Abstract
Background
Mastitis is one of the most prevalent diseases and causes considerable economic losses in the dairy farming sector and dairy industry. Presently, antibiotic treatment is still the ...main method to control this disease, but it also brings bacterial resistance and drug residue problems.
Lactobacillus plantarum
(
L. plantarum
) is a multifunctional probiotic that exists widely in nature. Due to its anti-inflammatory potential,
L. plantarum
has recently been widely researched in complementary therapies for various inflammatory diseases. In this study, the apoptotic ratio, the expression levels of various inflammatory mediators and key signalling pathway proteins in
Escherichia coli
-induced bovine mammary epithelial cells (BMECs) under different doses of
L. plantarum
17–5 intervention were evaluated.
Results
The data showed that
L. plantarum
17–5 reduced the apoptotic ratio, downregulated the mRNA expression levels of
TLR2
,
TLR4
,
MyD88
,
IL1β
,
IL6
,
IL8
,
TNFα
,
COX2
,
iNOS
,
CXCL2
and
CXCL10
, and inhibited the activation of the NF-κB and MAPK signalling pathways by suppressing the phosphorylation levels of p65, IκBα, p38, ERK and JNK.
Conclusions
The results proved that
L. plantarum
17–5 exerted alleviative effects in
Escherichia coli
-induced inflammatory responses of BMECs.
The formation of functionally versatile protein complexes underlies almost every biological process. The estimation of how fast these complexes can be formed has broad implications for unravelling ...the mechanism of biomolecular recognition. This kinetic property is traditionally quantified by association rates, which can be measured through various experimental techniques. To complement these time-consuming and labor-intensive approaches, we developed a coarse-grained simulation approach to study the physical processes of protein-protein association. We systematically calibrated our simulation method against a large-scale benchmark set. By combining a physics-based force field with a statistically-derived potential in the simulation, we found that the association rates of more than 80% of protein complexes can be correctly predicted within one order of magnitude relative to their experimental measurements. We further showed that a mixture of force fields derived from complementary sources was able to describe the process of protein-protein association with mechanistic details. For instance, we show that association of a protein complex contains multiple steps in which proteins continuously search their local binding orientations and form non-native-like intermediates through repeated dissociation and re-association. Moreover, with an ensemble of loosely bound encounter complexes observed around their native conformation, we suggest that the transition states of protein-protein association could be highly diverse on the structural level. Our study also supports the idea in which the association of a protein complex is driven by a "funnel-like" energy landscape. In summary, these results shed light on our understanding of how protein-protein recognition is kinetically modulated, and our coarse-grained simulation approach can serve as a useful addition to the existing experimental approaches that measure protein-protein association rates.
In this study, the influence of nanocrystalline structure on the plasma nitriding (PN) behavior of 17-4PH steel and corresponding corrosion mechanisms under different treatments were systematically ...investigated. The results showed that nanocrystalline structures introduced by ultrasonic surface rolling process (USRP) would affect the nitrides morphology, composition and distribution via accelerating element diffusion. The fabricated nanocrystalline structures could enhance the corrosion resistance of original and plasma-nitrided 17-4PH steel, which was attributed to its various microstructures. Homogeneous microstructures suppressed or alleviated the formation of micro-galvanic couple in USRP-treated 17-4PH steel and USRP-15 + PN specimen.
The development of artificial protein cages has recently gained massive attention due to their promising application prospect as novel delivery vehicles for therapeutics. These nanoparticles are ...formed through a process called self‐assembly, in which individual subunits spontaneously arrange into highly ordered patterns via non‐covalent but specific interactions. Therefore, the first step toward the design of novel engineered protein cages is to understand the general mechanisms of their self‐assembling dynamics. Here we have developed a new computational method to tackle this problem. Our method is based on a coarse‐grained model and a diffusion–reaction simulation algorithm. Using a tetrahedral cage as test model, we showed that self‐assembly of protein cage requires of a seeding process in which specific configurations of kinetic intermediate states are identified. We further found that there is a critical concentration to trigger self‐assembly of protein cages. This critical concentration allows that cages can only be successfully assembled under a persistently high concentration. Additionally, phase diagram of self‐assembly has been constructed by systematically testing the model across a wide range of binding parameters. Finally, our simulations demonstrated the importance of protein's structural flexibility in regulating the dynamics of cage assembly. In summary, this study throws lights on the general principles underlying self‐assembly of large cage‐like protein complexes and thus provides insights to design new nanomaterials.
