Protein and Peptide Letters - Volume 28, Issue 5, 2021

Background: Activation of mitogen-activated protein kinases (MAPKs) is regulated by a phosphorylation cascade comprising three kinases, MAPK kinase kinase (MAP3K), MAPK kinase (MAP2K), and MAPK. MAP2K1 and MAPK2K2, also known as MEK1 and MEK2, activate ERK1 and ERK2. The structure of the MAPK signaling cascade has been studied, but high-resolution structural studies of MAP2Ks have often focused on kinase domains or docking sites, but not on full-length proteins. Objective: To understand the conformational dynamics of MEK1. Methods: Full-length MEK1 was purified from Escherichia coli (BL21), and its conformational dynamics were analyzed using hydrogen/deuterium exchange mass spectrometry (HDX-MS). The effects of ATP binding were examined by co-incubating MEK1 and adenylyl-imidodiphosphate (AMP- PNP), a non-hydrolysable ATP analog. Results: MEK1 exhibited mixed EX1/EX2 HDX kinetics within the N-terminal tail through β1, αI, and the C-terminal helix. AMP-PNP binding was found to reduce conformational dynamics within the glycine-rich loop and regions near the DFG motif, along with the activation lip. Conclusion: We report for the first time that MEK1 has regions that slowly change its folded and unfolded states (mixed EX1/EX2 kinetics) and also report the conformational effects of ATP-binding to MEK1.

Background: Physical parameters like pH and temperature play a major role in the design of an industrial enzymatic process. Enzyme stability and activity are greatly influenced by these parameters; hence optimization and control of these parameters becomes a key point in determining the economic feasibility of the process. Objective: This study was taken up with the objective to optimize physical parameters for maximum stability and activity of xylose reductase from D. nepalensis NCYC 3413 through separate and simultaneous optimization studies and comparison thereof. Methods: Effects of pH and temperature on the activity and stability of xylose reductase from Debaryomyces nepalensis NCYC 3413 were investigated by enzyme assays and independent variables were optimised using surface response methodology. Enzyme activity and stability were optimised separately and concurrently to decipher the appropriate conditions. Results: Optimized conditions of pH and temperature for xylose reductase activity were determined to be 7.1 and 27 °C respectively, with predicted responses of specific activity (72.3 U/mg) and half-life time (566 min). The experimental values (specific activity 50.2 U/mg, half-life time 818 min) were on par with predicted values indicating the significance of the model. Conclusion: Simultaneous optimization of xylose reductase activity and stability using statistical methods is effective as compared to optimisation of the parameters separately.

Background: The prediction of a protein's secondary structure from its amino acid sequence is an essential step towards predicting its 3-D structure. The prediction performance improves by incorporating homologous multiple sequence alignment information. Since homologous details not available for all proteins. Therefore, it is necessary to predict the protein secondary structure from single sequences. Objective and Methods: Protein secondary structure predicted from their primary sequences using n-gram word embedding and deep recurrent neural network. Protein secondary structure depends on local and long-range neighbor residues in primary sequences. In the proposed work, the local contextual information of amino acid residues captures variable-length character n-gram words. An embedding vector represents these variable-length character n-gram words. Further, the bidirectional long short-term memory (Bi-LSTM) model is used to capture the long-range contexts by extracting the past and future residues information in primary sequences. Results: The proposed model evaluates on three public datasets ss.txt, RS126, and CASP9. The model shows the Q3 accuracy of 92.57%, 86.48%, and 89.66% for ss.txt, RS126, and CASP9. Conclusion: The proposed model performance compares with state-of-the-art methods available in the literature. After a comparative analysis, it observed that the proposed model performs better than state-of-the-art methods.

