Ni-nitrilotriacetic Acid Research Articles

A cell-penetrating NS5B-specific nanobody inhibits bovine viral diarrhea virus replication

Bovine viral diarrhea virus (BVDV) causes one of the significant devastating diseases for the cattle industry worldwide. The virus can cross the placenta and result in the persistent infection of the fetus, which has hampered the efficacy and the development of vaccines. Hence, efficient antiviral strategies are urgently needed. In our previous work, a specific nanobody Nb1 against nonstructural protein 5 (NS5B) was successfully isolated, and the replication of BVDV was significantly reduced in the MDBK cell line stably expressing Nb1. Nevertheless, the Nb1 protein itself cannot enter the cells autonomously, which has severely hampered the application of the Nb1. In this work, Nb1fuses with a trans-activating transduction (TAT) peptide to form the TAT-Nb1. The TAT-Nb1 was expressed in Escherichia coli, and then purified by Ni-nitrilotriacetic acid (Ni-NTA) resin. We showed that TAT successfully delivered Nb1 into the MDBK cells, and the TAT-Nb1 efficiently inhibited the replication of BVDV in a dose-and time-dependent manner. Furthermore, the recognition site of Nb1 to NS5B was identified as NS5Baa186-487 by the yeast two-hybrid assay. In summary, this study indicates that the TAT-Nb1 can potentially to be an antiviral drug against BVDV infection, and this research may accelerate the process of Nb1 for clinical use.

Combining the Benefits of Biotin-Streptavidin Aptamer Immobilization with the Versatility of Ni-NTA Regeneration Strategies for SPR.

The high affinity of the biotin-streptavidin interaction has made this non-covalent coupling an indispensable strategy for the immobilization and enrichment of biomolecular affinity reagents. However, the irreversible nature of the biotin-streptavidin bond renders surfaces functionalized using this strategy permanently modified and not amenable to regeneration strategies that could increase assay reusability and throughput. To increase the utility of biotinylated targets, we here introduce a method for reversibly immobilizing biotinylated thrombin-binding aptamers onto a Ni-nitrilotriacetic acid (Ni-NTA) sensor chip using 6xHis-tagged streptavidin as a regenerable capture ligand. This approach enabled the reproducible immobilization of aptamers and measurements of aptamer-protein interaction in a surface plasmon resonance assay. The immobilized aptamer surface was stable during five experiments over two days, despite the reversible attachment of 6xHis-streptavidin to the Ni-NTA surface. In addition, we demonstrate the reproducibility of this immobilization method and the affinity assays performed using it. Finally, we verify the specificity of the biotin tag-streptavidin interaction and assess the efficiency of a straightforward method to regenerate and reuse the surface. The method described here will allow researchers to leverage the versatility and stability of the biotin-streptavidin interaction while increasing throughput and improving assay efficiency.

A Step-by-Step Guide for the Production of Recombinant Fluorescent TAT-HA-Tagged Proteins and their Transduction into Mammalian Cells.

Investigating the function of target proteins for functional prospection or therapeutic applications typically requires the production and purification of recombinant proteins. The fusion of these proteins with tag peptides and fluorescently derived proteins allows the monitoring of candidate proteins using SDS-PAGE coupled with western blotting and fluorescent microscopy, respectively. However, protein engineering poses a significant challenge for many researchers. In this protocol, we describe step-by-step the engineering of a recombinant protein with various tags: TAT-HA (trans-activator of transduction-hemagglutinin), 6×His and EGFP (enhanced green fluorescent protein) or mCherry. Fusion proteins are produced in E. coli BL21(DE3) cells and purified by immobilized metal affinity chromatography (IMAC) using a Ni-nitrilotriacetic acid (NTA) column. Then, tagged recombinant proteins are introduced into cultured animal cells by using the penetrating peptide TAT-HA. Here, we present a thorough protocol providing a detailed guide encompassing every critical step from plasmid DNA molecular assembly to protein expression and subsequent purification and outlines the conditions necessary for protein transduction technology into animal cells in a comprehensive manner. We believe that this protocol will be a valuable resource for researchers seeking an exhaustive, step-by-step guide for the successful production and purification of recombinant proteins and their entry by transduction within living cells. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: DNA cloning, molecular assembly strategies, and protein production Basic Protocol 2: Protein purification Basic Protocol 3: Protein transduction in mammalian cells.

