Mechanism of site-directed protein cross-linking. protein-directed selectivity in reactions of hemoglobin with aryl trimesates

Site-directed cross-linking of hemoglobin has become an efficient way to produce a structurally defined altered protein with desirable functional properties. The reagent trimesoyl tris(3, 5-dibromosalicylate) (1) introduces a bis amide cross-link derived from the epsilon-amino groups of the side chains of the two beta-Lys-82 residues in human hemoglobin. The basis of its specificity was investigated using a set of analogues of 1 (2-12). There are marked differences in the reaction patterns of these compounds with amino groups in hemoglobin compared to reactions with n-propylamine. The compounds that effectively modify the protein contain a carboxyl group ortho to the phenolic oxygen of the ester, while materials with meta or para carboxyl groups give little or no reaction. In contrast, the reactions with n-propylamine are slowest with the ortho carboxyl materials. Addition of the unreactive compound 5 to a solution containing hemoglobin reduces the ability of 1 to modify the protein, showing that the unreactive compound binds but does not react. On the basis of these observations and the known reaction patterns of salicylates, it is clear that the environment in the protein controls the reaction, regardless of the inherent reactivity of the reagent. We propose that the carboxyl group positions the reagent critically within the protein. Only the ortho arrangement permits transfer of the acyl function to the nucleophile.     

Reactive Acrylamide-Modified DNA Traps for Accurate Cross-Linking with Cysteine Residues in DNA–Protein Complexes Using Mismatch Repair Protein MutS as a Model

Covalent protein capture (cross-linking) by reactive DNA derivatives makes it possible to investigate structural features by fixing complexes at different stages of DNA–protein recognition. The most common cross-linking methods are based on reactive groups that interact with native or engineered cysteine residues. Nonetheless, high reactivity of most of such groups leads to preferential fixation of early-stage complexes or even non-selective cross-linking. We synthesised a set of DNA reagents carrying an acrylamide group attached to the C5 atom of a 2′-deoxyuridine moiety via various linkers and studied cross-linking with MutS as a model protein. MutS scans DNA for mismatches and damaged nucleobases and can form multiple non-specific complexes with DNA that may cause non-selective cross-linking. By varying the length of the linker between DNA and the acrylamide group and by changing the distance between the reactive nucleotide and a mismatch in the duplex, we showed that cross-linking occurs only if the distance between the acrylamide group and cysteine is optimal within the DNA–protein complex. Thus, acrylamide-modified DNA duplexes are excellent tools for studying DNA–protein interactions because of high selectivity of cysteine trapping.     

LASER CROSS-LINKING OF PROTEINS TO NUCLEIC ACIDS: PHOTODEGRADATION AND ALTERNATIVE PHOTOPRODUCTS OF THE BACTERIOPHAGE T4 GENE 32 PROTEIN

Pulsed laser cross-linking provides a means of introducing a covalent bond between proteins and the nucleic acids to which they are bound. This rapid cross-linking effectively traps the equilibrium that exists at the moment of irradiation and thus allows examination of the protein-nucleic acid interactions that existed. Laser irradiation may also induce photodestruction of protein and we have used the bacteriophage T4 gene 32 protein to investigate this phenomenon. Our results show that both nonspecific and specific photoproducts can occur, specifically at wavelengths where the peptide backbone of proteins is known to absorb. These results demonstrate that nonspecific photodegradation can be correlated with the formation of a specific photodegradation product. The formation of this product was monitored to show that product yield is nonlinearly dependent on laser power and wavelength. We have also investigated an unexpected photoproduct whose formation is dependent on the length of the polynucleotide to which the gene 32 protein binds and that further demonstrates the complexities of analyzing protein-nucleic acid interactions through the use of UV laser cross-linking. These data provide essential information for the establishment of appropriate conditions for future studies that use UV cross-linking of protein-nucleic acid complexes.     

A minimal model for stabilization of biomolecules by hydrocarbon cross-linking

Programmed cell death regulating protein motifs play an essential role in the development of an organism, its immune response, and disease-related cellular mechanisms. Among those motifs the BH3 domain of the BCL-2 family is found to be of crucial importance. Recent experiments showed how the isolated, otherwise unstructured BH3 peptide can be modified by a hydrocarbon linkage to regain function. We parametrized a reduced, dynamic model for the stability effects of such covalent cross-linking and confirmed that the model reproduces the reinforcement of the structural stability of the BH3 motif by cross-linking. We show that an analytically solvable model for thermostability around the native state is not capable of reproducing the stabilization effect. This points to the crucial importance of the peptide dynamics and the fluctuations neglected in the analytic model for the cross-linking system to function properly. This conclusion is supported by a thorough analysis of a simulated Go model. The resulting model is suitable for rational design of generic cross-linking systems in silicio.     

