Homobifunctional Cross-linker Research Articles

Pronounced Toxicity Differences between Homobifunctional Protein Cross-Linkers and Analogous Monofunctional Electrophiles

Bifunctional electrophiles have been used in various chemopreventive, chemotherapeutic, and bioconjugate applications. Many of their effects in biological systems are traceable to their reactive properties, whereby they can modify nucleophilic sites in DNA, proteins, and other cellular molecules. Previously, we found that two different bifunctional electrophiles--diethyl acetylenedicarboxylate and divinyl sulfone--exhibited a strong enhancement of toxicity when compared with analogous monofunctional electrophiles in both human colorectal carcinoma cells and baker's yeast. Here, we have compared the toxicities for a broader panel of homobifunctional electrophiles bearing diverse electrophilic centers (e.g., isothiocyanate, isocyanate, epoxide, nitrogen mustard, and aldehyde groups) to their monofunctional analogues. Each bifunctional electrophile showed at least a 3-fold enhancement of toxicity over its monofunctional counterpart, although in most cases, the differences were even more pronounced. To explain their enhanced toxicity, we tested the ability of each bifunctional electrophile to cross-link recombinant yeast thioredoxin 2 (Trx2), a known intracellular target of electrophiles. The bifunctional electrophiles were capable of cross-linking Trx2 to itself in vitro and to other proteins in cells exposed to toxic concentrations. Moreover, most cross-linkers were preferentially reactive with thiols in these experiments. Collectively, our results indicate that thiol-reactive protein cross-linkers in general are much more potent cytotoxins than analogous monofunctional electrophiles, irrespective of the electrophilic group studied.

Surfactant-Free Synthesis of Biodegradable, Biocompatible, and Stimuli-Responsive Cationic Nanogel Particles

Nanogels have attracted much attention lately because of their many potential applications, including as nanocarriers for drug and gene delivery. Most nanogels reported previously, however, are not biodegradable, and their synthesis often requires the use of surfactants. Herein we report a surfactant-free method for the preparation of biodegradable, biocompatible, and stimuli-responsive cationic nanogels. The nanogels were synthesized by simply coaservating linear polymer precursors in mixed solvents followed by in situ cross-linking with homobifunctional cross-linkers. The versatility of this approach has been demonstrated by employing two different polymers and various cross-linkers to prepare nanogel particles with diameters ranging from 170 to 220 nm. Specifically, disulfide-containing tetralysine (TetK)- and oligoethylenimine (OEI)-based prepolymers were prepared and the subsequent nanogels were formed by covalently cross-linking the polymer coacervate phase. Nanogel particles are responsive to pH changes, increasing in size and zeta-potential with concomitant lowering of solution pH. Furthermore, as revealed by AFM imaging, nanogel particles were degradable in the presence of glutathione at concentrations similar to those in intracellular environment (10 mM). Both the nanogel and the polymer precursors were determined to exhibit minimal cytotoxicity against fibroblast 3T3 cells by flow cytometric analyses and fluorescent imaging. This study demonstrates a new surfactant-free method for preparing biodegradable, biocompatible, and stimuli-responsive nanogels as potential nanocarriers for the delivery of drugs and genes.

Targeting EGFR-overexpressed A431 cells with EGF-labeled silica-coated magnetic nanoparticles

Human epidermal growth-factor receptor (EGFR) has emerged as an attractive target for cancer therapy. In this study, amino- or carboxyl-functionalized silica-coated maghemite nanoparticles were conjugated with epidermal growth-factor (EGF) using five different binding modes: carbodiimide chemistry, two types of homo-bifunctional cross-linking reagents, and electrostatic interactions between the nanoparticles and the EGF. The nanoparticles and their aqueous suspensions were characterized by transmission electron microscopy, zeta-potential measurements and dynamic light scattering. The binding efficiency of the EGF to the nanoparticles was measured by flow cytometry using a specific anti-EGF antibody. The ability of EGF bioconjugates to target the EGF receptors was tested using EGFR over-expressing A431 cells in comparison to EGFR negative HeLa cells. Our results showed that the bioconjugates where the EGF was bonded by carbodiimide chemistry are the most effective for the specific targeting of EGFR-expressing cells in vitro.

Abstract 898: Probing accessibility and conformational changes in ATP-binding sites during the catalytic cycle of human P-glycoprotein (ABCB1).

