BACKGROUND: Inappropriate antibiotic treatment for patients with viral infections has led to a surge in antimicrobial resistance, increasing mortality and healthcare costs. Viral and bacterial infections are often dif...BACKGROUND: Inappropriate antibiotic treatment for patients with viral infections has led to a surge in antimicrobial resistance, increasing mortality and healthcare costs. Viral and bacterial infections are often difficult to distinguish. Myxovirus resistance protein A(MxA), an essential antiviral factor induced by interferon after viral infection, holds promise for distinguishing between viral and bacterial infections. This study aimed to determine the ability of Mx A to distinguish viral from bacterial infections.METHODS: We quantified MxA in 121 infected patients via dry immunofluorescence chromatography. The Kruskal-Wallis test and receiver operating characteristic(ROC) curve analysis were used to determine the diagnostic value of Mx A, either alone or in combination with C-reactive protein(CRP) or procalcitonin(PCT), in patients with viral, bacterial, or co-infections.RESULTS: The value of MxA(ng/mL) was significantly higher in patients with viral infections than in those with bacterial and co-infections(82.3 [24.5–182.9] vs. 16.4 [10.8–26.5], P<0.0001)(82.3 [24.5–182.9] vs. 28.5 [10.2–106.8], P=0.0237). The area under the curve(AUC) of the ROC curve for distinguishing between viral and bacterial infections was 0.799(95% confidence interval [95% CI] 0.696–0.903), with a sensitivity of 68.9%(95% CI 54.3%–80.5%) and specificity of 90.0%(95% CI 74.4%–96.5%) at the threshold of 50.3 ng/mL. Combining the MxA level with the CRP or PCT level improved its ability. MxA expression was low in cytomegalovirus(15.8 [9.6–47.6] ng/mL) and Epstein-Barr virus(12.9 [8.5–21.0] ng/mL) infections.CONCLUSION: Our study showed the diagnostic efficacy of Mx A in distinguishing between viral and bacterial infections, with further enhancement when it was combined with CRP or PCT. Moreover, EpsteinBarr virus and human cytomegalovirus infections did not elicit elevated Mx A expression.展开更多
Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have b...Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have been proposed to identify essential proteins. Unfortunately, most methods based on network topology only consider the interactions between a protein and its neighboring proteins, and not the interactions with its higher-order distance proteins. In this paper, we propose the DSEP algorithm in which we integrated network topology properties and subcellular localization information in protein–protein interaction(PPI) networks based on four-order distances, and then used random walks to identify the essential proteins. We also propose a method to calculate the finite-order distance of the network, which can greatly reduce the time complexity of our algorithm. We conducted a comprehensive comparison of the DSEP algorithm with 11 existing classical algorithms to identify essential proteins with multiple evaluation methods. The results show that DSEP is superior to these 11 methods.展开更多
Previous research reported litchi thaumatin-like protein(LcTLP)could lead to inflammation,which is a factor causing the adverse reactions after excessive intake of litchi.As a main amino acid in litchi pulp,γ-aminobu...Previous research reported litchi thaumatin-like protein(LcTLP)could lead to inflammation,which is a factor causing the adverse reactions after excessive intake of litchi.As a main amino acid in litchi pulp,γ-aminobutyric acid(GABA)was found with anti-inflammatory effect.Therefore,this study aimed to investigate the effects of GABA on LcTLP-induced inflammation through RAW264.7 macrophages and C57BL mice models.In vitro study showed GABA could effectively regulate the level of inflammatory cytokines(interleukin(IL)-1β,IL-6,IL-10,and prostaglandin E2)and Ca2+in cells,and inhibit the phosphorylation of p65,IκB,p38,c-Jun N-terminal kinase(JNK)and extracellular signal-regulated kinase(ERK).These results indicate GABA alleviated inflammation through nuclear factor-κB and mitogen-activated protein kinase pathway signaling pathways.In vivo experiment was performed to verify the anti-inflammatory effect of GABA,and the results demonstrated that GABA reduced the inflammation and oxidative stress in the liver of LcTLP-treated mice,as it down-regulated the pro-inflammatory cytokines,malondialdehyde,aspartate transferase,and alanine transaminase.The relative expression of phosphorylated p38,JNK and ERK in mice liver with GABA treatment were reduced to 65%,39%and 80%of the control group,respectively.Furthermore,GABA treatment enriched probiotic bacteria and decreased pathogenic bacteria in mice gut,which reveals GABA could effectively reduce the translocation of gut microbiota.展开更多
Single-molecule magnetic tweezers(MTs) have revealed multiple transition barriers along the unfolding pathway of several two-state proteins, such as GB1 and Csp. In this study, we utilized MTs to measure the force-dep...Single-molecule magnetic tweezers(MTs) have revealed multiple transition barriers along the unfolding pathway of several two-state proteins, such as GB1 and Csp. In this study, we utilized MTs to measure the force-dependent folding and unfolding rates of both protein L(PLWT) and its Y47W mutant(PLY47W) where the mutation point is not at the force-bearing β-strands. The measurements were conducted within a force range of 3–120 pN. Notably, the unfolding rates of both PLWT and PWY47W exhibit distinct force sensitivities below 50 pN and above 60 pN, implying a two-barrier free energy landscape. Both PLWT and PLY47W share the same force-dependent folding rate and the same transition barriers,but the unfolding rate of PLY47W is faster than that of PLWT. Our finding demonstrates that the residue outside of the force-bearing region will also affect the force-induced unfolding dynamics.展开更多
In this study,we investigated the effects of major royal jelly proteins(MRJPs)on the estrogen,gut microbiota,and immunological responses in mice.Mice given 250 or 500 mg/kg,not 125 mg/kg of MRJPs,enhanced the prolifer...In this study,we investigated the effects of major royal jelly proteins(MRJPs)on the estrogen,gut microbiota,and immunological responses in mice.Mice given 250 or 500 mg/kg,not 125 mg/kg of MRJPs,enhanced the proliferation of splenocytes in response to mitogens.The splenocytes and mesenteric lymphocytes activated by T-cell mitogens(Con A and anti-CD3/CD28 antibodies)released high levels of IL-2 but low levels of IFN-γand IL-17A.The release of IL-4 was unaffected by MRJPs.Additionally,splenocytes and mesenteric lymphocytes activated by LPS were prevented by MRJPs at the same dose as that required for producing IL-1βand IL-6,two pro-inflammatory cytokines.The production of IL-1β,IL-6,and IFN-γwas negatively associated with estrogen levels,which were higher in the MRJP-treated animals than in the control group.Analysis of the gut microbiota revealed that feeding mice 250 mg/kg of MRJPs maintained the stability of the natural intestinal microflora of mice.Additionally,the LEf Se analysis identified biomarkers in the MRJP-treated mice,including Prevotella,Bacillales,Enterobacteriales,Gammaproteobacteria,Candidatus_Arthromitus,and Shigella.Our results showed that MRJPs are important components of royal jelly that modulate host immunity and hormone levels and help maintain gut microbiota stability.展开更多
