Dual Functionality of Poloxamer 188 in Freeze-Dried Protein Formulations: A Stabilizer in Frozen Solutions and a Bulking Agent in Lyophiles

Poloxamer 188 (P188) was hypothesized to be a dual functional excipient, (i) a stabilizer in frozen solution to prevent ice-surface-induced protein destabilization and (ii) a bulking agent to provide elegant lyophiles. Based on X-ray diffractometry and differential scanning calorimetry, sucrose, in a concentration-dependent manner, inhibited P188 crystallization during freeze-drying, while trehalose had no such effect. The recovery of lactate dehydrogenase (LDH), the model protein, was evaluated after reconstitution. While low LDH recovery (∼60%) was observed in the lyophiles prepared with P188, the addition of sugar improved the activity recovery to >85%. The secondary structure of LDH in the freeze-dried samples was assessed using infrared spectroscopy, and only moderate structural changes were observed in the lyophiles formulated with P188 and sugar. Thus, P188 can be a promising dual functional excipient in freeze-dried protein formulations. However, P188 alone does not function as a lyoprotectant and needs to be used in combination with a sugar.

Disulfide Bonds of Thyroid Peroxidase Are Critical Elements for Subcellular Localization, Proteasome-Dependent Degradation, and Enzyme Activity

Background: Congenital hypothyroidism (CH) is caused by mutations in cysteine residues, including Cys655 and Cys825 that form disulfide bonds in thyroid peroxidase (TPO). It is highly likely that these disulfide bonds could play an important role in TPO activity. However, to date, no study has comprehensively analyzed cysteine mutations that form disulfide bonds in TPO. In this study, we induced mutations in cysteine residues involved in disulfide bonds formation and analyzed their effect on subcellular localization, degradation, and enzyme activities to evaluate the importance of disulfide bonds in TPO activity. Methods: Vector plasmid TPO mutants, C655F and C825R, known to occur in CH, were transfected into HEK293 cells. TPO activity and protein expression levels were measured by the Amplex red assay and Western blotting. The same procedure was performed in the presence of MG132 proteasome inhibitor. Subcellular localization was determined using immunocytochemistry and flow cytometry. The locations of all disulfide bonds within TPO were predicted using in silico analysis. All TPO mutations associated with disulfide bonds were induced. TPO activity and protein expression levels were also measured in all TPO mutants associated with disulfide bonds using the Amplex red assay and Western blotting. Results: C655F and C825R showed significantly decreased activity and protein expression compared with the wild type (WT) (p < 0.05). In the presence of the MG132 proteasome inhibitor, the protein expression level of TPO increased to a level comparable with that of the WT without increases in its activity. The degree of subcellular distribution of TPO to the cell surface in the mutants was lower compared with the WT TPO. Twenty-four cysteine residues were involved in the formation of 12 disulfide bonds in TPO. All TPO mutants harboring an amino acid substitution in each cysteine showed significantly reduced TPO activity and protein expression levels. Furthermore, the differences in TPO activity depended on the position of the disulfide bond. Conclusions: All 12 disulfide bonds play an important role in the activity of TPO. Furthermore, the mutations lead to misfolding, degradation, and membrane insertion.

Stratification of ovarian cancer patients from the prospect of drug target-related transcription factor protein activity: the prognostic and genomic landscape analyses

The expression and activity of transcription factors, which directly mediate gene transcription, are strictly regulated to control numerous normal cellular processes. In cancer, transcription factor activity is often dysregulated, resulting in abnormal expression of genes related to tumorigenesis and development. The carcinogenicity of transcription factors can be reduced through targeted therapy. However, most studies on the pathogenic and drug-resistant mechanisms of ovarian cancer have focused on the expression and signaling pathways of individual transcription factors. To improve the prognosis and treatment of patients with ovarian cancer, multiple transcription factors should be evaluated simultaneously to determine the effects of their protein activity on drug therapies. In this study, the transcription factor activity of ovarian cancer samples was inferred from virtual inference of protein activity by enriched regulon algorithm using mRNA expression data. Patients were clustered according to their transcription factor protein activities to investigate the association of transcription factor activities of different subtypes with prognosis and drug sensitivity for filtering subtype-specific drugs. Meanwhile, master regulator analysis was utilized to identify master regulators of differential protein activity between clustering subtypes, thereby identifying transcription factors associated with prognosis and assessing their potential as therapeutic targets. Master regulator risk scores were then constructed for guiding patients' clinical treatment, providing new insights into the treatment of ovarian cancer at the level of transcriptional regulation.

