 vs. 13.1 ± 4.2 mm-2 , p < .05; and 37.5 ± 5.8 µm vs. 27.8 ± 4.9 µm, p < .05). CONCLUSION: Compared with venous superdrainage, distal arterial supercharging in the potential territory resulted in better survival of an extended dorsal perforator flap in a rat model.

[Study progressing on the effect of bone structural abnormalities on the distal radioulnar joint stability].

The distal radioulnar joint is not only the main load-bearing joint in the wrist, but also the pivot of the rotation of the forearm. It is one of the most important and unique joints in the body. Maintaining the stability of the distal radioulnar joint is very important for our daily life. The tissue to stabilize the distal radioulnar joint includes bone structures and soft tissue structures. Although the contribution of soft tissue structures to its stability is far exceeding that of bone structures, the influence of abnormal bone structure on the distal radioulnar joint cannot be ignored. By reviewing the relevant literatures, this article divides the bone structural abnormalities into congenital and acquired bone structural abnormalities. The effects of congenital and acquiredbone structural abnormalities on the distal radioulnar joint stability are analysized and collated in this article, and its clinical symptoms, clinical grading, clinical treatments are also summerized. The problems of distal radioulnar joint instability in clinical practicing and its future researching directions are briefly described in order to provide some suggestions for future clinical applications.

Global and Kinetic Profiles of Substrate Diffusion in Candida antarctica Lipase B: Molecular Dynamics with the Markov-State Model.

Profiling substrate diffusion pathways with kinetic information, which accounts for the dynamic nature of enzyme-substrate interaction, can enable molecular reengineering of enzymes and process optimization of enzymatic catalysis. Candida antarctica lipase B (CALB) is extensively used for producing various chemicals because of its rich catalytic mechanisms, broad substrate spectrum, thermal stability, and tolerance to organic solvents. In this study, an all-atom molecular dynamics (MD) combined with Markov-state models (MSMs) implemented in pyEMMA was proposed to simulate diffusion pathways of 4-nitrophenyl ester (4NPE), a commonly used substrate, from the surface into the active site of CALB. Six important metastable conformations of CALB were identified in the diffusion process, including a closed state. An induced-fit mechanism incorporating multiple pathways with molecular information was proposed, which might find unprecedented applications for the rational design of lipase for green catalysis.

In Situ Oxidation of Cu2O Crystal for Electrochemical Detection of Glucose.

The development of a sensitive, quick-responding, and robust glucose sensor is consistently pursued for use in numerous applications. Here, we propose a new method for preparing a Cu2O electrode for the electrochemical detection of glucose concentration. The Cu2O glucose electrode was prepared by in situ electrical oxidation in an alkaline solution, in which Cu2O nanoparticles were deposited on the electrode surface to form a thin film, followed by the growth of Cu(OH)2 nanorods or nanotubes. The morphology and electrocatalytic activity of a Cu2O glucose electrode can be tuned by the current density, reaction time, and NaOH concentration. The results from XRD, SEM, and a Raman spectrum show that the electrode surface was coated with cubic Cu2O nanoparticles with diameters ranging from 50 to 150 nm. The electrode exhibited a detection limit of 0.0275 mM, a peak sensitivity of 2524.9 µA·cm-2·mM-1, and a linear response range from 0.1 to 1 mM. The presence of high concentrations of ascorbic acid, uric acid, dopamine and lactose appeared to have no effects on the detection of glucose, indicating a high specificity and robustness of this electrode.

Coordination design of cadmium ions at the 4-fold axis channel of the apo-ferritin cage.

Spherical protein cages with highly symmetrical structures provide unique environments for the conjugation of metal ions and metal nanoparticles. Ferritin has been widely studied as a template for the coordination of metal ions and metal nanoparticles in fundamental research and applications. However, it remains difficult to design metal coordination sites precisely. In this work, we describe the design and construction of new metal coordination sites by introducing Cys residues at the 4-fold symmetrical hydrophobic channel of apo-ferritin. X-ray crystal structure analyses of the mutants containing Cd(ii) ions show that the four or eight binding sites for Cd(ii) ions are located at the 4-fold symmetrical axis channel of apo-ferritin. It was found that the coordination number and configuration of Cd(ii) ions can be varied by adjusting the positions of the Cys residues at the symmetrical channels of the apo-ferritin cage.

