S. Shirin Shahangian - Academia.edu (original) (raw)

Papers by S. Shirin Shahangian

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy

International Journal of Biological Macromolecules

Process Biochemistry

Abstract The dnaK gene of Bacillus persicus strain B48(T) was cloned, sequenced, and functionally... more Abstract The dnaK gene of Bacillus persicus strain B48(T) was cloned, sequenced, and functionally characterized in the present study. The gene was 1836 bp in length, encoding a polypeptide of 611 amino acid residues. The 3D structure of protein predicted by I-TASSER represented the similarity of the overall structures of DnaK from B. persicus strain B48(T) and human protein Hsp70 (BiP) with a homology of 89 %. Based on the results, refolding heat-denatured carbonic anhydrase increased significantly up to 80 % in the presence of the purified recombinant DnaK. In addition, salt resistance experiments demonstrated a 2.7-fold increase in the survival of recombinant E. coli BL21–DnaK in the presence of 0.4 M NaCl for 60 h compared to that of the control cells. Further, Cd2+ failed to affect DnaK refolding function, while Hg2+ ion reflected a biphasic effect (inhibiting and stimulating at lower and higher than 100 nM concentrations, respectively). Finally, DnaK from B. persicus can potentially be used for improving the functional properties of enzymes and proteins through increasing folding activity and enhancing stress tolerance.

Journal of Aquatic Food Product Technology

ABSTRACT Bioactive peptides from marine protein sources hold tremendous promise as potent antioxi... more ABSTRACT Bioactive peptides from marine protein sources hold tremendous promise as potent antioxidant agents with plausible anticancer activity. Herein, the antioxidant activities of crab protein hydrolysate and its ultrafiltration fractions at different molecular weights (>30 kDa,10–30 kDa,3–10 kD and<3 kDa) using various methods (DPPH, ABTS and FRAP assay) were investigated carefully. The results showed that although all peptide fractions from the crab hydrolysate showed some activity, the low molecular weight fractions (3–10 kDa and <3 kDa) generated the highest antioxidant activity, with a high content of hydrophobic amino acids (48.87% for 3–10 and 46.26% for <3 kDa). Interestingly, both low molecular weight peptide fractions showed a remarkable cytotoxic effect against the MCF-7 cells, while the 3–10 kDa peptide fraction proved to be more effective. Phase-contrast microscopy of treated MCF7 cells with the 3–10 peptide fraction confirmed various morphological alterations and cell damages. Overall, the study suggested that the low molecular weight peptide fractions of rocky shore crab Grapsus albolineatus hydrolysate could be considered as a natural antioxidant candidate in the prevention of cancer by reducing free radicals production, as well as an anticancer agent in cancer treatment by cytotoxic effect on cancer cells.

Journal of Molecular Liquids

Process Biochemistry, 2021

Abstract A novel xylanase gene of 870bp was isolated and cloned from the thermophilic bacteria Co... more Abstract A novel xylanase gene of 870bp was isolated and cloned from the thermophilic bacteria Cohnella sp.A01 that encodes an enzyme comprising 290 amino acid residues and belonging to the GH10 family of xylanases. The enzyme was efficiently expressed in Escherichia coli BL21, then purified using one-step chromatography. The recombinant XynB-A01 not only exhibited significant thermostability but also showed to be stable in a broad range of pH (3.0–10.0), the presence of some detergents, and organic solvents. Although XynB-A01 demonstrated significant activity toward both beechwood and oat spelt xylans, it showed a stronger affinity and higher activity toward the former. HPLC analysis of beechwood xylan hydrolysis revealed that xylotetraose, xylobiose, and xylose are the major hydrolysis products. The investigation of XynB-A01 in pulp biobleaching showed effectiveness in the release of reducing sugars and chromophores. Simple purification, stability over a broad range of pH and temperature, cellulase-free character, and the capacity to produce xylooligosaccharides are some of the advantages of the xylanase of Cohnella sp.A01, suggesting that it may be a promising candidate for biobleaching of paper pulps, producing xylooligosaccharides, and applying in other industries.