NaRnEA: An Information Theoretic Framework for Gene Set Analysis

Gene sets are being increasingly leveraged to make high-level biological inferences from transcriptomic data; however, existing gene set analysis methods rely on overly conservative, heuristic approaches for quantifying the statistical significance of gene set enrichment. We created Nonparametric analytical-Rank-based Enrichment Analysis (NaRnEA) to facilitate accurate and robust gene set analysis with an optimal null model derived using the information theoretic Principle of Maximum Entropy. By measuring the differential activity of ~2500 transcriptional regulatory proteins based on the differential expression of each protein's transcriptional targets between primary tumors and normal tissue samples in three cohorts from The Cancer Genome Atlas (TCGA), we demonstrate that NaRnEA critically improves in two widely used gene set analysis methods: Gene Set Enrichment Analysis (GSEA) and analytical-Rank-based Enrichment Analysis (aREA). We show that the NaRnEA-inferred differential protein activity is significantly correlated with differential protein abundance inferred from independent, phenotype-matched mass spectrometry data in the Clinical Proteomic Tumor Analysis Consortium (CPTAC), confirming the statistical and biological accuracy of our approach. Additionally, our analysis crucially demonstrates that the sample-shuffling empirical null models leveraged by GSEA and aREA for gene set analysis are overly conservative, a shortcoming that is avoided by the newly developed Maximum Entropy analytical null model employed by NaRnEA.

Functioning of P-Glycoprotein during Pregnancy in Rabbits

The level P-glycoprotein (Pgp) in organs of pregnant rabbits and its content and activity in the placental barrier at different stages of pregnancy were studied. An increase in Pgp content in the jejunum on days 7, 14, 21, and 28 of pregnancy in comparison with this parameter non-pregnant females was revealed by ELISA; in the liver, Pgp content was higher on day 7 and tended to increase on day 14; in the kidney and cerebral cortex, Pgp content was higher on day 28 of pregnancy in parallel with an increase in serum progesterone concentration. We also observed a decrease in Pgp content in the placenta on days 21 and 28 of pregnancy in comparison with day 14 and a decrease in Pgp activity in the placental barrier, which was confirmed by enhanced penetration of fexofenadine (Pgp substrate) through the barrier.

Thermofluor-Based Optimization Strategy for the Stabilization of Recombinant Human Soluble Catechol-O-Methyltransferase

Catechol-O-methyltransferase (COMT) has been involved in a number of medical conditions including catechol-estrogen-induced cancers and a great range of cardiovascular and neurodegenerative diseases such as Parkinson's disease. Currently, Parkinson's disease treatment relies on a triple prophylaxis, involving dopamine replacement by levodopa, the use of aromatic L-amino acid decarboxylase inhibitors, and the use of COMT inhibitors. Typically, COMT is highly thermolabile, and its soluble isoform (SCOMT) loses biological activity within a short time span preventing further structural and functional trials. Herein, we characterized the thermal stability profile of lysate cells from Komagataella pastoris containing human recombinant SCOMT (hSCOMT) and enzyme-purified fractions (by Immobilized Metal Affinity Chromatography-IMAC) upon interaction with several buffers and additives by Thermal Shift Assay (TSA) and a biological activity assessment. Based on the obtained results, potential conditions able to increase the thermal stability of hSCOMT have been found through the analysis of melting temperature (T_m) variations. Moreover, the use of the ionic liquid 1-butyl-3-methylimidazolium chloride [C₄mim]Cl (along with cysteine, trehalose, and glycerol) ensures complete protein solubilization as well as an increment in the protein Tm of approximately 10 °C. Thus, the developed formulation enhances hSCOMT stability with an increment in the percentage of activity recovery of 200% and 70% when the protein was stored at 4 °C and -80 °C, respectively, for 12 h. The formation of metanephrine over time confirmed that the enzyme showed twice the productivity in the presence of the additive. These outstanding achievements might pave the way for the development of future hSCOMT structural and biophysical studies, which are fundamental for the design of novel therapeutic molecules.

