Site-specific Covalent Attachment Research Articles

Live-Cell Mitochondrial Targeted NIR Fluorescent Covalent Labeling of Specific Proteins Using a Dual Localization Effect.

Here, our designed water-soluble NIR fluorescent unsymmetrical Cy-5-Mal/TPP+ consists of a lipophilic cationic TPP+ subunit that can selectively target and accumulate in a live-cell inner mitochondrial matrix where a maleimide residue of the probe undergoes faster chemoselective and site-specific covalent attachment with the exposed Cys residue of mitochondrion-specific proteins. On the basis of this dual localization effect, Cy-5-Mal/TPP+ molecules remain for a longer time period even after membrane depolarization, enabling long-term live-cell mitochondrial imaging. Due to the adequate concentration of Cy-5-Mal/TPP+ reached in live-cell mitochondria, it facilitates site-selective NIR fluorescent covalent labeling with Cys-exposed proteins, which are identified by the in-gel fluorescence assay and LC-MS/MS-based proteomics and supported by a computational method. This dual targeting approach with admirable photostability, narrow NIR absorption/emission bands, bright emission, long fluorescence lifetime, and insignificant cytotoxicity has been shown to improve real-time live-cell mitochondrial tracking including dynamics and interorganelle crosstalk with multicolor imaging applications.

Nuclear ADP-ribosylation drives IFN\u03b3-dependent STAT1\u03b1 enhancer formation in macrophages

STAT1α is a key transcription factor driving pro-inflammatory responses in macrophages. We found that the interferon gamma (IFNγ)-regulated transcriptional program in macrophages is controlled by ADP-ribosylation (ADPRylation) of STAT1α, a post-translational modification resulting in the site-specific covalent attachment of ADP-ribose moieties. PARP-1, the major nuclear poly(ADP-ribose) polymerase (PARP), supports IFNγ-stimulated enhancer formation by regulating the genome-wide binding and IFNγ-dependent transcriptional activation of STAT1α. It does so by ADPRylating STAT1α on specific residues in its DNA-binding domain (DBD) and transcription activation (TA) domain. ADPRylation of the DBD controls STAT1α binding to its cognate DNA elements, whereas ADPRylation of the TA domain regulates enhancer activation by modulating STAT1α phosphorylation and p300 acetyltransferase activity. Loss of ADPRylation at either site leads to diminished IFNγ-dependent transcription and downstream pro-inflammatory responses. We conclude that PARP-1-mediated ADPRylation of STAT1α drives distinct enhancer activation mechanisms and is a critical regulator of inflammatory responses in macrophages.

Remote Regulation of Membrane Channel Activity by Site-Specific Localization of Lanthanide-Doped Upconversion Nanocrystals.

The spatiotemporal regulation of light-gated ion channels is a powerful tool to study physiological pathways and develop personalized theranostic modalities. So far, most existing light-gated channels are limited by their action spectra in the ultraviolet (UV) or visible region. Simple and innovative strategies for the specific attachment of photoswitches on the cell surface without modifying or genetically encoding channel structures, and more importantly, that enable the remote activation of ion-channel functions within near-infrared (NIR) spectral window in living systems, remain a challenging concern. Herein, metabolic glycan biosynthesis is used to achieve site-specific covalent attachment of near-infrared-light-mediated lanthanide-doped upconversion nanocrystals (UCNs) to the cell surface through copper-free click cyclization. Upon irradiation with 808 nm light, the converted emission at 480 nm could activate a light-gated ion channel, channelrhodopsins-2 (ChR2), and thus remotely control the cation influx. This unique strategy provides valuable insights on the specific regulation membrane-associated activities in vivo.

Effects of Selective Biotinylation on the Thermodynamic Stability of Human Serum Albumin