Biotechnology and Applied Biochemistry, 2019

The effects of 17 kinds of additive mixtures have been studied on refolding and aggregation of a ... more The effects of 17 kinds of additive mixtures have been studied on refolding and aggregation of a model protein, lysozyme. Most of the prepared mixtures were efficient in inhibiting aggregation of the protein and surprisingly, 4 novel additive mixtures, i.e. lactic acid: L-This article is protected by copyright. All rights reserved. arginine, lactic acid: L-glutamine, choline chloride: lactic acid and imidazolium salt: βcyclodextrin as well as choline chloride: urea exhibited a more remarkable efficacy in suppressing aggregation. Among these, lactic acid: L-arginine was identified as the most efficient additive, and lactic acid: L-glutamine and choline chloride: lactic acid were inefficient to recover the enzyme activity. In contrast, choline chloride: ethylene glycol: imidazole, choline chloride: glycerol: imidazole, imidazole: betaine: ethylene glycol were found to be less effective mixtures in preventing enzyme aggregation. Totally, it was demonstrated that the protective effects of the mixtures were improved as their concentrations increased. The improvement was more remarkable for imidazolium salt: β-cyclodextrin and choline chloride: urea, where the denatured lysozyme was reactivated and recovered up to 85% of its initial activity by enhancing their concentrations from 1 to 5% (V/V). It is suggested that such solution additives may be further employed as artificial chaperones in order to assist protein folding and stability.

Journal of Biomolecular Structure and Dynamics, 2020

Stress tolerance is one of the most prominent and interesting topics in biology since many macroa... more Stress tolerance is one of the most prominent and interesting topics in biology since many macroand micro-adaptations have evolved in resistant organisms that are worth studying. When it comes to confronting various environmental stressors, the extremophile Artemia is unrivaled in the animal kingdom. In the present review, the evolved molecular and cellular basis of stress tolerance in resistant biological systems are described, focusing on Artemia cyst as an excellent biological model. The main purpose of the review is to discuss how the structure and physicochemical characteristics of protective factors such as late embryogenesis abundant proteins (LEAPs), small heat shock proteins (sHSPs) and trehalose are related to their functions and by which mechanisms, they exert their functions. In addition, some metabolic depressors in Artemia encysted embryos are also mentioned, indirectly playing important roles in stress tolerance. Importantly, a great deal of attention is given to the LEAPs, exhibiting distinctive folding behaviors and mechanisms of actions. For instance, molecular shield function, chaperone-like activity, moonlighting property, sponging and snorkeling capabilities of the LEAPs are delineated here. Moreover, the molecular interplay between some of these factors is mentioned, leading to their synergistic effects. Interestingly, Artemia life cycle adapts to environmental conditions. Diapause is the defense mode of this life cycle, safeguarding Artemia encysted embryos against various environmental stressors.

International Journal of Aquatic Biology, 2020

Antibacterial and antioxidant activity of the rocky shore crab , Grapsus albolineathus , protein ... more Antibacterial and antioxidant activity of the rocky shore crab , Grapsus albolineathus , protein hydrolysate (CPH), with different degree of hydrolysis (DH) prepared using alcalase was investigated. The results showed that by increasing DH with reaction time up to 90 min, the DPPH radical scavenging activity of the hydrolysates raise, followed by a decrease in the next stages from 90 to 180 min.Interestingly, ABTS radical scavenging of the hydrolysates increase up to 120 min, and CPH 120 show the highest activity with no significant difference with CPH 90 and CPH 180 . The degree of hydrolysis applied a significant influence on the antibacterial activity of crab hydrolysates against gram-positive bacteria, with a significant increase up to 90 min. The maximum zone of inhibitions was recorded against Listeria monocytogene for CPH 90 :14.55 mm. The results suggest that the alcalase hydrolysis of rocky shore crab can produce bioactive peptides with potent antioxidant and antibacterial ...

