Efficient generation of dendritic arrays of cross-linked hemoglobin: symmetry and redundancy

Chemically connected protein arrays have significant diverse applications including the production of red cell substitutes, bioconjugate drug delivery, and protein therapies. In order to make materials of defined structure, there is a need for efficient and accessible reagents. While chemical cross-linking with a multi-subunit protein can be achieved in high yield, connecting proteins to one another in a dendritic assembly along with concurrent cross-linking has met with limited success. This has now been overcome through the design and implementation of a readily prepared reagent with added reaction sites that compensate for competing hydrolysis. N,N',N'-Tris[bis(sodium methyl phosphate)isophthalyl]-1,3,5-benzenetricarboxamide (1), a hexakis(methyl phosphate) isophthalyl trimesoyl tris-amide, was designed and synthesized in high yield in three stages from a reactive trimesoyl core. This material has three pairs of coplanar cross-linking reaction sites in a symmetrical array. The presence of three sets of sites greatly increases the probability that at least two sets will produce cross-links within hemoglobin tetramers (in competition with hydrolysis) and thereby connect two cross-linked tetramers at the same time. Reaction of 1 with deoxyhemoglobin at pH 8.5 gives a material that contains two cross-linked hemoglobin tetramers connected to one another and to a constituent alphabeta dimer. Products were characterized by SDS-PAGE, MS, enzyme digestion and HPLC. The isolated dendritic-hemoglobin with 2.5 tetrameric components has the same oxygen affinity as native hemoglobin (P50 = 5.0 torr) and retains cooperativity (n50 = 2.0). Analysis of circular dichroism spectra indicates that the assembly retains proper folding of the globin chains while the hemes are in an altered environment.     

Preparation of monodisperse poly(N-isopropylacrylamide) microgel particles with homogenous cross-link density distribution

Monodisperse microgel latex with homogeneous cross-link density distribution within the particles was prepared by feeding the monomer and cross-linker into the reaction mixture in a regulated way during the polymerization. To determine the appropriate monomer feeding parameters, the kinetics of the particle formation was investigated by HPLC. The swelling and optical characteristics of the prepared homogenously cross-linked microgel particles were compared to the properties of inhomogenously cross-linked microgels prepared by the normal precipitation polymerization method. The distribution of the cross-link density within the particles inserts a great influence on the characteristics of the system. The degree of swelling of the homogeneous particles is significantly higher than that of the heterogeneous microgel particles. Furthermore, at room temperature the pNIPAm latex containing the homogeneously cross-linked particles is transparent, while the heterogeneously cross-linked particles form a highly turbid system at the same 0.1 wt% concentration.     

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.     

Synthesis of oligonucleotides containing an O-G-alkyl-O-G interstrand cross-link

A methodology to synthesize oligonucleotides containing an alkyl interstrand cross-link between the two O6 atoms of deoxyguanosine has been developed. This cross-link is designed to serve as a stable structural mimic of the lesion formed in duplex DNA with the bifunctional alkylating agent hepsulfam. The O6-alkyl coupling is performed via a Mitsunobu reaction between a nucleoside and mono-protected 1,7-heptanediol. Solid-phase oligonucleotide synthesis using a nucleoside bis-phosphoramidite allows for the assembly of the cross-linked duplex. Sufficient quantities of this cross-linked duplex were obtained for various structural and biological investigations.     

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.     

Mispair-aligned N3T-alkyl-N3T interstrand cross-linked DNA: synthesis and characterization of duplexes with interstrand cross-links of variable lengths