Abstract P-glycoprotein (P-gp) is an ATP-binding cassette (ABC) efflux transporter implicated in the development of multidrug resistance in cancer cells. The catalytic cycle of P-gp is still not fully understood. Both the C431 and C1074 residues in the Walker A motifs of nucleotide-binding domains (NBDs) are highly conserved in P-gp from different species and these residues are excellent reporter sites to study the interaction between the two NBDs during the catalytic cycle. Using homo-bifunctional crosslinkers, disulfide crosslinking of the 431C and 1074C residues in a cysless background can be observed in the presence of copper phenanthroline (CuP) and M17M, which have spacer arm lengths of 0 Å and 25 Å, respectively. However, crosslinking with M17M was prevented in the ADP-vanadate-trapped (closed) conformation, indicating that the distance between 431C and 1074C or the accessibility of these residues changes upon ATP hydrolysis. In addition, the accessibility of the residues, separately or together (431C/1074C) in both the apo and closed conformations was determined with fluorescein-5-maleimide (FM) and methanethio-sulfonate derivatives of rhodamine (MTS-rhodamine) and verapamil (MTS-verapamil), which exhibit different physical properties. The crosslinking of cysteine residues with thiol-reactive compounds is observed both in apo (open) and ADP-vanadate-trapped (closed) conformations, though at a reduced level in the latter case, indicating the flexible nature of the cysteines in Walker A domains. Consistent with these findings, the docking of FM in a homology model of human P-gp ATP sites shows that the sulfur atoms of 431C or 1074C can be oriented either facing the ATP pocket or facing away from the pocket. A different degree of labeling was observed between the two residues; for 1074C having 1.4- fold and 2-fold higher labeling with FM compared to 431C in the apo and closed conformations respectively, suggesting that accessibility of 1074C is greater than that of 431C in both conformations. In the presence of the transport substrate cyclosporine A (50 μM), crosslinking is still observed with CuP and M17M, suggesting that the binding of substrates to the drug-binding site in the transmembrane domains does not change the accessibility of the cysteines in the NBDs. In summary, the cysteines in the Walker A motifs of human P-gp are flexible and differentially accessible in the apo and closed conformations. In addition, the NBDs of human P-gp are closer together (20-25 Å) than the NBDs observed in the X-ray structure of mouse P-gp (36 Å). Citation Format: Hong-May Sim, Jaya Bhatnagar, Samantha A. Green, Adam Gonzalez, Eduardo E. Chufan, Suresh V. Ambudkar. Probing accessibility and conformational changes in ATP-binding sites during the catalytic cycle of human P-glycoprotein (ABCB1). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 898. doi:10.1158/1538-7445.AM2013-898

Sarcolipin Protein Interaction with Sarco(endo)plasmic Reticulum Ca2+ATPase (SERCA) Is Distinct from Phospholamban Protein, and Only Sarcolipin Can Promote Uncoupling of the SERCA Pump

Sarco(endo)plasmic reticulum Ca(2+)ATPase (SERCA) pump activity is modulated by phospholamban (PLB) and sarcolipin (SLN) in cardiac and skeletal muscle. Recent data suggest that SLN could play a role in muscle thermogenesis by promoting uncoupling of the SERCA pump (Lee, A.G. (2002) Curr. Opin. Struct. Biol. 12, 547-554 and Bal, N. C., Maurya, S. K., Sopariwala, D. H., Sahoo, S. K., Gupta, S. C., Shaikh, S. A., Pant, M., Rowland, L. A., Bombardier, E., Goonasekera, S. A., Tupling, A. R., Molkentin, J. D., and Periasamy, M. (2012) Nat. Med. 18, 1575-1579), but the mechanistic details are unknown. To better define how binding of SLN to SERCA promotes uncoupling of SERCA, we compared SLN and SERCA1 interaction with that of PLB in detail. The homo-bifunctional cross-linker (1,6-bismaleimidohexane) was employed to detect dynamic protein interaction during the SERCA cycle. Our studies reveal that SLN differs significantly from PLB: 1) SLN primarily affects the Vmax of SERCA-mediated Ca(2+) uptake but not the pump affinity for Ca(2+); 2) SLN can bind to SERCA in the presence of high Ca(2+), but PLB can only interact to the ATP-bound Ca(2+)-free E2 state; and 3) unlike PLB, SLN interacts with SERCA throughout the kinetic cycle and promotes uncoupling of the SERCA pump. Using SERCA transmembrane mutants, we additionally show that PLB and SLN can bind to the same groove but interact with a different set of residues on SERCA. These data collectively suggest that SLN is functionally distinct from PLB; its ability to interact with SERCA in the presence of Ca(2+) causes uncoupling of the SERCA pump and increased heat production.