Thermal denaturation and stability of two commercially available preparations of Human Serum Albumin (HSA), differing in their advertised level of purity, were investigated by differential scanning calorimetry (DSC). These protein samples were 99% pure HSA (termed HSA99) and 96% pure HSA (termed HSA96). According to the supplier, the 3% difference in purity between HSA96 and HSA99 is primarily attributed to the presence of globulins and fatty acids. Our primary aim was to investigate the utility of DSC in discerning changes in HSA that occur when the protein is specifically adducted, and determine how adduct formation manifests itself in HSA denaturation curves, or thermograms, measured by DSC. Effects of site specific covalent attachment of biotin (the adduct) on the thermodynamic stability of HSA were investigated. Each of the HSA preparations was modified by biotinylation targeting a single site, or multiple sites on the protein structure. Thermograms of both modified and unmodified HSA samples successfully demonstrated the ability of DSC to clearly discern the two HSA preparations and the presence or absence of covalent modifications. DSC thermogram analysis also provided thermodynamic characterization of the different HSA samples of the study, which provided insight into how the two forms of HSA respond to covalent modification with biotin. Consistent with published studies [1] HSA96, the preparation with contaminants that contain globulins and fatty acids seems to be comprised of two forms, HSA96-L and HSA96-H, with HSA96-L more stable than HSA99. The effect of multisite biotinylation is to stabilize HSA96-L and destabilize HSA96-H. Thermodynamic analysis suggests that the binding of ligands comprising the fatty acid and globulin-like contaminant contributes approximately 6.7 kcal/mol to the stability HSA96-L.

Site-specific covalent attachment of an engineered Z-domain onto a solid matrix: An efficient platform for 3D IgG immobilization

Immobilized antibodies with oriented and homogeneous patterns are crucial to solid-phase molecular recognition assay. Antibody binding protein-based immobilization can effectively present the desired antibodies. However, steadily installing the stromatoid protein with site-specific attachment manner onto a matrix surface remains to be elucidated. In this study, we present an optimal protocol to tightly attach an immunoglobulin G (IgG)-binding protein (Z-domain) through covalent incorporation of Cys-tag and maleimide group onto polystyrene surface to guarantee site-specific, oriented, and irreversible attachment, resulting in a highly efficient platform for three-dimensional IgG immobilization. The actual IgG-binding characteristic of immobilized Z-Cys was investigated by employing affinity chromatography and size exclusion chromatography. And the efficacy and potential of this platform was demonstrated by applying it to the analysis of interaction between rabbit anti-HRP IgG and its binding partner HRP. The proposed approach may be an attractive strategy to construct high performance antibody arrays and biosensors given that the antibody is compatible with the Z-domain.

Dynamic and bio-orthogonal protein assembly along a supramolecular polymer

Dynamic protein assembly along supramolecular columnar polymers has been achieved through the site-specific covalent attachment of different SNAP-tag fusion proteins to self-assembled benzylguanine-decorated discotics. The self-assembly of monovalent discotics into supramolecular polymers creates a multivalent, bio-orthogonal and self-regulating framework for protein assembly. The intrinsic reversibility of supramolecular interactions results in reorganization and exchange of building blocks allowing for dynamic intermixing of protein-functionalized discotics between different self-assembled polymers, leading to self-optimization of protein arrangement and distance as evidenced by efficient energy transfer between fluorescent proteins.

Self‐Assembly of Thermally Responsive Nanoparticles of a Genetically Encoded Peptide Polymer by Drug Conjugation

Chimeric polypeptides (CPs) that are derived from elastin-like polypeptides (ELPs) can self-assemble to form nanoparticles by site-specific covalent attachment of hydrophobic molecules to one end of the biopolymer backbone. Molecules with a distribution coefficient greater than 1.5 impart sufficient amphiphilicity to drive self-assembly into sub-100 nm nanoparticles.

Site-specific covalent attachment of heme proteins on self-assembled monolayers

Naturally occurring hemin cofactor has been functionalized to introduce two terminal alkyne groups. This modified hemin has been successfully covalently attached to mixed self-assembled monolayers of alkanethiols and azide-terminated alkanethiols on gold electrodes using a Cu(I)-catalyzed 1,3-cycloaddition reaction. However these hemin-modified electrodes could not be used to reconstitute apomyoglobin on gold electrodes owing to the hydrophobicity of the alkane thiol self-assembled monolayer. Modification of existing techniques allowed covalent attachment of alkyne-terminated electroactive species onto mixed monolayers of azidothiols and carboxylatoalkanethiols on electrodes using the same Cu(I)-catalyzed 1,3-cycloaddition reaction. Apomyoglobin could be reconstituted using the hemin covalently attached to these hydrophilic electrodes. The electrochemical data, UV-vis absorption data, surface-enhanced resonance Raman spectroscopy data, and atomic force microscopy data indicate the presence of these modified myoglobin proteins on these electrodes. The direct attachment of the heme cofactor of these modified myoglobin proteins to the electrode allows fast electron transfer to the heme center from the electrode and affords efficient O(2)-reducing bioelectrodes under physiological conditions.