Therapeutic bifunctional alkylating agents generate interstrand cross-links in duplex DNA. As part of our continuing studies on DNA duplexes that contain alkyl interstrand cross-links, we have synthesized a cross-link that bridges the N(3) positions of a mismatched thymidine base pair. This cross-link, which is similar to the N(3)C-alkyl-N(3)C cross-link that has been observed between mismatched cytosine base pairs, was introduced by first incorporating a cross-linked phosphoramidite unit at the 5'-end of an oligonucleotide chain. Fully cross-linked duplexes were then synthesized using an orthogonal approach to selectively remove protecting groups, thus allowing construction of the cross-linked duplex via conventional solid-phase oligonucleotide synthesis. Short DNA duplexes with alkyl cross-links of various lengths (two, four, and seven methylene units) were prepared, and their physical properties were studied via UV thermal denaturation and circular dichroism spectroscopy. These linkers were found to stabilize the duplexes by 37, 31, and 16 degrees C for the two-, four-, and seven-carbon linkers, respectively, relative to a non-cross-linked duplex. Circular dichroism spectra suggested that these lesions induce very little deviation in the global structure relative to the non-cross-linked duplex DNA control. Molecular models show that the two-carbon cross-link spans the distance between the N(3) atoms of the T-T mismatch without perturbing the helix structure, whereas the longer linkers, particularly the seven-carbon linker, tend to push the thymines apart, creating a local distortion. This perturbation may account for the lower thermal stability of the seven-carbon versus two-carbon cross-linked duplex.     

Synthesis and characterization of DNA duplexes containing an N(4)C-ethyl-N(4)C interstrand cross-link

Short DNA duplexes containing an N(4)C-ethyl-N(4)C interstrand cross-link, C-C, were synthesized on controlled pore glass supports. Duplexes having two, three, or four A/T base pairs on either side of the C-C cross-link and terminating with a C(4) overhang at their 5'-ends were prepared. The cross-link was introduced using a convertible nucleoside approach. Thus, an oligonucleotide terminating at its 5'-end with O(4)-triazoyl-2'-deoxyuridine was first prepared on the support. The triazole group of support-bound oligomer was displaced by the aminoethyl group of 5'-dimethoxytrityl-3'-O-tert-butyldimethylsilyl-N(4)-(2-aminoethyl)deoxycytidine to give the cross-link. The dimethoxytrityl group was removed, and the upper and lower strands of the duplex were extended from two 5'-hydroxyl groups of the cross-link using protected nucleoside 3'-phosphoramidites. The tert-butyldimethylsilyl group of the resulting partial duplex was then removed, and the chain was extended in the 3'-direction from the resulting 3'-hydroxyl of the cross-link using protected nucleoside 5'-phosphoramidites. The cross-linked duplexes were purified by HPLC and characterized by enzymatic digestion and MALDI-TOF mass spectrometry. Duplexes with three or four A/T base pairs on either side of the C-C cross-link gave sigmoidal shaped A(260) profiles when heated, a behavior consistent with cooperative denaturation of the A/T base pairs. Each cross-linked duplex could be ligated to an acceptor duplex using T4 DNA ligase, a result that suggests that the C-C cross-link does not interfere with the ligation reaction, even when it is located only two base pairs from the site of ligation. The ability to synthesize duplexes with a defined interstrand cross-link and to incorporate these duplexes into longer pieces of DNA should enable preparation of substrates that can be used for a variety of biophysical and biochemical experiments, including studies of DNA repair.     

Analytical characterisation of glutardialdehyde cross-linking products in gelatine-gum arabic complex coacervates

Encapsulates having shells of cross-linked mixtures of proteins and polysaccharides are widely used in the food and pharmaceutical industry for controlled release of actives and flavour compounds. In order to be able to predict the behaviour and the release characteristics of the microcapsules, a better understanding of the nature and extent of the cross-linking reaction is needed. Several analytical techniques were applied for the characterisation of glutardialdehyde (GDA) cross-linked encapsulates made of gelatine and gum arabic. To allow the use of sensitive, high-resolution methods such as chromatography and mass spectrometry, the sample first had to be hydrolysed. In this way, a mixture of amino acids, small peptides and the cross-link moieties was obtained. High-resolution liquid chromatography coupled to high-resolution mass spectrometry (HPLC-MS) was applied to detect possible cross-link markers through a comparison of HPLC-MS mass-chromatograms obtained for cross-linked and non-cross-linked coacervates. HPLC-MS/MS was used to identify the species responsible for the differences. Cross-linking occurred between GDA molecules and lysine and hydroxylysine epsilon-amino groups, and up to eight cross-link products of different nature could be identified. They included pyridinium ions and Schiff bases, and also unreacted GDA condensation products. Next, based on the insight gained in the possible chemical structures present in the cross-link markers, methods for selective labelling of these functionalities were employed to allow easier detection of related reaction products. Both liquid chromatography (LC) and gas chromatography (GC) were used in these experiments. Unfortunately, these approaches failed to detect new cross-link markers, most likely as a result of the low levels at which these are present.     