ATP Alone Triggers the Outward Facing Conformation of the Maltose ATP-binding Cassette Transporter

The maltose transporter MalFGK(2) is a study prototype for ABC importers. During catalysis, the MalFG membrane domain alternates between inward and outward facing conformations when the MalK dimer closes and hydrolyzes ATP. Because a rapid ATP hydrolysis depends on MalE and maltose, it has been proposed that closed liganded MalE facilitates the transition to the outward facing conformation. Here we find that, in contrast to the expected, ATP is sufficient for the closure of MalK and for the conversion of MalFG to the outward facing state. The outward facing transporter binds MalE with nanomolar affinity, yet neither MalE nor maltose is necessary or facilitates the transition. Thus, the rapid hydrolysis of ATP observed in the presence of MalE and maltose is not because closed liganded MalE accelerates the formation of the outward facing conformation. These findings have fundamental implications for the description of the transport reaction.

High-density immobilization of antibodies onto nanobead-coated cyclic olefin copolymer plastic surfaces for application as a sensitive immunoassay chip

Our research efforts have been devoted to development of nanobead multilayer-based sensitive immunoassays on cyclic olefin copolymer (COC) plastic surfaces. To facilitate nanobead attachment and impart antibiofouling properties to a COC substrate, we used an amphiphilic copolymer comprising benzyl, polyethylene glycol, and reactive ester moieties to coat the hydrophobic COC surface in an aqueous environment. Subsequently, NH2-modified polystyrene nanobeads were reacted with the polymer-coated COC surface and further assembled into multilayers that increased the overall surface area available for attaching capture antibodies. After treatment of the nanobead multilayers with an amine-reactive homobifunctional crosslinker, a model capture antibody (anti-rabbit IgG) was covalently immobilized onto the activated surface of nanobeads. Finally, a sandwich immunoassay was carried out using rabbit IgG as a target analyte and rhodamine-labeled anti-rabbit IgG as a probe. Compared with a nanobead-free, polymer-coated COC surface, the nanobead multilayer-based immunoassay exhibited ~4-fold higher fluorescence intensity. In addition, our nanobead-based assay system exhibited a wide dynamic range of detection (0.1 to 1,000ng/mL) and high specificity for rabbit IgG. Furthermore, much better detection sensitivity for rabbit IgG was attained in the nanobead multilayer-based immunoassay than with a conventional ELISA system (0.1ng/mL versus 10ng/mL), indicating the potential value of the proposed immunoassay system in plastic-based portable biochip applications.

Designer reagents for mass spectrometry-based proteomics: clickable cross-linkers for elucidation of protein structures and interactions.

We present novel homobifunctional amine-reactive clickable cross-linkers (CXLs) for investigation of three-dimensional protein structures and protein-protein interactions (PPIs). CXLs afford consolidated advantages not previously available in a simple cross-linker, including (1) their small size and cationic nature at physiological pH, resulting in good water solubility and cell-permeability, (2) an alkyne group for bio-orthogonal conjugation to affinity tags via the click reaction for enrichment of cross-linked peptides, (3) a nucleophilic displacement reaction involving the 1,2,3-triazole ring formed in the click reaction, yielding a lock-mass reporter ion for only clicked peptides, and (4) higher charge states of cross-linked peptides in the gas-phase for augmented electron transfer dissociation (ETD) yields. Ubiquitin, a lysine-abundant protein, is used as a model system to demonstrate structural studies using CXLs. To validate the sensitivity of our approach, biotin-azide labeling and subsequent enrichment of cross-linked peptides are performed for cross-linked ubiquitin digests mixed with yeast cell lysates. Cross-linked peptides are detected and identified by collision induced dissociation (CID) and ETD with linear quadrupole ion trap (LTQ)-Fourier transform ion cyclotron resonance (FTICR) and LTQ-Orbitrap mass spectrometers. The application of CXLs to more complex systems (e.g., in vivo cross-linking) is illustrated by Western blot detection of Cul1 complexes including known binders, Cand1 and Skp2, in HEK 293 cells, confirming good water solubility and cell-permeability.