Effect of the Competing Ligand on Ni-NTA/Histag Strength Revealed by Click Chemistry-Based Force Spectroscopy.

The specific interaction between Ni-nitrilotriacetic acid and the six-histidine tag may be one of the most important coordination bonds utilized in biological research because of its wide application for recombinant protein purification. The complex stability is critical for target protein binding. Thus, measurement of the mechanical stability of the system was attempted soon after the invention of atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) two decades ago. Moreover, the competing ligand imidazole and protons are the two critical factors for target protein elution. However, the mechanochemistry between the system and the imidazole/proton has not been determined. Here, an AFM-SMFS system using strain-promoted alkyne-azide cycloaddition and Cu-free click chemistry was used to characterize the system. Consequently, the destabilizing effect of the imidazole and proton on the interaction was revealed quantitatively, leading to a 3-fold increase in the bond dissociation rate.

Expression and Enzyme Kinetics of Fused Plasmodium falciparum Orotate Phosphoribosyltransferase and Orotidine 5′-monophosphate Decarboxylase in Different Escherichia Coli

Background: Fusion of the last two enzymes in the pyrimidine biosynthetic pathway in the inverse order by having COOH-terminal orotate phosphoribosyltransferase (OPRT) and NH2-terminal orotidine 5′-monophosphate decarboxylase (OMPDC), as OPRT-OMPDC, has been described in many organisms. Objective: The study aimed to select the optimum host cell and temperature for expressing the recombinant fusion OMPDC-OPRT having the enzymatic activity. Methods: We constructed gene fusions of the human malaria parasite Plasmodium falciparum OMPDC-OPRT (1,836 bp) in the pTrcHisA vector and expressed it as a 6xHis-tag bifunctional protein in three Escherichia coli strains (BL21(DE3), TOP10, Rosetta) at 18°C and 25°C. The recombinant bifunctional protein was partially purified by Ni-nitrilotriacetic acid affinity chromatography and confirmed via Western blot and LC-MS/MS. The enzyme kinetics of OPRT and OMPDC was assessed. Results: Specific enzymatic activities of both OPRT and OMPDC domains expressed in E. coli BL21(DE3) cells were approximately eight-to-nine-fold higher than those in the TOP10 cells at 18°C. However, the specific activities of both domains expressed in the TOP10 cells were twice higher than those of the BL21(DE3) cells at 25°C. Very low and no enzymatic activities were observed when the constructed vector was expressed in the Rosetta cells at both induction temperatures. The bifunctional enzyme had specific activities of the OPRT and OMPDC domains in a ratio of 1:2. Kinetic study values of the OPRT domain in the bifunctional OMPDC-OPRT enzyme were found to be relatively low at µM level and at the perfect catalytic efficiency (kcat/Km). Conclusion: The recombinant fusion of OMPDC-OPRT exhibited a high expression level of E. coli BL21(DE3) at 18°C. The kinetic parameter is greater than 108M-1s-1.

Molecular cloning, and optimized production and characterization of recombinant cyclodextrin glucanotransferase from Bacillus sp. T1.

The online version contains supplementary material available at 10.1007/s13205-022-03111-8.

Duck Complement Factor H Binds to Outer Membrane Protein Omp24 of Riemerella anatipestifer.

The resistance to serum complement-mediated killing is a vital virulence property of microbial pathogens. Complement factor H (FH) is a key negative regulator of the complement alternative pathway (AP) that prevents formation and accelerates the decay of AP C3 convertase and acts as a cofactor in the inactivation of C3b. Pathogens can recruit host FH through their surface proteins to escape the clearance of the complement system. Riemerella anatipestifer could also evade the complement system attack to achieve host infection, but the mechanism is still unclear. In this study, the R. anatipestifer proteins that could interact with FH in host serum were screened and analyzed, and the functions were determined. Affinity chromatography with a Ni-nitrilotriacetic acid Sefinose column and mass spectrometry identified three outer membrane proteins (Omp) of R. anatipestifer, Omp54, Omp53, and Omp24, as potential FH-binding proteins. We then successfully conducted the prokaryotic expression and polyclonal antibody preparation of three candidate proteins. Indirect immunofluorescence assay showed that three candidate proteins were all present in R. anatipestifer. The affinity blotting assay, anti-serum-inhibiting assay, and serum bactericidal assay presented evidence that Omp24 could bind FH. Moreover, FH bound to Omp24 was associated with resistance to the alternative pathway and functional for R. anatipestifer survival in the normal duck serum. These results suggested that R. anatipestifer Omp24 was a FH-binding protein and the interaction with FH blocked the alternative pathway. Recruitment of complement regulatory proteins may facilitate better R. anatipestifer resistance to this vital line of host defense.

