Estimation of the molecular weights of proteins by Sephadex gel-filtration

Recombinant production, purification, and biochemical characterization of a novel L-lactate dehydrogenase from Bacillus cereus NRC1 and inhibition study of mangiferin

Lactate dehydrogenase (LDH, EC 1.1.1.27) is one of the vital glycolytic conditions, especially during anaerobic conditions. It is a significant diagnostic, prognostic, and monitoring biomarker parameter. A 950-bp DNA fragment containing the gene (LDH) encoding LDH was amplified from Bacillus cereus NRC1. The deduced amino acid sequence reveals that B. cereus LDH (Bc-LDH) is highly homologous to the LDHs of Bacillus organisms. All LDH enzymes have a significant degree of conservation in their active site and several additional domains with unidentified functions. The gene for LDH, which catalyzes lactate synthesis, was cloned, sequenced (accession number: LC706200.1), and expressed in Escherichia coli BL21 (DE3). In this investigation, Bc-LDH was purified to homogeneity with a specific activity of 22.7 units/mg protein and a molecular weight of 35 kDa. It works optimally at pH 8.0. The purified enzyme was inhibited by FeCl2, CuCl2, ZnCl2, and NiCl, whereas CoCl2 was found to boost the activity of Bc-LDH. The molecular docking of the 3D model of the Bc-LDH structure with a natural inhibitor, mangiferin, demonstrated excellent LDH inhibition, with a free binding energy of −10.2 kcal/mol. Moreover, mangiferin is a potent Bc-LDH inhibitor that inhibits Bc-LDH competitively and has one binding site with a Ki value of 0.075 mM. The LDH-mangiferin interaction exhibits a low RMSF value (>1.5 Å), indicating a stable contact at the residues. This study will pave the way for more studies to improve the understanding of mangiferin, which could be considered an intriguing candidate for creating novel and improved LDH inhibitors.

Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors

G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.

Barley Nepenthesin-Like Aspartic Protease HvNEP-1 Degrades Fusarium Phytase, Impairs Toxin Production, and Suppresses the Fungal Growth

Nepenthesins are categorized under the subfamily of the nepenthesin-like plant aspartic proteases (PAPs) that form a distinct group of atypical PAPs. This study describes the effect of nepenthesin 1 (HvNEP-1) protease from barley (Hordeum vulgare L.) on fungal histidine acid phosphatase (HAP) phytase activity. Signal peptide lacking HvNEP-1 was expressed in Pichia pastoris and biochemically characterized. Recombinant HvNEP-1 (rHvNEP-1) strongly inhibited the activity of Aspergillus and Fusarium phytases, which are enzymes that release inorganic phosphorous from phytic acid. Moreover, rHvNEP-1 suppressed in vitro fungal growth and strongly reduced the production of mycotoxin, 15-acetyldeoxynivalenol (15-ADON), from Fusarium graminearum. The quantitative PCR analysis of trichothecene biosynthesis genes (TRI) confirmed that rHvNEP-1 strongly repressed the expression of TRI4, TRI5, TRI6, and TRI12 in F. graminearum. The co-incubation of rHvNEP-1 with recombinant F. graminearum (rFgPHY1) and Fusarium culmorum (FcPHY1) phytases induced substantial degradation of both Fusarium phytases, indicating that HvNEP-1-mediated proteolysis of the fungal phytases contributes to the HvNEP-1-based suppression of Fusarium.

Topological Sieving of Rings According to Their Rigidity

We present a novel mechanism for resolving the mechanical rigidity of nanoscopic circular polymers that flow in a complex environment. The emergence of a regime of negative differential mobility induced by topological interactions between the rings and the substrate is the key mechanism for selective sieving of circular polymers with distinct flexibilities. A simple model accurately describes the sieving process observed in molecular dynamics simulations and yields experimentally verifiable analytical predictions, which can be used as a reference guide for improving filtration procedures of circular filaments. The topological sieving mechanism we propose ought to be relevant also in probing the microscopic details of complex substrates.