Enzymatic hydrolysis of proteins can enhance their emulsifying properties and antioxidant activities.However,the problem related to the hydrolysis of proteins was the generation of the bitter taste.Recently,high hydro...Enzymatic hydrolysis of proteins can enhance their emulsifying properties and antioxidant activities.However,the problem related to the hydrolysis of proteins was the generation of the bitter taste.Recently,high hydrostatic pressure(HHP)treatment has attracted much interest and has been used in several studies on protein modification.Hence,the study aimed to investigate the effects of enzymatic hydrolysis by Corolase PP under different pressure treatments(0.1,100,200,and 300 MPa for 1-5 h at 50℃)on the emulsifying property,antioxidant activity,and bitterness of soybean protein isolate hydrolysate(SPIH).As observed,the hydrolysate obtained at 200 MPa for 4 h had the highest emulsifying activity index(47.49 m^(2)/g)and emulsifying stability index(92.98%),and it had higher antioxidant activities(44.77%DPPH free radical scavenging activity,31.12%superoxide anion radical scavenging activity,and 61.50%copper ion chelating activity).At the same time,the enhancement of emulsion stability was related to the increase of zeta potential and the decrease of mean particle size.In addition,the hydrolysate obtained at 200 MPa for 4 h had a lower bitterness value and showed better palatability.This study has a broad application prospect in developing food ingredients and healthy foods.展开更多
A Pickering emulsion based on sodium starch octenyl succinate(SSOS)was prepared and its effects on the physicochemical properties of hairtail myofibrillar protein gels(MPGs)subjected to multiple freeze-thaw(F-T)cycles...A Pickering emulsion based on sodium starch octenyl succinate(SSOS)was prepared and its effects on the physicochemical properties of hairtail myofibrillar protein gels(MPGs)subjected to multiple freeze-thaw(F-T)cycles were investigated.The whiteness,water-holding capacity,storage modulus(G')and texture properties of the MPGs were significantly improved by adding 1%-2%Pickering emulsion(P<0.05).Meanwhile,Raman spectral analysis demonstrated that Pickering emulsion promoted the transformation of secondary structure,enhanced hydrogen bonds and hydrophobic interactions,and promoted the transition of disulfide bond conformation from g-g-g to g-g-t and t-g-t.At an emulsion concentration of 2%,theα-helix content decreased by 10.37%,while theβ-sheet content increased by 7.94%,compared to the control.After F-T cycles,the structure of the MPGs was destroyed,with an increase in hardness and a decrease in whiteness and water-holding capacity,however,the quality degradation of MPGs was reduced with 1%-2%Pickering emulsion.These findings demonstrated that SSOS-Pickering emulsions,as potential fat substitutes,can enhance the gel properties and the F-T stability of MPGs.展开更多
Protein sequences as special heterogeneous sequences are rare in the amino acid sequence space. The specific sequen- tial order of amino acids of a protein is essential to its 3D structure. On the whole, the correlati...Protein sequences as special heterogeneous sequences are rare in the amino acid sequence space. The specific sequen- tial order of amino acids of a protein is essential to its 3D structure. On the whole, the correlation between sequence and structure of a protein is not so strong. How well would a protein sequence contain its structural information？ How does a sequence determine its native structure？ Keeping the globular proteins in mind, we discuss several problems from sequence to structure.展开更多
As the climate crisis continues to escalate, there has been a growing emphasis on the development of electrode materials that are environmentally friendly and sustainable. Biomolecules, such as proteins,peptides, and ...As the climate crisis continues to escalate, there has been a growing emphasis on the development of electrode materials that are environmentally friendly and sustainable. Biomolecules, such as proteins,peptides, and amino acids, have emerged as promising alternatives to metal oxide and metal hydroxide-based energy storage systems. These biomolecules offer several advantages, such as high safety, non-toxicity, abundant raw material sources, and ease of device fabrication. In this review, we highlighted the recent advancements in amino acid, peptide, and protein-based materials for lithiumion batteries, supercapacitors, and fuel cells. We delve into the synthetic strategies employed and their impact on factors such as active potential window, solubility in the electrolyte, and electrochemical performance. Our focus is on the development, composition, and performance of biomolecules, as well as the various approaches taken for their application in batteries, supercapacitors, and fuel cells. Finally, we discuss key considerations that must be taken into account to promote the design, synthesis and development for future practical applications of lithium-ion batteries, supercapacitors, and fuel cells.展开更多
The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample pre...The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample preparation workflow for mass spectrometry-based proteomics.Using HeLa cells as an example,we found that the method employing the mass spectrometry-compatible surfactant BT reagent significantly reduces the total time consumed for protein extraction and minimizes protein losses during the sample preparation process.Further integrating the four protein extraction methods,we identified over 7000 proteins from HeLa cells without relying on pre-fractionation techniques,and 2990 of them were quantified using label-free quantification.It is worth noting that the BT and SDS methods demonstrate higher efficiency in extracting membrane proteins,while the Urea and Trizol methods are more effective in extracting proteins from nuclear and cytoplasmic fractions.In summary,this study provides a novel solution for deep proteome coverage,particularly in the context of cellular protein extraction,by integrating mass spectrometry-compatible surfactants with traditional extraction methods to effectively enhance protein identification numbers.展开更多
Globally,the prevalence of anxiety and depression has reached epidemic proportions.Food-derived protein hydrolysates and peptides delivered through dietary supplementation can avoid the negative risks associated with ...Globally,the prevalence of anxiety and depression has reached epidemic proportions.Food-derived protein hydrolysates and peptides delivered through dietary supplementation can avoid the negative risks associated with traditional pharmaceuticals while delivering superior anxiolytic and antidepressant effects.This review summarizes current research on food-derived anxiolytic and antidepressant protein hydrolysates and peptides,and subsequently analyses their physicochemical characteristics and elaborates on their mechanisms.The aim of this work is to contribute to the in-depth study and provide a theoretical foundation for the development of related products to better serve patients with anxiety and depression.展开更多