Mapping low-resolution three-dimensional protein structures using chemical cross-linking and Fourier transform ion-cyclotron resonance mass spectrometry

Techniques in mass spectrometry (MS) combined with chemical cross-linking have proven to be efficient tools for the rapid determination of low-resolution three-dimensional (3-D) structures of proteins. The general procedure involves chemical cross-linking of a protein followed by enzymatic digestion and MS analysis of the resulting peptide mixture. These experiments are generally fast and do not require large quantities of protein. However, the large number of peptide species created from the digestion of cross-linked proteins makes it difficult to identify relevant intermolecular cross-linked peptides from MS data. We present a method for mapping low-resolution 3-D protein structures by combining chemical cross-linking with high-resolution FTICR (Fourier transform ion-cyclotron resonance) mass spectrometry using cytochrome c and hen egg lysozyme as model proteins. We applied several homo-bifunctional, amine-reactive cross-linking reagents that bridge distances from 6 to 16 A. The non-digested cross-linking reaction mixtures were monitored by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to determine the extent of cross-linking. Enzymatically digested reaction mixtures were separated by nano-high-performance liquid chromatography (nano-HPLC) on reverse-phase columns applying water/acetonitrile gradients with flow rates of 200 nL/min. The nano-HPLC system was directly coupled to an FTICR mass spectrometer equipped with a nano-ESI (electrospray ionization) source. Cross-linking products were identified using a combination of the GPMAW software and ExPASy Proteomics tools. For correct assignment of the cross-linking products the key factor is to rely on a mass spectrometric method providing both high resolution and high mass accuracy, such as FTICRMS. By combining chemical cross-linking with FTICRMS we were able to rapidly define several intramolecular constraints for cytochrome c and lysozyme.     

Mapping protein interfaces by a trifunctional cross-linker combined with MALDI-TOF and ESI-FTICR mass spectrometry

Chemical cross-linking of protein complexes has gained renewed interest in combination with mass spectrometric analysis of the reaction products as it allows a rapid mapping of protein interfaces, which is crucial for understanding protein/protein interactions. The identification of cross-linking products from the complex mixtures created after the cross-linking reaction, however, remains a daunting task. To facilitate the identification of cross-linking products, we explore the use of the commercially available biotinylated cross-linking reagent sulfo-SBED (sulfosuccinimidyl-2-[6-(biotinamido)-2-(p-azidobenzamido)-hexanoamido]ethyl-1,3'-dithiopropionate). This trifunctional cross-linker possesses one amine-reactive and one photo-reactive site and, additionally, allows an affinity-based enrichment of cross-linker containing species. As a model system, we chose the Ca(2+)-dependent complex between calmodulin and its target peptide M13, which represents a part of the C-terminal sequence of the skeletal muscle myosin light chain kinase. After the cross-linking reaction, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and one-dimensional gel electrophoresis were employed to check for the extent of cross-linking product formation. The cross-linking reaction mixtures were subjected to tryptic in-solution digestion. Biotinylated peptides, e.g., peptides that had been modified by the cross-linker as well as cross-linked peptides, were enriched on monomeric avidin beads after several washing steps had been performed. Peptide mixtures were analyzed by MALDI-TOFMS, nano-high-performance liquid chromatography (HPLC)/nano-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS), and tandem MS. We demonstrate that an enrichment of cross-linker containing species allows a more efficient identification of interacting amino acid sequences in protein complexes. This strategy is expected to be especially beneficial for investigating large protein assemblies.     

Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes

Chemical cross-linking of proteins, an established method in protein chemistry, has gained renewed interest in combination with mass spectrometric analysis of the reaction products for elucidating low-resolution three-dimensional protein structures and interacting sequences in protein complexes. The identification of the large number of cross-linking sites from the complex mixtures generated by chemical cross-linking, however, remains a challenging task. This review describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the strategies employing intra- or intermolecular chemical cross-linking and mass spectrometry. The various approaches described in the literature to facilitate detection of cross-linking products and also computer software for data analysis are reviewed. Cross-linking techniques combined with mass spectrometry and bioinformatic methods have the potential to provide the basis for an efficient structural characterization of proteins and protein complexes.     