Drug Metabolism Reviews, 2021

Abstract Developing effective strategies to confront coronavirus disease 2019 (COVID-19) has beco... more Abstract Developing effective strategies to confront coronavirus disease 2019 (COVID-19) has become one of the greatest concerns of the scientific community. In addition to the vast number of global mortalities due to COVID-19, since its outbreak, almost every aspect of human lives has changed one way or another. In the present review, various defensive and offensive strategies developed to confront COVID-19 are illustrated. The Administration of immune-boosting micronutrients/agents, as well as the inhibition of the activity of incompetent gatekeepers, including some host cell receptors (e.g. ACE2) and proteases (e.g. TMPRSS2), are some efficient defensive strategies. Antibody/phage therapies and specifically vaccines also play a prominent role in the enhancement of host defense against COVID-19. Nanotechnology, however, can considerably weaken the virulence of SARS-CoV-2, utilizing fake cellular locks (compounds mimicking cell receptors) to block the viral keys (spike proteins). Generally, two strategies are developed to interfere with the binding of spike proteins to the host cell receptors, either utilizing fake cellular locks to block the viral keys or utilizing fake viral keys to block the cellular locks. Due to their evolutionary conserved nature, viral enzymes, including 3CLpro, PLpro, RdRp, and helicase are highly potential targets for drug repurposing strategy. Thus, various steps of viral replication/transcription can effectively be blocked by their inhibition, leading to the elimination of SARS-CoV-2. Moreover, RNA decoy and CRISPR technologies likely offer the best offensive strategies after viral entry into the host cells, inhibiting the viral replication/assembly in the infected cells and substantially reducing the quantity of viral progeny.

Iranian Biomedical Journal, 2021

Background: This study was devoted to assessing the inhibitory potential of acetone, methanol, an... more Background: This study was devoted to assessing the inhibitory potential of acetone, methanol, and ethanol extracts of Acroptilon repens against disease-associated enzymes, as well as their antioxidant/antibacterial activity and phytochemical composition. Methods: Comparative assessment using various antioxidant evaluation methods, including FRAP, scavenging ability on DPPH radical and hydrogen peroxide, and RP, indicated that the acetone extract presented the highest antioxidant activity, due to its highest total antioxidant content. Results: The TPC and TFC of these extracts were 3.44 ± 0.32 mg GAE/g DW and 2.09 ± 0.2 mg QE/g DW, respectively. The hydrodistillation essential oil from A. repens was analyzed by GC/MS, and 17 compounds were identified. All extracts showed good inhibitory activities against disease-related enzyme acetylcholinesterase and α-amylase, with the lowest IC 50 for acetonic extract. Extracts of A. repens exhibited inhibiting activities against the Gram-positive bacteria, with the most effect of acetone extract. Conclusion: Our findings suggest A. repens as a promising source of natural antioxidant, antimicrobial, anti-cholinesterase and anti-amylase agents for the management of oxidative damage, and pharmaceutical, food, and cosmeceutical purposes.

Asian Pacific Journal of Cancer Prevention, 2020

Long non-coding RNAs (lncRNAs) are RNA molecules (>200 nucleotides in length) with no protein-cod... more Long non-coding RNAs (lncRNAs) are RNA molecules (>200 nucleotides in length) with no protein-coding capacity. Recent studies have demonstrated that lncRNAs involve in the regulation of their target genes at transcriptional, post-transcriptional and epigenetic levels. The aim of this case-control study was to explore whether growth arrest-specific 5 (GAS5) lncRNA 5-bp Ins/Del (rs145204276) polymorphism is involved in the breast cancer susceptibility. A total of 170 cases and 220 age matched controls were recruited in this study. GAS5 lncRNA polymorphism was genotyped using tetra primers amplification refractory mutation system polymerase chain reaction (T-ARMS-PCR) method. Statistical analysis was performed using SPSS. The distribution of the genotype ins/ins, ins/ del and del/del were %75.29, 21.76% and 2.94% and 52.27%, 39.55% and 8.81% in the cases and controls, respectively. The ins/del or del/del genotype had a significantly decreased risk of breast cancer as compared with the ins/ins genotype under a codominant model (OR=0.38, 95%CI 0.24-0.60, p=0.0001; OR= 0.25, 95%CI 0.09-0.69, p=0.008, respectively). Moreover, the deletion allele of this polymorphic site is associated with a protective effect (OR=0.41, 95%CI 0.28-0.60, p=0.0001). Our study provided the first evidence that the deletion allele of GAS5 rs145204276 may have a protective role in mediating individual susceptibility to breast cancer. However, further comprehensive studies are warranted in a larger sample.