Profiling the protein composition of bacteria is essential for understanding their biology,physiology and interaction with environment.Mass spectrometry has become a pivotal tool for protein analysis,facilitating the ...Profiling the protein composition of bacteria is essential for understanding their biology,physiology and interaction with environment.Mass spectrometry has become a pivotal tool for protein analysis,facilitating the examination of expression levels,molecular masses and structural modifications.In this study,we compared the performance of three widely-used mass spectrometry methods,i.e.,matrix-assisted laser desorption/ionization(MALDI)protein fingerprinting,top-down proteomics and bottom-up proteomics,in the profiling of bacterial protein composition.It was revealed that bottom-up proteomics provided the highest protein coverage and exhibited the greatest protein profile overlap between bacterial species.In contrast,MALDI protein fingerprinting demonstrated superior detection reproducibility and effectiveness in distinguishing between bacterial species.Although top-down proteomics identified fewer proteins than bottom-up approach,it complemented MALDI fingerprinting in the discovery of bacterial protein markers,both favoring abundant,stable,and hydrophilic bacterial ribosomal proteins.This study represents the most systematic and comprehensive comparison of mass spectrometry-based protein profiling methodologies to date.It provides valuable guidelines for the selection of appropriate profiling strategies for specific analytical purposes.This will facilitate studies across various fields,including infection diagnosis,antimicrobial resistance detection and pharmaceutical target discovery.展开更多
The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational biology.One of the most cutting-edge and important applications of ML is its integration with...The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational biology.One of the most cutting-edge and important applications of ML is its integration with molecular simulations to improve the sampling efficiency of the vast conformational space of large biomolecules.This review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational landscape.We first highlight the recent development of ML-aided enhanced sampling methods,including heuristic algorithms and neural networks that are designed to refine the selection of reaction coordinates for the construction of bias potential,or facilitate the exploration of the unsampled region of the energy landscape.Further,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein conformations.Lastly,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann weights.Collectively,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins.展开更多
The traditional nutritional and medical hemp(Cannabis sativa L.)seed protein were explored for the discovery and directional preparation of new xanthine oxidase inhibitory(XOI)peptides by structure-based virtual scree...The traditional nutritional and medical hemp(Cannabis sativa L.)seed protein were explored for the discovery and directional preparation of new xanthine oxidase inhibitory(XOI)peptides by structure-based virtual screening,compound synthesis,in vitro bioassay and proteolysis.Six subtypes of hemp seed edestin and albumin were in silico hydrolyzed by 29 proteases,and 192 encrypted bioactive peptides were screened out.Six peptides showed to be XOI peptides,of which four(about 67%)were released by elastase hydrolysis.The peptide DDNPRRFY displayed the highest XOI activity(IC50=(2.10±0.06)mg/mL),acting as a mixed inhibitor.The pancreatic elastase directionally prepared XOI hemp seed protein hydrolysates,from which 6 high-abundance XOI peptides encrypted 3 virtually-screened ones including the DDNPRRFY.The novel outstanding hemp seed protein-derived XOI peptides and their virtual screening and directed preparation methods provide a promising and applicable approach to conveniently and efficiently explore food-derived bioactive peptides.展开更多
Plant protein beverage adulteration occurs frequently,which may cause health problems for consumers due to the hidden allergens.Hence,a novel method was developed for authentication by ultra-performance liquid chromat...Plant protein beverage adulteration occurs frequently,which may cause health problems for consumers due to the hidden allergens.Hence,a novel method was developed for authentication by ultra-performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS).Almond,peanut,walnut and soybean were hydrolyzed,followed by separation by NanoLC-Triple TOF MS.The obtained fingerprints were identified by ProteinPilotTM combined with Uniprot,and 16 signature peptides were selected.Afterwards,plant protein beverages treated by trypsin hydrolysis were analyzed with UPLC-MS/MS.This method showed a good linear relationship with R2>0.99403.The limit of quantification(LOQ)were 0.015,0.01,0.5 and 0.05 g/L for almond,peanut,walnut and soybean,respectively.Mean recoveries ranged from 84.77%to 110.44%with RSDs<15%.The developed method was successfully applied to the adulteration detection of 31 plant protein beverages to reveal adulteration and false labeling.Conclusively,this method could provide technical support for authentication of plant protein beverages to protect the rights and health of consumers.展开更多
To explore the oxidation mechanism of wooden breast myofibrillar protein(WBMP),oxidative breast MP(OBMP)was obtained from different doses(3,10,and 20 mmol/L)of H2O2 oxidized normal breast MP(NBMP).The results showed t...To explore the oxidation mechanism of wooden breast myofibrillar protein(WBMP),oxidative breast MP(OBMP)was obtained from different doses(3,10,and 20 mmol/L)of H2O2 oxidized normal breast MP(NBMP).The results showed that the Zeta-potential,particle size,solubility,sulfhydryl,and carbonyl contents of OBMP-3(3 mmol/L,low-dose free radicals)and WBMP were similar.Fluorescence spectrum analysis showed that the oxidation of low-dose free radicals led to a significant increase in the surface hydrophobicity(from 214.03±10.03 to 393.50±10.33)and tryptophan fluorescence intensity(from 185.71 to 568.32).In addition,theα-helix content of WBMP decreased significantly from(37.46±1.15)%(NBMP)to(34.70±2.04)%,whileβ-sheet and random coil contents increased significantly(P<0.05)from(14.37±0.69)%and(22.24±0.78)%(NBMP)to(17.70±0.87)%and(25.20±1.47)%(WBMP).In summary,low-dose free radical oxidation attacks protein groups,inducing secondary and tertiary structural changes,leading to the formation of WBMP.This work will provide a theoretical basis at the molecular level for exploring the mechanism of functional degradation of WBMP.展开更多
