FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization.

Overproduction of desired native or nonnative biochemical(s) in (micro)organisms can be achieved through metabolic engineering. Appropriate rewiring of cell metabolism is performed by making rational changes such as insertion, up-/down-regulation and knockout of genes and consequently metabolic reactions. Finding appropriate targets (including proper sets of reactions to be knocked out) for metabolic engineering to design optimal production strains has been the goal of a number of computational algorithms. We developed FastKnock, an efficient next-generation algorithm for identifying all possible knockout strategies (with a predefined maximum number of reaction deletions) for the growth-coupled overproduction of biochemical(s) of interest. We achieve this by developing a special depth-first traversal algorithm that allows us to prune the search space significantly. This leads to a drastic reduction in execution time. We evaluate the performance of the FastKnock algorithm using various Escherichia coli genome-scale metabolic models in different conditions (minimal and rich mediums) for the overproduction of a number of desired metabolites. FastKnock efficiently prunes the search space to less than 0.2% for quadruple- and 0.02% for quintuple-reaction knockouts. Compared to the classic approaches such as OptKnock and the state-of-the-art techniques such as MCSEnumerator methods, FastKnock found many more beneficial and important practical solutions. The availability of all the solutions provides the opportunity to further characterize, rank and select the most appropriate intervention strategy based on any desired evaluation index. Our implementation of the FastKnock method in Python is publicly available at https://github.com/leilahsn/FastKnock .

Interaction of gallium, indium, and vanadyl curcumin complexes with hen egg-white lysozyme (HEWL): Mechanistic aspects and evaluation of antiamyloidogenic activity.

Many proteins and peptides can aggregate into amyloid fibrils with high-ordered and cross-ß rich structure characteristics. Amyloid deposition is a common feature of neurodegenerative diseases called amyloidosis. Various natural polyphenolic compounds such as curcumin exhibited antiamyloidogenic activities, but less researches were focused on the metal complexes of these compounds. In this study, the inhibitory effects of gallium curcumin (Ga(cur)3), indium curcumin (In(cur)3), and vanadyl curcumin (VO(cur)2) on the amyloid fibrillation of hen egg white lysozyme (HEWL) have been investigated. Moreover, the details of binding interactions of these metal complexes with HEWL have been explored. The results of fluorescence quenching analyses revealed that In(cur)3 and VO(cur)2 have much higher binding affinities than Ga(cur)3 toward HEWL. The interactions of these metal complexes were accompanied by partial conformational changes in the tertiary structure of HEWL. The kinetic curves of the fibrillation process demonstrated that In(cur)3 and VO(cur)2 have higher inhibitory effects than Ga(cur)3 on the amyloid fibrillation of HEWL. The strength of binding to HEWL is completely in accordance with inhibitory activities of these metal complexes of curcumin.

FastKnock: An efficient next-generation approach to identify all knockout strategies for strain optimization.

Overproduction of desired native or nonnative biochemical(s) in (micro)organisms can be achieved through metabolic engineering. Appropriate rewiring of cell metabolism is performed making rational changes such as insertion, up-/down-regulation and knockout of genes and consequently metabolic reactions. Finding appropriate targets (including proper sets of reactions to be knocked out) for metabolic engineering to design optimal production strains has been the goal of a number of computational algorithms. We developed FastKnock, an efficient next-generation algorithm for identifying all possible knockout strategies for the growth-coupled overproduction of biochemical(s) of interest. We achieve this by developing a special depth-first traversal algorithm that allows us to prune the search space significantly. This leads to a drastic reduction in execution time. We evaluate the performance of the FastKnock algorithm using three Escherichia coli genome-scale metabolic models in different conditions (minimal and rich mediums) for the overproduction of a number of desired metabolites. FastKnock efficiently prunes the search space to less than 0.2% for quadruple and 0.02% for quintuple-reaction knockouts. Compared to the classic approaches such as OptKnock and the state-of-the-art techniques such as MCSEnumerator methods, FastKnock found many more useful and important practical solutions. The availability of all the solutions provides the opportunity to further characterize and select the most appropriate intervention strategy based on any desired evaluation index. Our implementation of the FastKnock method in Python is publicly available at https://github.com/leilahsn/FastKnock.