Aim: To identify and characterize peptide binders to truncated recombinant chikungunya virus envelope protein 2. Background: Despite extensive research on the chikungunya virus (CHIKV), the specific antiviral treatment’s unavailability has stressed the need for the urgent development of therapeutics. The Envelope protein 2 (E2) of CHIKV that displays putative receptor binding sites and specific epitopes for virus neutralizing antibodies is a critical target for the therapeutic intervention. Objective: The study aims to identify the unique peptides that can bind to truncated E2 protein of CHIKV and further explore their properties as potential therapeutic candidate. Methods: A stretch of CHIKV-E2 (rE2), which is prominently exposed on the surface of virion, was used as bait protein to identify peptide binders to the CHIKV-rE2 using a 12-mer phage display peptide library. Three rounds of biopanning yielded several peptide binders to CHIKV-rE2 and their binding affinities were compared by phage ELISA. Additionally, a fully flexible-blind docking simulation investigated the possible binding modes of the selected peptides. Furthermore, the selected peptides were characterized and their ADMET properties were explored in silico. Results: Five peptides were identified as potential binders based on their robust reactivity to the bait protein. The selected peptides appeared to interact with the crucial residues that were notably exposed on the surface of E1-E2 trimeric structure. The explored in silico studies suggested their non-allergenicity, non-toxicity and likeliness to be antiviral. Conclusion: The potential binding peptides of CHIKV-rE2 protein were identified using phage display technology and characterized in silico. The selected peptides could be further used for the development of therapeutics against the CHIKV infection.

Background: Enzymes are efficient biocatalysis that catalysis a large number of reactions due to their chemical, regional, or stereo specifities and selectivity. Their usage in bioreactor or biosensor systems has great importance. Carbonic anhydrase enzyme catalyzes the interconversion between carbon dioxide and water and the dissociated ions of carbonic acid. In organisms, the carbonic anhydrase enzyme has crucial roles connected with pH and CO2 homeostasis, respiration, and transport of CO2/bicarbonate, etc. So, immobilization of the enzyme is important in stabilizing the catalyst against thermal and chemical denaturation in bioreactor systems when compared to the free enzyme that is unstable at high temperatures and extreme pH values, as well as in the presence of organic solvents or toxic reagents. Nano-scale composite materials have attracted considerable attention in recent years, and electrospinning based all-nanocomposite materials have a wide range of applications. In this study, electrospun nanofibers were fabricated and used for the supporting media for carbonic anhydrase enzyme immobilization to enhance the enzyme storage and usage facilities. Objective: In this article, our motivation is to obtain attractive electrospun support for carbonic anhydrase enzyme immobilization to enhance the enzyme reusability and storage ability in biocatalysis applications. Methods: In this article, we propose electrospun nanofibers for carbonic anhydrase carrying support for achieving our aforementioned object. In the first part of the study, agar with polyacrylonitrile (PAN) nanofibers was directly fabricated from an agar-PAN mixture solution using the electrospinning method, and fabricated nanofibers were cross-linked via glutaraldehyde (GA). The morphology, chemical structure, and stability of the electrospun nanofibers were characterized. In the second part of the study, the carbonic anhydrase enzyme was immobilized onto fabricated electrospun nanofibers. Then, enzyme activity, the parameters that affect enzyme immobilization such as pH, enzyme amount, immobilization time, etc. and reusability were investigated. Results: When the scanning electron microscopy (SEM) and Fourier-transform infrared spectroscopy (FTIR) analysis results are combined in the characterization process of the synthesized electrospun nanofibers, the optimum cross-linking time is found to be 8 hours using 5% glutaraldehyde cross-linking agent. Then, thermal stability measurements showed that the thermal stability of electrospun nanofibers has an excellent characteristic for biomedical applications. The optimum temperature value was found 37°C, pH 8 was determined as an optimum pH, and 100 ppm carbonic anhydrase enzyme concentration was found to be optimum enzyme concentration for the carbonic anhydrase enzyme immobilization. According to the kinetic data, carbonic anhydrase immobilized electrospun nanofibers acted as a biocatalyst in the conversion of the substrate to the product in 83.98%, and immobilized carbonic anhydrase enzyme is reusable up to 9 cycles in biocatalysis applications. Conclusion: After applying the framework, we get a new biocatalysis application platform for carbonic anhydrase enzyme. Electrospun nanofibers were chosen as the support material for enzyme immobilization. By using this approach, the carbonic anhydrase enzyme could easily be used in the industrial area by cost-effective advantageous aspects.

