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1.
Combining the properties of a zero‐length cross‐linker with cleavability by tandem mass spectrometry (MS/MS) poses great advantages for protein structure analysis using the cross‐linking/MS approach. These include a reliable, automated data analysis and the possibility to obtain short‐distance information of protein 3D‐structures. We introduce 1,1′‐carbonyldiimidazole (CDI) as an easy‐to‐use and commercially available, low‐cost reagent that ideally fulfils these features. CDI bridges primary amines and hydroxy groups in proteins with the lowest possible spacer length of one carbonyl unit (ca. 2.6 Å). The cross‐linking reaction can be conducted under physiological conditions in the pH range between 7.2 and 8. Urea and carbamate cross‐linked products are cleaved upon collisional activation during MS/MS experiments generating characteristic product ions, greatly improving the unambiguous identification of cross‐links. Our innovative analytical concept is exemplified and applied for bovine serum albumin (BSA), wild‐type tumor suppressor p53, an intrinsically disordered protein, and retinal guanylyl cyclase activating protein‐2 (GCAP‐2).  相似文献   

2.
Chemical cross‐linking combined with a subsequent enzymatic digestion and mass spectrometric analysis of the created cross‐linked products presents an alternative approach to assess low‐resolution protein structures. By covalently connecting pairs of functional groups within a protein or a protein complex a set of structurally defined interactions is built up. We synthesized the heterobifunctional amine‐reactive photo‐cross‐linker N‐succinimidyl p‐benzoyldihydrocinnamate as a non‐deuterated (SBC) and doubly deuterated derivative (SBDC). Applying a 1:1 mixture of SBC and SBDC for cross‐linking experiments aided the identification of cross‐linked amino acids in the mass spectra based on the characteristic isotope patterns of fragment ions. The cross‐linker was applied to the calcium‐binding protein calmodulin with a subsequent analysis of cross‐linked products by nano‐high‐performance liquid chromatography matrix‐assisted laser desorption/ionization tandem time‐of‐flight mass spectrometry (nano‐HPLC/MALDI‐TOF/TOF‐MS) and nano‐HPLC/nano‐electrospray ionization (ESI)‐LTQ‐Orbitrap‐MS. Copyright © 2009 John Wiley & Sons, Ltd.  相似文献   

3.
Chemical cross‐linking combined with mass spectrometry (XL‐MS) and computational modeling has evolved as an alternative method to derive protein 3D structures and to map protein interaction networks. Special focus has been laid recently on the development and application of cross‐linkers that are cleavable by collisional activation as they yield distinct signatures in tandem mass spectra. Building on our experiences with cross‐linkers containing an MS‐labile urea group, we now present the biuret‐based, CID‐MS/MS‐cleavable cross‐linker imidodicarbonyl diimidazole (IDDI) and demonstrate its applicability for protein cross‐linking studies based on the four model peptides angiotensin II, MRFA, substance P, and thymopentin.  相似文献   

4.
The fragmentation behavior of a novel thiourea‐based cross‐linker molecule specifically designed for collision‐induced dissociation (CID) MS/MS experiments is described. The development of this cross‐linker is part of our ongoing efforts to synthesize novel reagents, which create either characteristic fragment ions or indicative constant neutral losses (CNLs) during tandem mass spectrometry allowing a selective and sensitive analysis of cross‐linked products. The new derivatizing reagent for chemical cross‐linking solely contains a thiourea moiety that is flanked by two amine‐reactive N‐hydroxy succinimide (NHS) ester moieties for reaction with lysines or free N‐termini in proteins. The new reagent offers simple synthetic access and easy structural variation of either length or functionalities at both ends. The thiourea moiety exhibits specifically tailored CID fragmentation capabilities—a characteristic CNL of 85 u—ensuring a reliable detection of derivatized peptides by both electrospray ionization (ESI) and matrix‐assisted laser desorption/ionization (MALDI) tandem mass spectrometry and as such possesses a versatile applicability for chemical cross‐linking studies. A detailed examination of the CID behavior of the presented thiourea‐based reagent reveals that slight structural variations of the reagent will be necessary to ensure its comprehensive and efficient application for chemical cross‐linking of proteins. Copyright © 2010 John Wiley & Sons, Ltd.  相似文献   