A top down approach to protein structural studies using chemical cross-linking and Fourier transform mass spectrometry

Mass spectrometric analysis of wild-type proteins that have been covalently modified by bifunctional cross-linking reagents and then digested proteolytically can be used to obtain low-resolution distance constraints, which can be useful for protein structure determination. Limitations of this approach include time-consuming separation steps, such as the separation of internally cross-linked protein monomers from covalent dimers, and a susceptibility to artifacts due to low levels of natural and man-made peptide modifications that can be mistaken for cross-linked species. The results presented here show that when a crude cross-linked protein mixture is injected into an electrospray ionization Fourier transform mass spectrometry (ESI-FTMS) instrument, the cross-link positions can be localized by fragmentation and mass spectrometry on the 'gas-phase purified' singly internally cross-linked monomer. Our results show that reaction of ubiquitin with the homobifunctional lysine-lysine cross-linking reagent dissuccinimidyl suberate (DSS) resulted in two cross-links consistent with the known ubiquitin tertiary structure (K6-K11 and K48-K63). Because no protein or peptide chemistry steps are needed, other than the initial cross-linking, this new top down approach appears well suited for high-throughput experiments with multiple cross-linkers and reaction conditions. Published in 2002 by John Wiley & Sons, Ltd.     

Formation and characterization of polyglutamate core-shell microspheres

The need for organ-targeted delivery of drugs and imaging agents creates an interest in biocompatible, biodegradable vesicles. We make protein microspheres using high-intensity ultrasound; these microspheres have a protein shell and a hydrophobic interior, making them ideal for delivering hydrophobic materials. We have previously shown that various proteins, e.g., bovine serum albumin (BSA), form a microsphere shell stabilized by interprotein cross-linking of cysteine residues. In this study, polyglutamate was used to form core-shell microspheres at slightly basic pH using sonication. These particles are smaller than our previous protein microspheres and are stable under conditions encountered in vivo. The stability of polyglutamate microspheres appears to be due to hydrogen bonding networks and not covalent cross-linking.     

Does chemical cross-linking with NHS esters reflect the chemical equilibrium of protein-protein noncovalent interactions in solution?

Chemical cross-linking in combination with mass spectrometry has emerged as a powerful tool to study noncovalent protein complexes. Nevertheless, there are still many questions to answer. Does the amount of detected cross-linked complex correlate with the amount of protein complex in solution? In which concentration and affinity range is specific cross-linking possible? To answer these questions, we performed systematic cross-linking studies with two complexes, using the N-hydroxysuccinimidyl ester disuccinimidyl suberate (DSS): (1) NCoA-1 and mutants of the interacting peptide STAT6Y, covering a K_D range of 30 nM to >25 μM, and (2) α-thrombin and basic pancreatic trypsin inhibitor (BPTI), a system that shows a buffer-dependent K_D value between 100 and 320 μM. Samples were analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). For NCoA-1· STAT6Y, a good correlation between the amount of cross-linked species and the calculated fraction of complex present in solution was observed. Thus, chemical cross-linking in combination with MALDI-MS can be used to rank binding affinities. For the mid-affinity range up to about K_D ≈ 25 μM, experiments with a nonbinding peptide and studies of the concentration dependence showed that only specific complexes undergo cross-linking with DSS. To study in which affinity range specific cross-linking can be applied, the weak α-thrombin · BPTI complex was investigated. We found that the detected complex is a nonspecifically cross-linked species. Consequently, based on the experimental approach used in this study, chemical cross-linking is not suitable for studying low-affinity complexes with K_D ? 25 μM.     

Cross-linking the protein precursor of marine mussel adhesives: bulk measurements and reagents for curing

Marine mussels affix themselves to surfaces by use of a highly cross-linked, protein-based adhesive. Metal levels (e.g., Fe, Zn, Cu, Mn) of the cured glue are significantly concentrated relative to surrounding waters. Specific details on the reagents used by mussels to induce protein cross-linking are not known at this time. To provide insight on the cross-linking agents and reactions taking place while curing mussel glues, we performed a study in which various compounds were tested for the ability to bring about protein curing. A precursor to adhesion, with proteins containing the unusual amino acid 3,4-dihydroxyphenylalanine, was extracted from mussel feet. Potential cross-linking agents were mixed with this gelatinous pellet. The compressibility and shear properties of the resulting material were investigated by use of a penetration test. The reagents examined included simple metal ions (e.g., Na+, Zn2+), oxidizing transition metals (e.g., Fe3+, Cr2O7(2-)), nonmetallic oxidants (e.g., H2O2,IO4-), and oxidizing enzymes (e.g., tyrosinase). We found that protein curing was brought about by simple oxidants and transition metal ions. The results show that optimal curing occurs when the reagent is an oxidizing metal ion (e.g., MnO4-, Fe3+). We conclude that marine mussels are likely to employ Mn3+ and Fe3+ for protein cross-linking and adhesive synthesis.     