Cross-linked bis-hemoglobins: connections and oxygen binding

Covalently linked pairs of cross-linked hemoglobin tetramers ("bis-tetramers", shown schematically as 6-8) were prepared by reacting hemoglobin A with tetrakis acyl phosphate esters (3-5). The effects of the link between tetramers are observed in the oxygen-binding properties of the bis-tetramers: they bind oxygen cooperatively but with Hill coefficients (n(50)) lower than that of the native protein and with a high average affinity. The bis-tetramers with longer connections between tetramers show a higher n(50), suggesting that steric interactions between the tetramers affect cooperativity. These results correlate to the observed reduced vasoactivity of heterogeneous solutions of oligomeric cross-linked hemoglobin tetramers.     

Protein diffusion in charged polyacrylamide gels. Visualization and analysis

Protein diffusion in anionic, cross-linked polyacrylamide-based gels supported in fused-silica capillaries was characterized by a direct visualization method. Microphotography was used to obtain transient protein concentration profiles in these gels using cytochrome c as a probe molecule. Gels based on acrylamido-methylpropane sulfonic acid with 2.5-10% N,N'-methylene-bisacrylamide as a cross-linker and with a total polymer concentration of 0.21 g/cm3 yielded diffuse protein concentration profiles which were quantitatively consistent with a Fickian diffusion model. An analytical method was developed to calculate the diffusivity as a function of protein concentration in the gel from the experimental profiles. The diffusivity was found to assume values in the range 2.5-5.5x10(-8) cm2/s and varied somewhat with the protein concentration in the gel. The effects of some of the polymer properties, such as cross-link density, polymer concentration and charge, were also investigated for a limited range of conditions to derive qualitative trends. Results showed that the transport rates increased with a decrease in the cross-link density, were extremely reduced when the polymer concentration was doubled, and were slightly increased when the charge density was decreased by half by polymerizing a 1:1 mixture of acrylamide and acrylamido-methylpropane sulfonic acid monomers.     

固化反应产物网络结构的表征

本文论证了在交联点为三分枝的固化反应中,每一对未反应的基团使固化产物有效链损失数目为常数3。ΣA_(ai)—ΣB_(bj) 型固化反应的交联密度是官能团密度、有效数均官能度、配料比、固化体系凝胶分数、A(或B)基凝胶相反应程度、A_(ai)(或B_(bj))链节凝胶分数的函数。后两个不能直接测定的参数,可通过测定固化反应体系溶胶分数及溶胶相 A 基和 B 基的反应程度而获得。     

Highly efficient sequence-specific DNA interstrand cross-linking by pyrrole/imidazole CPI conjugates

