Intrinsic BET inhibitor resistance in SPOP-mutated prostate cancer is mediated by BET protein stabilization and AKT-mTORC1 activation

Subject Code:H16With the support by the National Natural Science Foundation of China,a collaborative study by the research groups led by Prof.Wang Chenji(王陈继)from Fudan University,Prof.Huang Haojie(黄浩杰)from Mayo Clinic and Sun Yinhao(孙颖浩)from the Second Military Medical University have

Light Promotes Protein Stability of Auxin Response Factor 7#

Light is an environmental signaling,whereas Aux/IAA proteins and Auxin Response Factors(ARFs)are regulators of auxin signalling.Aux/IAA proteins are unstable,and their degradation dependents on 26S ubiquitin-proteasome and is promoted by Auxin.Auxin binds directly to a SCF-type ubiquitin-protein ligase,TIR1,facilitates the interaction between Aux/IAA proteins and TIR1,and then the degradation of Aux/IAA proteins.A few studies have reported that some ARFs are also unstable proteins,and their degradation is also mediated by 26S proteasome.In this study,by using of antibodies recognizing endogenous ARF7 proteins,we found that protein stability of ARF7 was affected by light.By expressing MYC tagged ARF activators in protoplasts,we found that degradation of ARF7 was inhibited by 26 proteasome inhibitors.In addition,at least ARF5 and ARF19 were also unstable proteins,and degradation of ARF5 via 26S proteasome was further confirmed by using stable transformed plants overexpressing ARF5 with a GUS tag.

Using NMR-detected hydrogen-deuterium exchange to quantify protein stability in cosolutes,under crowded conditions in vitro and in cells

We review the use of nuclear magnetic resonance(NMR)spectroscopy to assess the exchange of amide protons for deuterons(HDX)in efforts to understand how high concentration of cosolutes,especially macromolecules,affect the equilibrium thermodynamics of protein stability.HDX NMR is the only method that can routinely provide such data at the level of individual amino acids.We begin by discussing the properties of the protein systems required to yield equilibrium thermodynamic data and then review publications using osmolytes,sugars,denaturants,synthetic polymers,proteins,cytoplasm and in cells.

Protein A-based ligands for affinity chromatography of antibodies

Protein A chromatography is a key technology in the industrial production of antibodies,and a variety of commercial protein A adsorbents are available in shelf.High stability and binding capacity of a protein A adsorbent are two key issues for successful practice of protein A chromatography.Earlier versions of protein A adsorbents ever exhibited serious fragility to typical cleaning-in-place protocols(e.g.washing with sodium hydroxide solution),and suffered from low binding capacity,harsh elution,ligand leakage and other problems involved in industrial applications.During the last three decades,various techniques and approaches have been applied in the improvement of chemical stability and enhancement of binding capacity of protein A-based ligands and adsorbents for antibody purifications.This mini-review focuses on the technical explorations in protein A-based affinity adsorbents,especially protein A-based ligands,including the efforts to increase the chemical stability by site-directed mutations and to improve the binding capacity by ligand polymerization and site-directed immobilization.Moreover,the efforts to develop short peptide ligands based on the structure of protein A,including the biomimetic design strategies and the synthesis of peptide-mixed mode hybrid ligands are discussed.These peptide and peptidebased hybrid ligands exhibit high affinity and selectivity to antibodies,but noteworthy differences in the binding mechanism of antibody from protein A.As a result,bound antibody to the ligands could be effectively eluted under mild conditions.Perspectives for the development of the protein A-based peptide ligands have been extensively discussed,suggesting that the ligands represent a direction for technological development of antibody purification.

