Novel antibody derivatives for proteome and high-content analysis

The understanding of cellular processes and their pathophysiological alterations requires comprehensive data on the abundance, distribution, modification, and interaction of all cellular components. On the one hand, artificially introduced fluorescent fusion proteins provide information about their distribution and dynamics in living cells but not about endogenous factors. On the other hand, antibodies can detect endogenous proteins, posttranslational modifications, and other cellular components but mostly in fixed and permeabilized cells. Here we highlight a new technology based on the antigen-binding domain of heavy-chain antibodies (V_HH) from Camelidae. These extremely stable V_HH domains can be produced in bacteria, coupled to matrices, and used for affinity purification and proteome studies. Alternatively, these V_HH domains can be fused with fluorescent proteins and expressed in living cells. These fluorescent antigen-binding proteins called “chromobodies” can be used to detect and trace proteins and other cellular components in vivo. Chromobodies can, in principle, detect any antigenic structure, including posttranslational modifications, and thereby dramatically expand the quality and quantity of information that can be gathered in high-content analysis. Depending on the epitope chosen, chromobodies can also be used to modulate protein function in living cells.     

Direct monitoring of the expression of the green fluorescent protein-extracellular signal-regulated kinase 2 fusion protein in transfected cells using capillary electrophoresis with laser-induced fluorescence detection

Proper subcellular localization of the extracellular signal-regulated kinases (ERKs) is important in regulating physiological functions such as proliferation and differentiation in the pheochromocytoma cell line (PC12 cells). Thus, a direct visualization method is necessary to observe ERK localization within the cell or in crude cellular extracts. In this paper, a determination method was established for the detection of ERK2 localization in PC12 cells using green fluorescent protein (GFP) and capillary electrophoresis with laser-induced fluorescence (LIF). GFP as a reporter or labeling tag for gene expression in biochemistry and cell biology was used for the detection of ERK2 localization in PC12 cells. PC12 cells were transfected with GFP-ERK2 plasmid construct that was inserted into a variant GFP gene (enhanced green fluorescent protein), and successfully expressed GFP-ERK2 fusion proteins. GFP-ERK2 fusion proteins were detected within 5 min by CE analysis using an uncoated fused-silica capillary with LIF. Optimum conditions for GFP-ERK2 fusion proteins detection were 100 mM 3-(cyclohexylamino)-1-propanesulfonic acid buffer containing 100 mM sodium dodecylsulfate, pH 11, running at 20 degrees C. This result offers new opportunity in screening for the determination of localization of intracellular components, protein-protein interactions and kinase activity within the cells.     

Stable Isotope Labeling Strategy for Protein–Ligand Binding Analysis in Multi-Component Protein Mixtures

Described here is a stable isotope labeling protocol that can be used with a chemical modification- and mass spectrometry-based protein–ligand binding assay for detecting and quantifying both the direct and indirect binding events that result from protein–ligand binding interactions. The protocol utilizes an H₂¹⁶O₂ and H₂¹⁸O₂ labeling strategy to evaluate the chemical denaturant dependence of methionine oxidation in proteins both in the presence and absence of a target ligand. The differential denaturant dependence to the oxidation reactions performed in the presence and absence of ligand provides a measure of the protein stability changes that occur as a result of direct interactions of proteins with the target ligand and/or as a result of indirect interactions involving other protein–ligand interactions that are either induced or disrupted by the ligand. The described protocol utilizes the ¹⁸O/¹⁶O ratio in the oxidized protein samples to quantify the ligand-induced protein stability changes. The ratio is determined using the isotopic distributions observed for the methionine-containing peptides used for protein identification in the LC-MS-based proteomics readout. The strategy is applied to a multi-component protein mixture in this proof-of-principle experiment, which was designed to evaluate the technique’s ability to detect and quantify the direct binding interaction between cyclosporin A and cyclophilin A and to detect the indirect binding interaction between cyclosporin A and calcineurin (i.e., the protein–protein interaction between cyclophilin A and calcineurin that is induced by cyclosporin A binding to cyclophilin A).     