Physicochemical studies on the structural stability of the HIV-1 vaccine candidate recombinant Tat protein.

HIV-1 transactivator of transcription protein is one of the most promising AIDS vaccine candidates and plays central roles in the virus life cycle and pathogenesis. Understanding structural properties of vaccine candidate antigens leads to rational design of vaccines which improves their presentation to immune system and facilitates their manufacturing and storage. This study aims to investigate structural properties and stability of one variant of HIV-1 Tat recombinant protein using different spectroscopic, electrophoretic, and microscopic methods. Therefore, after the gene transformation, protein expression was optimized in E. coli cells and the C-terminal His6-tagged protein was purified using Ni-NTA resin. The structural stability of the pure protein was then investigated under different conditions including pH, Zn2+ ions, thermal and chemical stress. Acidic and alkaline pHs affects spectroscopic properties of the vaccine in different ways. The structure unfolding experiment shows relatively poor stability of the zinc-free protein sample compared to the ion-containing one. According to the quenching experiment and also thermal stability study results, the protein has attained more structural compactness in the presence of Zn2+. Secondary structure of the protein is mainly disordered and didn't significantly affect under various conditions. Finally, different degrees of oligomerization and aggregation were found under physiological conditions.

An evolution-based designing and characterization of mutants of cyclomaltodextrinase: Molecular modeling and spectroscopic studies.

Cyclomaltodextrinase (CDase) is a member of the alpha-amylase family GH13, the subfamily GH13_20. In addition to CDase and neopullulanase, this subfamily also contains maltogenic amylase. They have common structural features, but different substrate specificity. In current work, a combination of bioinformatics and experimental tools were used for designing and constructions of single and double mutants of a new variant of CDase from Anoxybacillus flavithermus. Considering the evolutionary variable positions 123 and 127 at the dimer interface of subunits in the alpha-amylase family, these positions in CDase were modified and three mutants, including A123V, C127Q and A123V/C127Q were constructed. The tertiary structure of WT and mutants were made with the MODELLER program, and the phylogenetic tree of homologous protein sequences was built with selected programs in Phylip package. Enzyme kinetic studies revealed that the catalytic efficiency of mutants, especially double one, is lower than the WT enzyme. Heat-induced denaturation experiments were monitored by measuring the UV/Vis signal at 280 nm, and it was found that WT protein is structurally more stable at 25 °C. However, it is more susceptible to changes in temperature compared to the double mutant. It was concluded that the positions 123 and 127 at the dimeric interface of CDase, not only could affect the conformational stability; but also; the catalytic properties of the enzyme by setting up the active site configuration in the dimeric state.

The Effect of Chronic Consumption of Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Antagonists on Blood Pressure and Inotrope Consumption After Separation from Cardiopulmonary Bypass.

BACKGROUND: Chronic use of renin-angiotensin system (RAS) antagonists (angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor antagonists (ARAS)) can cause hypotension during anesthesia. In some studies hemodynamic instability, including hypotension and its effects on the clinical outcome in patients treated with these drugs during coronary artery bypass graft (CABG) and need to excessive vasoactive drugs in these patient population, has been described. The aim of this study was to evaluate the effect of chronic consumption of ACEIs and ARAS on blood pressure and inotrope consumption during coronary artery bypass graft under cardiopulmonary bypass. METHODS: A total of 200 patients undergoing coronary artery bypass graft surgery, who were treated with either ARAS or ACEIs (n = 100) over at least 2 months, or who were not treated with any RAS antagonists (control group, n = 100) were enrolled. The mean arterial blood pressure, central venous pressure, and need for vasoactive drugs, were measured after induction of anesthesia (T1) before cardiopulmonary bypass (T2) and after separation from (CPB), (T3). RESULTS: There were no significant differences regarding the mean arterial pressure (case group: T1: 84 ± 7 mmHg, T2: 77 ± 6 mmHg, T3: 83 ± 8 mmHg), (control group: T1: 85 ± 7 mmHg, T2: 81 ± 7 mmHg, T3:84 ± 6 mmHg) between two groups (P > 0.05). Also there were no significant differences regarding mean central venous pressure, mean heart rate, and vasoactive drug consumption between the two groups during the time of intervals. CONCLUSIONS: We found that preoperative (RAS) antagonist's continuation have not profound hemodynamic changes during coronary artery bypass graft under cardiopulmonary bypass and so we conclude that omitting these drugs before surgery did not have a sufficient advantage to be recommended routinely.