Analytical and Bioanalytical Chemistry, 2020

Because of the critical role of vascular endothelial growth factor (VEGF) in angiogenesis and its... more Because of the critical role of vascular endothelial growth factor (VEGF) in angiogenesis and its significantly increased serum levels in early stages of cancer, VEGF is considered an important prognostic biomarker in different cancers. Herein, the amplification power of PCR combined with phage displaying anti-VEGF VHH, a sensitive real-time immunoassay, was precisely designed based on phage display-mediated immuno-PCR (PD-IPCR) for the detection of VEGF. This system benefits from strong and specific binding of antigen and antibody in a sandwich immunosorbent assay platform using avastin (anti-VEGF monoclonal antibody) as the capture antibody. The anti-VEGF phage particles were used as both anti-VEGF agent and DNA template in the PD-IPCR. Anti-VEGF phage ELISA showed a linear range of 3-250 ng/ml and a limit of detection (LOD) of 1.1 ng/ml. Using the PD-IPCR method, the linear range of VEGF detection was found to be 0.06-700 ng/ml, with a detection limit of 3 pg/ml. The recovery rate in serum ranged from 83% to 99%, with a relative standard deviation of 1.2-4.9%. These values indicate that the method has good sensitivity for use in clinical analysis. The proposed method was successfully applied to the clinical determination of VEGF in human serum samples, and the results showed excellent correlation with conventional ELISA (R 2 = 0.995). The novel immunoassay provides a specific and sensitive immunoassay protocol for VEGF detection at very low levels.

ABSTRACTArtemin is an abundant thermostable protein in Artemia embryos and considered as a highly... more ABSTRACTArtemin is an abundant thermostable protein in Artemia embryos and considered as a highly efficient molecular chaperone against extreme environmental stress conditions. The dynamic conformational properties of artemin appear to play a critical role in its biological activities. In this study, we have investigated the conformational transitions and functional changes of artemin under heat and oxidative stress to find some evidence of the relationship between the structure and function of artemin. The tertiary and quaternary structures of artemin have been evaluated by fluorescence measurements, protein cross-linking analysis, and dynamic light scattering. Based on the structural analysis, artemin showed irreversible substantial conformational lability in response to heat and oxidant which mainly mediated through the hydrophobic interactions and dimerization of the chaperone. In addition, the chaperone-like activity of the heated and oxidized artemin was examined using lysozym...

British Journal of Biomedical Science, 2019

ABSTRACT Background: MicroRNAs (miRNAs) participate in gene regulation and the control of cancer-... more ABSTRACT Background: MicroRNAs (miRNAs) participate in gene regulation and the control of cancer-related mechanisms such as apoptosis, invasion and differentiation. Single nucleotide polymorphisms (SNP) of the miRNA encoding genes may influence the development of cancer. We hypothesized a link between miR-559 SNP rs58450758 and breast cancer. Materials & methods: Bioinformatics analyses were performed to predict the miR-559 target genes and the effect of the rs58450758 SNP on the stem-loop structure. A total of 129 breast cancer cases and 153 controls were genotyped using PCR-RFLP. Results: The recessive genotype (TT) was more common among breast cancer patients (23.3%) than among controls (2%). The non-dominant genotypes (CT+TT) were associated with breast cancer in patients (OR 3.62; 95% CI, 1.95–6.69; p < 0.0001). Bioinformatics analyses suggested that rs58450758 changes miR-559 secondary structure and forms new DICER sites in the pre-miRNA. Conclusion: The miR-559 rs58450758 variant is linked to breast cancer.

Cell Stress and Chaperones, 2018

Encysted embryos of Artemia are among the most stress-resistant eukaryotes partly due to the mass... more Encysted embryos of Artemia are among the most stress-resistant eukaryotes partly due to the massive amount of a cysteine-rich protein termed artemin. High number of cysteine residues in artemin and their intramolecular spatial positions motivated us to investigate the role of the cysteine residues in the chaperone-like activity of artemin. According to the result of Ellman's assay, there are nine free thiols (seven buried and two exposed) and one disulfide bond per monomer of artemin. Subsequent theoretical analysis of the predicted 3D structure of artemin confirmed the data obtained by the spectroscopic study. Native and reduced/ modified forms of artemin were also compared with respect to their efficiency in chaperoning activity, tertiary structure, and stability. Since the alkylation and reduction of artemin diminished its chaperone activity, it appears that its chaperoning potential depends on the formation of intermolecular disulfide bond and the presence of cysteine residues. Comparative fluorescence studies on the structure and stability of the native and reduced protein revealed some differences between them. Due to the redoxdependent functional switching of artemin from the less to more active form, it can be finally suggested as a redox-dependent chaperone.