5.
Chemical cross‐linking combined with mass spectrometry (MS) has been used to elucidate protein structures and protein‐protein interactions. However, heterogeneity of the samples and the relatively low abundance of cross‐linked peptides make this approach challenging. As an effort to overcome this hurdle, we have synthesized lysine‐reactive homobifunctional cross‐linkers with the biotin in the middle of the linker and used them to enrich cross‐linked peptides. The reaction of biotin‐tagged cross‐linkers with purified HIV‐1 CA resulted in the formation of hanging and intramolecular cross‐links. The peptides modified with biotinylated cross‐linkers were effectively enriched and recovered using a streptavidin‐coated plate and MS‐friendly buffers. The enrichment of modified peptides and removal of the dominantly unmodified peptides simplify mass spectra and their analyses. The combination of the high mass accuracy of Fourier transform ion cyclotron resonance (FT‐ICR) MS and the tandem mass spectrometric (MS/MS) capability of the linear ion trap allows us to unambiguously identify the cross‐linking sites and additional modification, such as oxidation. Copyright © 2009 John Wiley & Sons, Ltd.  相似文献   

6.
The use of mass spectrometry coupled with chemical cross‐linking of proteins has become one of the most useful tools for proteins structure and interactions studies. One of the challenges in these studies is the identification of the cross‐linked peptides. The interpretation of the MS/MS data generated in cross‐linking experiments using N‐hydroxy succinimide esters is not trivial once a new amide bond is formed allowing new fragmentation pathways, unlike linear peptides. Intermolecular cross‐linked peptides occur when two different peptides are connected by the cross‐linker and they yield information on the spatial proximity of different domains (within a protein) or proteins (within a complex). In this article, we report a detailed fragmentation study of intermolecular cross‐linked peptides, generated from a set of synthetic peptides, using both ESI and MALDI to generate the precursor ions. The fragmentation features observed here can be helpful in the interpretation and identification of cross‐linked peptides present in cross‐linking experiments and be further implemented in search engine's algorithms. Copyright © 2011 John Wiley & Sons, Ltd.  相似文献   

7.
A series of novel organotin‐containing core‐cross‐linked knedels and shell‐cross‐linked knedels were first synthesized facilely from poly(styrene)‐b‐poly(acrylate acid) nanoparticles in different selective solvents [Tetrahydrofuran (THF)/H2O or THF/n‐octane] by using organotin compound 1,3‐dichloro‐tetra‐n‐butyl‐distannoxane as a new cross‐linker. The formation of the 1‐chloro‐3‐carboxylato‐tetra‐n‐butyl‐distannoxane layer in our cross‐linking reaction was supported by Fourier transform infrared (FT‐IR) and inductive coupled plasma emission spectrometer (ICP) analysis of the resulting shell‐cross‐linked knedels and core‐cross‐linked knedels. Transmission electron microscopy (TEM) study showed the spherical morphology and the size of the core‐cross‐linked knedels and shell‐cross‐linked knedel. Especially, the layer structure of the core‐cross‐linked knedels was clearly displayed in TEM image. The increase of extent of cross‐linking lead to the increasing of diameter for the shell‐cross‐linked knedels, whereas there was no significant effect on the core‐cross‐linked knedels. Dynamic light scattering (DLS) measurements gave hydrodynamic diameters of the core‐cross‐linked knedels that were in agreement with the TEM diameters. Moreover, the wall thickness of the shell layer of the core‐cross‐linked knedels could be easily modified by varying the block copolymer composition. Notably, the organotin‐containing core‐cross‐linked knedel exhibited highly efficient catalytic activity for the aqueous esterification reaction under nearly neutral conditions. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010  相似文献   