Effect of Sterilization Process and Storage on the Antioxidative Properties of Runner Bean

In this study, we investigated the effect of standard preservation of bean seeds on changes in contents and activity of their selected components: dry matter, ash, different forms of nitrogen, composition of protein fractions; total phenolics and condensed tannins; ability to chelate iron(II) ions; antiradical activity against ABTS•+ and DPPH•; and capability for inhibiting autoxidation and enzymatic oxidation of linoleic acid. The conducted technological process caused various changes in contents of nitrogen forms and partial loss of phenolic compounds. The antiradical and antioxidative activity of the extracts decreased significantly, while an increase was observed in their ability to chelate Fe(II). These changes were due to the migration of active compounds to the brine, and to their structural transformations and degradation. Longer storage of the sterilized product caused restoration of part of the antiradical activity of the seeds.

A brief practical review of size exclusion chromatography: Rules of thumb, limitations, and troubleshooting

Through years of research, teaching, troubleshooting, and editing, I have developed a solid working understanding of many aspects of protein purification and protein biochemistry. I have also found that many researchers do not understand the basics, let alone the pitfalls, of the techniques they use. In the case of size exclusion chromatography (SEC), I summarize below some of the rules of thumb, suggestions, limitations and troubleshooting I have found most useful in helping my students and colleagues carry out successful SEC.

Vicilin-A major storage protein of mungbean exhibits antioxidative potential, antiproliferative effects and ACE inhibitory activity

Enzymatic hydrolysates of different food proteins demonstrate health benefits. Search for diet related food protein hydrolysates is therefore of interest within the scope of functional foods. Mungbean is one of the popular foods in India because of rich protein source. In this study, mungbean vicilin protein (MBVP) was enzymatically hydrolysed by alcalase and trypsin under optimal conditions. We have studied the antioxidant, antiproliferative and angiotensin-converting enzyme (ACE) inhibitory activities of mungbean vicilin protein hydrolysate (MBVPH) vis-a-vis alcalase-generated mungbean vicilin protein hydrolysate (AMBVPH) and trypsin-generated mungbean vicilin protein hydrolysate (TMBVPH). The results showed that MBVPH exhibited higher antioxidant potential, ACE inhibitory and antiproliferative activities than MBVP. The alcalase treated hydrolysate displayed highest ACE inhibitory activity with IC50 value of 0.32 mg protein/ml. The MBVP showed significant antiproliferative activity against both MCF-7 and MDA-MB-231 breast cancer cells at the doses between 0.2-1.0 mg/ml. The data suggested that MBVPH can be utilized as physiologically active functional foods with sufficient antihypertensive activity. The results indicate that mungbean can be utilized as a rich resource of functional foods.

In vivo fluorescence bioimaging of ascorbic acid in mice: Development of an efficient probe consisting of phthalocyanine, TEMPO, and albumin

After a groundbreaking study demonstrated that a high dose of ascorbic acid selectively kills cancer cells, the compound has been tested in the clinic against various forms of cancers, with some success. However, in vivo tracing of intravenously injected ascorbic acid has not been achieved. Herein, we successfully imaged ascorbic acid intravenously injected into mice based on the discovery of a novel, highly sensitive, and appropriately selective fluorescent probe consisting of silicon phthalocyanine (SiPc) and two 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) radicals, i.e., R2c. The radicals in this R2c were encapsulated in dimeric bovine serum albumin, and the sensitivity was >100-fold higher than those of other R2c-based probes. Ascorbic acid intravenously injected into mice was efficiently transported to the liver, heart, lung, and cholecyst. The present results provide opportunities to advance the use of ascorbic acid as cancer therapy.