Biochemical characterization and overexpression of an α-amylase (BmAmy) in silkworm, Bombyx mori

Silkworm (Bombyx mori) is the only fully domesticated insect. As an economically important insect, nutrition utilization is important for its productivity. Hence, the present study investigated the expression pattern of BmAmy, an α-amylase, in B. mori. BmAmy protein purification and biochemical characterization were performed, and effects of BmAmy overexpression were assessed. Real-time quantitative reverse transcription polymerase chain reaction indicated that BmAmy transcription was positively correlated with the silkworm's food intate. Moreover, enzymatic activity assay results showed that BmAmy had significant α-amylase activity of about 1 mg/min/mg protein. Furthermore, treatment with mulberry amylase inhibitors MnAI1 and MnAI2 resulted to 89.92% and 93.67% inhibition in BmAmy activity, respectively, and the interaction between BmAmy and MnAI was also confirmed by protein docking analysis. A silkworm line that specifically overexpressed BmAmy in the midgut was generated through piggyBac-based transgenic technology, and compared to those of non-transgenic silkworms, the whole cocoon and cocoon shell weights of these transgenic silkworms increased by 10.13% and 18.32%, respectively, in the female group, and by 5.83% and 6.00%, respectively, in the male group. These results suggested that BmAmy may be a suitable target for breeding better silkworm varieties in the future.

[Cloning, expression and activity analysis of cutinase from Sclerotinia sclerotiorum]

Cutinase can degrade aliphatic and aromatic polyesters, as well as polyethylene terephthalate. Lack of commercially available cutinase calls for development of cost-effective production of efficient cutinase. In this study, eight cutinase genes were cloned from Sclerotinia sclerotiorum. The most active gene SsCut-52 was obtained by PCR combined with RT-PCR, expressed in Escherichia coli BL21 and purified by Ni-NTA affinity chromatography to study its characteristics and pathogenicity. Sscut-52 had a total length of 768 bp and 17 signal peptides at the N terminals. Phylogenetic analysis showed that its amino acid sequence had the highest homology with Botrytis keratinase cutinase and was closely related to Rutstroemia cutinase. Sscut-52 was highly expressed during the process of infecting plants by Sclerotinia sclerotiorum. Moreover, the expression level of Sscut-52 was higher than those of other cutinase genes in the process of sclerotia formation from mycelium. The heterologously expressed cutinase existed in the form of inclusion body. The renatured SsCut-52 was active at pH 4.0-10.0, and mostly active at pH 6.0, with a specific activity of 3.45 U/mg achieved. The optimum temperature of SsCut-52 was 20-30 ℃, and less than 60% of the activity could be retained at temperatures higher than 50 ℃. Plant leaf infection showed that SsCut-52 may promote the infection of Banlangen leaves by Sclerotinia sclerotiorum.

Variation of BMP2 Concentration and Its Activity in Bone Grafts Obtained from Patients Undergoing Hip Replacement Surgery

AIM

Bone morphogenetic protein 2 (BMP2) is a member of a subgroup of the transforming growth factor beta superfamily and triggers various signaling events which in turn stimulate chondrogenesis, osteogenesis, angiogenesis and extracellular matrix remodeling leading to fracture healing. In this study, we quantified the concentration of BMP2 in fresh human bone grafts obtained from 40 patients undergoing hip replacement surgery. Besides the concentration, the activity of the detected BMP2 was also investigated.

MATERIALS AND METHODS

In this study, the concentration of BMP2 in fresh human bone grafts obtained from 40 patients undergoing hip replacement surgery was quantified. Human BMP2 enzyme-linked immunosorbent assays and bicinchoninic acid quantification was used to determine the total concentration of protein present in each sample. To determine the activity of the BMP2 found in each bone sample, alkaline phosphatase activity was measured by colorimetric assay.