Enhanced Bioactivity of a Human GHR Antagonist Generated by Solid-Phase Site-Specific PEGylation.

Growth hormone (GH) has been implicated in cancer progression andis a potential target for anticancer therapy. Currently, pegvisomant is the only GH receptor (GHR) antagonist approved for clinical use. Pegvisomant is a mutated GH molecule (B2036) which is PEGylated on amine groups to extend serum half-life. However, PEGylation significantly reduces the bioactivity of the antagonist in mice. To improve bioactivity, we generated a series of B2036 conjugates with the site-specific attachment of 20, 30, or 40 kDa methoxyPEG maleimide (mPEG maleimide) by introduction of a cysteine residue at amino acid 144 (S144C). Recombinant B2036-S144C was expressed in Escherichia coli, purified, and then PEGylated using cysteine-specific conjugation chemistry. To avoid issues with dimerization due to the introduced cysteine, B2036-S144C was PEGylated while immobilized on an Ni-nitrilotriacetic (Ni-NTA) acid column, which effectively reduced disulfide-mediated dimer formation and allowed efficient conjugation to mPEG maleimide. Following PEGylation, the IC50 values for the 20, 30, and 40 kDa mPEG maleimide B2036-S144C conjugates were 66.2 ± 3.8, 106.1 ± 7.1, and 127.4 ± 3.6 nM, respectively. The circulating half-life of the 40 kDa mPEG conjugate was 58.3 h in mice. Subcutaneous administration of the 40 kDa mPEG conjugate (10 mg/kg/day) reduced serum insulin-like growth factor I (IGF-I) concentrations by 50.6%. This in vivo reduction in serum IGF-I was at a considerably lower dose compared to the higher doses required to observe comparable activity in studies with pegvisomant. In conclusion, we have generated a novel PEGylated GHR antagonist by the solid-phase site-specific attachment of mPEG maleimide at an introduced cysteine residue, which effectively reduces serum IGF-I in vivo.

Ni-Nitrilotriacetic Acid Affinity SELEX Method for Selection of DNA Aptamers Specific to the N-Cadherin Protein.

Nucleic acid aptamers are single-stranded oligonucleotides that may be evolved for affinity and specificity for their targets and can be easily produced, regenerated, and stabilized. In this study, we adapted Ni-NTA (nickle-charged nitrilotriacetic acid) affinity-chromatography in the development of single-stranded DNA aptamers against N-cadherin protein by systematic evolution of ligands by exponential enrichment (SELEX). After ten rounds of selection, two aptamers, designated NS13 and NC23, were selected, which showed low dissociation constants of 93 and 174 nM, respectively. The 5'-carboxyfluorescein-labeled NS13 was used for the sensitive detection of N-cadherin protein by the enzyme-linked oligonucleotide assay (ELONA) method.

Proteomics analysis of host cell proteins after immobilized metal affinity chromatography: Influence of ligand and metal ions