BACKGROUND:Patients with diabetes mellitus(DM)are vulnerable to community-acquired pneumonia(CAP),which have a high mortality rate.We aimed to investigate the value of heparin-binding protein(HBP)as a prognostic marke...BACKGROUND:Patients with diabetes mellitus(DM)are vulnerable to community-acquired pneumonia(CAP),which have a high mortality rate.We aimed to investigate the value of heparin-binding protein(HBP)as a prognostic marker of mortality in patients with DM and CAP.METHODS:This retrospective study included CAP patients who were tested for HBP at intensive care unit(ICU)admission from January 2019 to April 2020.Patients were allocated to the DM or non-DM group and paired with propensity score matching.Baseline characteristics and clinical outcomes up to 90 days were evaluated.The primary outcome was the 10-day mortality.Receiver operating characteristic(ROC)curves,Kaplan-Meier analysis,and Cox regression were used for statistical analysis.RESULTS:Among 152 enrolled patients,60 pairs were successfully matched.There was no significant difference in 10-day mortality,while more patients in the DM group died within 28 d(P=0.024)and 90 d(P=0.008).In the DM group,HBP levels at ICU admission were higher in 10-day non-survivors than in 10-day survivors(median 182.21[IQR:55.43-300]ng/ml vs.median 66.40[IQR:34.13-107.85]ng/mL,P=0.019),and HBP levels could predict the 10-day mortality with an area under the ROC curve of 0.747.The cut-off value,sensitivity,and specificity were 160.6 ng/mL,66.7%,and 90.2%,respectively.Multivariate Cox regression analysis indicated that HBP was an independent prognostic factor for 10-day(HR 7.196,95%CI:1.596-32.455,P=0.01),28-day(HR 4.381,95%CI:1.449-13.245,P=0.009),and 90-day mortality(HR 4.581,95%CI:1.637-12.819,P=0.004)in patients with DM.CONCLUSION:Plasma HBP at ICU admission was associated with the 10-day,28-day,and 90-day mortality,and might be a prognostic factor in patients with DM and CAP.展开更多
The hydroxyl-terminated self-assembled monolayer(OH-SAM),as a surface resistant to protein adsorption,exhibits substantial potential in applications such as ship navigation and medical implants,and the appropriate str...The hydroxyl-terminated self-assembled monolayer(OH-SAM),as a surface resistant to protein adsorption,exhibits substantial potential in applications such as ship navigation and medical implants,and the appropriate strategies for designing anti-fouling surfaces are crucial.Here,we employ molecular dynamics simulations and alchemical free energy calculations to systematically analyze the factors influencing resistance to protein adsorption on the SAMs terminated with single or double OH groups at three packing densities(∑=2.0 nm^(-2),4.5 nm^(-2),and 6.5 nm^(-2)),respectively.For the first time,we observed that the compactness and order of interfacial water enhance its physical barrier effect,subsequently enhancing the resistance of SAM to protein adsorption.Notably,the spatial hindrance effect of SAM leads to the embedding of protein into SAM,resulting in a lack of resistance of SAM towards protein.Furthermore,the number of hydroxyl groups per unit area of double OH-terminated SAM at ∑=6.5 nm^(-2) is approximately 2 to 3 times that of single OH-terminated SAM at ∑=6.5 nm^(-2) and 4.5 nm^(-2),consequently yielding a weaker resistance of double OH-terminated SAM towards protein.Meanwhile,due to the structure of SAM itself,i.e.,the formation of a nearly perfect ice-like hydrogen bond structure,the SAM exhibits the weakest resistance towards protein.This study will complement and improve the mechanism of OH-SAM resistance to protein adsorption,especially the traditional barrier effect of interfacial water.展开更多
The aim of this study is to investigate the feasibility of Maillard reaction products of Haematococcus pluvialis protein and galactose(HPP-GAL)for improving the bioactivities of curcumin(CUR)for alleviating alcoholic ...The aim of this study is to investigate the feasibility of Maillard reaction products of Haematococcus pluvialis protein and galactose(HPP-GAL)for improving the bioactivities of curcumin(CUR)for alleviating alcoholic liver damage.CUR was embedded into HPP-GAL nanoparticles by the self-assembly of hydrogen bonding and hydrophobic interaction with the particle size around 200 nm.HPP-GAL enhanced the encapsulation efficiency and loading amount of CUR with the value of(89.21±0.33)%and(0.500±0.004)%,respectively.The stabilities of CUR under strong acid,salt ion stability and ultraviolet irradiation conditions were improved by the encapsulation.HPP-GAL-CUR nanoparticles exhibited excellent concentration-dependent in vitro antioxidant activities including DPPH and ABTS scavenging rates,and better protective effect on CUR against gastric acid environment as well as longer release of CUR in simulated intestinal fluid.In addition,the HPPGAL-CUR delivery system possessed liver targeting property due to the existence of GAL,which could effectively alleviate the alcohol-induced liver damage and the inflammation indexes by inhibiting the oxidative stress.Therefore,HPP-GAL-CUR nanoparticles might be a potential candidate system for the prevention of alcoholic liver damage in the future.展开更多
基金supported by the National Natural Science Foundation of China (82272196 and 82272220)。
文摘BACKGROUND: Inappropriate antibiotic treatment for patients with viral infections has led to a surge in antimicrobial resistance, increasing mortality and healthcare costs. Viral and bacterial infections are often difficult to distinguish. Myxovirus resistance protein A(MxA), an essential antiviral factor induced by interferon after viral infection, holds promise for distinguishing between viral and bacterial infections. This study aimed to determine the ability of Mx A to distinguish viral from bacterial infections.METHODS: We quantified MxA in 121 infected patients via dry immunofluorescence chromatography. The Kruskal-Wallis test and receiver operating characteristic(ROC) curve analysis were used to determine the diagnostic value of Mx A, either alone or in combination with C-reactive protein(CRP) or procalcitonin(PCT), in patients with viral, bacterial, or co-infections.RESULTS: The value of MxA(ng/mL) was significantly higher in patients with viral infections than in those with bacterial and co-infections(82.3 [24.5–182.9] vs. 16.4 [10.8–26.5], P<0.0001)(82.3 [24.5–182.9] vs. 28.5 [10.2–106.8], P=0.0237). The area under the curve(AUC) of the ROC curve for distinguishing between viral and bacterial infections was 0.799(95% confidence interval [95% CI] 0.696–0.903), with a sensitivity of 68.9%(95% CI 54.3%–80.5%) and specificity of 90.0%(95% CI 74.4%–96.5%) at the threshold of 50.3 ng/mL. Combining the MxA level with the CRP or PCT level improved its ability. MxA expression was low in cytomegalovirus(15.8 [9.6–47.6] ng/mL) and Epstein-Barr virus(12.9 [8.5–21.0] ng/mL) infections.CONCLUSION: Our study showed the diagnostic efficacy of Mx A in distinguishing between viral and bacterial infections, with further enhancement when it was combined with CRP or PCT. Moreover, EpsteinBarr virus and human cytomegalovirus infections did not elicit elevated Mx A expression.