Background: Human growth hormone (hGH) is the first recombinant protein approved for the treatment of human growth hormone deficiency. However, expression in inclusion bodies and low expression levels are enormous challenges for heterologous expression of hGH in Escherichia coli. Objective: To increase the soluble expression of recombinant hGH with correct folding in E. coli. Methods: We constructed a new recombinant expression plasmid containing the coding sequence of the outer membrane protein A (ompA3) which was used for the expression in Transetta (DE3) E. coli. In order to simplify the purification process and cleavage of recombinant proteins, the fusion sequence should contain hexahistidine-tag (His6) and enterokinase recognition sites (D4K). The effect of different expression conditions on recombinant hGH expression was optimized in flask cultivations. Furthermore, the periplasmic solution containing soluble hGH was purified by Ni-NTA affinity chromatography. Circular dichroism (CD), western blot and mass spectrometry analyses were used to characterize the protein. Moreover, the growth-promoting effect of the purified hGH was also evaluated by cell proliferation assay. Results: High-level expression (800 μg/mL) was achieved by induction with 0.5 mM IPTG at 30°C for 10 hours. The purity of hGH was over 90%. The immunological activity, secondary structure and molecular weight of the purified hGH were consistent with native hGH. The purified hGH was found to promote the growth of MC3T3-E1 cells, and was found to show the highest activity at a concentration of 100 ng/mL. Conclusion: Our research provides a feasible and convenient method for the soluble expression of recombinant hGH in E. coli, and may lay a foundation for the production and application of hGH in the industry.

Background: Reversibly glycosylated polypeptide (RGP), a kind of hydrosoluble and plasmodesmal-associated protein found in plants, plays a crucial role in the development of pollen. Objective: A novel RGP 2 was isolated and identified from rape (Brassica napus L.) bee pollen. Methods: RGP2 was isolated and purified by ion-exchange column and gel filtration chromatography, and characterized by MALDI-TOF-MS, LC-MS, immunological histological chemistry, and transmission electron microscope. Results: Our results indicated that the RGP2 is an acidic protein (pI=5.46) with the molecular weight 42388 Da. It contained 17 kinds of amino acids, among which aspartic acid had the highest amount (71.56 mg/g). Homologous alignment of amino acid sequence results showed that RGP2 was 80.33%, 85.02%, 86.06%, and 88.93% identical to Arabidopsis thaliana RGP2 (AtRGP2), Oryza sativa RGP (OsRGP), Triticum aestivum RGP (TaRGP), and Zea maize RGP (ZmRGP), respectively. The localization results showed that RGP2 in rape anther existed in exine and intine of anther cells of rape flower by immunological histological chemistry and the subcellular localization identified that RGP2 appeared around the Golgi apparatus in cytoplasm by transmission electron microscope. Conclusion: RGP2 has a highly conserved sequence of amino acid residues and potential glycosylation sites.

Background: The purification of expressed proteins is the most critical part of subunit-- vaccine production. Protein-purification methods such as affinity chromatography and ion exchange still have the shortcomings of being time consuming and complicated. With the rapid development of computational molecular-simulation technology, structure-based peptide-ligand design has become feasible. Objection: We aimed to apply molecular docking for a peptide ligand designed for classical swine fever virus (CSFV) E2 purification. Methods: Computational-derived peptides were synthesized, and the in vitro binding interaction with E2 was investigated. The effects of purification on E2 were also evaluated. Results: The best peptide recognizing E2 was P6, which had a sequence of KKFYWRYWEH. Based on kinetic surface plasmon resonance (SPR) analysis, the apparent affinity constant of P6 was found to be 148 nM. Importantly, P6 showed suitable binding affinity and specificity for E2 purification from transgenic rice seeds. Evaluation of immune antibodies in mice showed that the antibody- blocking rate on day 42 after inoculation reached 86.18% and 90.68%. Conclusion: The computational-designed peptide in this study has high sensitivity and selectivity and is thus useful for the purification of CSFV E2. The novel method of design provided a broad platform and powerful tool for protein-peptide screening, as well as new insights into CSFV vaccine design.