RESULTS

The amount of BMP2 seemed to vary slightly between the patients. Taking into consideration the patient's gender, we observed that male patients presented slightly more BMP2 in comparison with females. When analyzing the activity of BMP2, we observed that in female patients, the activity was slightly higher in comparison to males. This variation may be caused by a number of factors, including but not limited to gender, age, osteoporosis and previous diseases. This information shows that the osteogenic potential of different bone graft samples is not consistent.

CONCLUSION

The activity of BMP2 in femur heads obtained from patients undergoing total hip replacement surgery showed significant variation according to gender and age. The measurement of bone proteins activity might be promising as a qualitative method in bone banks and should be further investigated.

Activity of Deposited Lysozyme on Contemporary Soft Contact Lenses Exposed to Differing Lens Care Systems

Purpose

The amount of protein deposition on soft contact lenses and to what extent the proteins are denatured may have an impact on comfortable wearing times of contact lenses. The purpose of this study was to evaluate the effects of two lens care systems on total protein and the quantity and activity of lysozyme deposited on worn senofilcon A, silicone hydrogel contact lenses.

Participants and Methods

Thirty symptomatic soft contact lens wearers were enrolled into a 4-week prospective, randomized, bilateral eye, daily-wear, crossover, double-masked study. Participants were fitted with biweekly senofilcon A lenses and were assigned either a polyquaternium-1 and myristamidopropyl dimethylamine-containing system (OPTI-FREE RepleniSH) or a peroxide-based system (CLEAR CARE). After each wear period, proteins were extracted from the lenses and analyzed for total protein, total lysozyme quantity and activity.

Results

The use of either the peroxide-based system or the polyquaternium-1 and myristamidopropyl dimethylamine-containing system resulted in no difference (P>0.05) to the amount of total protein deposited on the lenses (6.7 ± 2.8 micrograms/lens versus 7.3 ± 2.8 micrograms/lens, respectively) or to the amount of denatured lysozyme deposits (0.8 ± 0.7 versus 0.9 ± 0.7 micrograms/lens), respectively. The total amount of lysozyme deposited on the lenses was significantly lower when using the peroxide-based system (1.3 ± 0.9 micrograms/lens) compared to the polyquaternium-1 and myristamidopropyl dimethylamine-containing system (1.7 ± 1.0 micrograms/lens) (P=0.02).

Conclusion

The inactivation of lysozyme deposited on senofilcon A lenses when disinfected with the peroxide-based or the polyquaternium-1 and myristamidopropyl dimethylamine-containing systems were neither statistically nor clinically significant and the overall amounts of denatured lysozyme recovered from the lenses were low (<1 microgram/lens).

Beyond the Roles in Biomimetic Chemistry: An Insight into the Intrinsic Catalytic Activity of an Enzyme for Tumor-Selective Phototheranostics

Protein-assisted biomimetic synthesis has been an emerging offshoot of nanofabrication in recent years owing to its features of green chemistry, facile process, and ease of multi-integration. As a result, many proteins have been used for biomimetic synthesis of varying kinds of nanostructures. Although the efforts on exploring new proteins and investigating their roles in biomimetic chemistry are increasing, the most essential intrinsic properties of proteins are largely neglected. Herein we report a frequently used enzyme (horseradish peroxidase, HRP) to demonstrate the possibility of enzymatic activity retaining after accomplishing the roles in biomimetic synthesis of ultrasmall gadolinium (Gd) nanodots and stowing its substrate 2,2'-Azinobis (3-ethylbenzothiazoline-6-sulfonic acid ammonium salt) (ABTS), denoted as Gd@HRP^ABTS. It was found that ca. 70% of the enzymatic activity of HRP was preserved. The associated changes of protein structure with chemical treatments were studied by spectroscopic analysis. Leveraging on the highly retained catalytic activity, Gd@HRP^ABTS exerts strong catalytic oxidation of peroxidase substrate ABTS into photoactive counterparts in the presence of intrinsic H₂O₂ inside the tumor, therefore enabling tumor-selective catalytic photoacoustic (PA) imaging and photothermal therapy (PTT). In addition, the MR moiety of Gd@HRP^ABTS provides guidance for PTT and further diagrams that Gd@HRP^ABTS is clearable from the body via kidneys. Preliminary toxicity studies show no observed adverse effects by administration of them. This study demonstrates beyond the well-known roles in biomimetic chemistry that HRP can also preserve its enzymatic activity for tumor catalytic theranostics.