基金Project supported by the Gansu Province Industrial Support Plan (Grant No.2023CYZC-25)the Natural Science Foundation of Gansu Province (Grant No.23JRRA770)the National Natural Science Foundation of China (Grant No.62162040)。
文摘Essential proteins are inseparable in cell growth and survival. The study of essential proteins is important for understanding cellular functions and biological mechanisms. Therefore, various computable methods have been proposed to identify essential proteins. Unfortunately, most methods based on network topology only consider the interactions between a protein and its neighboring proteins, and not the interactions with its higher-order distance proteins. In this paper, we propose the DSEP algorithm in which we integrated network topology properties and subcellular localization information in protein–protein interaction(PPI) networks based on four-order distances, and then used random walks to identify the essential proteins. We also propose a method to calculate the finite-order distance of the network, which can greatly reduce the time complexity of our algorithm. We conducted a comprehensive comparison of the DSEP algorithm with 11 existing classical algorithms to identify essential proteins with multiple evaluation methods. The results show that DSEP is superior to these 11 methods.
基金supported by China Agriculture Research System of MOF and MARA(CARS-32)the Guangzhou Wanglaoji Lychee Industry Research Project(5100-H220577)+2 种基金the Science and Technology Planning Project of Guangzhou City of China(202103000054)the National Natural Science Foundation of China(32202022)the Dongguan Key R&D Programme(2022120030008).
文摘Previous research reported litchi thaumatin-like protein(LcTLP)could lead to inflammation,which is a factor causing the adverse reactions after excessive intake of litchi.As a main amino acid in litchi pulp,γ-aminobutyric acid(GABA)was found with anti-inflammatory effect.Therefore,this study aimed to investigate the effects of GABA on LcTLP-induced inflammation through RAW264.7 macrophages and C57BL mice models.In vitro study showed GABA could effectively regulate the level of inflammatory cytokines(interleukin(IL)-1β,IL-6,IL-10,and prostaglandin E2)and Ca2+in cells,and inhibit the phosphorylation of p65,IκB,p38,c-Jun N-terminal kinase(JNK)and extracellular signal-regulated kinase(ERK).These results indicate GABA alleviated inflammation through nuclear factor-κB and mitogen-activated protein kinase pathway signaling pathways.In vivo experiment was performed to verify the anti-inflammatory effect of GABA,and the results demonstrated that GABA reduced the inflammation and oxidative stress in the liver of LcTLP-treated mice,as it down-regulated the pro-inflammatory cytokines,malondialdehyde,aspartate transferase,and alanine transaminase.The relative expression of phosphorylated p38,JNK and ERK in mice liver with GABA treatment were reduced to 65%,39%and 80%of the control group,respectively.Furthermore,GABA treatment enriched probiotic bacteria and decreased pathogenic bacteria in mice gut,which reveals GABA could effectively reduce the translocation of gut microbiota.
基金supported by the National Natural Science Foundation of China(Grant Nos.12174322 to HC and 12204124 to ZG)111 Project(Grant No.B16029)+1 种基金the Graduate Scientific Research Foundation of Wenzhou University(Grant No.3162023003034 to JH)research grant from Wenzhou Institute。
文摘Single-molecule magnetic tweezers(MTs) have revealed multiple transition barriers along the unfolding pathway of several two-state proteins, such as GB1 and Csp. In this study, we utilized MTs to measure the force-dependent folding and unfolding rates of both protein L(PLWT) and its Y47W mutant(PLY47W) where the mutation point is not at the force-bearing β-strands. The measurements were conducted within a force range of 3–120 pN. Notably, the unfolding rates of both PLWT and PWY47W exhibit distinct force sensitivities below 50 pN and above 60 pN, implying a two-barrier free energy landscape. Both PLWT and PLY47W share the same force-dependent folding rate and the same transition barriers,but the unfolding rate of PLY47W is faster than that of PLWT. Our finding demonstrates that the residue outside of the force-bearing region will also affect the force-induced unfolding dynamics.