8.
This contribution is part of our ongoing efforts to develop innovative cross‐linking (XL) reagents and protocols for facilitated peptide mixture analysis and efficient assignment of cross‐linked peptide products. In this report, we combine in‐source Paternò‐Büchi (PB) photo‐chemistry with a tandem mass spectrometry approach to selectively address the fragmentation of a tailor‐made cross‐linking reagent. The PB photochemistry, so far exclusively used for the identification of unsaturation sites in lipids and in lipidomics, is now introduced to the field of chemical cross‐linking. Based on trans‐3‐hexenedioic acid, an olefinic homo bifunctional amine reactive XL reagent was designed and synthesized for this proof‐of‐principle study. Condensation products of the olefinic reagent with a set of exemplary peptides are used to test the feasibility of the concept. Benzophenone is photochemically reacted in the nano‐electrospray ion source and forms oxetane PB reaction products. Subsequent CID‐MS triggered retro‐PB reaction of the respective isobaric oxetane molecular ions and delivers reliably and predictably two sets of characteristic fragment ions of the cross‐linker. Based on these signature ion sets, a straightforward identification of covalently interconnected peptides in complex digests is proposed. Furthermore, CID‐MSn experiments of the retro‐PB reaction products deliver peptide backbone characteristic fragment ions. Additionally, the olefinic XL reagents exhibit a pronounced robustness upon CID‐activation, without previous UV‐excitation. These experiments document that a complete backbone fragmentation is possible, while the linker‐moiety remains intact. This feature renders the new olefinic linkers switchable between a stable, noncleavable cross‐linking mode and an in‐source PB cleavable mode.  相似文献   

9.
Chemical cross‐linking, combined with mass spectrometry, has been applied to map three‐dimensional protein structures and protein–protein interactions. Proper choice of the cross‐linking agent, including its reactive groups and spacer arm length, is of great importance. However, studies to understand the details of reactivity of the chemical cross‐linkers with proteins are quite sparse. In this study, we investigated chemical cross‐linking from the aspects of the protein structures and the cross‐linking reagents involved, by using two structurally well‐known proteins, glyceraldehyde 3‐phosohate dehydrogenase and ribonuclease S. Chemical cross‐linking reactivity was compared using a series of homo‐ and hetero‐bifunctional cross‐linkers, including bis(sulfosuccinimidyl) suberate, dissuccinimidyl suberate, bis(succinimidyl) penta (ethylene glycol), bis(succinimidyl) nona (ethylene glycol), m‐maleimidobenzoyl‐N‐hydroxysulfosuccinimide ester, 2‐pyridyldithiol‐tetraoxaoctatriacontane‐N‐hydrosuccinimide and succinimidyl‐[(N‐maleimidopropionamido)‐tetracosaethyleneglycol]ester. The protein structure itself, especially the distances between target amino acid residues, was found to be a determining factor for the cross‐linking efficiency. Moreover, the reactive groups of the chemical cross‐linker also play an important role; a higher cross‐linking reaction efficiency was found for maleimides compared to 2‐pyrimidyldithiols. The reaction between maleimides and sulfhydryl groups is more favorable than that between N‐hydroxysuccinimide esters and amine groups, although cysteine residues are less abundant in proteins compared to lysine residues. Copyright © 2013 John Wiley & Sons, Ltd.  相似文献   

10.
We present an integrated approach for investigating the topology of proteins through native mass spectrometry (MS) and cross‐linking/MS, which we applied to the full‐length wild‐type p53 tetramer. For the first time, the two techniques were combined in one workflow to obtain not only structural insight in the p53 tetramer, but also information on the cross‐linking efficiency and the impact of cross‐linker modification on the conformation of an intrinsically disordered protein (IDP). P53 cross‐linking was monitored by native MS and as such, our strategy serves as a quality control for different cross‐linking reagents. Our approach can be applied to the structural investigation of various protein systems, including IDPs and large protein assemblies, which are challenging to study by the conventional methods used for protein structure characterization.  相似文献   