Characterizing Phospholamban to Sarco(endo)plasmic Reticulum Ca2+-ATPase 2a (SERCA2a) Protein Binding Interactions in Human Cardiac Sarcoplasmic Reticulum Vesicles Using Chemical Cross-linking

Chemical cross-linking was used to study protein binding interactions between native phospholamban (PLB) and SERCA2a in sarcoplasmic reticulum (SR) vesicles prepared from normal and failed human hearts. Lys(27) of PLB was cross-linked to the Ca(2+) pump at the cytoplasmic extension of M4 (at or near Lys(328)) with the homobifunctional cross-linker, disuccinimidyl glutarate (7.7 Å). Cross-linking was augmented by ATP but abolished by Ca(2+) or thapsigargin, confirming in native SR vesicles that PLB binds preferentially to E2 (low Ca(2+) affinity conformation of the Ca(2+)-ATPase) stabilized by ATP. To assess the functional effects of PLB binding on SERCA2a activity, the anti-PLB antibody, 2D12, was used to disrupt the physical interactions between PLB and SERCA2a in SR vesicles. We observed a tight correlation between 2D12-induced inhibition of PLB cross-linking to SERCA2a and 2D12 stimulation of Ca(2+)-ATPase activity and Ca(2+) transport. The results suggest that the inhibitory effect of PLB on Ca(2+)-ATPase activity in SR vesicles results from mutually exclusive binding of PLB and Ca(2+) to the Ca(2+) pump, requiring PLB dissociation for catalytic activation. Importantly, the same result was obtained with SR vesicles prepared from normal and failed human hearts; therefore, we conclude that PLB binding interactions with the Ca(2+) pump are largely unchanged in failing myocardium.

Biochemical Crosslinking and Liquid Chromatography-Mass Spectrometry Demonstrate a Rhodopsin Dimerization Interface Mediated by Helices 1 and 8

Heptahelical G protein-coupled receptors (GPCRs) can exist as monomers and a ternary complex of ligand, GPCR and heterotrimeric G protein is the basic signaling unit. GPCRs also tend to form dimers and higher-order oligomers in membranes, although the functional consequences of these interactions are in most cases unknown. Furthermore, the precise protein-protein interface(s) in receptor dimers and the mechanisms mediating dimerization remain controversial. Two-dimensional and three-dimensional densities obtained from electron microscopy, as well as X-ray data on packing of rhodopsin crystals, suggest that the primary dimer contacts involve transmembrane helix (H) 1 and cytoplasmic H8. Biochemical crosslinking studies with dopamine D2 receptors hint that this interface may be broadly significant. We crosslinked rhodopsin dimers in native rod outer segment disk membranes to demonstrate the proximity of H8 between adjacent receptors. Four homobifunctional cysteine-reactive crosslinkers were used, two with maleimide groups and two with methanethiosulfonate groups. The formation of dimers and oligomers was verified by SDS-PAGE, size-exclusion chromatography, and immunoblot analysis. We used partial proteolysis and high-resolution liquid chromatography-mass spectrometry (LC-MS) to identify the site of a crosslink between Cys316-Cys316. Cys316 is one of two reactive cysteines in rhodopsin and is located in H8. The spacer length of the crosslinkers that formed the intermolecular Cys316-Cys316 crosslink is consistent with the distance predicted in a H1/H8 dimer model. This result corroborates findings from coarse-grained molecular dynamics (CGMD) potential of mean force (PMF) calculations, which show that the H1/H8 orientation is by far the most stable among the possible dimer orientations tested. Together these results strongly suggest the existence of this interface in native membranes. Given the high degree of homology across class A GPCRs, these results may be relevant for other receptors.

Synthesis and reactivity of a bis-sultone cross-linker for peptideconjugation and [18F]-radiolabelling via unusual “double click” approach

A novel homobifunctional cross-linker based on a bis-sultone benzenic scaffold was synthesised. The potential utility of this bioconjugation reagent was demonstrated through the preparation of an original prosthetic group suitable for the [(18)F]-labelling of peptides. The labelling strategy is based on the nucleophilic fluorination via the ring-opening of a first sultone moiety followed by the nucleophilic ring-opening of the second remanent sultone by a reactive amine of the biopolymer. Beyond the one-step radiolabelling of the peptide, the second main advantage of this strategy is the release of free sulfonic acid moieties making the separation of the targeted [(18)F]-tagged sulfonated compound from its non-sulfonated precursor easier and thus faster. This first report of the successful use of a bis-sultone moiety as a versatile bioconjugatable group was demonstrated through a comprehensive reactivity study involving various nucleophiles, especially those commonly found in biopolymers. An illustrative example, highlighting the potential of this unusual and promising "double click" conjugation approach, was devoted to the radiolabelling of a biological relevant peptide.