Purification and characterization of a novel tannase produced by Kluyveromyces marxianus using olive pomace as solid support, and its promising role in gallic acid production

Tannase is considered one of the most important industrial enzymes that find great applications in various sectors. Production of tannases through solid state fermentation (SSF) using agro-industrial wastes is an eco-friendly and cheap technology. Tannase was produced by the yeast Kluyveromyces marxianus using olive pomace as a solid support under SSF. It was purified using ammonium sulfate fractional precipitation followed by Sephadex G-200 gel filtration resulting in 64.6% enzyme yield with 1026.12U/mg specific activity and 24.21 purification fold. Pure tannase had molecular weight of 65 KDa and 66.62 KDa by SDS-PAGE and gel filtration, respectively. It showed a maximal activity at 35°C having two different pH optima, one of which is acidic (4.5) and the other one is alkaline (8.5). The enzyme was stable in the acidic range of pH (4.0-5.5) for 30min, and thermostable within the temperature range 30-70°C. Using tannic acid, the enzyme had a Km value of 0.77mM and Vmax of 263.20μmolemin^-1ml^-1. The effect of different metal ions on enzymatic activity was evaluated. HPLC analysis data indicated that the purified enzyme could carry out 24.65% tannic acid conversion with 5.25 folds increase in gallic acid concentration within 30min only.

Binding of NAD+-Glycohydrolase to Streptolysin O Stabilizes Both Toxins and Promotes Virulence of Group A Streptococcus

The globally dominant, invasive M1T1 strain of group A Streptococcus (GAS) harbors polymorphisms in the promoter region of an operon that contains the genes encoding streptolysin O (SLO) and NAD⁺-glycohydrolase (NADase), resulting in high-level expression of these toxins. While both toxins have been shown experimentally to contribute to pathogenesis, many GAS isolates lack detectable NADase activity. DNA sequencing of such strains has revealed that reduced or absent enzymatic activity can be associated with a variety of point mutations in nga, the gene encoding NADase; a commonly observed polymorphism associated with near-complete abrogation of activity is a substitution of aspartic acid for glycine at position 330 (G330D). However, nga has not been observed to contain early termination codons or mutations that would result in a truncated protein, even when the gene product contains missense mutations that abrogate enzymatic activity. It has been suggested that NADase that lacks NAD-glycohydrolase activity retains an as-yet-unidentified inherent cytotoxicity to mammalian cells and thus is still a potent virulence factor. We now show that expression of NADase, either enzymatically active or inactive, augments SLO-mediated toxicity for keratinocytes. In culture supernatants, SLO and NADase are mutually interdependent for protein stability. We demonstrate that the two proteins interact in solution and that both the translocation domain and catalytic domain of NADase are required for maximal binding between the two toxins. We conclude that binding of NADase to SLO stabilizes both toxins, thereby enhancing GAS virulence.

The global increase in invasive GAS infections in the 1980s was associated with the emergence of an M1T1 clone that harbors a 36-kb pathogenicity island, which codes for increased expression of toxins SLO and NADase. Polymorphisms in NADase that render it catalytically inactive can be detected in clinical isolates, including invasive strains. However, such isolates continue to produce full-length NADase. The rationale for this observation is not completely understood. This study characterizes the binding interaction between NADase and SLO and reports that the expression of each toxin is crucial for maximal expression and stability of the other. By this mechanism, the presence of both toxins increases toxicity to keratinocytes and is predicted to enhance GAS survival in the human host. These observations provide an explanation for conservation of full-length NADase expression even when it lacks enzymatic activity and suggest a critical role for binding of NADase to SLO in GAS pathogenesis.