ChemistrySelect, 2018

Despite research efforts to unravel the role of naturally occurring deep eutectic solvents (NADES... more Despite research efforts to unravel the role of naturally occurring deep eutectic solvents (NADESs) in living cells, there are still many questions left unanswered. The proposed hypothesis about the role of NADESs in cryopreservation and resistance of cells motivated us to investigate whether DESs might possess chaperoning activity. Accordingly, here, the chaperone-like activity of a well-known DES, urea-choline chloride DES (UC), on a model protein, lysozyme, has been evaluated. The results showed that UC DES was not only capable of suppressing lysozyme aggregation almost completely, but also efficiently enhanced the refolding yield of the denatured enzyme by nearly 95%, thereby suggesting the chaperoning potency of DESs. The refolding promotion of lysozyme was also verified through fluorescence study. The results may introduce DESs as new generation chaperones and shed light on their role in cell resistance under stress conditions.

British Journal of Biomedical Science, 2018

Infertility is defined as the failure to establish a pregnancy after a year of regular and unprot... more Infertility is defined as the failure to establish a pregnancy after a year of regular and unprotected sexual intercourse [1]. Males are solely responsible for 20–30% of infertility cases but contr...

International Journal of Biological Macromolecules, 2019

Due to the need for calf rennet alternatives, many attempts have been made to find new proteases.... more Due to the need for calf rennet alternatives, many attempts have been made to find new proteases. A novel cysteine protease with milk-clotting activity was purified from Ficus johannis by cation exchange chromatography. The protease was stable in various pH (3.0-10.5) with the optimum at 6.5 and showed its maximum activity at 60 °C. The K m and V max values of the enzyme were obtained to be 0.604 mg/ml and 0.0273 µmol Tyr/min, respectively. The purified protease exhibited considerable activity towards κ-casein in comparison to α-casein and β-casein. The enzyme was almost completely active in the presence of high salt concentrations. Besides, it had high stability against autodigestion. The content of free amino acids was determined by HPLC, where leucine, lysine, valine, γaminobutyric acid and tyrosine were the most abundant amino acids. The cheese manufactured by using the purified protease showed similar textural properties and physico-chemical compositions to cheese produced using commercial rennet. Considering the special characteristics, including high milkclotting activity, considerable stability over wide ranges of pH and temperature, resistance towards solvents, salts, and surfactants, the new protease might be the promising candidate for the dairy industry as well as other food and biotechnological industries.

Chemical Biology & Drug Design, 2018

Due to its crucial role in DNA synthesis, thymidylate synthase (TS) has been considered as a pote... more Due to its crucial role in DNA synthesis, thymidylate synthase (TS) has been considered as a potential therapeutic target. Inhibition of the enzyme is a promising strategy for the treatment of some hyper-proliferative diseases, including infections. Since TS species-specific inhibitors would be able to distinguish between the host and the pathogens, developing highly Accepted Article This article is protected by copyright. All rights reserved. selective inhibitors is of great clinical importance. TS is among the most highly conserved enzymes over evolutionary history, making the design of its species-selective inhibitor significantly challenging. The chemical interaction space, governed by a set of non-selective TS inhibitors, has been explored for human TS and its homologous proteins in both T. gondii and E. coli using proteochemometrics modeling (PCM). Validity, robustness and prediction power of the PCM model have been assessed applying a diverse set of internal/external validation approaches. Our PCM model has provided major structural information, which is indeed of great help to design new TS species-specific inhibitors with the simultaneous inhibition ability towards both T. gondii and E. coli. To show applicability of the PCM model, new compounds have been designed based on structural information provided by the constructed model. Final results have been very promising with regard to selectivity ratios of the designed compounds for different TS isoforms, confirming the applicability of the PCM model.