NF-E2:a Novel Regulator of Alpha-hemoglobin Stabilizing Protein Gene Expression

Objective To investigate whether α-hemoglobin stabilizing protein (AHSP), the α-globin-specific molecular chaperone, is regulated by erythroid transcription factor NF-E2. Methods We established the stable cell line with NF-E2p45 (the larger subunit of NF-E2) short hairpin RNA to silence its expression. Western blot, real-time polymerase chain reaction, and chromatin immunoprecipitation (ChIP) analysis were performed to detect the expression of AHSP, the histone modifications at AHSP gene locus, and the binding of GATA-1 at the AHSP promoter with NF-E2p45 deficiency. ChIP was also carried out in dimethyl sulfoxide (DMSO)-induced DS19 cells and estrogen-induced G1E-ER4 cells to examine NF-E2 binding to the AHSP gene locus and its changes during cell erythroid differentiation. Finally, luciferase assay was applied in HeLa cells transfected with AHSP promoter fragments to examine AHSP promoter activity in the presence of exogenous NF-E2p45. Results We found that AHSP expression was highly dependent on NF-E2p45. NF-E2 bound to the regions across AHSP gene locus in vivo, and the transcription of AHSP was transactivated by exogenous NF-E2p45. In addition, we observed the decrease of H3K4 trimethylation and GATA-1 occupancy at the AHSP gene locus in NF-E2p45-deficient cells. Restoration of GATA-1 in G1E-ER4 cells in turn led to increased DNA binding of NF-E2p45. Conclusion NF-E2 may play an important role in AHSP gene regulation, providing new insights into the molecular mechanisms underlying the erythroid-specific expression of AHSP as well as new possibilities for β-thalassemia treatment.

Solution pH jump during antibody and Fc-fusion protein thaw leads to increased aggregation

Freeze-thaw cycles impact the amount of aggregation observed in antibodies and Fc-fusion proteins. Various formulation strategies are used to mitigate the amount of aggregation that occurs upon putting a protein solution through a freeze-thaw cycle. Additionally, low pH solutions cause native antibodies to unfold, which are prone to aggregate upon pH neutralization, There is great interest in the mechanism that causes therapeutic proteins to aggregate since aggregate species can cause unwanted immunogenicity in patients, Herein, an increase in aggregation is reported when the pH is adjusted from pH 3 up to a pH ranging from pH 4 to pH 7 during the thaw process of a frozen antibody solution, Raising the pH during the thaw process caused a significant increase in the percent aggregation observed. Two antibodies and one Fc-fusion protein were evaluated during the pH jump thaw process and similar effects were observed. The results provide a new tool to study the kinetics of therapeutic protein ag- gregation upon pH increase,

A retrospective investigation on the phenotype and stability of the E-protein gene in Japanese Encephalitis (JE) virus strain SA14-14-2 used live-attenuated JE vaccine

To detect retrospectively the phenotype and stability of the E-protein gene in Japanese Encephalitis （JE） virus strain SA14-14-2 used in the live-attenuated JE vaccine prepears, the viral titer was titrated by plaque formation in BHK-21 cell cultures, and the neuro-virulence of viruses was assayed in mice with body weight of 12-14 g by intracerebral inoculation. Meanwhile, the total RNA of virus gene was extracted and amplified by RT-PCR with the designed primers, and then it was purified and cloned to the expression vector pGEM-T. The recombinant plasmid was purified and sequenced. It was found that the loss of viral titer of vaccines stored in -20℃ for longer than 10 years was less than 0.5 Lg PFU/ml. No mice inoculated intracerebrally showed signs of illness or even death. The size of plagues of the vaccine virus remained to be small, and the E genes of primary virus seed SA14-14-2 and the vaccines prepared at different years （1987-2001） were unchanged, in- cluding the 8 critical amino acid sites which were different from the parent wild virus strain SA14 and the related neuro-virulence. These results indicate that the genotypic and biological characteristics of the attenuated JE virus strain SA14-14-2 and its vaccines sion noted. prepared are quite stable without any reversion noted.