Structure of a Cannabinoid Receptor Subtype 2 Homodimer Determined by Cysteine and Homobifunctional Crosslinking Experiments Combined with Computational Studies

The cannabinoid CB2 receptor is a Class A GPCR that is highly expressed in the immune system (Galiegue et al., 1995) and couples via Gi proteins (Glass and Northup, 1999). In a project to determine the stoichiometry of the CB2/ Gi protein complex, we first performed crosslinking experiments using a homobifunctional Lys-Lys linker, disuccinimidyl suberate combined with MS/MS analysis. We identified the following crosslinks: (1) Gi: K349 / CB2: K6.35(245) and (2) Gi: K317 / CB2: K5.64 (215). Using HgCl2 (and verified via MS/MS analysis), we also found disulfide bridge formation between Gi: C351 / CB2: C3.53(134). A computer model of the CB2/G-protein complex was constructed using our CB2 inactive (R) and active (R∗) state models (Hurst et al., 2010), along with the crystal structure of Gαi1β1γ2 (Wall et al., 1995). Our modelling revealed that achieving all three crosslinks at the same time would require CB2 to be in a homodimeric form, with one monomer in the inactive state, while the second monomer is in the activated state, coupled to G protein. This arrangement is consistent with the homodimeric signalling unit proposed by Javitch and Weinstein (Han et al., 2009). Further, to satisfy all of the experimental restraints, the interface of the CB2 homodimer had to be at TMH5-TMH6. This interface is similar to that found for the chemokine CXCR4 receptor (Wu et al., 2010). Monomer crosslinking studies were then undertaken to identify the homodimer interface in CB2. Substituted cysteine experiments revealed that in the presence of HgCl2, CB2 can dimerize at H6.57(267)C and at A6.60(270)C. These results are in agreement with the dimer interface chosen above to satisfy all of the CB2/G-protein crosslinks. [Support: RO1 DA003934 and KO5 DA021358 (PHR)].

Comparative Study of Random and Oriented Antibody Immobilization as Measured by Dual Polarization Interferometry and Surface Plasmon Resonance Spectroscopy

Dual polarization interferometry (DPI) is used for a detailed study of antibody immobilization with and without orientation control, using prostate specific antigen (PSA) and its antibody as model. Thiol modified DPI chips were activated by a heterobifunctional cross-linker (sulfo-GMBS). PSA antibody was either directly immobilized via covalent binding or coupled via the Fc-fragment to protein G covalently attached to the activated chip. The direct covalent binding leads to a random antibody orientation and the coupling through protein G leads to an end-on orientation. Ethanolamine (ETH) was used to block remaining active sites following the direct antibody immobilization and protein G immobilization. A homobifunctional cross-linker (BS3) was used to stabilize the antibody layer coupled on protein G. DPI provides a real-time measurement of the stepwise molecular binding processes and gives detailed geometrical and structural values of each layer, i.e., thickness, mass, and density. These values evidence the end-on orientation of closely packed antibody on protein G layer and reveal structural effects of ETH blocking/deactivation and BS3 stabilization. With the end-on immobilized antibody, PSA at 10 pg/mL can be detected by DPI through a sandwich complex that satisfies the clinical requirement (assuming <30 pg/mL as clinically safe). However, the randomly immobilized antibody failed to detect PSA at 1 ng/mL. In a parallel study using surface plasmon resonance (SPR) spectroscopy, random and end-on antibody immobilization on streptavidin-modified gold surface was evaluated to further validate the importance of antibody orientation control. With the closely packed antibody layer on protein G surface, SPR can also detect PSA at 10 pg/mL.