A Negative Ion Mass Spectrometry Approach to Identify Cross-Linked Peptides Utilizing Characteristic Disulfide Fragmentations

Chemical cross-linking combined with mass spectrometry (MS) is an analytical tool used to elucidate the topologies of proteins and protein complexes. However, identification of the low abundance cross-linked peptides and modification sites amongst a large quantity of proteolytic fragments remains challenging. In this work, we present a strategy to identify cross-linked peptides by negative ion MS for the first time. This approach is based around the facile cleavages of disulfide bonds in the negative mode, and allows identification of cross-linked products based on their characteristic fragmentations. MS(3) analysis of the cross-linked peptides allows for their sequencing and identification, with residue specific location of cross-linking sites. We demonstrate the applicability of the commercially available cystine based cross-linking reagent dithiobis(succinimidyl) propionate (DSP) and identify cross-linked peptides from ubiquitin. In each instance, the characteristic fragmentation behavior of the cross-linked species is described. The data presented here indicate that this negative ion approach may be a useful tool to characterize the structures of proteins and protein complexes, and provides the basis for the development of high throughput negative ion MS chemical cross-linking strategies.     

Bovine red blood cell starvation age discrimination through a glutaraldehyde-amplified dielectrophoretic approach with buffer selection and membrane cross-linking

We report a novel buffer electric and dielectric relaxation time tuning technique, coupled with a glutaraldehyde (Glt.) cross-linking cell fixation reaction that allows for sensitive dielectrophoretic analysis and discrimination of bovine red blood cells of different starvation age. Guided by a single-shell oblate spheroid model, a zwitterion buffer composition is selected to ensure that two measurable crossover frequencies (cof's) near 500 kHz exist for dielectrophoresis (DEP) within a small range of each other. It is shown that the low cof is sensitive to changes in the cell membrane dielectric constant, in which cross-linking by Glt. reduces the dielectric constant of the cell membrane from 10.5 to 3.8, while the high cof is sensitive to cell cytoplasm conductivity changes. We speculate that this enhanced particle polarizability that results from the cross-linking reaction is because younger (reduced starvation time) cells possess more amino groups that the reaction can release to enhance the cell interior ionic strength. Such sensitive discrimination of cells with different age (surface protein density) by DEP is not possible without the zwitterion buffer and cleavage by Glt. treatment. It is then expected that rapid identification and sorting of healthy from diseased cells can be similarly sensitized.     

Emulsion-templated fully reversible protein-in-oil gels

We have developed a new method allowing us to transform low-viscous apolar fluids into elastic solids with a shear elastic modulus of the order of 10(3)-10(5) Pa. The elasticity of the elastic solid is provided by a percolating 3D network of proteins, which are originally adsorbed at the interface of an oil-in-water emulsion template. By cross-linking the protein films at the interface and upon removal of water, the template is driven into a structure resembling a dry foam where the protein interfaces constitute the walls of the foam and the air is replaced by oil confined within polyhedral, closely packed droplets. Depending on the density of the protein network, the final material consists of chemically unmodified oil in a proportion of 95 to 99.9%. The physical properties of the elastic solid obtained can be tuned by changing either the average diameter size of the emulsion template or the cross-linking process of the protein film. However, the original low-viscosity emulsion can be restored by simply rehydrating the solidified fluid. Therefore, the present procedure offers an appealing strategy to build up solid properties for hydrophobic liquids while preserving the low viscosity and ease of manufacturing.     

CROSS-LINKING OF MEMBRANE PROTEINS AND PROTOPORPHYRIN-SENSITIZED PHOTOHEMOLYSIS*

Abstract— Irradiation of protoporphyrin-sensitized red cells with blue light in the presence of oxygen alters many components of their membranes and eventually leads to hemolysis. Extensive cross-linking of membrane proteins can be observed before hemolysis occurs (Girotti, 1976).
Facile oxidative hemolysis can be achieved without observable cross-linking of membrane proteins upon incubation (37°C) of red cells containing membrane-bound 3ß-hydroxy-5α-hydroperoxy-△⁶-cholcstene. Thus, protein cross-linking is not obligatory for oxidative lysis. Deoxygenation by Ar bubbling strongly retards the light-induced increase in osmotic fragility and strongly inhibits eventual hemolysis of protoporphyrin-sensitized erythrocytes. However, similar reduction in oxygen concentration only partially inhibits cross-linking of membrane proteins. These results suggest that membrane protein cross-linking and photohemolysis are not coupled processes.     