11.
We have synthesized a homobifunctional active ester cross‐linking reagent containing a TEMPO (2,2,6,6‐tetramethylpiperidine‐1‐oxy) moiety connected to a benzyl group (Bz), termed TEMPO‐Bz‐linker. The aim for designing this novel cross‐linker was to facilitate MS analysis of cross‐linked products by free radical initiated peptide sequencing (FRIPS). The TEMPO‐Bz‐linker was reacted with all 20 proteinogenic amino acids as well as with model peptides to gain detailed insights into its fragmentation mechanism upon collision activation. The final goal of this proof‐of‐principle study was to evaluate the potential of the TEMPO‐Bz‐linker for chemical cross‐linking studies to derive 3D‐structure information of proteins. Our studies were motivated by the well documented instability of the central NO―C bond of TEMPO‐Bz reagents upon collision activation. The fragmentation of this specific bond was investigated in respect to charge states and amino acid composition of a large set of precursor ions resulting in the identification of two distinct fragmentation pathways. Molecular ions with highly basic residues are able to keep the charge carriers located, i.e. protons or sodium cations, and consequently decompose via a homolytic cleavage of the NO―C bond of the TEMPO‐Bz‐linker. This leads to the formation of complementary open‐shell peptide radical cations, while precursor ions that are protonated at the TEMPO‐Bz‐linker itself exhibit a charge‐driven formation of even‐electron product ions upon collision activation. MS3 product ion experiments provided amino acid sequence information and allowed determining the cross‐linking site. Our study fully characterizes the CID behavior of the TEMPO‐Bz‐linker and demonstrates its potential, but also its limitations for chemical cross‐linking applications utilizing the special features of open‐shell peptide ions on the basis of selective tandem MS analysis. Copyright © 2015 John Wiley & Sons, Ltd.  相似文献   

12.
Structure elucidation of tertiary or quaternary protein structures by chemical cross‐linking and mass spectrometry (MS) has recently gained importance. To locate the cross‐linker modification, dedicated software is applied to analyze the mass or tandem mass spectra (MS/MS). Such software requires information on target amino acids to limit the data analysis time. The most commonly used homobifunctional N‐hydroxy succinimide (NHS) esters are often described as reactive exclusively towards primary amines, although side reactions with tyrosine and serine have been reported. Our goal was to systematically study the reactivity of NHS esters and derive some general rules for their attack of nucleophilic amino acid side chains in peptides. We therefore studied the cross‐linking reactions of synthesized and commercial model peptides with disuccinimidyl suberate (DSS). The first reaction site in all cases was expectedly the α‐NH2‐group of the N‐terminus or the ε‐NH2‐group of lysine. As soon as additional cross‐linkers were attached or loops were formed, other amino acids were also involved in the reaction. In addition to the primary amino groups, serine, threonine and tyrosine showed significant reactivity due to the effect of neighboring amino acids by intermediate or permanent Type‐1 cross‐link formation. The reactivity is highly dependent on the pH and on adjacent amino acids. Copyright © 2009 John Wiley & Sons, Ltd.  相似文献   

13.
A new G‐quadruplex (G‐4)‐directing alkylating agent BMVC‐C3M was designed and synthesized to integrate 3,6‐bis(1‐methyl‐4‐vinylpyridinium iodide)carbazole (BMVC) with aniline mustard. Various telomeric G‐4 structures (hybrid‐2 type and antiparallel) and an oncogene promoter, c‐MYC (parallel), were constructed to react with BMVC‐C3M, yielding 35 % alkylation yield toward G‐4 DNA over other DNA categories (<6 %) and high specificity under competition conditions. Analysis of the intact alkylation adducts by electrospray ionization mass spectroscopy (ESI‐MS) revealed the stepwise DNA alkylation mechanism of aniline mustard for the first time. Furthermore, the monoalkylation sites and intrastrand cross‐linking sites were determined and found to be dependent on G‐4 topology based on the results of footprinting analysis in combination with mass spectroscopic techniques and in silico modeling. The results indicated that BMVC‐C3M preferentially alkylated at A15 (H26), G12 (H24), and G2 (c‐MYC), respectively, as monoalkylated adducts and formed A15–C3M–A21 (H26), G12–C3M–G4 (H24), and G2–C3M–G4/G17 (c‐MYC), respectively, as cross‐linked dialkylated adducts. Collectively, the stability and site‐selective cross‐linking capacity of BMVC‐C3M provides a credible tool for the structural and functional characterization of G‐4 DNAs in biological systems.  相似文献   