A Magnetofluorescent Nanoparticle for <I>Ex-Vivo</I> Cell Labeling by Covalently Linking the Drugs Protamine and Feraheme

We synthesized a nanoparticle (NP) for ex-vivo cell labeling and MRI tracking by covalently coupling the C-terminus of a rhodamine-labeled protamine (ProRho) to Feraheme (FH) in order to yield the nanoparticle denoted ProRho-FH. Since protamine can adsorb to certain charged surfaces, we confirmed a covalent interaction between ProRho and FH by heparin affinity chromatography. ProRho-FH lacks a net charge (zeta potential approximately 0) due to the combination of negative FH and positive ProRho charges. ProRho-FH was readily internalized by U87 cells and mouse mesenchymal stem cells as determined by FACS and MR relaxometry. Finally, some 4,000 stem cells were implanted in a mouse brain and imaged by MRI. Due to its lack of net surface charge, ProRho-FH relies on the internalizing properties of the surface guanidinium groups present in the arginine-rich protamine to induce NP uptake. ProRho-FH is a unique cell-labeling agent due to its synthesis using two approved drugs, magnetofluorescence, site-specific covalent attachment chemistry, and lack of surface charge.

Site-specific covalent attachment of DNA to proteins using a photoactivatable Tus–Ter complex

Investigations into the photocrosslinking kinetics of the protein Tus with various bromodeoxyuridine-substituted Ter DNA variants highlight the potential use of this complex as a photoactivatable connector between proteins of interest and specific DNA sequences.

Recent developments in the site‐specific immobilization of proteins onto solid supports

Immobilization of proteins onto surfaces is of great importance in numerous applications, including protein analysis, drug screening, and medical diagnostics, among others. The success of all these technologies relies on the immobilization technique employed to attach a protein to the corresponding surface. Non-specific physical adsorption or chemical cross-linking with appropriate surfaces results in the immobilization of the protein in random orientations. Site-specific covalent attachment, on the other hand, leads to molecules being arranged in a definite, orderly fashion and allows the use of spacers and linkers to help minimize steric hindrances between the protein and the surface. The present work reviews the latest chemical and biochemical developments for the site-specific covalent attachment of proteins onto solid supports.

Monospecific bivalent scFv-SH: Effects of linker length and location of an engineered cysteine on production, antigen binding activity and free SH accessibility

Development of tumor targeting pharmaceuticals on a modular platform is an attractive paradigm. Design choices for bispecific (anti-tumor and anti-chelate) pretargeting molecules are increased by the use of scFvs. Because a scFv is monovalent and small in size, its functional affinity and in vivo residence time can be improved through multimerization. ScFv multimers can be covalent or non-covalent. In vivo studies indicate that covalent scFv multimers are preferable. Attachment of scFv modules to scaffolds offers a wide range of possibilities for size and valency. A free thiol introduced at the C terminal end of a scFv (scFv-SH) allows for site-specific covalent attachment to a PEG scaffold without interfering with its antigen (Ag) binding. Although in theory, multimerization of 3 or 4 scFvs can be achieved by direct conjugation, as scFv-SH, to a tri or tetrafunctionalized PEG, it is not a practical option since homogeneous tri and tetrafunctionalized PEG are not readily available. However, the generation of (scFv) 3–4-PEG molecules through attachment of combinations of di-scFv-SH (tandemly expressed scFvs) and scFv-SH or 2 di-scFv-SH to a bifunctional PEG is a sound approach that also allows for better control of the scFv-PEG conjugate molecular composition. Optimization of the molecular format of the di-scFv-SH module for production as soluble proteins in E. coli, Ag binding and conjugation is reported in this study. ScFvs in the VH-VL format were used for the di-scFv constructs since Fv domain inversion to VL-VH, while not yielding more protein, also abolished Ag binding. The effects on production yield, Ag binding and conjugation potential of the scFv joining linker length and the presence and location of an engineered cysteine were assessed in vitro. Our data indicate that for di-scFv-SH, an increase of the scFv joining linker length results in higher production and better Ag binding; a 20 aa long linker (G 4S) 4 was the longest linker tested. For the engineered cysteine, three locations were tested; within the scFv joining linker, at the C terminus upstream of the E Tag and as the carboxy terminal aa. The accessibility of the free SH assessed by conjugation of di-scFv-SH to HRP-Mal demonstrated that di-scFv-HRP conjugates are formed with comparable efficiencies when the cysteine is located at the scFv carboxy end. This empirical work provides a framework for the development of bispecific scFv multimers via site-specific attachment of scFv-SH and di-scFv-SH modules to a scaffold.