基金financially supported by the National Natural Science Foundation of China(U2004104)the Natural Science Foundation of Henan Province(202300410080)+2 种基金the Key Project of Henan Education Committee(21A310005)the Internal Fund of Hebei University of Economics and Business(2020ZD10)the Postgraduate“Talent Program”of Henan University(SYL20060187 and SYL20060189)。
文摘In this study,we investigated the effects of major royal jelly proteins(MRJPs)on the estrogen,gut microbiota,and immunological responses in mice.Mice given 250 or 500 mg/kg,not 125 mg/kg of MRJPs,enhanced the proliferation of splenocytes in response to mitogens.The splenocytes and mesenteric lymphocytes activated by T-cell mitogens(Con A and anti-CD3/CD28 antibodies)released high levels of IL-2 but low levels of IFN-γand IL-17A.The release of IL-4 was unaffected by MRJPs.Additionally,splenocytes and mesenteric lymphocytes activated by LPS were prevented by MRJPs at the same dose as that required for producing IL-1βand IL-6,two pro-inflammatory cytokines.The production of IL-1β,IL-6,and IFN-γwas negatively associated with estrogen levels,which were higher in the MRJP-treated animals than in the control group.Analysis of the gut microbiota revealed that feeding mice 250 mg/kg of MRJPs maintained the stability of the natural intestinal microflora of mice.Additionally,the LEf Se analysis identified biomarkers in the MRJP-treated mice,including Prevotella,Bacillales,Enterobacteriales,Gammaproteobacteria,Candidatus_Arthromitus,and Shigella.Our results showed that MRJPs are important components of royal jelly that modulate host immunity and hormone levels and help maintain gut microbiota stability.
基金supported by the Doctoral Research Foundation of Bohai University (05013/0520bs006)the Science and Technology Project of“Unveiling and Commanding”Liaoning Province (2021JH1/10400033)the Scientific Research Project from Education Department of Liaoning Province (LJ2020010)。
文摘Enzymatic hydrolysis of proteins can enhance their emulsifying properties and antioxidant activities.However,the problem related to the hydrolysis of proteins was the generation of the bitter taste.Recently,high hydrostatic pressure(HHP)treatment has attracted much interest and has been used in several studies on protein modification.Hence,the study aimed to investigate the effects of enzymatic hydrolysis by Corolase PP under different pressure treatments(0.1,100,200,and 300 MPa for 1-5 h at 50℃)on the emulsifying property,antioxidant activity,and bitterness of soybean protein isolate hydrolysate(SPIH).As observed,the hydrolysate obtained at 200 MPa for 4 h had the highest emulsifying activity index(47.49 m^(2)/g)and emulsifying stability index(92.98%),and it had higher antioxidant activities(44.77%DPPH free radical scavenging activity,31.12%superoxide anion radical scavenging activity,and 61.50%copper ion chelating activity).At the same time,the enhancement of emulsion stability was related to the increase of zeta potential and the decrease of mean particle size.In addition,the hydrolysate obtained at 200 MPa for 4 h had a lower bitterness value and showed better palatability.This study has a broad application prospect in developing food ingredients and healthy foods.
基金supported by the National Natural Science Foundation of China(U20A2067,32272360)。
文摘A Pickering emulsion based on sodium starch octenyl succinate(SSOS)was prepared and its effects on the physicochemical properties of hairtail myofibrillar protein gels(MPGs)subjected to multiple freeze-thaw(F-T)cycles were investigated.The whiteness,water-holding capacity,storage modulus(G')and texture properties of the MPGs were significantly improved by adding 1%-2%Pickering emulsion(P<0.05).Meanwhile,Raman spectral analysis demonstrated that Pickering emulsion promoted the transformation of secondary structure,enhanced hydrogen bonds and hydrophobic interactions,and promoted the transition of disulfide bond conformation from g-g-g to g-g-t and t-g-t.At an emulsion concentration of 2%,theα-helix content decreased by 10.37%,while theβ-sheet content increased by 7.94%,compared to the control.After F-T cycles,the structure of the MPGs was destroyed,with an increase in hardness and a decrease in whiteness and water-holding capacity,however,the quality degradation of MPGs was reduced with 1%-2%Pickering emulsion.These findings demonstrated that SSOS-Pickering emulsions,as potential fat substitutes,can enhance the gel properties and the F-T stability of MPGs.
基金supported by the National Natural Science Foundation of China (Grant Nos. 11175224 and 11121403)
文摘Protein sequences as special heterogeneous sequences are rare in the amino acid sequence space. The specific sequen- tial order of amino acids of a protein is essential to its 3D structure. On the whole, the correlation between sequence and structure of a protein is not so strong. How well would a protein sequence contain its structural information？ How does a sequence determine its native structure？ Keeping the globular proteins in mind, we discuss several problems from sequence to structure.
基金financial support from The Director, CSIR-IICT (MS No. IICT/Pubs./2024/043) Hyderabad, IndiaUniversity Grant Commission (UGC) Faculty Research Program, New Delhi, India (F.4-5(50-FRP) (IV-Cycle)/2017(BSR)) for an award of Professorship。
文摘As the climate crisis continues to escalate, there has been a growing emphasis on the development of electrode materials that are environmentally friendly and sustainable. Biomolecules, such as proteins,peptides, and amino acids, have emerged as promising alternatives to metal oxide and metal hydroxide-based energy storage systems. These biomolecules offer several advantages, such as high safety, non-toxicity, abundant raw material sources, and ease of device fabrication. In this review, we highlighted the recent advancements in amino acid, peptide, and protein-based materials for lithiumion batteries, supercapacitors, and fuel cells. We delve into the synthetic strategies employed and their impact on factors such as active potential window, solubility in the electrolyte, and electrochemical performance. Our focus is on the development, composition, and performance of biomolecules, as well as the various approaches taken for their application in batteries, supercapacitors, and fuel cells. Finally, we discuss key considerations that must be taken into account to promote the design, synthesis and development for future practical applications of lithium-ion batteries, supercapacitors, and fuel cells.
文摘The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample preparation workflow for mass spectrometry-based proteomics.Using HeLa cells as an example,we found that the method employing the mass spectrometry-compatible surfactant BT reagent significantly reduces the total time consumed for protein extraction and minimizes protein losses during the sample preparation process.Further integrating the four protein extraction methods,we identified over 7000 proteins from HeLa cells without relying on pre-fractionation techniques,and 2990 of them were quantified using label-free quantification.It is worth noting that the BT and SDS methods demonstrate higher efficiency in extracting membrane proteins,while the Urea and Trizol methods are more effective in extracting proteins from nuclear and cytoplasmic fractions.In summary,this study provides a novel solution for deep proteome coverage,particularly in the context of cellular protein extraction,by integrating mass spectrometry-compatible surfactants with traditional extraction methods to effectively enhance protein identification numbers.