Different degrees of protein purity have been observed in immobilized metal affinity chromatography ranging from extremely high purity to moderate and low purity. It has been hypothesized that the host cell protein composition and the metal ligands are factors governing the purity of a protein obtained after immobilized metal affinity chromatography (IMAC). Ni nitrilotriacetic acid (NTA) has become the first choice for facile His-tagged protein purification, but alternative ligands such as iminodiacetic acid (IDA) with other immobilized metal ions such as Zn, Cu and Co are valuable options when the expected purity or binding capacity is not reached. Especially Cu and Zn are very attractive, due to their reduced environmental and safety concerns compared to Ni. Co and Zn are more selective than Ni and Cu. This increased selectivity comes at the cost of weaker binding. In this work, the influence of ligand choice on protein purity after IMAC was evaluated by several methods, including peptide mapping. His-tagged GFP was used as model protein. We found that host cell protein (HCP) content varies drastically between ligands, as IDA eluates generally showing higher HCP concentrations than NTA. The relative content of the key amino acids His, Cys and Trp in the sequence of the co-eluted protein does not suffice to explain co-eluting propensity. The co-elution of HCPs is mostly influenced by metal binding clusters on the protein surface and not by total content or surface concentration of metal interacting amino acids. Prediction of co-elution is not dependent on these clusters alone, due to protein-protein interactions, indicted by a relative low metal binding cluster score but high co-elution propensity and in a lot of cases these proteins are often part of complex such as ribosome and chaperones. The different co-eluting proteins were presented by a heatmap with a dendrogram. Ward's linkage method was used to calculate the distance between groups of co-eluting proteins. Clustering of co-eluting HCPs was observed according to ligand and by metal ions, with Zn and Co forming one cluster and Ni and Cu another. The co-elution of host cell proteins can be explained by clusters of metal interacting amino acids on the protein surface and by protein-protein interactions. While Ni NTA still appears to be highly advantageous, it might not be the cure-all for all applications.

Soluble expression and purification of high-bioactivity recombinant human bone morphogenetic protein-2 by codon optimisation in Escherichia coli.

We developed a simple method of preparing recombinant human bone morphogenetic protein-2 (rhBMP-2) with high biological activity. This rhBMP-2 was overproduced in Escherichia coli as a fusion protein with thioredoxin 6xHis-tag at its amino terminus. The cDNA fragment of human bone morphogenetic protein-2 (hBMP-2) fused to the secretion signal of alkaline phosphatase (PhoA) was expressed under T7 promoter in E. coli. After DNA sequence confirmation, the recombinant vector pETpho-bmp2 was transformed into E. coli BL21 (DE3). rhBMP-2 was produced by the recombinant strain pETpho-bmp2/BL21 (DE3) in a soluble form with an yield of 6.2mg/L culture. Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) results showed that the molecular weight of the product was approximately 28 kD. Moreover, rhBMP-2 was secreted as a dimer with a natural structure. rhBMP-2, purified by Ni Nitrilotriacetic acid Agarose (Ni-NTA) affinity chromatography, was used to examine osteosarcoma MG-63 cells and assay the alkaline phosphatase (ALP) activity. Results showed that rhBMP-2 induced MG-63 cell differentiation. When the final concentration was 500ng/mL, the effect was more remarkable and ALP activity reached 525% compared with that of the control group.

Covalent affixation of histidine-tagged proteins tethered onto Ni-nitrilotriacetic acid sensors for enhanced surface plasmon resonance detection of small molecule drugs and kinetic studies of antibody/antigen interactions.

The Ni2+-histidine (His) chelation yields a more uniform and predicable orientation of immobilized protein molecules than an amine-coupling reaction in surface plasmon resonance (SPR) analyses. However, the gradual dissociation of His-tagged proteins leads to a long and sloped baseline, which adversely affects kinetic studies. Furthermore, as shown in this work for the first time, the strong binding affinity between the histidine-rich Fc domain of immunoglobulin-type antibodies and Ni-nitrilotriacetic acid (NTA) interferes with the kinetic studies of these antibodies and their His-tagged antigens. By performing an amine-coupling reaction immediately after the Ni2+-His chelation, essentially all of the Ni2+-tethered protein molecules can be covalently linked to the carboxyl groups on the underlying carboxymethylated dextran surface. The sequential injections of pH 8.6 phosphate-buffered saline provided additional time to ensure a higher amine coupling efficiency and reverted NHS esters on the protein molecules to carboxyl groups. The application of our method to antibody/antigen interactions is demonstrated with the kinetic analysis of His-tagged t-DARPP protein/anti-t-DARPP interactions. In a separate experiment, the highly efficient immobilization method resulted in a higher immobilization density of His-tagged human carbonic anhydrase (HCA) II, affording accurate kinetic measurements for the binding of 4-carboxybenzenesulfonamide. In addition, the higher HCA II density enhanced the SPR sensitivity, allowing 4-carboxybenzenesulfonamide to be determined with a remarkable detection limit (14 nM).