Expression and Secretion of a CB4-1 scFv–GFP Fusion Protein by Fission Yeast

There is a rapidly growing demand for fluorescent single-chain Fv (scFv) antibody fragments for many applications. Yeasts have developed into attractive hosts for recombinant production of these functionalized proteins because they provide several advantages over prokaryotes and higher eukaryotes as expression systems, e.g., being capable of high-level secretion of heterologous proteins. In this study, we report Schizosaccharomyces pombe as a new host organism for secretory production of scFv-green fluorescent protein (GFP) fusions and compare it with previously described yeast expression systems. We cloned a plasmid for the expression and secretion of the anti-p24 (human immunodeficiency virus 1) CB4-1 scFv fused to GFP. After expression of the scFv–GFP fused to an N-terminal Cpy1 secretion signal sequence, fluorescence microscopy of living yeast cells indicated that the heterologous protein entered the secretory pathway. Western blot analysis of cell-free culture supernatants confirmed that the scFv–GFP was efficiently secreted with yields up to 5 mg/L. In addition, fluorescence measurements of culture supernatants demonstrated that the GFP moiety of the scFv–GFP protein is fully functional after secretion. Our data suggest that S. pombe has the potential for being used as alternative expression host in recombinant antibody fragment production by ensuring efficient protein processing and secretion.     

Reversible immobilization of proteins with streptavidin affinity tags on a surface plasmon resonance biosensor chip

Dissociation of biotin from streptavidin is very difficult due to their high binding affinity. The re-use of streptavidin-modified surfaces is therefore almost impossible, making devices containing them (e.g. surface plasmon resonance (SPR) sensor chips) expensive. This paper describes a new protocol for reversible and site-directed immobilization of proteins with streptavidin affinity tags on the streptavidin-coated SPR biosensor chip (SA chip). Two streptavidin affinity tags, nano-tag and streptavidin-binding peptide (SBP tag), were applied. They both can specifically interact with streptavidin but have weaker binding force compared to the biotin–streptavidin system, thus allowing association and dissociation under controlled conditions. The SA chip surface could be regenerated repeatedly without loss of activity by injection of 50 mM NaOH solution. The fusion construct of a SBP tag and a single-chain antibody to mature bovine prion protein (scFv-Z186-SBP) interacts with the SA chip, resulting in a single-chain-antibody-modified surface. The chip showed kinetic response to the prion antigen with equilibrium dissociation constant K _D≈4.01×10⁻⁷. All results indicated that the capture activity of the SA chip has no irreversible loss after repeated immobilization and regeneration cycles. The method should be of great benefit to various biosensors, biochips and immunoassay applications based on the streptavidin capture surface.     

Structure and thermodynamics of hydrocarbon liquids: Computer simulation based on rism theory

A system of Ornstein-Zernike integral equations is solved numerically to determine the heats of vaporization ΔH_V of liquid ethane, propane, and n-butane. It is shown that the calculations (the deformations of valence bonds and bond angles in the liquid-phase molecules are ignored) give rather accurate values of ΔH_V, which are in agreement with the corresponding experimental data. On the other hand, it is established that if there are intramolecular rotational degrees of freedom, ΔH_V depends on the angle of internal rotation ϕ. The function ΔH_V(ϕ) is minimum for trans-conformations (ϕ=0) and maximum for cis-conformations (ϕ=180°). Hence, intermolecular interactions stabilize compact (convolute) conformations. The energy of this effect is of the order of 1 kJ/mole. Tver State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 5, pp. 808–813, September–October, 1995. Translated by I. Izvekova     

Versatile and Efficient Site‐Specific Protein Functionalization by Tubulin Tyrosine Ligase

A novel chemoenzymatic approach for simple and fast site‐specific protein labeling is reported. Recombinant tubulin tyrosine ligase (TTL) was repurposed to attach various unnatural tyrosine derivatives as small bioorthogonal handles to proteins containing a short tubulin‐derived recognition sequence (Tub‐tag). This novel strategy enables a broad range of high‐yielding and fast chemoselective C‐terminal protein modifications on isolated proteins or in cell lysates for applications in biochemistry, cell biology, and beyond, as demonstrated by the site‐specific labeling of nanobodies, GFP, and ubiquitin.     

Oxidation with the “O2−H2O2—vanadium complex—pyrazine-2-carboxylic acid” reagent

The vanadium complex—pyrazine-2-carboxylic acid (PCA) system catalyzes oxidation of styrenes PhRC=CHR′ (R=H, Me; R′=H, Ph), or phenylacetylenes PhC=CR (R=H, Ph) with hydrogen peroxide in air to give aldehydes, ketones, and carboxylic acids. The reaction begins with H₂O₂ coordination to the vanadium ion followed by the formation of hydroxyl radicals. Catalytic action of PCA facilitates the reduction of the V^V complex to the V^IV complex and/or the stage of the formation of a peroxide derivative of vanadium.     