We have developed a novel type of DNA interstrand cross-linking agent by synthesizing dimers of a pyrrole (Py)/imidazole (Im)-diamide-CPI conjugate, ImPyLDu86 (1), connected using seven different linkers. The tetramethylene linker compound, 7b, efficiently produces DNA interstrand cross-links at the nine-base-pair sequence, 5'-PyGGC(T/A)GCCPu-3', only in the presence of a partner triamide, ImImPy. For efficient cross-linking by 7b with ImImPy, one A.T base pair between two recognition sites was required to accommodate the linker region. Elimination of the A.T base pair and insertion of an additional A.T base pair and substitution with a G.C base pair significantly reduced the degree of cross-linking. The sequence specificity of the interstrand cross-linking by 7b was also examined in the presence of various triamides. The presence of ImImIm slightly reduced the formation of a cross-linked product compared to ImImPy. The mismatch partners, ImPyPy and PyImPy, did not produce an interstrand cross-link product with 7b, whereas ImPyPy and PyImPy induced efficient alkylation at their matching site with 7b. The interstrand cross-linking abilities of 7b were further examined using denaturing polyacrylamide gel electrophoresis with 5'-Texas Red-labeled 400- and 67-bp DNA fragments. The sequencing gel analysis of the 400-bp DNA fragment with ImImPy demonstrated that 7b alkylates several sites on the top and bottom strands, including one interstrand cross-linking match site, 5'-PyGGC(T/A)GCCPu-3'. To obtain direct evidence of interstrand cross-linkages on longer DNA fragments, a simple method using biotin-labeled complementary strands was developed, which produced a band corresponding to the interstrand cross-linked site on both top and bottom strands. Densitometric analysis indicated that the contribution of the interstrand cross-link in the observed alkylation bands was approximately 40%. This compound efficiently cross-linked both strands at the target sequence. The present system consisted of a 1:2 complex of the alkylating agent and its partner ImImPy and caused an interstrand cross-linking in a sequence-specific fashion according to the base-pair recognition rule of Py-Im polyamides.     

Initiated chemical vapor deposition of linear and cross-linked poly(2-hydroxyethyl methacrylate) for use as thin-film hydrogels

Initiated chemical vapor deposition (iCVD) is able to synthesize linear and cross-linked poly(2-hydroxyethyl methacrylate) (PHEMA) thin films, in one step, from vapors of 2-hydroxyethyl methacrylate (HEMA), ethylene glycol diacrylate (EGDA), and tert-butyl peroxide (TBPO) without using any solvents. This all-dry technique also allows control of the cross-link density by adjusting the partial pressure of the cross-linking agent EGDA in the vapor phase. Films with specific cross-link densities and hence thermal, wetting, and swelling properties can be created in one single vacuum processing step. Through selective thermal decomposition of the initiator TBPO, films with well-defined chemical structures and full functionality retention can be deposited, which is evident in the Fourier transform infrared (FTIR) and X-ray photoelectron spectroscopy (XPS) analyses. These spectroscopic methods also facilitate determination of EGDA incorporation in the cross-linked films based on the fact that HEMA contains a hydroxyl group but EGDA does not. For the linear PHEMA depositions, the growth rate was found to be nonlinear in the partial pressure of HEMA, possibly due to nonlinear multilayer adsorption and/or primary termination. The EGDA/HEMA ratio in the films systematically increased from 0.00 to 0.46 as the EGDA partial pressure was raised. The onset temperatures of decomposition were between 270 and 302 degrees C for the linear and the most cross-linked films, respectively. Thermal annealing at approximately 430 degrees C resulted in minuscule amounts of residue for all films, linear or cross-linked. The most cross-linked film had approximately 99.50% thickness removed after annealing. The contact angle was found to increase with increasing cross-link density. Significant contact-angle hysteresis was observed, indicating surface reconfiguration, and the lowest receding angle was 17 degrees for the linear film. Swelling measurements using spectroscopic ellipsometry showed that the degree of swelling decreased with increasing EGDA incorporation. The water content decreased from 35% (v/v) for the linear film to below 10% (v/v) for the most cross-linked film. These results show that iCVD is able to produce PHEMA thin films that function as hydrogels when soaked in water. The spectroscopic results, the contact-angle results, and the swelling analysis altogether prove the retention of the hydrophilic pendant groups in the iCVD process.     

REPAIR IN Escherichia coli OF A PSORALEN-DNA INTERSTRAND CROSSLINK SITE SPECIFICALLY INTRODUCED INTO T410A411 OF THE PLASMID pUC 19

Abstract— Escherichia coli was transformed with a pUC 19 plasmid which contained a 4,5',8-trimethylpsoralen cross-link specifically at position T₄₁₀-A₄₁₁, and transformants in which the cross-link had been repaired were scored on the basis of ampicillin resistance. Repair was only seen after induction of the SOS-system by shortwave ultraviolet irradiation. The repair efficiency was 6%, and of 100 colonies analyzed only two was found to be mutated at the cross-linked site: a T-A transversion was observed at position 410. A repair mechanism which does not involve recombination is proposed.     