Perspectives of inclusion bodies for bio-based products: curse or blessing?

The bacterium Escherichia coli is a major host for recombinant protein production of non-glycosylated products. Depending on the expression strategy, the recombinant protein can be located intracellularly, which often leads to protein aggregates inside of the cytoplasm, forming so the called inclusion bodies (IBs). When compared to other protein expression strategies, inclusion body formation allows high product titers and also the possibility of expressing proteins being toxic for the host. In the past years, the comprehension of inclusion bodies being only inactive protein aggregates changed, and the new term of non-classical inclusion bodies emerged. These inclusion bodies are believed to contain a reasonable amount of active protein within their structure. However, subsequent downstream processing, such as homogenisation of cells, centrifugation or solubilisation of IBs, is prone to variable process performance and is often known to result in low extraction yields. It is hypothesised that variations in IB quality attributes are responsible for those effects and that such attributes can be controlled by upstream process conditions. In this review, we address the impact of process design (process parameters) in the upstream on defined inclusion body quality attributes. The following topics are therefore addressed: (i) an overview of the range of inclusion body applications (including emerging technologies); (ii) analytical methods to determine quality attributes; and (iii) screws in process engineering to achieve the desired quality attributes for different inclusion body-based applications. Process parameters in the upstream can be used to trigger different quality attributes including protein activity, but are not exploited to a satisfying content yet. Design by quality approaches in the upstream are already considered for a multitude of existing processes. Further intensifying this approach may pave the industrial application for new IB-based products and improves IB processing, as discussed within this review.

Semiconducting Polymer Nanoenzymes with Photothermic Activity for Enhanced Cancer Therapy

Regulation of enzyme activity is fundamentally challenging but practically meaningful for biology and medicine. However, noninvasive remote control of enzyme activity in living systems has been rarely demonstrated and exploited for therapy. Herein, we synthesize a semiconducting polymer nanoenzyme with photothermic activity for enhanced cancer therapy. Upon near-infrared (NIR) light irradiation, the activity of the nanoenzyme can be enhanced by 3.5-fold to efficiently digest collagen in the tumor extracellular matrix (ECM), leading to enhanced nanoparticle accumulation in tumors and consequently improved photothermal therapy (PTT). This study thus provides a promising strategy to remotely regulate enzyme activity for cancer therapy.

The consequences of deglycosylation of recombinant intra-melanosomal domain of human tyrosinase

Tyrosinase, a melanosomal glycoenzyme, catalyzes initial steps of the melanin biosynthesis. While glycosylation was previously studied in vivo, we present three recombinant mutant variants of human tyrosinase, which were obtained using multiple site-directed mutagenesis, expressed in insect larvae, purified and characterized biochemically. The mutagenesis demonstrated the reduced protein expression and enzymatic activity due to possible loss of protein stability and protein degradation. However, the complete deglycosylation of asparagine residues in vitro, including the residue in position 371, interrupts tyrosinase function, which is consistent with a melanin loss in oculocutaneous albinism type 1 (OCA1) patients.

Determinants and Regulation of Protein Turnover in Yeast

Protein turnover maintains the recycling needs of the proteome, and its malfunction has been linked to aging and age-related diseases. However, not all proteins turnover equally, and the factors that contribute to accelerate or slow down turnover are mostly unknown. We measured turnover rates for 3,160 proteins in exponentially growing yeast and analyzed their dependence on physical, functional, and genetic properties. We found that functional characteristics, including protein localization, complex membership, and connectivity, have greater effect on turnover than sequence elements. We also found that protein turnover and mRNA turnover are correlated. Analysis under nutrient perturbation and osmotic stress revealed that protein turnover highly depends on cellular state and is faster when proteins are being actively used. Finally, stress-induced changes in protein and transcript abundance correlated with changes in protein turnover. This study provides a resource of protein turnover rates and principles to understand the recycling needs of the proteome under basal conditions and perturbation.