Psb27, a transiently associated protein, binds to the chlorophyll binding protein CP43 in photosystem II assembly intermediates

Photosystem II (PSII), a large multisubunit pigment-protein complex localized in the thylakoid membrane of cyanobacteria and chloroplasts, mediates light-driven evolution of oxygen from water. Recently, a high-resolution X-ray structure of the mature PSII complex has become available. Two PSII polypeptides, D1 and CP43, provide many of the ligands to an inorganic Mn(4)Ca center that is essential for water oxidation. Because of its unusual redox chemistry, PSII often undergoes degradation followed by stepwise assembly. Psb27, a small luminal polypeptide, functions as an important accessory factor in this elaborate assembly pathway. However, the structural location of Psb27 within PSII assembly intermediates has remained elusive. Here we report that Psb27 binds to CP43 in such assembly intermediates. We treated purified genetically tagged PSII assembly intermediate complexes from the cyanobacterium Synechocystis 6803 with chemical cross-linkers to examine intermolecular interactions between Psb27 and various PSII proteins. First, the water-soluble 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) was used to cross-link proteins with complementary charged groups in close association to one another. In the His27△ctpAPSII preparation, a 58-kDa cross-linked species containing Psb27 and CP43 was identified. This species was not formed in the HT3△ctpA△psb27PSII complex in which Psb27 was absent. Second, the homobifunctional thiol-cleavable cross-linker 3,3'-dithiobis(sulfosuccinimidylpropionate) (DTSSP) was used to reversibly cross-link Psb27 to CP43 in His27△ctpAPSII preparations, which allowed the use of liquid chromatography/tandem MS to map the cross-linking sites as Psb27K(63)↔CP43D(321) (trypsin) and CP43K(215)↔Psb27D(58)AGGLK(63)↔CP43D(321) (chymotrypsin), respectively. Our data suggest that Psb27 acts as an important regulatory protein during PSII assembly through specific interactions with the luminal domain of CP43.

Piezoelectric immunosensor for direct and rapid detection of staphylococcal enterotoxin A (SEA) at the ng level

A direct, label-free immunosensor was designed for the rapid detection and quantification of staphylococcal enterotoxin A (SEA) in buffered solutions using quartz crystal microbalance with dissipation (QCM-D) as transduction method. The sensing layer including the anti-SEA antibody was constructed by chemisorption of a self-assembled monolayer of cysteamine on the gold electrodes placed over the quartz crystal sensor followed by activation of the surface amino groups with the rigid homobifunctional cross-linker 1,4-phenylene diisothiocyanate (PDITC) and covalent linking of binding protein (protein A or protein G). Four anti-SEA antibodies (two of which from commercial source) have been selected to set up the most sensitive detection device. With the optimized sensing layer, a standard curve for the direct assay of SEA was established from QCM-D responses within a working range of 50–1000 or 2000ngml−1 with a detection limit of 20ngml−1. The total time for analysis was 15min. Using a sandwich type assay, the response was ca. twice higher and consequently the lowest measurable concentration dropped down to 7ngml−1 for a total assay time of 25min.

Preparation of epoxy‐based macroporous monolithic columns for the fast and efficient immunofiltration of Staphylococcus aureus

Macroporous epoxy-based monolithic columns were used for immunofiltration of bacteria. The prepared monolithic polymer support is hydrophilic and has large pore sizes of 21 μm without mesopores. A surface chemistry usually applied for immobilization of antibodies on glass slides is successfully transferred to monolithic columns. Step-by-step, the surface of the epoxy-based monolith is hydrolyzed, silanized, coated with poly(ethylene glycol diamine) and activated with the homobifunctional crosslinker di(N-succinimidyl)carbonate for immobilization of antibodies on the monolithic columns. The functionalization steps are characterized to ensure the coating of each monolayer. The prepared antibody-immobilized monolithic column is optimized for immunofiltration to enrich Staphylococcus aureus as an important food contaminant. Different kinds of geometries of monolithic columns, flow rates and elution buffers are tested with the goal to get high recoveries in the shortest enrichment time as possible. An effective capture of S. aureus was achieved at a flow rate of 7.0 mL/min with low backpressures of 20.1±5.4 mbar enabling a volumetric enrichment of 1000 within 145 min. The bacteria were quantified by flow cytometry using a double-labeling approach. After immunofiltration the sensitivity was significantly increased and a detection limit of the total system of 42 S. aureus/mL was reached.