Characterization of a novel allergenic protein from the octocoral Scleronephthya gracillima (Kuekenthal) that corresponds to a new GFP-like family named Akane

Certain marine organisms have been known to cause allergic reactions among occupational fishermen. We have previously reported that bronchial asthma among the workers engaged in spiny lobster fishing in Japan was caused by octocorals such as Dendronephthya sp. and Scleronephthya gracillima (previously named Alcyonium gracillimum). Now we have found another octocoral, Scleronephthya gracillima (Kuekenthal), which causes the allergic disease in fishermen. The octocoral was characterized as a new green fluorescent protein (GFP)-like family. The new allergen has a molecular mass of 27 kDa in 1D and 2D SDS-PAGE under reduced conditions. The 27 kDa component was determined to be an allergen by western blotting, ECL immune staining method and absorption of patient sera with the antigen. Furthermore, the combination of analysis with LC-ESI-MS/MS and MASCOT search in the NCBInr database concluded the 27 kDa component had the sequence YPADI/LPDYFK, and that the 22 kDa component had the sequence QSFPEGFSWER, which both matched a GFP-like protein in Acropora aculeus and in Montastraea annularis. Further analysis by MALDI-TOF/MS/MS and MASCOT search in the NCBInr database of all 27 kDa eight spot components from 2D SDS-PAGE indicated that the sequence QSFPEGFSWER also matched as GFP-like protein in Lobophyllia hemprichii and Scleractinia sp. To our knowledge, this is the first report of the new allergenic protein that corresponds to a new GFP-like protein named Akane, and which has fluorescent emissions in the red and green part of the spectra at 628 nm and 508 nm, respectively.

Study of Different Variants of Mo Enzyme crARC and the Interaction with Its Partners crCytb5-R and crCytb5-1

The mARC (mitochondrial Amidoxime Reducing Component) proteins are recently discovered molybdenum (Mo) Cofactor containing enzymes. They are involved in the reduction of several N-hydroxylated compounds (NHC) and nitrite. Some NHC are prodrugs containing an amidoxime structure or mutagens such as 6-hydroxylaminopurine (HAP). We have studied this protein in the green alga Chlamydomonas reinhardtii (crARC). Interestingly, all the ARC proteins need the reducing power supplied by other proteins. It is known that crARC requires a cytochrome b₅ (crCytb5-1) and a cytochrome b₅ reductase (crCytb5-R) that form an electron transport chain from NADH to the substrates. Here, we have investigated NHC reduction by crARC, the interaction with its partners and the function of important conserved amino acids. Interactions among crARC, crCytb5-1 and crCytb5-R have been studied by size-exclusion chromatography. A protein complex between crARC, crCytb5-1 and crCytb5-R was identified. Twelve conserved crARC amino acids have been substituted by alanine by in vitro mutagenesis. We have determined that the amino acids D182, F210 and R276 are essential for NHC reduction activity, R276 is important and F210 is critical for the Mo Cofactor chelation. Finally, the crARC C-termini were shown to be involved in protein aggregation or oligomerization.

Oligomeric state of hypoxanthine-guanine phosphoribosyltransferase from Mycobacterium tuberculosis

Sedimentation equilibrium and size-exclusion chromatography experiments on Mycobacterium tuberculosis hypoxanthine-guanine phosphoribosyltransferase (MtHGPRT) have established the existence of this enzyme as a reversibly associating mixture of dimeric and tetrameric species in 0.1 M Tris-HCl-0.012 M MgCl₂, pH 7.4. Displacement of the equilibrium position towards the larger oligomer by phosphate signifies the probable existence of MtHGPRT as a tetramer in the biological environment. These data thus add credibility to the relevance of considering enzyme function in the light of a published tetrameric structure deduced from X-ray crystallography. Failure of 5-phospho-α-d-ribosyl-1-pyrophosphate (PRib-PP) to perturb the dimer-tetramer equilibrium position indicates the equivalence and independence of binding for this substrate (the first to bind in an ordered sequential mechanism) to the two oligomers. By virtue of the displacement of the equilibrium position towards dimer that is affected by removing MgCl₂ from the Tris-HCl buffer, it can be concluded that divalent metal ions, as well as phosphate, can affect the oligomerization. These characteristics of MtHGPRT in solution are correlated with published crystal structures of four enzyme-ligand complexes.