Kinetics, structure, and dynamics of Renilla luciferase solvated in binary mixtures of glycerol and water and the mechanism by which glycerol obstructs the enzyme emitter site.

Renilla Luciferase is a bioluminescent enzyme which is broadly implemented as protein reporter in biology-related researches. In this study, new evidences on the kinetics, structure, and dynamics of Renilla luciferase solvated in binary mixtures of glycerol and water using MD simulation along with experimental procedures including fluorescence and CD spectroscopy were obtained. The results indicated that the Renilla luciferase activity decreased at 0.8 and 1.2 M of glycerol through the obstruction of enzyme emitter site. The present study may describe a new molecular mechanism of decreasing enzyme activity in the presents of glycerol.

Toward Escherichia coli bacteria machine for water oxidation.

Nature uses a Mn oxide-based catalyst for water oxidation in plants, algae, and cyanobacteria. Mn oxides are among major candidates to be used as water-oxidizing catalysts. Herein, we used two straightforward and promising methods to form Escherichia coli bacteria/Mn oxide compounds. In one of the methods, the bacteria template was intact after the reaction. The catalysts were characterized by X-ray photoelectron spectroscopy, visible spectroscopy, scanning electron microscopy, high-resolution transmission electron microscopy, diffuse reflectance infrared Fourier transform spectroscopy, Raman spectroscopy, and X-ray diffraction spectrometry. Electrochemical properties of the catalysts were studied, and attributed redox potentials were assigned. The water oxidation of the compounds was examined under electrochemical condition. Linear sweep voltammetry showed that the onsets of water oxidation in our experimental condition for bacteria and Escherichia coli bacteria/Mn oxide were 1.68 and 1.56 V versus the normal hydrogen electrode (NHE), respectively. Thus, the presence of Mn oxide in the catalyst significantly decreased (~ 120 mV) the overpotential needed for water oxidation.

Inhibition of amyloid fibrillation of lysozyme by bisdemethoxycurcumin and diacetylbisdemethoxycurcumin.

Amyloid deposition, arising from the fibrillogenesis of proteins in organs and tissues of the body, causes several neurodegenerative disorders. One therapeutic approach is based on the use of polyphenols and their derivatives for suppressing and inhibiting the accumulation of these toxic fibrils in tissues. In the present study, the anti-amyloidogenic activities of bisdemethoxycurcumin (BDMC), a natural polyphenolic compound, and diacetylbisdemethoxycurcumin (DABC), a synthetic derivative of curcumin, on the amyloid fibrillation of hen egg white lysozyme (HEWL) is studied in depth using thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), circular dichroism spectroscopy (CD), molecular docking and Ligplot calculations. The binding parameters such as binding constants and the number of substantive binding sites were obtained experimentally. It could be shown from docking simulation that four hydrogen bonds via the two phenolic OH groups of BDMC and two ß-diketone moiety of BDMC are formed with the Asp-101, Trp-63, Asn-59 and Glu-35 of HEWL, whereas, two hydrogen bonds formed via two ß-diketone moiety of DABC with Asn-39 and Trp-63 of HEWL. The short FÓ§rster's distance (r) between donor and acceptor, the binding constant values and also the nature of interaction, demonstrate strong interaction between these two curcuminoids and lysozyme. According to amyloid fibrillation and binding results, the interaction of BDMC with HEWL is stronger than that of DABC and amyloid fibrillation of HEWL was inhibited more effectively by BDMC than DABC. It can be suggested that the more inhibitory activity of BDMC than DABC is correlated to the stronger interaction of BDMC with HEWL. These natural polyphenolic compounds are thus good candidates for inhibiting of amyloid formation. The inhibitory activities of BDMC and DABC can be used in drug formulation against the dangerous amyloid-related diseases and provide health promotion for organs and tissues of the body.