[cDNA cloning, expression and determination of substrate specificity of mice selenocysteine-containing protein SelV (Selenoprotein V)]

To date various bioinformatics tools allowed to identify 25 selenocysteine-containing mammalian proteins. The name of these proteins assumes that they contain the amino acid selenocysteine (Sec). Functionally characterized selenocysteine-containing proteins are oxidoreductases with various functions, including glutathione peroxidases, thioredoxin reductases, deiodinases etc. However, the functions of more than half of identified proteins are still unclear, and mammalian selenoprotein SeIV is among them. We studied the selV in all stages of postnatal development with the maximum level of mRNA expression during puberty, whereas in adult mice (8-18 months) we observed a gradual decrease of expression. In order to get closer to the functional role of Selenoprotein V, we have carried out experiments on the substrate specificity and enzymatic activity measurement of this selenocysteine-containing protein. It was shown that SelV posseses glutathionperoxidase and thioredoxinreductase activities.

Improvement in the Thermal Stability of Pyrophosphatase by Conjugation to Poly(N-isopropylacrylamide): Application to the Polymerase Chain Reaction

Polymerase chain reaction (PCR) is a powerful method for nucleic acid amplification. However, the PCR is inhibited in its yield due to its byproduct, pyrophosphate (PPi), a byproduct of the reaction; the yield is thereby limited. The conventional method for hydrolysis of PPi by pyrophosphatase (PPase) is not well adapted for operation at elevated temperatures over long times as required during the PCR. In this work, we reported a strategy to improve the PCR yield using a conjugate of the enzyme with the thermally responsive polymer poly(N-isopropylacrylamide) (PNIPAM). Pyrophosphatase (PPase) was conjugated to PNIPAM site-specifically near the active center. As compared to the free enzyme, the optimum temperature of the conjugate was shown to increase from 45 to 60 °C. For the conjugate, about 77% enzyme activity was retained after incubation at 60 °C for 3 h, representing a 6.8-fold increase as compared to the unconjugated enzyme. For the PCR using the conjugate, the yield was 1.5-fold greater than using the unconjugated enzyme. As well as improving the yield of the PCR (and possibly other biological reactions) at elevated temperature, polymer conjugation may also provide a strategy to improve the heat resistance of proteins more generally.

Temperature-Responsive Poly(N-isopropylacrylamide) Modified Gold Nanoparticle-Protein Conjugates for Bioactivity Modulation

It is important to effectively maintain and modulate the bioactivity of protein-nanoparticle conjugates for their further and intensive applications. The strategies of controlling protein activity via "tailor-made surfaces" still have some limitations, such as the difficulties in further modulation of the bioactivity and the proteolysis by some proteases. Thus, it is essential to establish a responsive protein-nanoparticle conjugate system to realize not only controllable modulations of protein activity in the conjugates by incorporating sensitivity to environmental cues but also high resistance to proteases. In the work reported here, Escherichia coli (E. coli) inorganic pyrophosphatase (PPase) and poly(N-isopropylacrylamide) (pNIPAM) were both fabricated onto gold nanoparticles (AuNPs), forming AuNP-PPase-pNIPAM conjugates. The bioactivity-modulating capability of the conjugates with changes in temperature was systematically investigated by varying the molecular weight of pNIPAM, the PPase/pNIPAM molar ratio on AuNP, and the orientation of the proteins. Under proper conditions, the activity of the conjugate at 45 °C was approximately 270% of that at 25 °C. In the presence of trypsin digestion, much less conjugate activity than protein activity was lost. These findings indicate that the fabrication of AuNP-protein-pNIPAM conjugates can both modulate protein activity on a large scale and show much higher resistance to protease digestion, exhibiting great potential in targeted delivery, controllable biocatalysis, and molecular/cellular recognition.