Stereoselective and regioselective reaction of cyclic ortho esters with phenols

Cyclic ortho esters undergo stereoselective and regioselective reaction with phenols when treated with BF(3) x OEt(2) at low temperatures. Attack of the phenol on the ortho ester occurs at an open carbon para to electron-donating groups on the phenol ("C-addition") or at the phenolic hydroxyl group ("O-addition") depending on the nature of the cation formed from reaction of the ortho ester and BF(3) x OEt(2). Products resulting from O-addition undergo reversion to a mixture of starting phenol, C-addition product, and O-addition product if treated with BF(3) x OEt(2) at room temperature, but C-addition products are stable under the same conditions. X-ray structural analysis of the C-addition compound indicates that its stereochemistry is opposite to that observed in reaction of similar ortho esters with chloride from TMSCl. However, the stereochemistry of the reaction can be rationalized by the ability of the ortho ester to isomerize via an intermediate benzylic cation and examination of the preferred trajectory of attack of the nucleophile on the intermediate oxonium ion.     

Pd-catalyzed amidation of aryl chlorides using monodentate biaryl phosphine ligands: a kinetic, computational, and synthetic investigation

We present results on the amidation of aryl halides and sulfonates utilizing a monodentate biaryl phosphine-Pd catalyst. Our results are in accord with a previous report that suggests that the formation of kappa(2)-amidate complexes is deleterious to the effectiveness of a catalyst for this transformation and that their formation can be prevented by the use of appropriate bidentate ligands. We now provide data that suggest that the use of certain monodentate ligands can also prevent the formation of the kappa(2)-amidate complexes and thereby generate more stable catalysts for the amination of aryl chlorides. Furthermore, computational studies shed light on the importance of the key feature(s) of the biaryl phosphines (a methyl group ortho to the phosphorus center) that enable the coupling to occur. The use of ligands that possess a methyl group ortho to the phosphorus center allows a variety of aryl and heteroaryl chlorides with various amides to be coupled in high yield.     

Improvement of the surface of polyethylene foamed sheet by irradiation

The manufacturing methods of cross-linked polyethylene foams are classified into two categories based on a type of cross-linking. One is chemical cross-linking by using peroxide as a cross-linking agent. The other method is cross-linking by irradiation. As for chemical cross-linking, a fairly thick foam sheet can be produced, and a comparatively high degree of cross-linking can be achieved. This means chemical cross-linking excels in thermo-forming but, due to a rough surface, the product is lacking in adhesive property and printability. We studied how to improve the surface condition of foam sheet without damaging the features proceeding from chemical cross-linking. As a result, it has been revealed that at the pre-stage of foaming, and by irradiating the surface at low voltage, the resultant foamed sheet with smooth surfaces and excelling in mechanical properties can be produced.     

Protein release from poly(ortho ester) extruded rods

Poly(ortho ester) rods containing 15 wt% FITC‐BSA were prepared by extruding an intimate mixture of finely powdered polymer and protein at a temperature where protein activity is retained. After an induction period, linear in vitro release kinetics were obtained with concomitant polymer weight loss.     

Chemistry of periodate-mediated cross-linking of 3,4-dihydroxylphenylalanine-containing molecules to proteins

Chemical cross-linking is an attractive approach to map peptide-protein and protein-protein complexes. Previously, we explored 3,4-dihydroxylphenylalanine (DOPA) as a protein cross-linking agent upon periodate oxidation (Burdine, L.; Gillette, T. G.; Lin, H.-J.; Kodadek, T. J. Am. Chem. Soc. 2004, 126, 11442-11443). We report here a study on the chemistry of DOPA-protein cross-linking. First, using a peptide nucleic acid templated system, we identified the alpha-amino, epsilon-amino of Lys, imidazole of His, and thiol of Cys as functional groups capable of attacking DOPA ortho-quinone. Second, we demonstrated that periodate-induced DOPA-protein cross-linking could be carried out efficiently at neutral pH in the presence of excess aliphatic 1,2-diols such as ethylene glycol, lactose, and adenosine triphosphate. This result indicated that DOPA-protein cross-linking and 1,2-diol oxidative cleavage proceed via different mechanisms and that carbohydrates will not interfere with this process when carried out in crude cell extracts or on intact cells.