Developing Bright Green Fluorescent Protein (GFP)-like Fluorogens for Live-Cell Imaging with Nonpolar Protein−Chromophore Interactions

Fluorescence-activating proteins (FAPs) that bind a chromophore and activate its fluorescence have gained popularity in bioimaging. The fluorescence-activating and absorption-shifting tag (FAST) is a light-weight FAP that enables fast reversible fluorogen binding, thus advancing multiplex and super-resolution imaging. However, the rational design of FAST-specific fluorogens with large fluorescence enhancement (FE) remains challenging. Herein, a new fluorogen directly engineered from green fluorescent protein (GFP) chromophore by a unique double-donor-one-acceptor strategy, which exhibits an over 550-fold FE upon FAST binding and a high extinction coefficient of approximately 100,000 M⁻¹ cm⁻¹, is reported. Correlation analysis of the excited state nonradiative decay rates and environmental factors reveal that the large FE is caused by nonpolar protein−fluorogen interactions. Our deep insights into structure-function relationships could guide the rational design of bright fluorogens for live-cell imaging with extended spectral properties such as redder emissions.     

Isolation and Functional Characterization of Single Domain Antibody Modulators of Caspase-3 and Apoptosis

Apoptosis, or programmed cell death, is an essential process affecting homeostasis of cell growth, development, and the elimination of damaged or dangerous cells. Inappropriate cell death caused by oxidative stress has been implicated in the development of neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and stroke. On the other hand, a defect in the cell death process leads to the development of cancer. For example, the main player of apoptosis, p53, is defective in many of the human cancers. Apoptosis is regulated by the interplay of pro-apoptotic and anti-apoptotic proteins from the Bcl-2 family and caspases. In particular, specific modulators of the activity of Caspase 3 could be very important for the development of therapies for diseases such as neurodegeneration and cancer. In this study, two V_HHs specific to Caspase 3 (VhhCasp31 and VhhCasp32) were isolated from a heavy chain antibody variable domain (V_HH) phage display library and tested for their apoptosis-modulating effects. While VhhCasp31 was found to be antagonistic towards Caspase 3, VhhCasp32 was agonistic. Furthermore, when expressed as intrabodies in SHSY-5Y neuroblastoma cells, VhhCasp31 rendered cells resistant to oxidative-stress-induced apoptosis, whereas VhhCasp32 resulted in apoptosis. These V_HH antagonist and agonist of apoptosis could have potential for the development of therapeutics for neurodegenerative diseases and cancer, respectively.     

Synthesis, Crystal Structure, and IR Spectroscopic Characterization of 1,6-Hexanediammonium Dihydrogendecavanadate

 Anhydrous 1,6-hexanediammonium dihydrogendecavanadate ((HdaH₂)₂H₂V₁₀O₂₈, 1) was prepared by reaction of V₂O₅ with 1,6-hexanediamine in aqueous solution. The crystal structure of 1 was determined, and the proton positions in the H₂V₁₀O₂₈ ⁴⁻ anion were calculated by the bond length/bond number method. The protons are bound to the centrosymmetrically oriented μ–OV₃ groups of the decavanadate anion. Based on the analysis of IR spectra of 1 prepared from H₂O and D₂O, the absorption band at 871 cm⁻¹ can be attributed to δ(V–O_b–H) vibrations.     

Synthesis, Crystal Structure, and IR Spectroscopic Characterization of 1,6-Hexanediammonium Dihydrogendecavanadate

Summary.  Anhydrous 1,6-hexanediammonium dihydrogendecavanadate ((HdaH₂)₂H₂V₁₀O₂₈, 1) was prepared by reaction of V₂O₅ with 1,6-hexanediamine in aqueous solution. The crystal structure of 1 was determined, and the proton positions in the H₂V₁₀O₂₈ ⁴⁻ anion were calculated by the bond length/bond number method. The protons are bound to the centrosymmetrically oriented μ–OV₃ groups of the decavanadate anion. Based on the analysis of IR spectra of 1 prepared from H₂O and D₂O, the absorption band at 871 cm⁻¹ can be attributed to δ(V–O_b–H) vibrations. Received August 3, 2001. Accepted (revised) October 8, 2001     