An inter-subunit disulfide bond of artemin acts as a redox switch for its chaperone-like activity.

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 redox-dependent functional switching of artemin from the less to more active form, it can be finally suggested as a redox-dependent chaperone.

Interaction of aurein 1.2 and its analogue with DPPC lipid bilayer.

Antibacterial peptides have potential as novel therapeutic agents for bacterial infections. Aurein 1.2 is one of the smallest antibacterial peptides extracted from an anuran. LLAA is a more active analogue of aurein 1.2. Antibacterial peptides usually accomplish their function by interacting with bacterial membrane selectively. In this study, we tried to find the reasons for the stronger antibacterial activity of LLAA compared with aurein 1.2. For this purpose, the interaction of aurein 1.2 and LLAA with dipalmitoylphosphatidylcholine (DPPC) was investigated by molecular dynamics (MD) simulation. In addition, the structure of peptides and their antibacterial activity were investigated by circular dichroism (CD) and dilution test method, respectively. MD results showed that LLAA is more flexible compared with aurein 1.2. Furthermore, LLAA loses its structure more than aurein 1.2 in the DPPC bilayer. A higher amount of water molecules penetrate into bilayer in the presence of LLAA relative to aurein 1.2. According to the antibacterial result that indicated LLAA is remarkably more active than aurein 1.2, it can be concluded that flexibility of the peptide is a determining factor in antibacterial activity. Probably, flexibility of the peptides facilitates formation of effective pores in the lipid bilayer.

Interaction of hemin with quadruplex DNA.

A DNA enzyme with peroxidase activity is a G-quadruplex-based DNAzyme formed by hemin and G-quadruplex DNA. Activity of peroxide DNAzymes can be influenced by the structure of quadruplex DNA. In this investigation, the interaction of hemin with T30695 G-quadruplex DNA is evaluated. Molecular dynamic simulation indicates that the binding mode of hemin to G-quadruplex DNA is end-stacking, which is consistent with absorption spectroscopy. Based on fluorescence spectroscopy, hemin ejects thiazole orange from bases of four-strand DNA. Circular dichroism spectra showed that no alteration occurs in this type of DNA structure. Graphical Abstract Peroxidase DNAzyme is formed by hemin and G-quadruplex DNA.

The biological effects of vanadyl curcumin and vanadyl diacetylcurcumin complexes: the effect on structure, function and oxidative stability of the peroxidase enzyme, antibacterial activity and cytotoxic effect.

Curcumin has multiple pharmacological effects, but it has poor stability. Complexation of curcumin with metals improves its stability. Here, the effects of vanadyl curcumin and vanadyl diacetylcurcumin on the function and structure of horseradish peroxidase enzyme were evaluated by spectroscopic techniques. Cytotoxic effect of the complexes was also assessed on MCF-7 breast cancer, bladder and LNCaP prostate carcinoma cell line. The results showed that the complexes improve catalytic activity of HRP, and also increase its tolerance against the oxidative condition. The result also indicated that the affinity of HRP for hydrogen peroxide substrate decreases, while the affinity increases for phenol substrate. Circular dichroism and fluorescence spectroscopies showed that compactness of the enzyme structure around the catalytic heme group and the distance between the heme group and tryptophan residue decreases after the binding. The antibacterial and cytotoxic results indicated that the complexes have anticancer potential, but they have no considerable antibacterial activity.