The mechanical properties of biomolecules play pivotal roles in regulating cellular functions. For instance, extracellular mechanical stimuli are converted to intracellular biochemical activities by ...membrane receptors and their downstream adaptor proteins during mechanotransduction. In general, proteins favor the conformation with the lowest free energy. External forces modify the energy landscape of proteins and drive them to unfolded or deformed conformations that are of functional relevance. Therefore, the study of the physical properties of proteins under external forces is of fundamental importance to understand their functions in cellular mechanics. Here, a coarse-grained computational model was developed to simulate the unfolding or deformation of proteins under mechanical perturbation. By applying this method to unfolding of previously studied proteins or protein fragments with external forces, we demonstrated that our results are quantitatively comparable to previous experimental or all-atom computational studies. The model was further extended to the problem of elastic deformation of large protein complexes formed between membrane receptors and their ligands. Our studies of binding between T cell receptor (TCR) and major histocompatibility complex (MHC) illustrated that stretching of MHC ligand initially lowers its binding energy with TCR, supporting the recent experimental report that TCR/MHC complex is formed through the catch-bond mechanism. Finally, the method was, for the first time, applied to pulling of an eight-cadherin cluster that was formed by their
trans
and
cis
binding interfaces. Our simulation results show that mechanical properties of adherens junctions are functionally important to cell adhesion.
Proteins carry out their diverse functions in cells by forming interactions with each other. The dynamics of these interactions are quantified by the measurement of association and dissociation rate ...constants. Relative to the efforts made to model the association of biomolecules, little has been studied to understand the principles of protein complex dissociation. Using the interaction between colicin E9 endonucleases and immunity proteins as a test system, here we develop a coarse-grained simulation method to explore the dissociation mechanisms of protein complexes. The interactions between proteins in the complex are described by the knowledge-based potential that was constructed by the statistics from available protein complexes in the structural database. Our study provides the supportive evidences to the dual recognition mechanism for the specificity of binding between E9 DNase and immunity proteins, in which the conserved residues of helix III of Im2 and Im9 proteins act as the anchor for binding, while the sequence variations in helix II make positive or negative contributions to specificity. Beyond that, we further suggest that this binding specificity is rooted in the process of complex dissociation instead of association. While we increased the flexibility of protein complexes, we further found that they are less prone to dissociation, suggesting that conformational fluctuations of protein complexes play important functional roles in regulating their binding and dissociation. Our studies therefore bring new insights to the molecule mechanisms of protein-protein interactions, while the method can serve as a new addition to a suite of existing computational tools for the simulations of protein complexes.
The fabrication of porous structures on aluminum surfaces can be performed readily and routinely using anodic oxidation technology. However, the design and preparation of smooth and compact films on ...the porous structures is difficult to achieve. In this work, by replacing Al cathode with graphite cathode and also by tailoring the Al
3+
concentration, anodic oxide films (AOFs) possessing novel multilayer structures which contain compact surface layers, porous sublayers and barrier layers and which show excellent wear resistance were fabricated
via
common anodic oxidation technology. The surface morphologies and chemical compositions of the as-prepared films were investigated by scanning electron microscopy, energy dispersive spectroscopy, X-ray photoelectron spectroscopy and X-ray diffraction. The results showed that the surface layer was amorphous aluminum oxide. The surface microhardness of the as-prepared AOFs was 2 to 7 times that of the untreated Al alloys. The thicknesses of the surface layer and porous sublayer were manipulated by the anodic current density and the concentration of sulfuric acid. The wear resistance properties of the anodic oxide film were characterized using a UMT-3 tribometer. When the sample was anodized in a 90 mg mL
−1
sulfuric acid bath and the current density was 5 A dm
−2
(AOF2-A), the wear rate significantly decreased to 1.81 × 10
−5
mm
3
N
−1
m
−1
under dry sliding and 7.54 × 10
−6
mm
3
N
−1
m
−1
under seawater sliding. The wear rate of the AOF2-A sample was 3 orders of magnitude lower than that of 2024 Al alloys. It was found that the surface layer of the AOF2-A sample, which showed high hardness and excellent toughness, presented the lowest wear rate owing to columnar wear debris in the wear track, which acted as a rolling log in the sliding process. The influences of the anodic oxidation current density and the concentration of sulfuric acid on the wear resistance and the self-lubrication mechanism of desquamated wear debris in the sliding process were discussed in detail.
Anodic oxide films contain novel multilayer structure were fabricated by replacing Al cathode with graphite cathode and also tailoring the Al
3+
concentration using common anodic oxidation technology.