基金supported by the National Key Research and Development Program of China (2021YFD2100402)the National Natural Science Foundation of China (81903275)the Fund of the Cultivation Project of Double First-Class Disciplines of Food Science and Engineering,Beijing Technology&Business University (BTBUYXTD202203)。
文摘Globally,the prevalence of anxiety and depression has reached epidemic proportions.Food-derived protein hydrolysates and peptides delivered through dietary supplementation can avoid the negative risks associated with traditional pharmaceuticals while delivering superior anxiolytic and antidepressant effects.This review summarizes current research on food-derived anxiolytic and antidepressant protein hydrolysates and peptides,and subsequently analyses their physicochemical characteristics and elaborates on their mechanisms.The aim of this work is to contribute to the in-depth study and provide a theoretical foundation for the development of related products to better serve patients with anxiety and depression.
文摘Profiling the protein composition of bacteria is essential for understanding their biology,physiology and interaction with environment.Mass spectrometry has become a pivotal tool for protein analysis,facilitating the examination of expression levels,molecular masses and structural modifications.In this study,we compared the performance of three widely-used mass spectrometry methods,i.e.,matrix-assisted laser desorption/ionization(MALDI)protein fingerprinting,top-down proteomics and bottom-up proteomics,in the profiling of bacterial protein composition.It was revealed that bottom-up proteomics provided the highest protein coverage and exhibited the greatest protein profile overlap between bacterial species.In contrast,MALDI protein fingerprinting demonstrated superior detection reproducibility and effectiveness in distinguishing between bacterial species.Although top-down proteomics identified fewer proteins than bottom-up approach,it complemented MALDI fingerprinting in the discovery of bacterial protein markers,both favoring abundant,stable,and hydrophilic bacterial ribosomal proteins.This study represents the most systematic and comprehensive comparison of mass spectrometry-based protein profiling methodologies to date.It provides valuable guidelines for the selection of appropriate profiling strategies for specific analytical purposes.This will facilitate studies across various fields,including infection diagnosis,antimicrobial resistance detection and pharmaceutical target discovery.
基金Project supported by the National Key Research and Development Program of China(Grant No.2023YFF1204402)the National Natural Science Foundation of China(Grant Nos.12074079 and 12374208)+1 种基金the Natural Science Foundation of Shanghai(Grant No.22ZR1406800)the China Postdoctoral Science Foundation(Grant No.2022M720815).
文摘The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational biology.One of the most cutting-edge and important applications of ML is its integration with molecular simulations to improve the sampling efficiency of the vast conformational space of large biomolecules.This review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational landscape.We first highlight the recent development of ML-aided enhanced sampling methods,including heuristic algorithms and neural networks that are designed to refine the selection of reaction coordinates for the construction of bias potential,or facilitate the exploration of the unsampled region of the energy landscape.Further,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein conformations.Lastly,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann weights.Collectively,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins.
基金funded by National Natural Science Foundation of China(21868003)Bama County Program for Talents in Science and Technology(BaRenKe20210045).
文摘The traditional nutritional and medical hemp(Cannabis sativa L.)seed protein were explored for the discovery and directional preparation of new xanthine oxidase inhibitory(XOI)peptides by structure-based virtual screening,compound synthesis,in vitro bioassay and proteolysis.Six subtypes of hemp seed edestin and albumin were in silico hydrolyzed by 29 proteases,and 192 encrypted bioactive peptides were screened out.Six peptides showed to be XOI peptides,of which four(about 67%)were released by elastase hydrolysis.The peptide DDNPRRFY displayed the highest XOI activity(IC50=(2.10±0.06)mg/mL),acting as a mixed inhibitor.The pancreatic elastase directionally prepared XOI hemp seed protein hydrolysates,from which 6 high-abundance XOI peptides encrypted 3 virtually-screened ones including the DDNPRRFY.The novel outstanding hemp seed protein-derived XOI peptides and their virtual screening and directed preparation methods provide a promising and applicable approach to conveniently and efficiently explore food-derived bioactive peptides.
基金supported by the High-level Talent Funding Project of Hebei Province(A202005015)Youth Top Talent Support Plan of Hebei Province.
文摘Plant protein beverage adulteration occurs frequently,which may cause health problems for consumers due to the hidden allergens.Hence,a novel method was developed for authentication by ultra-performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS).Almond,peanut,walnut and soybean were hydrolyzed,followed by separation by NanoLC-Triple TOF MS.The obtained fingerprints were identified by ProteinPilotTM combined with Uniprot,and 16 signature peptides were selected.Afterwards,plant protein beverages treated by trypsin hydrolysis were analyzed with UPLC-MS/MS.This method showed a good linear relationship with R2>0.99403.The limit of quantification(LOQ)were 0.015,0.01,0.5 and 0.05 g/L for almond,peanut,walnut and soybean,respectively.Mean recoveries ranged from 84.77%to 110.44%with RSDs<15%.The developed method was successfully applied to the adulteration detection of 31 plant protein beverages to reveal adulteration and false labeling.Conclusively,this method could provide technical support for authentication of plant protein beverages to protect the rights and health of consumers.
基金supported by the Shandong Modern Agricultural Technology and Industry System(SDAIT-11-11)China Agricultural Research System(CARS-41-Z06)Natural Science Foundation of Shandong Province(ZR2022MC087).