14.
《先进技术聚合物》2018,29(1):575-586
In this work, a new surface‐initiating system was constituted on the surfaces of cross‐linked polyvinyl alcohol (CPVA) microspheres, and on this basis, papain surface‐imprinted material was successfully prepared in aqueous solution. CPVA microspheres were modified with chlorethamin as reagent, and so a mass of primary amino group was introduced onto CPVA microspheres. Whereupon, a surface initiating system (−NH2/S2O82−) was formed at the interface between the microspheres and aqueous solution, in which papain as template protein, 4‐styrene sulfonate (SSS) as functional monomer, N,N′‐methylenebisacrylamide (MBA) as cross‐linker and (NH4)2S2O8 as initiator were all dissolved. In neutral solution, the polypeptide chains of papain as a basic protein were positively charged, and the molecules of anionic monomer SSS would spontaneously gather around papain polypeptide chain, forming complex by right of strong electrostatic interaction. The free radicals produced on CPVA microspheres initiated the monomer SSS around papain polypeptide chain and the cross‐linker MBA to produce graft/cross‐linking polymerization, and at the same time, papain macromolecules were embed in the cross‐linked networks. As a result, the graft/cross‐linking polymerizing of SSS and the molecule imprinting of papain were synchronously carried out, and papain surface‐imprinted material, MIP‐PSSS/CPVA microspheres, was obtained. The experimental results show that the papain surface‐imprinted material has excellent binding affinity and high recognition selectivity for papain. The binding capacity of MIP‐PSSS/CPVA microspheres for papain reaches 44 mg/g, and relative to another basic protein, trypsin (TRY) as contrast protein, the selectivity coefficient of MIP‐PSSS/CPVA microspheres for papain is 14.35, displaying very high recognition specificity.  相似文献   

15.
An efficient cross‐linked polymer support for solid‐phase synthesis was prepared by introducing glycerol dimethacrylate cross‐linker to polystyrene network using free radical aqueous suspension polymerization. The support was characterized by various spectroscopic methods. Morphological feature of the resin was analyzed by microscopy. The polymerization reaction was investigated with respect to the effect of amount of cross‐linking agent, which in turn vary the swelling, loading, and the mechanical stability of the resin. The solvent uptake of the polymer was studied in relation to cross‐linking and compared with Merrifield resin. The stability of the resin was tested in different synthetic conditions used for solid‐phase peptide synthesis. Hydroxy group of the support was derivatized to chloro and then amino groups using different reagents and reaction conditions. Efficiency of the support was tested and compared with TentaGel? resin by following different steps involved in the synthesis of the 65–74 fragment of acyl carrier protein. The results showed that the poly(styrene‐co‐glycerol dimethacrylate) (GDMA‐PS) is equally efficient as TentaGel resin in peptide synthesis. The purity of the peptides was analyzed by HPLC and identities were determined by mass spectroscopy and amino acid analysis. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4382–4392, 2005  相似文献   

16.
We developed a simple route to prepare stabilized micelles and nanovesicles in aqueous solutions. A hydrophobic poly(succinimide) (PSI) was conjugated with the hydrophilic poly(ethylene glycol) (PEG) as a new type of cross‐linkable unit. Spherical aggregates were formed when dissolving the amphiphilic PEG682b‐PSI130 copolymer in aqueous solutions directly, and polymer nanovesicles were prepared by a precipitation‐dialysis method using PEG455b‐PSI130 copolymer. Bifunctional primary amine was added to the micelle or nanovesicle solutions to prepare cross‐linked structures via aminolysis reaction of the succinimide units. The degree of cross‐linking was controlled by adjusting the molar ratio of the cross‐linker to the succinimide units. Increasing the degree of cross‐linking leads to the compaction of the micelle core thus reduced diameter. The cross‐linked polymer micelles or nanovesicles maintained their morphology in extremely diluted solutions because of their structural stability. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010  相似文献   