Dual-Valve and Counter-Flow Surface Plasmon Resonance.

Two six-port injector valves and one selector valve commonly used in flow injection analysis are combined with a surface plasmon resonance (SPR) instrument wherein solutions introduced from the two inlets counter-flow inside the flow cell. The system is versatile as the same or different solutions can be rapidly and repeatedly introduced to the two fluidic channels in series or in parallel. Unlike most commercial SPR instruments employing a single injector valve, solutions separately injected from the two injector valves can be readily exchanged (<1 s) between the two channels. This new method, referred to as the alternate injection mode, not only saves analysis time but also facilitates efficient and facile surface reactions for ligand immobilization and prevents immobilized species from desorbing. These advantages are demonstrated with the measurements of binding of acetazolamide (222.2 Da) to histidine-tagged human carbonic anhydrase II (his-tagged HCA). Amine-containing residues of his-tagged HCA molecules tethered at Ni-nitrilotriacetic acid (NTA) sensors were rapidly cross-linked to the underlying carboxymethylated dextran. The higher ligand densities and more stable surfaces are essential for SPR detection of small molecule binding. In a different application, microglobulin solutions of increasing concentrations were introduced for continuous binding to the preimmobilized antibody. The kinetic and affinity measurements can be conducted without performing repeated dissociation and surface regeneration reactions.

Molecular characterization of Babesia microti seroreactive antigen 5-1-1 and development of rapid detection methods for anti-B. microti antibodies in serum

Babesiosis has become a new global threat impacting human health, and most human babesiosis cases are caused by Babesia microti. Until now few antigens of B. microti have been described which can be used for the diagnosis of human babesiosis. In the present study, we report on the bioinformatic analysis, cloning and expression of the sequence encoding the B. microti seroreactive antigen 5-1-1 to investigate its potential incorporation in serologic diagnostic tools for babesiosis. Bioinformatic analysis and recombinant gene expression were performed to molecularly characterize seroreactive antigen 5-1-1. Enhanced chemiluminescence (ECL)-Western blot methods were used to detect specific antibodies in infected mice. Immunofluorescence antibody assays (IFA) were performed to detect the localization of BmSA5-1-1 in B. microti parasites. ELISA and immunochromatographic (ICT) tests were developed using recombinant BmSA5-1-1 to evaluate its potential use in rapid detection methods for B. microti antibodies and for the diagnosis of babesiosis. A recombinant expression plasmid was constructed by inserting the target gene fragment in the pET28a vector after double digestion with BamHI and XhoI restriction enzymes. The recombinant BmSA5-1-1 protein was expressed in Escherichia coli (rBmSA5-1-1) and purified by means of Ni-nitrilotriacetic acid (NTA) agarose columns. Polyclonal antibodies were generated against rBmSA5-1-1. Based on indirect immunofluorescence assay results, BmSA5-1-1 appeared to localize on the surface of B. microti. ELISA tests using the rBmSA5-1-1 antigen detected specific antibodies from infected mice as early as 4 days post-infection. Our results indicate that the two methods we developed can detect specific antibodies in mice at different stages of infection with sensitivities of 100% (rBmSA5-1-1 ELISA) and 90% (ICT). The specificity of the two methods was 100%. Sera of patients suffering from other closely related parasitic diseases, such as malaria and toxoplasmosis, produced negative results. In conclusion, seroreactive antigen 5-1-1, a member of the BMN1 protein family, is expressed on the outer surface of B. microti and is a promising candidate antigen for the early diagnosis of babesiosis. rBmSA5-1-1 ELISA and ICT methods show good potential for detecting specific antibodies in mice at different stages of infection.