NEW DEVELOPMENTS FOR THE SITE-SPECIFIC ATTACHMENT OF PROTEIN TO SURFACES

Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physical adsorption. However, since these interactions are weak, the molecules can get denatured or dislodged, thus causing loss of signal. They also result in random attachment of the protein to the surface. Site–specific covalent attachment of proteins onto surfaces, on the other hand, leads to molecules being arranged in a definite, orderly fashion and uses spacers and linkers to help minimize steric hindrances between the protein and the surface. This work reviews in detail some of the methods most commonly used as well as the latest developments for the site-specific covalent attachment of protein to solid surfaces.

High Z Metal Carbonyls for Imaging and Microspectroscopy

The power of microscopic and crystallographic techniques in structure-function analysis of multi-protein complexes can be greatly enhanced by the use of high Z or heavy atom labels introduced at specific sites. Heavy metal cluster complex labels that can be derivatized for site-specific covalent attachment to macromolecules have clear advantages over heavy metal salts. We have commercialized combined fluorescent and heavy metal probes that enable collection of complimentary sets of data, from fluorescence and electron microscopy, for correlative microscopic studies of biological targets at different spatial resolutions. We herein report combined heavy metal probes that will enable detection and spatially resolved chemical analysis of biological samples.

Solid-Phase Synthesis and Photophysical Properties of DNA Labeled at the Nucleobase with Ru(bpy)(2)(4-m-4'-pa-bpy)(2+).

A facile procedure for incorporating a Ru(diimine)(3)(2+) complex at the nucleobase in an oligonucleotide is reported that combines the advantages of Pd(0) cross-coupling and solid-phase DNA chemistries. These ruthenium-modified oligonucleotides form stable duplexes, and the favorable photophysical properties associated with the Ru(diimine)(3)(2+) complex are retained after site-specific covalent attachment.

Preparation and characterization of immunoconjugates for antibody-targeted photolysis

Monoclonal antibody (MAb)-dextran-tin(IV) chlorin e6 (SnCe6) immunoconjugates were prepared by a new technique involving the use of reducing, terminal-modified dextran carriers and site-specific modification of the Fc oligosaccharide moiety on the antibodies. Dextran carriers were synthesized to increase the number of SnCe6 molecules attached to a MAb. The dextran carriers were coupled to the MAb via a single, chain-terminal hydrazide group to prevent aggregation of MAbs. Conjugates were prepared with antimelanoma MAb 2.1 containing up to 18.9 SnCe6 molecules per MAb. Under neutral conditions, no hydrolysis of the hydrazone bond between the MAb and the dextran carrier could be detected, and the hydrazone was not stabilized by reduction with NaCNBH3 or NaBH4. Analysis of the purified immunoconjugates showed that approximately two dextran carrier chains were attached to a MAb regardless of the number of SnCe6 molecules linked to a dextran carrier. Site-specific covalent attachment of the SnCe6-dextran chains to the MAb was confirmed by SDS-PAGE. HPLC analysis of the conjugates gave a single species eluting in the range of 200-240 kDa. As determined by a competitive inhibition radioimmunoassay using viable SK-MEL-2 human malignant melanoma cells, the conjugates showed excellent retention of antigen-binding activity relative to unconjugated MAb.

The Use of a Photoaffinity Ligand to Compare Androgen-Binding Protein (ABP) Present in Rat Sertoli Cell Culture Media with ABP Present in Epididymal Cytosol*

The kinetic, binding, and physicochemical properties of androgen-binding protein (ABP) produced by rat Sertoli cells in culture [media ABP (mABP)] have been assessed and compared to ABP present in rat epididymal cytosol (eABP). Physicochemical studies were accomplished using ABP that had been covalently labeled using the photoaffinity probe 17β- hydroxy-[l,2-3H]4,6-androstadien-3-one ([3H]Δ6-testosterone). mABP was obtained from serum-free Sertoli cell culture media by ultrafiltration or precipitation with ammonium sulfate. mABP and eABP were photolyzed in the presence of [3H]Δ6- testosterone alone or together with nonphotoreactive 5α-dihydrotestosterone. Electrophoresis of photolabeled mABP and eABP on nondenaturing polyacrylamide gels (PAGE) showed similar mobilities. Site-specific covalent attachment of [3H]Δ6- testosterone to mABP and eABP was demonstrated by sodium dodecyl sulfate-PAGE. This analysis revealed the presence of 2 androgen-specific peaks corresponding to subunit molecular weights of appr...