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods

The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes.

Physico-chemical and in-silico analysis of a phytocystatin purified from Brassica juncea cultivar RoAgro 5444

This study describes the isolation and purification of a phytocystatin from seeds of Brassica juncea (Indian mustard; cultivar RoAgro 5444), which is an important oilseed crop both agriculturally and economically. The protein was purified by gel filtration chromatography with 24.3% yield and 204-fold purification, and visualised by 2D gel electrophoresis. The 18.1 kDa mustard cystatin was highly specific for cysteine proteinases. The plant cystatin inhibited cathepsin B, confirming its role in conferring pest resistance. The inhibitor was highly stable over a pH range of 3-10 and retained significant inhibitory potential up to 70 °C. The stoichiometry of its interaction with papain, determined by isothermal calorimetry, suggests a 1:1 complex. Secondary structural elements calculated by far-UV circular dichroism (CD) spectroscopy show an 18.8% α-helical and 21% β-sheet structure. The protein was a non-competitive inhibitor of thiol proteinases. The Stokes radius and frictional co-efficient were used to describe the shape and size of the protein. Homology modelling and docking studies proposed a prototype illustrating the Brassica phytocystatin mediated papain inhibition. Molecular dynamics (MD) study revealed the excellent stability of the papain-phytocystatin complex during a simulation for 100 ns. Detailed results identify the mustard cystatin as an important member of the phytocystatin family.

Characterization of Quinohemoprotein Amine Dehydrogenase from Pseudomonas putida

Quinohemoprotein amine dehydrogenase (AMDH) was purified and crystallized from the soluble fraction of Pseudomonas putida IFO 15366 grown on n-butylamine medium. AMDH gave a single component in analytical ultracentrifugation showing an intrinsic sedimentation coefficient of 5.8s. AMDH showed a typical absorption spectrum of cytochrome c showing maxima at 554, 522, 420, and 320 nm in the reduced form and one peak at 410 nm, a shoulder at 350 nm, and a broad hill around 530 nm in the oxidized form. The oxidized enzyme was specifically reduced by the addition of amine substrate. AMDH was composed of three different subunits, 60, 40, and 20 kDa, with the total molecular weight of 120,000. Two moles of heme c were detected per mole of AMDH and the 60-kDa subunit was found to be the heme c-carrying subunit. By redox-cycling quinone staining, a positive reaction band corresponding to the 20-kDa subunit was detected after developed by SDS-PAGE, but the 20 kDa band was scarcely stained by conventional protein staining. Only a silver staining method was possible to detect the subunit after the protein was developed by SDS-PAGE. p-Nitrophenylhydrazine-inhibited AMDH was dissociated into subunits and the 20-kDa subunit showed an absorption maximum at 455 nm, indicating Schiff base formation between the carbonyl cofactor in AMDH and the carbonyl reagent. Thus, AMDH is different from nonheme quinoprotein methylamine dehydrogenase and aromatic amine dehydrogenase in many respects. The presence of an azurin-like blue protein was identified and purified from the same cell-free extract of P. putida as AMDH was purified. The blue protein was reduced specifically during AMDH reaction, suggesting that the blue protein is the direct electron acceptor in amine oxidation. The amine oxidation system was reconstituted successfully only by AMDH, the blue protein, and the cytoplasmic membranes of the organism. The function of the 40-kDa subunit is unknown at the moment. The properties of AMDH were compared with other bacterial amine dehydrogenases so far reported.