Background: Proteases with keratinolytic activity are widely used in biotechnologies. The feather-degrading Bacillus thuringensis isolated from soil sample of a tea plantation produced high level of extracellular keratinase. Objective: This study aimed to analyze the properties by biochemical and enzymological methods to gain information for better utilization of the enzyme. Methods: The enzyme was purified with ion exchange and size exclusion chromatography. The substrate preference, optimal pH and temperature, and the effects of organic solvents and ions were checked. Circular dichroism was performed to compare the secondary structures of the native and apo-enzyme. Results: The enzyme worked best at 50°C, and it was an acidic serine protease with an optimal pH of 6.2. Ions Ca²⁺ and Mg²⁺ were essential for its activity. Organic solvents and other metal ions generally deactivated the enzyme in a concentration-dependent manner. However, Mn²⁺ and DMSO, which were frequently reported as inhibitors of protease, could activate the enzyme at low concentration (0.01 to 2 mmol/L of Mn²⁺; DMSO <2%, v/v). The enzyme exhibited high resistance to Al³⁺, which might be explained by the soil properties of its host’s residence. Circular dichroism confirmed the contribution of ions to the structure and activity. Conclusion: The enzyme was a thermostable aluminum-tolerant serine protease with unique biochemical properties.

Aims: The aim of this study was to create a new version of the PentaFOLD algorithm and to test its performance experimentally in several proteins and peptides. Background: Synthetic vaccines can cause production of neutralizing antibodies only in case if short peptides form the same secondary structure as fragments of full-length proteins. The Penta- FOLD 3.0 algorithm was designed to check stability of alpha helices, beta strands, and random coils using several propensity scales obtained during analysis of 1730 3D structures of proteins. Objective: The algorithm has been tested in the three peptides known to keep the secondary structure of the corresponding fragments of full-length proteins: the NY25 peptide from the Influenza H1N1 hemagglutinin, the SF23 peptide from the diphtheria toxin, the NQ21 peptide from the HIV1 gp120; as well as in the CC36 peptide from the human major prion protein. Methods: Affine chromatography for antibodies against peptides accompanied by circular dichroism and fluorescence spectroscopy were used to check the predictions of the algorithm. Results: Immunological experiments showed that all abovementioned peptides are more or less immunogenic in rabbits. The fact that antibodies against the NY25, the SF23, and the NQ21 form stable complexes with corresponding full-length proteins has been confirmed by affine chromatography. The surface of SARS CoV-2 spike receptor-binding domain interacting with hACE2 has been shown to be unstable according to the results of the PentaFOLD 3.0. Conclusion: The PentaFOLD 3.0 algorithm (http://chemres.bsmu.by/PentaFOLD30.htm) can be used with the aim to design vaccine peptides with stable secondary structure elements.

Background: Carbon monoxide (CO), which is well known as silent killer, has many toxic effects on organs with high rate of metabolism such as heart and brain. CO-induced cardiotoxicity resulted in a wide range of disabilities including electrocardiogram (ECG) abnormalities, elevation in level of cardiac enzymes, arrhythmias, impairment of left ventricular and myocardial infarction (MI). Cardio-protective effects of Granulocyte colony-stimulating factor (G-CSF) on infarcted heart was proved previously in various reports. Objective: In this study, possible effect of G-CSF on cardiac function of patients with moderate to severe acute CO poisoning was investigated. Methods: Cardioprotective effects of G-CSF in CO-poisoned patients was evaluated through ECG, Holter monitoring, echocardiography, and biochemical studies. Continuous intravenous infusion of G-CSF (90 μg/kg) and normal saline were administered respectively to treatment and placebo groups. Results: The results demonstrated that in moderate to severe CO poisoning, myocardial injury is common. ECG changes (e.g., ST-segment and T-wave changes, QTC), cardiac arrhythmias (e.g., heart blocks and ventricular arrhythmias), serum level of Troponin I, left ventricular ejection fraction were determined after G-CSF administration. Frequencies of ST depression, inversion or flatting of T wave and QTC in ECG were significantly reduced after G-CSF treatment. In addition, incidence of cardiac arrhythmias due to CO poisoning were reduced after G-CSF treatment. However, G-CSF did not exert protective effects on TPI level and function of left ventricular in CO-poisoned patients. Conclusion: GCSF could probably reduce CO-induced cardiac ischemia in patients with acute CO poisoning. Clinical Trial Registration: The trial protocol was registered in the Iranian Registry of Clinical Trials (http://www.irct.ir) registry (Irct ID: IRCT201607232083N7).