Investigating actinomycin D binding to G-quadruplex, i-motif and double-stranded DNA in 27-nt segment of c-MYC gene promoter.

c-MYC DNA is an attractive target for drug design, especially for cancer chemotherapy. Around 90% of c-MYC transcription is controlled by NHE III1, whose 27-nt purine-rich strand has the ability to form G-quadruplex structure. In this investigation, interaction of ActD with 27-nt G-rich strand (G/c-MYC) and its equimolar mixture with the complementary sequence, (GC/c-MYC) as well as related C-rich oligonucleotide (C/c-MYC) was evaluated. Molecular dynamic simulations showed that phenoxazine and lactone rings of ActD come close to the outer G-tetrad nucleotides indicating that ActD binds through end-stacking to the quadruplex DNA. RMSD and RMSF revealed that fluctuation of the quadruplex DNA increases upon interaction with the drug. The results of spectrophotometry and spectrofluorometry indicated that ActD most probably binds to the c-MYC quadruplex and duplex DNA via end-stacking and intercalation, respectively and polarity of ActD environment decreases due to the interaction. It was also found that binding of ActD to the GC-rich DNA is stronger than the two other forms of DNA. Circular dichroism results showed that the type of the three forms of DNA structures doesn't change, but their compactness alters due to their interaction with ActD. Finally, it can be concluded that ActD binds differently to double stranded DNA, quadruplex DNA and i-motif.

Investigating the effect of structural transition on aggregation of ß-lactoglobulin.

ß-lactoglobulin (BLG), the major bovine whey protein, is a well-characterized globular protein. It is a model protein for studying the structural transition and aggregation. BLG unfolds and aggregates through chemical and physical processes. It is a predominantly ß-sheet protein but, the non-native α-helical intermediate accumulates in its folding pathway. The present study aims to understand more about which stage of the protein folding is prone to aggregation. The intermediate states were trapped by TFE and their aggregation and structural changes evaluated, for this purpose. The experiments were carried out at various pH values, ionic strengths, protein concentrations and heating times by turbidity measurements, circular dichroism and fluorescence spectroscopy. Furthermore, the aggregated species at various molecular weights were detected by SDS-PAGE. Only a small change was observed in the secondary and tertiary structures of the protein at 10% TFE, but a further increase of TFE concentration results in induction of new α-helical structure and disruption of the rigid tertiary structure. The turbidity measurement indicated that the aggregation of BLG reaches a maximum level at 10% TFE on all experimental conditions and from this point forward, it decreases with increasing the amount of TFE. In conclusion, the results showed that the α-helical state is resistant to aggregation, in spite that its tertiary structure is partially unfolded. BLG becomes prone to aggregation, when its non-native α-helical structure converts to the ß-sheet structure.

Investigating the effect of gallium curcumin and gallium diacetylcurcumin complexes on the structure, function and oxidative stability of the peroxidase enzyme and their anticancer and antibacterial activities.

Curcumin has a wide spectrum of biological and pharmacological activities including anti-inflammatory, antioxidant, antiproliferative, antimicrobial and anticancer activities. Complexation of curcumin with metals has gained attention in recent years for improvement of its stability. In this study, the effect of gallium curcumin and gallium diacetylcurcumin on the structure, function and oxidative stability of horseradish peroxidase (HRP) enzyme were evaluated by spectroscopic techniques. In addition to the enzymatic investigation, the cytotoxic effect of the complexes was assessed on bladder, MCF-7 breast cancer and LNCaP prostate carcinoma cell lines by MTT assay. Furthermore, antibacterial activity of the complexes against S. aureus and E. coli was explored by dilution test method. The results showed that the complexes improve activity of HRP and also increase its tolerance against the oxidative condition. After addition of the complexes, affinity of HRP for hydrogen peroxide substrate decreases, while the affinity increases for phenol substrate. Circular dichroism, intrinsic and synchronous fluorescence spectra showed that the enzyme structure around the catalytic heme group becomes less compact and also the distance between the heme group and tryptophan residues increases due to binding of the complexes to HRP. On the whole, it can be concluded that the change in the enzyme structure upon binding to the gallium curcumin and gallium diacetylcurcumin complexes results in an increase in the antioxidant efficiency and activity of the peroxidise enzyme. The result of anticancer and antibacterial activities suggested that the complexes exhibit the potential for cancer treatment, but they have no significant antibacterial activity.

Preparation of polymeric particles in CO2 medium using non-toxic solvents: discussions on the mechanism of particle formation.