Computational Model-Based Analysis of Strategies to Enhance Scaffold Vascularization.

Stable and extensive blood vessel networks are required for cell function and survival in engineered tissues. A number of different strategies are currently being investigated to enhance biomaterial vascularization with screening primarily through extensive in vitro and in vivo experiments. In this article, we describe an agent-based model (ABM) developed to evaluate various strategies in silico, including design of optimal biomaterial structure, delivery of angiogenic factors, and application of prevascularized biomaterials. The model predictions are evaluated using experimental data. The ABM developed provides insight into different strategies currently applied for scaffold vascularization and will enable researchers to rapidly screen new hypotheses and explore alternative strategies for enhancing vascularization.

Agent-based modeling of porous scaffold degradation and vascularization: Optimal scaffold design based on architecture and degradation dynamics.

A multi-layer agent-based model (ABM) of biomaterial scaffold vascularization is extended to consider the effects of scaffold degradation kinetics on blood vessel formation. A degradation model describing the bulk disintegration of porous hydrogels is incorporated into the ABM. The combined degradation-angiogenesis model is used to investigate growing blood vessel networks in the presence of a degradable scaffold structure. Simulation results indicate that higher porosity, larger mean pore size, and rapid degradation allow faster vascularization when not considering the structural support of the scaffold. However, premature loss of structural support results in failure for the material. A strategy using multi-layer scaffold with different degradation rates in each layer was investigated as a way to address this issue. Vascularization was improved with the multi-layered scaffold model compared to the single-layer model. The ABM developed provides insight into the characteristics that influence the selection of optimal geometric parameters and degradation behavior of scaffolds, and enables easy refinement of the model as new knowledge about the underlying biological phenomena becomes available. STATEMENT OF SIGNIFICANCE: This paper proposes a multi-layer agent-based model (ABM) of biomaterial scaffold vascularization integrated with a structural-kinetic model describing bulk degradation of porous hydrogels to consider the effects of scaffold degradation kinetics on blood vessel formation. This enables the assessment of scaffold characteristics and in particular the disintegration characteristics of the scaffold on angiogenesis. Simulation results indicate that higher porosity, larger mean pore size, and rapid degradation allow faster vascularization when not considering the structural support of the scaffold. However, premature loss of structural support by scaffold disintegration results in failure of the material and disruption of angiogenesis. A strategy using multi-layer scaffold with different degradation rates in each layer was investigated as away to address this issue. Vascularization was improved with the multi-layered scaffold model compared to the single-layer model. The ABM developed provides insight into the characteristics that influence the selection of optimal geometric and degradation characteristics of tissue engineering scaffolds.

Over-expression of ROR2 and Wnt5a cooperatively correlates with unfavorable prognosis in patients with non-small cell lung cancer.

We investigated the expression of receptor tyrosine kinase-like orphan receptor (ROR) 2 and Wnt5a and their prognostic significance in non-small cell lung cancer (NSCLC). Tissue microarray-based immunohistochemical analysis was performed to determine the expression of ROR2 and Wnt5a in 219 patients. mRNA expression of ROR2 and Wnt5a was examined in 20 pairs of NSCLC and matched adjacent normal tissues by real-time PCR. Compared with non-tumorous tissues, both mRNA expression and protein product of ROR2 and Wnt5a genes were significantly increased in NSCLC. c2 analysis revealed that high ROR2 or Wnt5a expression in NSCLC was significantly associated with advanced TNM stage. High expression of both ROR2 and Wnt5a was also related to advanced TNM stage. Multivariate analyses suggested that ROR2, Wnt5a and TNM stage were independent prognostic factors in NSCLC. Our clinical findings suggest that high ROR2 or Wnt5a expression is associated with poor prognosis in NSCLC, and combined detection of ROR2 and Wnt5a is helpful in predicting the prognosis of NSCLC.