Architecture of a Full-length Retroviral Integrase Monomer and Dimer, Revealed by Small Angle X-ray Scattering and Chemical Cross-linking

We determined the size and shape of full-length avian sarcoma virus (ASV) integrase (IN) monomers and dimers in solution using small angle x-ray scattering. The low resolution data obtained establish constraints for the relative arrangements of the three component domains in both forms. Domain organization within the small angle x-ray envelopes was determined by combining available atomic resolution data for individual domains with results from cross-linking coupled with mass spectrometry. The full-length dimer architecture so revealed is unequivocally different from that proposed from x-ray crystallographic analyses of two-domain fragments, in which interactions between the catalytic core domains play a prominent role. Core-core interactions are detected only in cross-linked IN tetramers and are required for concerted integration. The solution dimer is stabilized by C-terminal domain (CTD-CTD) interactions and by interactions of the N-terminal domain in one subunit with the core and CTD in the second subunit. These results suggest a pathway for formation of functional IN-DNA complexes that has not previously been considered and possible strategies for preventing such assembly.

Chemical Trapping of the Dynamic MutS-MutL Complex Formed in DNA Mismatch Repair in Escherichia coli

The ternary complex comprising MutS, MutL, and DNA is a key intermediate in DNA mismatch repair. We used chemical cross-linking and fluorescence resonance energy transfer (FRET) to study the interaction between MutS and MutL and to shed light onto the structure of this complex. Via chemical cross-linking, we could stabilize this dynamic complex and identify the structural features of key events in DNA mismatch repair. We could show that in the complex between MutS and MutL the mismatch-binding and connector domains of MutS are in proximity to the N-terminal ATPase domain of MutL. The DNA- and nucleotide-dependent complex formation could be monitored by FRET using single cysteine variants labeled in the connector domain of MutS and the transducer domain of MutL, respectively. In addition, we could trap MutS after an ATP-induced conformational change by an intramolecular cross-link between Cys-93 of the mismatch-binding domain and Cys-239 of the connector domain.

Intra- and inter-molecular cross-linking of peptide ions in the gas phase: reagents and conditions.

Intra-molecular and inter-molecular cross-linking of protonated polypeptide ions in the gas phase via ion/ion reactions have been demonstrated using N-hydroxysulfosuccinimide (sulfo-NHS)- based reagent anions. The initial step in the ion/ion reaction involves the formation of a long-lived complex between the peptide and reagent, which is a prerequisite for the covalent bioconjugation chemistry. The sulfonate groups on the NHS rings of the homo-bifunctional cross-linking reagents have high affinity for the protonated sites in the peptide and, therefore, facilitate the long-lived complex formation. In addition to the formation of a long-lived chemical complex, intra-molecular cross-linking also requires two unprotonated primary amine sites within a molecule where the covalent modification takes place. Alternatively, inter-molecular cross-linking demands the availability of one neutral primary amine site in each of the two peptides that are being cross-linked. Nucleophilic displacement of two sulfo-NHS groups by the amine functionalities in the peptide is a signature of the covalent cross-linking chemistry in the gas phase. Upon removal of the two sulfo-NHS groups, two amide bonds are formed between an unprotonated, primary amine group of a lysine side chain in the peptide and the carboxyl group in the reagent.

Interactions between CusF and CusB Identified by NMR Spectroscopy and Chemical Cross-Linking Coupled to Mass Spectrometry

The Escherichia coli periplasmic proteins CusF and CusB, as part of the CusCFBA efflux system, aid in the resistance of elevated levels of copper and silver by direct metal transfer between the metallochaperone CusF and the membrane fusion protein CusB before metal extrusion from the periplasm to the extracellular space. Although previous in vitro experiments have demonstrated highly specific interactions between CusF and CusB that are crucial for metal transfer to occur, the structural details of the interaction have not been determined. Here, the interactions between CusF and CusB are mapped through nuclear magnetic resonance (NMR) spectroscopy and chemical cross-linking coupled with high-resolution mass spectrometry to better understand how recognition and metal transfer occur between these proteins. The NMR (1)H-(15)N correlation spectra reveal that CusB interacts with the metal-binding face of CusF. In vitro chemical cross-linking with a 7.7 Å homobifunctional amine-reactive cross-linker, BS(2)G, was used to capture the CusF/CusB interaction site, and mass spectral data acquired on an LTQ-Orbitrap confirm the following two cross-links: CusF K31 to CusB K29 and CusF K58 to CusB K32, thus revealing that the N-terminal region of CusB interacts with the metal-binding face of CusF. The proteins transiently interact in a metal-dependent fashion, and contacts between CusF and CusB are localized to regions near their respective metal-binding sites.