Recombinant expression of a functional myo-inositol-1-phosphate synthase (MIPS) in Mycobacterium smegmatis

Myo-inositol-1-phosphate synthase (MIPS, E.C. 5.5.1.4) catalyzes the first step in inositol production-the conversion of glucose-6-phosphate (Glc-6P) to myo-inositol-1-phosphate. While the three dimensional structure of MIPS from Mycobacterium tuberculosis has been solved, biochemical studies examining the in vitro activity have not been reported to date. Herein we report the in vitro activity of mycobacterial MIPS expressed in E. coli and Mycobacterium smegmatis. Recombinant expression in E. coli yields a soluble protein capable of binding the NAD(+) cofactor; however, it has no significant activity with the Glc-6P substrate. In contrast, recombinant expression in M. smegmatis mc(2)4517 yields a functionally active protein. Examination of structural data suggests that MtMIPS expressed in E. coli adopts a fold that is missing a key helix containing two critical (conserved) Lys side chains, which likely explains the inability of the E. coli expressed protein to bind and turnover the Glc-6P substrate. Recombinant expression in M. smegmatis may yield a protein that adopts a fold in which this key helix is formed enabling proper positioning of important side chains, thereby allowing for Glc-6P substrate binding and turnover. Detailed mechanistic studies may be feasible following optimization of the recombinant MIPS expression protocol in M. smegmatis.

A preliminary study on the antibacterial mechanism of Tegillarca granosa hemoglobin by derived peptides and peroxidase activity

The blood clam, Tegillarca granosa, is one of the few bivalve molluscs containing hemoglobin (Hb). In the present study, we purified two types of T. granosa hemoglobin, Tg-HbI and Tg-HbII, using size exclusion chromatography and measured their antibacterial and peroxidase activities. We also tested antibacterial activities of peptides prepared by trypsin digestion of purified Tg-Hb and reversed-phase high-performance liquid chromatography purification. Purified Tg-HbI and Tg-HbII showed antibacterial activity against Escherichia coli, Pseudomonas putida, Bacillus subtilis, and Bacillus firmus, with differences in minimal inhibitory concentrations (MICs), but lacked antibacterial activity against Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi and Staphylococcus aureus. In contrast, 7 Tg-Hb derived peptides exhibited varying degrees of antibacterial activity against V. alginolyticus (MICs: 12-200 μg/ml), V. parahaemolyticus (11-100 μg/ml) and V. harveyi (1-200 μg/ml). The antibacterial activity of Hb derived peptides was confirmed by fluorescence microscopy. In addition, peroxidase activity was detected in Tg-HbI and Tg-HbII. The results indicated that in addition to functioning as a respiratory protein T. granosa hemoglobins likely play a role in host antibacterial defense probably via a peroxidase activity of native molecules and some internal peptides released from the proteins.

Purification and biochemical characterization of phytocystatin from Brassica alba

Phytocystatins belong to the family of cysteine proteinases inhibitors. They are ubiquitously found in plants and carry out various significant physiological functions. These plant derived inhibitors are gaining wide consideration as potential candidate in engineering transgenic crops and in drug designing. Hence it is crucial to identify these inhibitors from various plant sources. In the present study a phytocystatin has been isolated and purified by a simple two-step procedure using ammonium sulfate saturation and gel filtration chromatography on Sephacryl S-100HR from Brassica alba seeds (yellow mustard seeds).The protein was purified to homogeneity with 60.3% yield and 180-fold of purification. The molecular mass of the mustard seed cystatin was estimated to be nearly 26,000 Da by sodium dodecyl sulfate polyacrylamide gel electrophoresis as well as by gel filtration chromatography. The stokes radius and diffusion coefficient of the mustard cystatin were found to be 23A° and 9.4 × 10(-7)  cm(2) s(-1) respectively. The isolated phytocystatin was found to be stable in the pH range of 6-8 and is thermostable up to 60 °C. Kinetic analysis revealed that the phytocystatin exhibited non-competitive type of inhibition and inhibited papain more efficiently (K(i)  = 3 × 10(-7)  M) than ficin (K(i)  = 6.6 × 10(-7)  M) and bromelain (K(i) = 7.7 × 10(-7)  M respectively). CD spectral analysis shows that it possesses 17.11% alpha helical content.