Development of single-chain variable fragment (scFv) antibodies against hapten benzo[a]pyrene: a binding study

Due to its highly carcinogenic and mutagenic effect on humans, a maximum tolerable limit of 10 ng/L of benzo[a]pyrene (B[a]P) in drinking water was set by the European Commission (Council Directive 98/83/EC). Although several polyclonal and monoclonal antibodies (mAb) for the detection of B[a]P and other polycyclic aromatic hydrocarbons (PAH) have been developed by others, a traditional enzyme-linked immunosorbent assay (ELISA) with a limit of quantification of 10 ng/L for monitoring B[a]P has not been developed. With this in mind, several single-chain variable fragment (scFv) antibodies were created using existing mAbs against the extremely hydrophobic hapten B[a]P, and their heavy and light chains recombined to make unique variable light (V_L) and heavy (V_H) chain combinations. Their binding behaviour was investigated using microtiter plate ELISA and surface plasmon resonance techniques. Specifically, the coding sequences for V_L and V_H chains of 10 murine anti-B[a]P antibody producing hybridoma cell lines were isolated by degenerate oligonucleotide primer sets, cloned in phagemid pIT2 and transferred into Escherichia coli HB2151. To systematically investigate the interaction of the V_L and V_H domains, three high-affinity B[a]P-specific and one nonspecific clone were selected and recombined to build a set of 16 different V_L and V_H combinations. On the basis of our data, it was shown that the V_H plays the major role for specific binding of B[a]P, whilst the V_L can, in some cases, increase the final sensitivity of the assay by one order of magnitude. Furthermore, the sequence analysis of scFvs indicates that the complementarity determining region H3 plays a major role in affinity, whilst cross-reactivity to seven other PAHs demonstrates the importance of the V_L in providing cross-reactivity.     

Porous Covalent Organic Framework Based Hydrogen-Bond Nanotrap for the Precise Recognition and Separation of Gold

Utilizing weak interactions to effectively recover and separate precious metals in solution is of great importance but the practice remains a challenge. Herein, we report a novel strategy to achieve precise recognition and separation of gold by regulating the hydrogen-bond (H-bond) nanotrap within the pore of covalent organic frameworks (COFs). It is found that both COF-HNU25 and COF-HNU26 can efficiently capture Au^III with fast kinetics, high selectivity, and uptake capacity. In particular, the COF-HNU25 with the high density of H-bond nanotraps exhibits an excellent gold uptake capacity of 1725 mg g⁻¹, which is significantly higher than that (219 mg g⁻¹) of its isostructural COF (COF-42) without H-bond nanostrap in the pores. Importantly, the uptake capacity is strongly correlated to the number of H-bonds between phenolic OH in the COF and [AuCl₄]⁻ in water, and multiple H-bond interactions are the key driving force for the excellent gold recovery and reusability of the adsorbent.     

Crystallographic evidence for intramolecular C−H...O interactions in principal nucleosides. Refinement of the crystal structure of thymidine

An analysis of crystallographic data for the major nucleosides has shown that their molecules (except for guanosine) exhibit specific intramolecular C−H...O interactions, which are weak hydrogen bonds. In purine nucleosides these interactions are rare and rather weak. For pyrimidine nucleosides, in addition to the previously known intramolecular interaction C₆−H₆...O_5′, we have revealed the intramolecular interactions C_1′−H_1′...O₂ and C₆−H₆...O_1′. The three interactions make approximately equal contributions to the stabilization of the anti-conformation in pyrimidine nucleosides and make this conformation prevailing. To enhance the reliability of the results of studying the C−H...O interactions in thymidine, we performed an additional, more exact, X-ray diffraction analysis of the substance. Institute of Physiologically Active Substances, Russian Academy of Sciences, Chernogolovka. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 1, pp. 178–184, January–February, 1995. Translated by I. Izvekova     

Application of a green fluorescent fusion protein to study protein-protein interactions by electrophoretic methods