Spectroscopic characterization of interstrand carbinolamine cross-links formed in the 5'-CpG-3' sequence by the acrolein-derived gamma-OH-1,N2-propano-2'-deoxyguanosine DNA adduct

The interstrand N2,N2-dG DNA cross-linking chemistry of the acrolein-derived gamma-OH-1,N2-propanodeoxyguanosine (gamma-OH-PdG) adduct in the 5'-CpG-3' sequence was monitored within a dodecamer duplex by NMR spectroscopy, in situ, using a series of site-specific 13C- and 15N-edited experiments. At equilibrium 40% of the DNA was cross-linked, with the carbinolamine form of the cross-link predominating. The cross-link existed in equilibrium with the non-crosslinked N2-(3-oxo-propyl)-dG aldehyde and its geminal diol hydrate. The ratio of aldehyde/diol increased at higher temperatures. The 1,N2-dG cyclic adduct was not detected. Molecular modeling suggested that the carbinolamine linkage should be capable of maintaining Watson-Crick hydrogen bonding at both of the tandem C x G base pairs. In contrast, dehydration of the carbinolamine cross-link to an imine (Schiff base) cross-link, or cyclization of the latter to form a pyrimidopurinone cross-link, was predicted to require disruption of Watson-Crick hydrogen bonding at one or both of the tandem cross-linked C x G base pairs. When the gamma-OH-PdG adduct contained within the 5'-CpG-3' sequence was instead annealed into duplex DNA opposite T, a mixture of the 1,N2-dG cyclic adduct, the aldehyde, and the diol, but no cross-link, was observed. With this mismatched duplex, reaction with the tetrapeptide KWKK formed DNA-peptide cross-links efficiently. When annealed opposite dA, gamma-OH-PdG remained as the 1,N2-dG cyclic adduct although transient epimerization was detected by trapping with the peptide KWKK. The results provide a rationale for the stability of interstrand cross-links formed by acrolein and perhaps other alpha,beta-unsaturated aldehydes. These sequence-specific carbinolamine cross-links are anticipated to interfere with DNA replication and contribute to acrolein-mediated genotoxicity.     

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.     

The Effect of Composition of Copolymeric Hydrogels on Their Physicochemical Parameters

Physicochemical characteristics of gel systems based on slightly cross-linked acrylamide-acrylic acid copolymers were studied and their dependences on such parameters as the cross-link density, the monomer ratio, and the total content of the monomers in a hydrogel were determined. A burn-healing hydrogel material developed on the basis of this study is nontraumatic, transparent; it is characterized by a high absorption capacity with respect to wound exudates and a delayed release of incorporated drugs.     

Reliable Identification of Cross-Linked Products in Protein Interaction Studies by 13C-Labeled p-Benzoylphenylalanine

We describe the use of the ¹³C-labeled artificial amino acid p-benzoyl-L-phenylalanine (Bpa) to improve the reliability of cross-linked product identification. Our strategy is exemplified for two protein–peptide complexes. These studies indicate that in many cases the identification of a cross-link without additional stable isotope labeling would result in an ambiguous assignment of cross-linked products. The use of a ¹³C-labeled photoreactive amino acid is considered to be preferred over the use of deuterated cross-linkers as retention time shifts in reversed phase chromatography can be ruled out. The observation of characteristic fragment ions additionally increases the reliability of cross-linked product assignment. Bpa possesses a broad reactivity towards different amino acids and the derived distance information allows mapping of spatially close amino acids and thus provides more solid structural information of proteins and protein complexes compared to the longer deuterated amine-reactive cross-linkers, which are commonly used for protein 3D-structure analysis and protein–protein interaction studies. Figure

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