HMW1555-914, HMW2553-916, and Hia585-705 as Subunit Vaccine Candidates of Nontypeable Haemophilus influenzae Induce Specific Antibody Responses with Bactericidal Activity in Balb/c

Background: Nontypeable Haemophilus influenzae (NTHi) is responsible for diseases such as otitis media, sinusitis, bronchitis, and pneumonia. Unlike H. influenzae Serotype b (Hib), there is no vaccine against diseases induced by NTHi. High molecular weight1 (HMW1), high molecular weight 2 (HMW2), and H. influenzae type a (Hia) proteins are critical protein adhesions of NTHi with the potentiality to provide the protection. Objectives: The current study aimed at investigating the potential of recombinant HMW1555-914, HMW2553-916, and Hia585-705 proteins as subunit vaccines to induce immune responses after active immunization in Bagg albino (inbred research mouse strain) or Balb/c mice. Methods: HMW1555-914, HMW2553-916, and Hia585-705 amplified by polymerase chain reaction (PCR) were cloned into pET28a. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and the Western blotting analysis were carried out to investigate the characteristics of proteins. Proteins were purified by Ni-nitrilotriacetic acid (Ni-NTA) as a gel matrix. Mice (Balb/c) were immunized subcutaneously with HMW1555-914, HMW2553-916, and Hia585-705 proteins, alone or in binary and ternary combinations. Eventually, specific antibody responses were evaluated by the enzyme-linked immunosorbent assay (ELISA) and serum bactericidal assay (SBA). Results: Antibody responses significantly increased in Balb/c immunized by ternary combination compared with the control group. IgG1/IgG2a ratio indicated that proteins directed immune responses toward T-helper 2. Antisera produced against purified proteins in ternary combination showed the highest bactericidal activity against NTHi strains with the titer of 1:32. Conclusions: The obtained results suggested that HMW1555-914, HMW2553-916, and Hia585-705 adhesins were the potential subunit vaccine candidates of NTHi and after further investigation could be considered for protection against NTHi infections.

An efficient strategy for the expression of Jingzhaotoxin-III in Escherichia coli

ABSTRACTJingzhaotoxin-III (JZTX-III), a 36-residue peptide cardiotoxin containing three pairs of disulphide bonds, has been characterized from the venom of the Chinese tarantula Chilobrachys jingzhao. JZTX-III is a promising target for drug development and clinical application, due to its specific inhibitory effects on the human voltage-gated potassium channel subtype hKv2.1 and sodium channel subtype hNav1.5, which are mainly expressed in the cardiac myocytes. The most direct way to obtain JZTX-III is by extraction from the native venom of the tarantula jingzhao, but the amount is often insufficient to meet research and clinical demands. Therefore, there is need for an efficient expression system that can provide a larger quantity of JZTX-III. In this paper, we utilized a galactose auto-induction system to assist the Escherichia coli strain SHuffle T7 Express to express recombinant JZTX-III, followed by in situ purification on a Ni-nitrilotriacetic acid (Ni-NTA) column. Subsequent experiments were performed to demonstrate the advantages of the galactose auto-induction method and to optimize the incubation conditions. Under the optimal expression conditions, the product of the purified bioactive recombinant JZTX-III reached 12.1 mg/L. Furthermore, it is expected that this expression method can be widely applied to the heterologous expression of other disulphide-bond-rich peptides.

Cloning, expression and mutation of a triazophos hydrolase gene from Burkholderia sp. SZL-1.

Triazophos is a broad-spectrum and highly effective insecticide, and the residues of triazophos have been frequently detected in the environment. A triazophos-degrading bacterium, Burkholderia sp. SZL-1, was isolated from a long-term triazophos-polluted soil. Strain SZL-1 could hydrolyze triazophos to 1-phenyl-3-hydroxy-1,2,4-triazole, which was further utilized as the carbon sources for growth. The triazophos hydrolase gene trhA, cloned from strain SZL-1, was expressed and homogenously purified using Ni-nitrilotriacetic acid affinity chromatography. TrhA is 55 kDa and displays maximum activity at 25°C, pH 8.0. This enzyme still has nearly 60% activity at the range of 15°C-50°C for 30 min. TrhA was mutated by sequential error prone PCR and screened for improved activity for triazophos degradation. One purified variant protein (Val89-Gly89) named TrhA-M1 showed up to 3-fold improvement in specific activity against triazophos, and the specificity constants of Kcat and Kcat/Km for TrhA-M1 were improved up to 2.3- and 8.28-fold, respectively, compared to the wild-type enzyme. The results in this paper provided potential material for the contaminated soil remediation and hydrolase genetic structure research.