The aim of this work was to develop a novel formulation method, termed modified-PGSS (modified-Particle from Gas Saturated Solution), for the encapsulation of protein into polymeric microparticles in CO2 medium. In this study, isosorbide dimethyl ether (DMI), a non-toxic water-miscible solvent, was used for the formulation and lysozyme was chosen as a model protein for encapsulation into PLGA microparticles. First, the mechanism of particle formation has been extensively studied and was discussed in detail. Phase behavior was investigated by measuring the solubility of CO2 in DMI and volumetric expansion of DMI saturated in CO2. Here, we demonstrate the consistency of the experimental values with the data obtained from the mathematical (such as the neural network) and thermodynamic (such as the Peng-Robinson equation of state) models. These models were built to develop predictive tools in the chosen experimental space for microparticle formulation. Furthermore, these microparticles were characterized in terms of size and zeta potential. The morphology and protein distribution within PLGA microparticles were determined using scanning electron microscopy and confocal microscopy, respectively. High encapsulation efficiency (65%) was obtained as confirmed by lysozyme quantification using a specific bioassay (M. lysodeikticus). Moreover, the in vitro protein release profile from loaded microparticles was presented. In this study, we report an innovative and green process for lysozyme encapsulation into PLGA microparticles. Thus, this process could be applied to the encapsulation of therapeutic proteins requiring protection and controlled release such as growth factors for regenerative medicine.

A spectroscopic investigation of the interaction between c-MYC DNA and tetrapyridinoporphyrazinatozinc(II).

The c-MYC gene plays an important role in the regulation of cell proliferation and growth and it is overexpressed in a wide variety of human cancers. Around 90% of c-MYC transcription is controlled by the nuclease-hypersensitive element III1 (NHE III1), whose 27-nt purine-rich strand has the ability to form a G-quadruplex structure under physiological conditions. Therefore, c-MYC DNA is an attractive target for drug design, especially for cancer chemotherapy. Here, the interaction of water-soluble tetrapyridinoporphyrazinatozinc(II) with 27-nt G-rich strand (G/c-MYC), its equimolar mixture with the complementary sequence (GC/c-MYC) and related C-rich oligonucleotide (C/c-MYC) is investigated. Circular dichroism (CD) measurements of the G-rich 27-mer oligonucleotide in 150 mM KCl, pH 7 demonstrate a spectral signature consistent with parallel G-quadruplex DNA. Furthermore, the CD spectrum of the GC rich oligonucleotide shows characteristics of both duplex and quadruplex structures. Absorption spectroscopy implies that the complex binding of G/c-MYC and GC/c-MYC is a two-step process; in the first step, a very small red shift and hypochromicity and in the second step, a large red shift and hyperchromicity are observed in the Q band. Emission spectra of zinc porphyrazine are quenched upon addition of three types of DNA. According to the results of spectroscopy, it can be concluded the dominant binding mode is probably, outside binding and end stacking.

Modification of lysine residues of horseradish peroxidase and its effect on stability and structure of the enzyme.

Biotechnology is consistently seeking improved enzyme stability. Enzymes have great properties, although their marginal stability limits their applications. Among the strategies for improving stability of the enzymes, chemical modification is a simple and effective technique. In the present study, chemical modification of horseradish peroxidase (HRP) was carried out with 2,3-dichloromaleic anhydride and 2,3-dimethylmaleic anhydride. HRP is an important heme-containing enzyme. It is widely applied in pharmacological, chemical, and medical industries. Here, thermal stability of HRP was investigated at different temperatures. In addition, the enzyme stability was evaluated in urea, DMSO, alkaline pH, and hydrogen peroxide solutions by spectroscopic techniques. Structural investigation indicated that the both anhydrides slightly decrease compactness of the enzyme structure. The results also indicated that 2,3-dichloromaleic anhydride increases thermal stability of the enzyme and its stability in urea and DMSO solutions, but 2,3-dimethylmaleic anhydride only stabilizes HRP in urea solution. Furthermore, the experiments implied that none of the modifiers are effective on the stability of HRP in extreme pH and oxidative condition. Catalytic efficiency and activation energy did not change remarkably following reaction of the enzyme with the both carboxylic anhydrides. Consequently, improvement in the stability of HRP depends on not only the type of modifier but also denaturing condition.