From the traditional way of pyrolysis to tunable photoluminescent water soluble carbon nano-onions for cell imaging and selective sensing of glucose

Water soluble photoluminescent carbon nano-onions were synthesized from vegetable ghee using traditional pyrolytic approach for imaging cells and selective-immediate detection of glucose via fluorescent “turn-off”/“turn-on” technique.

Evaluating the role of a trypsin inhibitor from soap nut (Sapindus trifoliatus L. Var. Emarginatus) seeds against larval gut proteases, its purification and characterization

BACKGROUND

The defensive capacities of plant protease Inhibitors (PI) rely on inhibition of proteases in insect guts or those secreted by microorganisms; and also prevent uncontrolled proteolysis and offer protection against proteolytic enzymes of pathogens.

METHODS

An array of chromatographic techniques were employed for purification, homogeneity was assessed by electrophoresis. Specificity, Ki value, nature of inhibition, complex formation was carried out by standard protocols. Action of SNTI on insect gut proteases was computationally evaluated by modeling the proteins by threading and docking studies by piper using Schrodinger tools.

RESULTS

We have isolated and purified Soap Nut Trypsin Inhibitor (SNTI) by acetone fractionation, ammonium sulphate precipitation, ion exchange and gel permeation chromatography. The purified inhibitor was homogeneous by both gel filtration and polyacrylamide gel electrophoresis (PAGE). SNTI exhibited a molecular weight of 29 kDa on SDS-PAGE, gel filtration and was negative to Periodic Acid Schiff's stain. SNTI inhibited trypsin and pronase of serine class. SNTI demonstrated non-competitive inhibition with a Ki value of 0.75 ± 0.05×10-10 M. The monoheaded inhibitor formed a stable complex in 1:1 molar ratio. Action of SNTI was computationally evaluated on larval gut proteases from Helicoverpa armigera and Spodoptera frugiperda. SNTI and larval gut proteases were modeled and docked using Schrodinger software. Docking studies revealed strong hydrogen bond interactions between Lys10 and Pro71, Lys299 and Met80 and Van Der Waals interactions between Leu11 and Cys76amino acid residues of SNTI and protease from H. Armigera. Strong hydrogen bonds were observed between SNTI and protease of S. frugiperda at positions Thr79 and Arg80, Asp90 and Gly73, Asp2 and Gly160 respectively.

CONCLUSION

We conclude that SNTI potentially inhibits larval gut proteases of insects and the kinetics exhibited by the protease inhibitor further substantiates its efficacy against serine proteases.

Toward structurally defined carbon dots as ultracompact fluorescent probes

There has been much discussion on the need to develop fluorescent quantum dots (QDs) as ultracompact probes, with overall size profiles comparable to those of the genetically encoded fluorescent tags. In the use of conventional semiconductor QDs for such a purpose, the beautifully displayed dependence of fluorescence color on the particle diameter becomes a limitation. More recently, carbon dots have emerged as a new platform of QD-like fluorescent nanomaterials. The optical absorption and fluorescence emissions in carbon dots are not bandgap in origin, different from those in conventional semiconductor QDs. The absence of any theoretically defined fluorescence color-dot size relationships in carbon dots may actually be exploited as a unique advantage in the size reduction toward having carbon dots serve as ultracompact QD-like fluorescence probes. Here we report on carbon dots of less than 5 nm in the overall dot diameter with the use of 2,2'-(ethylenedioxy)bis(ethylamine) (EDA) molecules for the carbon particle surface passivation. The EDA-carbon dots were found to be brightly fluorescent, especially over the spectral range of green fluorescent protein. These aqueous soluble smaller carbon dots also enabled more quantitative characterizations, including the use of solution-phase NMR techniques, and the results suggested that the dot structures were relatively simple and better-defined. The potential for these smaller carbon dots to serve as fluorescence probes of overall sizes comparable to those of fluorescent proteins is discussed.