Characterization of two halophilic adenylate cyclases from Thermobifida halotolerans and Haloactinopolyspora alba

Adenylate cyclase(AC)is the key enzyme that catalyzes the formation of cAMP from ATP.In this study,we discovered two novel class Ⅲ ACs with a halophilic property from Thermobifida halotolerans DSM 44931(ThAC)and Haloactinopolyspora alba DSM 45211(HaAC),respectively.The recombinant ThAC and HaAC were expressed in Escherichia coli with molecular weights of 36.1 and 36.0 kDa respectively.The presence of 2500 and 2200 mmol
L^(-1)1 NaCl significantly enhanced the enzyme activities of ThAC and HaAC,with 22-fold and 7.4-fold higher activities compared to those without NaCl,respectively.Several divalent metal ions were found to activate the recombinant ACs to different extents,and the optimal metal ion was Mg^(2+)for both ThAC and HaAC with concentrations of 80 mmol·L^(-1) and 40 mmol·L^(-1) respectively.Purified ThAC and HaAC had the optimal specific activities((4.59±0.35)×10^(4) and(7.76±0.52)×10^(4) U·mg^(-1))and catalytic efficiency(4.47 and 5.30 L·mmol^(-1)·s^(-1))at 45
℃ and 40
℃ respectively,while the optimum pH of both two recombinant ACs was 10.0.This is the first report of the halophilic Class III ACs,which could make new contributions to explore and study ACs for further associated investigations.

Regulating the bioactivity of non-glycosylated recombinant human bone morphogenetic protein-2 to enhance bone regeneration

Recombinant human bone morphogenetic protein-2(rhBMP-2)is the predominant growth factor that effectively induces osteogenic differentiation in orthopedic procedures.However,the bioactivity and stability of rhBMP-2 are intrinsically associated with its sequence,structure,and storage conditions.In this study,we successfully determined the amino acid sequence and protein secondary structure model of non-glycosylated rhBMP-2 expressed by an E.coli expression system through X-ray crystal structure analysis.Furthermore,we observed that acidic storage conditions enhanced the proliferative and osteoinductive activity of rhBMP-2.Although the osteogenic activity of non-glycosylated rhBMP-2 is relatively weaker compared to glycosylated rhBMP-2;however,this discrepancy can be mitigated by incorporating exogenous chaperone molecules.Overall,such information is crucial for rationalizing the design of stabilization methods and enhancing the bioactivity of rhBMP-2,which may also be applicable to other growth factors.

Genome-wide comparative analysis of type-A Arabidopsis response regulator genes by overexpression studies reveals their diverse roles and regulatory mechanisms in cytokinin signaling

Cytokinin is a critical growth regulator for various aspects of plant growth and development. In Arabidopsis, cytokinin signaling is mediated by a two-component system-based phosphorelay that transmits a signal from the receptors, through histidine phosphotransfer proteins, to the downstream response regulators （ARRs）. Of these ARRs, type-A ARR genes, whose transcription can be rapidly induced by cytokinin, act as negative regulators of eytokinin signaling. However, because of functional redundancy, the function of type-A ARR genes in plant growth and development is not well understood by analyzing loss-of-function mutants. In this study, we performed a comparative functional study on all ten type-A ARR genes by analyzing transgenic plants overexpressing these ARR genes fused to a MYC epitope tag. Overexpression of ARR genes results in a variety of cytokinin-associated phenotypes. Notably, overexpression of different ARR transgenes causes diverse phenotypes, even between phylogenetically closely-related gene pairs, such as within the ARR3-ARR4 and ARR5-ARR6 pairs. We found that the accumulation of a subset of ARR proteins （ARR3, ARR5, ARR7, ARR16 and ARR17; possibly ARR8 and ARR15） is increased by MG132, a specific proteasomal inhibitor, indicating that stability of these proteins is regulated by proteasomal degradation. Moreover, similar to that of previously characterized ARR5, ARR6 and ARR7, stability of ARR16 and ARR17, possibly including ARR8 and ARR15, is regulated by cytokinin. These results suggest that type-A ARR proteins are regulated by a combinatorial mechanism involving both the cytokinin and proteasome pathways, thereby executing distinctive functions in plant growth and development.

Molecular Dynamics Simulation on Stability of Insulin on Graphene

The adsorption dynamics of a model protein （the human insulin） onto graphene surfaces with different sizes was investigated by molecular dynamics simulations. During the adsorption, it has different effect on the stability of the model protein in the fixed and non-fixed graphene systems. The tertiary structure of the protein was destroyed or partially destroyed, and graphene surfaces shows the selective protection for some α-helices in non-fixed Systems but not in fixed systems by reason of the flexibility of graphene. As indicated by the interaction energy curve and trajectory animation, the conformation and orientation selection of the protein were induced by the properties and the texture of graphene surfaces. The knowledge of protein adsorption on graphene surfaces would be helpful to better understand stability of protein on graphene surfaces and facilitate potential applications of graphene in biotechnology.