A screening procedure for protein-protein interactions in cellular extracts using a green fluorescent protein (GFP) and affinity capillary electrophoresis (ACE) was established. GFP was fused as a fluorescent indicator to the C-terminus of a cyclophilin (rDmCyp20) from Drosophila melanogaster. Cyclophilins (Cyps) belong to the ubiquitously distributed enzyme family of peptidyl-prolyl cis/trans isomerases (PPlases) and are well known as cellular targets of the immunosuppressive drug cyclosporin A (CsA). The PPlase activity of the GFP fused rDmCyp20 as well as the high affinity to CsA remain intact. Using native gel electrophoresis and ACE mobility-shift assays, it was demonstrated that the known moderate affinity of Cyp20 to the capsid protein p24 of HIV-1 was detectable in the case of rDmCyp20 fused to the fluorescent tag. For the p24 / rDmCyp20-GFP binding an ACE method was established which allowed to determine a dissociation constant of Kd = 20+/-1.5 x 10(-6) M. This result was verified by size-exclusion chromatography and is in good agreement with published data for the nonfused protein. Moreover the fusion protein was utilized to screen rDmCyp20-protein interactions by capillary electrophoresis in biological matrices. A putative ligand of rDmCyp20 in crude extracts of embryonic D. melanogaster was discovered by mobility-shift assays using native gel electrophoresis with fluorescence imaging and ACE with laser-induced fluorescence detection. The approach seems applicable to a wide range of proteins and offers new opportunities to screen for moderate protein-protein interactions in biological samples.     

The Inducible Intein-Mediated Self-Cleaving Tag (IIST) System: A Novel Purification and Amidation System for Peptides and Proteins

An efficient self-cleavable purification tag could be a powerful tool for purifying recombinant proteins and peptides without additional proteolytic processes using specific proteases. Thus, the intein-mediated self-cleavage tag was developed and has been commercially available as the IMPACT™ system. However, uncontrolled cleavages of the purification tag by the inteins in the IMPACT™ system have been reported, thereby reducing final yields. Therefore, controlling the protein-splicing activity of inteins has become critical. Here we utilized conditional protein splicing by salt conditions. We developed the inducible intein-mediated self-cleaving tag (IIST) system based on salt-inducible protein splicing of the MCM2 intein from the extremely halophilic archaeon, Halorhabdus utahensis and applied it to small peptides. Moreover, we described a method for the amidation using the same IIST system and demonstrated ¹⁵N-labeling of the C-terminal amide group of a single domain antibody (V_HH).     

D<Subscript>2</Subscript>O — H<Subscript>2</Subscript>O Solvent Isotope Effects on the Apparent Molar Volumes of Tetramethyl-<Emphasis Type="Italic">bis</Emphasis>-urea (Mebicarum) Solutions

Densities of solutions of tetramethyl-bis-urea (TMbU) or “Mebicarum” in H₂O and D₂O, with solute mole fraction concentrations (x ₂) ranging up to 3.2 × 10⁻³, have been measured at 288.15, 298.15, 308.15 and 318.15 K using a precision vibrating-tube densimeter. The limiting apparent molar volumes, V _φ,2 ^∞, and expansibilities, E _{p, φ, 2} ^∞, of the solute have been calculated. The isotope effect δ V _φ,2 ^∞(H₂O → D₂O;T) is negative, monotonously decreases in magnitude with temperature and reverses sign at T ≈ 318 K. Water (H₂O, D₂O) and TMbU molecules in infinitely- and highly-dilute aqueous solutions form H(D)-bonded hydration complexes with a high packing density. The hydration of TMbU should be treated as a superposition of two mechanisms, hydrophobic and hydrophilic, with the latter one predominating.     

Oxidative Addition of Dihydrogen to Divanadium in Solid Ne: Multiple‐Bonded Triplet HVVH and Singlet V2(μ‐H)2

Dinuclear compounds of early transition metals with a high metal–metal bond order are of fundamental interest due to their intriguing bonding situation and of practical interest because of their potential involvement in catalytic processes. In this work, two isomers of V₂H₂ have been generated in solid Ne by the reaction between V₂ and H₂ and detected by infrared spectroscopy: the linear HVVH molecule (³Σ_g^? ground state), which is the product of the spin‐allowed reaction between V₂ (³Σ_g^? ground state) and H₂, and a lower‐energy, folded V₂(μ‐H)₂ isomer (¹A₁ ground state) with two bridging hydrogen atoms. Both isomers are characterized by metal–metal bonding with a high bond order; the orbital occupations point to quadruple bonding. Irradiation with ultraviolet light induces the transformation of linear HVVH to folded V₂(μ‐H)₂, whereas irradiation with visible light initiates the reverse reaction.