Biofunctionality of Calmodulin Immobilized on Gold Surface Studied by Surface-Enhanced Infrared Absorption Spectroscopy: Ca2+-Induced Conformational Change and Binding to a Target Peptide

Calcium ion (Ca2+)-induced functional expression of calmodulin (CaM), which is a signal transmitter in living cell, is known to be associated with its conformation change; however, it is difficult to correlate the conformational change and functional expression induced by Ca2+ reversibly as it is not easy to change the Ca2+ concentration while keeping the CaM concentration in solution. This can be done if CaM is immobilized on a solid surface while maintaining its function intact. Here CaM is immobilized on a self-assembled monolayer (SAM) of Ni-nitrilotriacetic acid (NTA) on a Au surface by histidine tag (His-tag) method. The conformational change of the immobilized CaM induced by the Ca2+ concentration change in solution was investigated using surface-enhanced infrared absorption spectroscopy (SEIRAS). The Ca2+-induced conformational change of CaM immobilized on the Au surface was followed by monitoring IR intensities at 1550 and 1645 cm–1, which originated from the Ca2+ binding site (EF hand) in CaM an...

Mechanistic Insights into Membrane Bending by Protein Crowding: Understanding the Role of Membrane Composition, Phase Separation and Free Energy of Protein Binding

Morphological changes in lipid membranes are hallmarks of a number of cellular processes like sorting, transport, etc. The dense crowding of the membrane environment with proteins and receptors has motivated many thorough academic investigations into the effects of macromolecular crowding on membrane surfaces. A number of recent studies have indicated that membrane reshaping could be driven by steric pressure between proteins co-localized on membrane domains. While these studies provide conclusive evidence for the membrane bending process, a detailed physical and mechanistic basis for this phenomenon is lacking. We provide a thermodynamic picture for this phenomenon through Isothermal Titration Calorimetry (ITC), Differential Scanning Calorimetry (DSC) and fluorescence microscopy using Ni-Nitrilotriacetic (NTA) acid and His-Tag interaction as a model system. Using ITC, we observe almost an order of magnitude increase in binding affinity for NTA-functionalized liposomes that display gel-fluid phase coexistence, as opposed to homogenous fluid compositions. This elevated affinity could be eliminated by thermal phase transition from gel-fluid to fluid, highlighting the importance of phase separation in modulating the strength of this binding interaction. DSC revealed that protein binding modulates the long-range lipid order substantially. In conjunction with the complicated nature of the binding isotherm, the DSC results indicate that the protein-binding event is coupled to a secondary exothermic process, presumably due to membrane deformation. Further ITC and fluorescence microscopy experiments reveal that the formation of membrane tubules upon protein binding is sensitive to membrane composition, phase separation and free energy of protein binding. Taken together with a predictive theoretical model that is currently under development, we believe that these results significantly advance our current understanding of the thermodynamics of membrane bending by protein crowding.

Characterization of a Novel Butachlor Biodegradation Pathway and Cloning of the Debutoxylase (Dbo) Gene Responsible for Debutoxylation of Butachlor in Bacillus sp. hys-1.

Bacillus sp. strain hys-1, which was isolated from active sludge, could degrade >90% butachlor at a concentration of 100 mg/L within 7 days. The present work revealed that strain hys-1 could mineralize butachlor via the following pathway: butachlor was initially metabolized to 2-chloro-N-(2,6-diethylphenyl)-N-methylacetamide by debutoxylation and then transformed to form 2-chloro-N-(2,6-diethylphenyl)acetamide by N-demethylation. Subsequently, it was converted to 2,6-diethylaniline and further mineralized into CO2 and H2O. In addition, the catalytic efficiency of crude cell extracts descended as follows: alachlor > acetochlor > butachlor. Furthermore, a novel 744 bp gene responsible for transforming butachlor into 2-chloro-N-(2,6-diethylphenyl)-N-methylacetamide was cloned from strain hys-1 and the encoding debutoxylase was designated Dbo. Then Dbo was expressed in Escherichia coli BL21 (DE3) and purified using Ni-nitrilotriacetic acid affinity chromatography. Dbo displayed the highest activity against butachlor at pH 6.5 and 30 °C. Metal ions played an important role in Dbo activity. To the best of the authors' knowledge, this is the first report that strain hys-1 can mineralize butachlor by a novel metabolic mechanism and the first identification of a gene encoding butachlor debutoxylase.