Covalent immobilization and characterization of Rhizopus oryzae lipase on core-shell cobalt ferrite nanoparticles for biodiesel production

Rhizopus oryzae lipase(ROL)was immobilized on the surface of silica coated amino modified CoFe_(2)O_4 nanoparticles and applied for biodiesel production.The results indicated more affinity of the ROL toward its substrate upon immobilization,as revealed by a lower Km value for the immobilized ROL compared to its free counterpart.Intrinsic fluorescence spectroscopy indicated a lower intensity for ROL immobilized on CoFe_(2)O_4 nanoparticles.Besides,immobilized ROL steady state anisotropy measurements presented lower values,which implied assembly of ROL molecules on magnetic nanoparticles upon immobilization as well as their restricted rotation upon covalent attachment.Thermal stability analysis revealed improved activity at higher temperatures for the immobilized enzyme compared to its free counterpart.Accordingly,Pace analysis to determine protein thermal stability revealed preservation of the protein conformation in the presence of increasing temperatures upon immobilization on nanoparticles.Finally,ROL immobilized on CoFe_(2)O_(4)nanoparticles exhibited improved efficiency of biodiesel production in agreement with thermal activity profile.Therefore,the authors suggest application of the lipase molecules immobilized on CoFe_(2)O_(4)nanoparticles for more efficient biodiesel production.

Effect of Excipients on Stability and Structure of rhCuZn-SOD Encapsulated in PLGA Microspheres

When a protein is encapsulated into poly( DL -lactide-co-glycolide)(PLGA) microspheres by means of the double-emulsion method,the harsh microspheres formation process including ultrasonification,exposure to an organic solvent and a polymer may cause the denaturation of the protein. In this study,we investigated the enzymatic activity change and the effect of the excipients on the stability of recombinant human Cu,Zn-superoxide dismutase(rhCu,Zn-SOD) during the emulsification. The specific activity recovery was found to be concentration dependent and the excipients involved such as PEG 600 and Tween 20,and trehalose were shown to increase the stability of rhCu,Zn-SOD. The protein structural integrity within the microspheres was analyzed by FTIR. The structure of rhCu,Zn-SOD within PLGA microspheres containing trehalose was found to be similar to that of the native solid state,whereas the protein encapsulated during the preparation in the absence of any excipient changed due to the possible hydrophobic interaction with the polymer. The results suggest that a rational stability strategy for protein to be encapsulated into microspheres should aim at different processes.

Common therapeutic target for both cancer and obesity

Obesity and cancer are two interrelated conditions of high epidemiological need, with studies showing that obesity is responsible for nearly 25% of the relative contribution to cancer incidence. Given the connection between these conditions, a drug that can operate on both obesity and cancer is highly desirable. Such a drug is accomplishablethrough the development of potent anti-angiogenesis agents due to the shared underlying role of angiogenesis in the development of both diseases. Prior research has demonstrated a key role of type-2 methionine aminopeptidase(Met AP2) for angiogenesis, which has led to the development of numerous of novel inhibitors. Several irreversible Met AP2 inhibitors have entered clinical trials without great success. Though this lack of success could be attributed to off-target adverse effects, the underlying causes remain unclear. More promising reversible inhibitors have been recently developed with excellent pre-clinical results. However, due to insufficient knowledge of the biological functions of N-terminal protein processing, it is hard to predict whether these novel inhibitors would successfully pass clinical trials and thereby benefit cancer and obesity patients. Significantly more efforts are needed to advance our understanding of the regulation of methionine aminopeptidases and the processes by which they govern the function of proteins.