The interactions between tumor necrosis factors (TNFs) and their corresponding receptors (TNFRs) play a pivotal role in inflammatory responses. Upon ligand binding, TNFR receptors were found to form ...oligomers on cell surfaces. However, the underlying mechanism of oligomerization is not fully understood. In order to tackle this problem, molecular dynamics (MD) simulations have been applied to the complex between TNF receptor‐1 (TNFR1) and its ligand TNF‐α as a specific test system. The simulations on both all‐atom (AA) and coarse‐grained (CG) levels achieved the similar results that the extracellular domains of TNFR1 can undergo large fluctuations on plasma membrane, while the dynamics of TNFα‐TNFR1 complex is much more constrained. Using the CG model with the Martini force field, we are able to simulate the systems that contain multiple TNFα‐TNFR1 complexes with the timescale of microseconds. We found that complexes can aggregate into oligomers on the plasma membrane through the lateral interactions between receptors at the end of the CG simulations. We suggest that this spatial organization is essential to the efficiency of signal transduction for ligands that belong to the TNF superfamily. We further show that the aggregation of two complexes is initiated by the association between the N‐terminal domains of TNFR1 receptors. Interestingly, the cis‐interfaces between N‐terminal regions of two TNF receptors have been observed in the previous X‐ray crystallographic experiment. Therefore, we provide supportive evidence that cis‐interface is of functional importance in triggering the receptor oligomerization. Taken together, our study brings insights to understand the molecular mechanism of TNF signaling.
Composite coatings are indispensable for protecting the offshore steel materials serviced in the splash zone. But the mechanical properties of conventional epoxy resin (EP) coatings are poor, which ...would lead to a short-term lifespan. The carbon fiber (CF) with excellent mechanical properties is an ideal filler to reinforce the EP coating, thus we chemically grafted Ti3C2Tx nanosheets onto CF via dopamine to enhance the interface adhesion and compatibility between CFs and EP, and improve the mechanical strength and erosion wear resistance of CF/Ti3C2Tx composite coating. The flexural property of CF/Ti3C2Tx@EP coating was evaluated by a three-point bending test, and its flexural strength was increased by 26.97% compared with pure epoxy resin coating. The tribological behaviors and erosion wear resistance of composite coatings were tested using a UMT-3 tribometer and erosion test rig. A UMT-3 tribometer and erosion test rig were used to evaluate the tribological performances and erosion wear resistance for composite coatings. When contrasted to EP coating, CF/Ti3C2Tx@EP′ wear rate was lowered by 79.39%, and its erosion mass and volume were reduced, respectively, by 21.31% and 66.85%, this was ascribed to its enhanced interfacial combination strength with Ti3C2Tx/CF hybrids and EP. We investigated failure behavior and revealed the interfacial strengthening mechanism of the CF/Ti3C2Tx@EP composite coating, which would evoke widespread interest in developing high-performance and long-term protective composite coatings used in the splash zone of the marine environment.
Display omitted
•Carbon fiber was modified by Ti3C2Tx with assistance of dopamine and introduced into the epoxy resin.•The erosion wear resistance mechanism of the CF/Ti3C2Tx@EP coating was studied in detail.•The fiber/epoxy interface properties influenced the improvement of mechanical and tribological performance of coatings.
In the innate immune system, the host defense from the invasion of external pathogens triggers the inflammatory responses. Proteins involved in the inflammatory pathways were often found to aggregate ...into supramolecular oligomers, called ‘inflammasome’, mostly through the homotypic interaction between their domains that belong to the death domain superfamily. Although much has been known about the formation of these helical molecular machineries, the detailed correlation between the dynamics of their assembly and the structure of each domain is still not well understood. Using the filament formed by the PYD domains of adaptor molecule ASC as a test system, we constructed a new multiscale simulation framework to study the kinetics of inflammasome assembly. We found that the filament assembly is a multi-step, but highly cooperative process. Moreover, there are three types of binding interfaces between domain subunits in the ASCPYD filament. The multiscale simulation results suggest that dynamics of domain assembly are rooted in the primary protein sequence which defines the energetics of molecular recognition through three binding interfaces. Interface I plays a more regulatory role than the other two in mediating both the kinetics and the thermodynamics of assembly. Finally, the efficiency of our computational framework allows us to design mutants on a systematic scale and predict their impacts on filament assembly. In summary, this is, to the best of our knowledge, the first simulation method to model the spatial-temporal process of inflammasome assembly. Our work is a useful addition to a suite of existing experimental techniques to study the functions of inflammasome in innate immune system.
•We constructed a new multiscale simulation framework to study the kinetics of ASC inflammasome assembly.•We show that the filament assembly of ASC inflammasome is a multi-step, but highly cooperative process.•We found a critical concentration in inflammasome assembly that assures a binary response to external stimulation.•We illustrated that the interaction along the same layer of filament facilitates inflammasome assembly.•The efficiency of our computational framework allows us to design mutants and predict their impacts on filament assembly.
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