17.
Crystallography and nuclear magnetic resonance are well‐established methods to study protein tertiary structure and interactions. Despite their usefulness, such methods are not applicable to many protein systems. Chemical cross‐linking of proteins coupled with mass spectrometry allows low‐resolution characterization of proteins and protein complexes based on measuring distance constraints from cross‐links. In this work, we have investigated cross‐linking by means of a heterobifunctional cross‐linker containing a traditional N‐hydroxysuccinimide (NHS) ester and a UV photoactivatable diazirine group. Activation of the diazirine group yields a highly reactive carbene species, with potential to increase the number of cross‐links compared with homobifunctional, NHS‐based cross‐linkers. Cross‐linking reactions were performed on model systems such as synthetic peptides and equine myoglobin. After reduction of the disulfide bond, the formation of intra‐ and intermolecular cross‐links was identified and the peptides modified with both NHS and diazirine moieties characterized. Fragmentation of these modified peptides reveals the presence of a marker ion for intramolecular cross‐links, which facilitates identification. Copyright © 2010 John Wiley & Sons, Ltd.  相似文献   

18.
Light‐induced release systems can be triggered remotely and are of interest for many controlled release applications due to the possibility for spatio‐temporal release control. In this study a biotin‐functionalized photocleavable macromer is incorporated with an o‐nitrobenzyl moiety into gelatin methacryloyl(‐acetyl) hydrogels via radical cross‐linking. Stronger immobilization of streptavidin‐coupled horseradish peroxidase occurs in linker‐functionalized hydrogels compared to pure gelatin methacryloyl(‐acetyl) hydrogels, and a controlled release of the streptavidin conjugate upon UV‐irradiation is possible. Liquid chromatography coupled to mass spectrometry (LC‐MS) analysis of aqueous linker solutions allows the identification of the main cleavage products and the cleavage kinetics. Thus, it is shown that a significant hydrolysis of the linker occurs at 37 °C. Nevertheless the system reported here is a promising controlled release scaffold for proteins and application in tissue engineering, if background releases of the immobilized drug are tolerable.  相似文献   

19.
A supramolecular cross‐linked cross‐linker, capable of introducing rotaxane cross‐links to vinyl polymers, has been developed for the rational synthesis of polyrotaxane networks. The experimental results reveal that the combination of an oligocyclodextrin (OCD) and a terminal bulky group‐tethering macromonomer (TBM) forms a polymer‐network structure having polymerizable moieties through supramolecular cross‐linking. Radical polymerization of a variety of typical vinyl monomers in the presence of the vinylic supramolecular cross‐linker (VSC) afforded the corresponding vinyl polymers cross‐linked through the rotaxane cross‐links (RCP) as transparent stable films in high yields under both photoinitiated and thermal polymerization conditions. A poly(N,N‐dimethylacrylamide)‐based hydrogel synthesized by using VSC, RCPDMAAm, displayed a unique mechanical property. The small‐angle X‐ray scattering (SAXS) results, indicating patterns characteristic of a polyrotaxane network, clearly suggested the presence and role of the rotaxane cross‐links. The confirmation of the introduction of rotaxane‐cross‐links into vinyl polymers strongly reveals the significant usefulness of VSC.  相似文献   

20.
In this paper, a novel highly cross‐linked porous monolithic stationary phase having a long alkyl chain ligand (C16) was introduced and evaluated in CEC. The monolithic stationary phase was prepared by in situ copolymerization of 1‐hexadecene, trimethylolpropane trimethacrylate, and 2‐acrylamido‐2‐methyl‐1‐propanesulfonic acid (AMPS) in the presence of ternary porogenic solvent (cyclohexanol/1,4‐butanediol/water). In preparing monoliths, the ternary cross‐linker trimethylolpropane trimethacrylate was usually applied to preparing molecularly imprinted polymers or molecularly imprinted solid‐phase extraction, instead of binary cross‐linker ethylene dimethacrylate. 1‐Hexadecene was introduced to provide the non‐polar sites (C16) for chromatographic retention, while AMPS was used to generate the EOF for transporting the mobile phase through the monolithic capillary. Monolithic columns were prepared by optimizing proportion of porogenic solvent and AMPS content in the polymerization solution as well as the cross‐linkers. The monolithic stationary phases could generate a strong and stable EOF in various pH values and exhibit an RP‐chromatographic behavior for neutral compounds. For charged compounds, the separation was mainly based on the association of hydrophobic, electrostatic and electrophoretic interaction.  相似文献   

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