Value of predictive bioinformatics in inherited metabolic diseases

Typically,inherited metabolic diseases arise from point mutations in genes encoding metabolic enzymes. Although some of these mutations directly affect amino acid residues in the active sites of these enzymes,the majority do not. It is now well accepted that the majority of these disease-associated mutations exert their effects through alteration of protein stability,which causes a reduction in enzymatic activity. This finding suggests a way to predict the severity of newly discovered mutations. In silico prediction of the effects of amino acid sequence alterations on protein stability often correlates with disease severity. However,no stability prediction tool is perfect and,in general,better results are obtained if the predictions from a variety of tools are combined and then interpreted. In addition to predicted alterations to stability,the degree of conservation of a particular residue can also be a factor which needs to be taken into account: alterations to highly conserved residues are more likely to be associated with severe forms of the disease. The approach has been successfully applied in a variety of inherited metabolic diseases,but further improvements are necessary to enable robust translation into clinically useful tools.

HOP co-chaperones contribute to GA signaling by promoting the accumulation of the F-box protein SNE in Arabidopsis

Gibberellins(GAs)play important roles in multiple developmental processes and in plant response to the environment.Within the GA pathway,a central regulatory step relies on GA-dependent degradation of the DELLA transcriptional regulators.Nevertheless,the relevance of the stability of other key proteins in this pathway,such as SLY1 and SNE(the F-box proteins involved in DELLA degradation),remains unknown.Here,we take advantage of mutants in the HSP70-HSP90 organizing protein(HOP)co-chaperones and reveal that these proteins contribute to the accumulation of SNE in Arabidopsis.Indeed,HOP proteins,along with HSP90 and HSP70,interact in vivo with SNE,and SNE accumulation is significantly reduced in the hop mutants.Concomitantly,greater accumulation of the DELLA protein RGA is observed in these plants.In agreement with these molecular phenotypes,hop mutants show a hypersensitive response to the GA inhibitor paclobutrazol and display a partial response to the ectopic addition of GA when GA-regulated processes are assayed.These mutants also display different phenotypes associated with alterations in the GA pathway,such as reduced germination rate,delayed bolting,and reduced hypocotyl elongation in response to warm temperatures.Remarkably,ectopic overexpression of SNE reverts the delay in germination and the thermally dependent hypocotyl elongation defect of the hop1 hop2 hop3 mutant,revealing that SNE accumulation is the key aspect of the hop mutant phenotypes.Together,these data reveal a pivotal role for HOP in SNE accumulation and GA signaling.

Effects of Selective Biotinylation on the Thermodynamic Stability of Human Serum Albumin

Thermal denaturation and stability of two commercially available preparations of Human Serum Albumin (HSA), differing in their advertised level of purity, were investigated by differential scanning calorimetry (DSC). These protein samples were 99% pure HSA (termed HSA99) and 96% pure HSA (termed HSA96). According to the supplier, the 3% difference in purity between HSA96 and HSA99 is primarily attributed to the presence of globulins and fatty acids. Our primary aim was to investigate the utility of DSC in discerning changes in HSA that occur when the protein is specifically adducted, and determine how adduct formation manifests itself in HSA denaturation curves, or thermograms, measured by DSC. Effects of site specific covalent attachment of biotin (the adduct) on the thermodynamic stability of HSA were investigated. Each of the HSA preparations was modified by biotinylation targeting a single site, or multiple sites on the protein structure. Thermograms of both modified and unmodified HSA samples successfully demonstrated the ability of DSC to clearly discern the two HSA preparations and the presence or absence of covalent modifications. DSC thermogram analysis also provided thermodynamic characterization of the different HSA samples of the study, which provided insight into how the two forms of HSA respond to covalent modification with biotin. Consistent with published studies [1] HSA96, the preparation with contaminants that contain globulins and fatty acids seems to be comprised of two forms, HSA96-L and HSA96-H, with HSA96-L more stable than HSA99. The effect of multisite biotinylation is to stabilize HSA96-L and destabilize HSA96-H. Thermodynamic analysis suggests that the binding of ligands comprising the fatty acid and globulin-like contaminant contributes approximately 6.7 kcal/mol to the stability HSA96-L.