文摘To explore the oxidation mechanism of wooden breast myofibrillar protein(WBMP),oxidative breast MP(OBMP)was obtained from different doses(3,10,and 20 mmol/L)of H2O2 oxidized normal breast MP(NBMP).The results showed that the Zeta-potential,particle size,solubility,sulfhydryl,and carbonyl contents of OBMP-3(3 mmol/L,low-dose free radicals)and WBMP were similar.Fluorescence spectrum analysis showed that the oxidation of low-dose free radicals led to a significant increase in the surface hydrophobicity(from 214.03±10.03 to 393.50±10.33)and tryptophan fluorescence intensity(from 185.71 to 568.32).In addition,theα-helix content of WBMP decreased significantly from(37.46±1.15)%(NBMP)to(34.70±2.04)%,whileβ-sheet and random coil contents increased significantly(P<0.05)from(14.37±0.69)%and(22.24±0.78)%(NBMP)to(17.70±0.87)%and(25.20±1.47)%(WBMP).In summary,low-dose free radical oxidation attacks protein groups,inducing secondary and tertiary structural changes,leading to the formation of WBMP.This work will provide a theoretical basis at the molecular level for exploring the mechanism of functional degradation of WBMP.
基金supported by the National Key Research and Development Program of China(2021YFC2501800)Leader Project of Henan Province Health Young and Middle-aged Professor(HNSWJW2020013).
文摘BACKGROUND:Patients with diabetes mellitus(DM)are vulnerable to community-acquired pneumonia(CAP),which have a high mortality rate.We aimed to investigate the value of heparin-binding protein(HBP)as a prognostic marker of mortality in patients with DM and CAP.METHODS:This retrospective study included CAP patients who were tested for HBP at intensive care unit(ICU)admission from January 2019 to April 2020.Patients were allocated to the DM or non-DM group and paired with propensity score matching.Baseline characteristics and clinical outcomes up to 90 days were evaluated.The primary outcome was the 10-day mortality.Receiver operating characteristic(ROC)curves,Kaplan-Meier analysis,and Cox regression were used for statistical analysis.RESULTS:Among 152 enrolled patients,60 pairs were successfully matched.There was no significant difference in 10-day mortality,while more patients in the DM group died within 28 d(P=0.024)and 90 d(P=0.008).In the DM group,HBP levels at ICU admission were higher in 10-day non-survivors than in 10-day survivors(median 182.21[IQR:55.43-300]ng/ml vs.median 66.40[IQR:34.13-107.85]ng/mL,P=0.019),and HBP levels could predict the 10-day mortality with an area under the ROC curve of 0.747.The cut-off value,sensitivity,and specificity were 160.6 ng/mL,66.7%,and 90.2%,respectively.Multivariate Cox regression analysis indicated that HBP was an independent prognostic factor for 10-day(HR 7.196,95%CI:1.596-32.455,P=0.01),28-day(HR 4.381,95%CI:1.449-13.245,P=0.009),and 90-day mortality(HR 4.581,95%CI:1.637-12.819,P=0.004)in patients with DM.CONCLUSION:Plasma HBP at ICU admission was associated with the 10-day,28-day,and 90-day mortality,and might be a prognostic factor in patients with DM and CAP.
基金Project supported by the National Natural Science Foundation of China (Grants No. 12075201)the Science and Technology Planning Project of Jiangsu Province, China (Grant No. BK20201428)+1 种基金the Postgraduate Research & Practice Innovation Program of Jiangsu Province, China (Grant No. KYCX21 3193)the Special Program for Applied Research on Supercomputation of the NSFC–Guangdong Joint Fund (the second phase)。
文摘The hydroxyl-terminated self-assembled monolayer(OH-SAM),as a surface resistant to protein adsorption,exhibits substantial potential in applications such as ship navigation and medical implants,and the appropriate strategies for designing anti-fouling surfaces are crucial.Here,we employ molecular dynamics simulations and alchemical free energy calculations to systematically analyze the factors influencing resistance to protein adsorption on the SAMs terminated with single or double OH groups at three packing densities(∑=2.0 nm^(-2),4.5 nm^(-2),and 6.5 nm^(-2)),respectively.For the first time,we observed that the compactness and order of interfacial water enhance its physical barrier effect,subsequently enhancing the resistance of SAM to protein adsorption.Notably,the spatial hindrance effect of SAM leads to the embedding of protein into SAM,resulting in a lack of resistance of SAM towards protein.Furthermore,the number of hydroxyl groups per unit area of double OH-terminated SAM at ∑=6.5 nm^(-2) is approximately 2 to 3 times that of single OH-terminated SAM at ∑=6.5 nm^(-2) and 4.5 nm^(-2),consequently yielding a weaker resistance of double OH-terminated SAM towards protein.Meanwhile,due to the structure of SAM itself,i.e.,the formation of a nearly perfect ice-like hydrogen bond structure,the SAM exhibits the weakest resistance towards protein.This study will complement and improve the mechanism of OH-SAM resistance to protein adsorption,especially the traditional barrier effect of interfacial water.
基金supported by the National Key Research and Development Program of China(2022YFF1100205)the National Natural Science Foundation of China(31972105)the National Science Fund for Distinguished Young Scholars of China(31925031).
文摘The aim of this study is to investigate the feasibility of Maillard reaction products of Haematococcus pluvialis protein and galactose(HPP-GAL)for improving the bioactivities of curcumin(CUR)for alleviating alcoholic liver damage.CUR was embedded into HPP-GAL nanoparticles by the self-assembly of hydrogen bonding and hydrophobic interaction with the particle size around 200 nm.HPP-GAL enhanced the encapsulation efficiency and loading amount of CUR with the value of(89.21±0.33)%and(0.500±0.004)%,respectively.The stabilities of CUR under strong acid,salt ion stability and ultraviolet irradiation conditions were improved by the encapsulation.HPP-GAL-CUR nanoparticles exhibited excellent concentration-dependent in vitro antioxidant activities including DPPH and ABTS scavenging rates,and better protective effect on CUR against gastric acid environment as well as longer release of CUR in simulated intestinal fluid.In addition,the HPPGAL-CUR delivery system possessed liver targeting property due to the existence of GAL,which could effectively alleviate the alcohol-induced liver damage and the inflammation indexes by inhibiting the oxidative stress.Therefore,HPP-GAL-CUR nanoparticles might be a potential candidate system for the prevention of alcoholic liver damage in the future.