Dynamic modulation of nodulation factor receptor levels by phosphorylation-mediated functional switch of a RING-type E3 ligase during legume nodulation

The precise control of receptor levels is crucial for initiating cellular signaling transduction in response to specific ligands;however,such mechanisms regulating nodulation factor(NF)receptor(NFR)-mediated perception of NFs to establish symbiosis remain unclear.In this study,we unveil the pivotal role of the NFR-interacting RING-type E3 ligase 1(NIRE1)in regulating NFR1/NFR5 homeostasis to optimize rhizobial infection and nodule development in Lotus japonicus.We demonstrated that NiRE1 has a dual function in this regulatory process.It associates with both NFR1 and NFR5,facilitating their degradation through K48-linked polyubiquitination before rhizobial inoculation.However,following rhizobial inoculation,NFR1 phosphorylates NIRE1ata conserved residue,Tyr-109,inducing a functional switch in NIRE1,which enables NIRE1tomediateK63-linkedpolyubiquitination,thereby stabilizing NFR1/NFR5 in infected root cells.The introduction of phospho-dead NIRE1Y1osF leads to delayed nodule development,underscoring the significance of phosphorylation at Tyr-1o9 in orchestrating symbiotic processes.Conversely,expression of the phospho-mimic NIRE1Y0E results in the formation of spontaneous nodules in L.japonicus,further emphasizing the critical role of the phosphorylation-dependent functional switch in NiRE1.In summary,these findings uncover a fine-tuned symbiotic mechanism that a single E3 ligase could undergo a phosphorylationdependent functional switch to dynamically and precisely regulate NF receptor protein levels.

Stability of proteins with multi-state unfolding behavior

A new model used to calculate the free energy change of protein unfolding is presented. In this model, proteins are considered to be composed of structural elements. The unfolding of a structural element obeys a two-state mechanism and the free energy change of the element can be obtained by a linear extrapolation method. If a protein consists of the same structural elements, its unfolding will displays a two-state process, and only the average structural element free energy change 〈△G0 element（H2O）〉 can be measured. If protein consists of completely different structural elements, its unfolding will show a multi-state behavior. When a protein consists of n structural elements its unfolding will shows a （n＋1）-state behavior. A least-squares fitting can be used to analyze the contribution of each structural element to the protein and the free energy change of each structural element can be obtained by using linear extrapolation to zero denaturant concentration, not to the start of each transition. The measured △Gn protein（H2O） is the sum of the free energy change for each structural element. Using this new model, we can not only analyze the stability of various proteins with similar structure and similar molecular weight, which undergo multi-state unfolding processes, but also compare the stability of proteins with different structures and molecular weights using the average structural element free energy change 〈△G0 element（H2O）〉. Although this method cannot completely provide the exact free energy of proteins, it is better than current methods.

Imidazolium-based ionic liquids as additives to preserve the Enhanced Green Fluorescent Protein fluorescent activity

Fluorescent Proteins(FP)can be applied as biomarkers and biosensors in the industrial and medical fields,but their large-scale use,especially for new industrial applications,is limited due to their low stability.Hence,the discovery of additives capable of preserving the activity of FP at room temperature and under stress conditions can help to expand and facilitate their commercial use.With this goal,we evaluated the application of 1-alkyl-3-methylimidazolium chloride-based([C_(n)mim]Cl)ionic liquids(ILs)as additives to preserve the activity of Enhanced Green Fluorescent Protein(EGFP)at different storage times and under unfavorable conditions.All[C_(n)mim]Cl solutions(at 0.100 mol L^(-1))were able to preserve EGFP fluorescence for longer than the phosphatesaline buffer(PBS)and NaCl solutions,increasing its fluorescence manifestation from 1 to 3 months.[C_(n)mim]Cl with shorter to medium cationic alkyl chains were the most effective in preserving EGFP fluorescence.[C_(n)mim]Cl also protected EGFP activity in the presence of the surfactant SDS,the acid guanidine hydrochloride,and H_(2)O_(2).Therefore,[C_(n)mim]Cl can be added to aqueous solutions to preserve EGFP fluorescence activity at room temperature for longer storage times and to reduce the negative impact of denaturing agents on EGFP.Therefore,there is a massive potential for the application of ILs as additives to preserve FP in the long-term without refrigeration and under unfavorable conditions,and this is fundamental to enable expansion of FP in industrial and commercial applications.