Preparing to read the ubiquitin code: characterization of ubiquitin trimers by top‐down mass spectrometry

The profound effects of ubiquitination on the movement and processing of cellular proteins depend exquisitely on the structures of monoubiquitin and polyubiquitin modifications. Unconjugated polyubiquitins also have a variety of intracellular functions. Structures and functions are not well correlated yet, because the structures of polyubiquitins and polyubiquitin modifications of proteins are difficult to decipher. We are moving towards a robust strategy to provide that structural information. In this report electron transfer dissociation mass spectra of six synthetic ubiquitin trimers (multiply branched proteins with molecular masses exceeding 25 600 Da) are examined using an Orbitrap Fusion Lumos instrument to determine how top‐down mass spectrometry can characterize the chain topology and linkage sites in a single, facile workflow. The efficacy of this method relies on the formation, detection, and interpretation of extensive fragmentation. Copyright © 2016 John Wiley & Sons, Ltd.     

Nonenzymatic assembly of natural polyubiquitin chains of any linkage composition and isotopic labeling scheme

Polymeric chains made of a small protein ubiquitin act as molecular signals regulating a variety of cellular processes controlling essentially all aspects of eukaryotic biology. Uncovering the mechanisms that allow differently linked polyubiquitin chains to serve as distinct molecular signals requires the ability to make these chains with the native connectivity, defined length, linkage composition, and in sufficient quantities. This, however, has been a major impediment in the ubiquitin field. Here, we present a robust, efficient, and widely accessible method for controlled iterative nonenzymatic assembly of polyubiquitin chains using recombinant ubiquitin monomers as the primary building blocks. This method uses silver-mediated condensation reaction between the C-terminal thioester of one ubiquitin and the ε-amine of a specific lysine on the other ubiquitin. We augment the nonenzymatic approaches developed recently by using removable orthogonal amine-protecting groups, Alloc and Boc. The use of bacterially expressed ubiquitins allows cost-effective isotopic enrichment of any individual monomer in the chain. We demonstrate that our method yields completely natural polyubiquitin chains (free of mutations and linked through native isopeptide bonds) of essentially any desired length, linkage composition, and isotopic labeling scheme, and in milligram quantities. Specifically, we successfully made Lys11-linked di-, tri-, and tetra-ubiquitins, Lys33-linked diubiquitin, and a mixed-linkage Lys33,Lys11-linked triubiquitin. We also demonstrate the ability to obtain, by high-resolution NMR, residue-specific information on ubiquitin units at any desired position in such chains. This method opens up essentially endless possibilities for rigorous structural and functional studies of polyubiquitin signals.     

Preparing to read the ubiquitin code: a middle‐out strategy for characterization of all lysine‐linked diubiquitins

Multiple studies demonstrate that ubiquitination of proteins codes for regulation of cell differentiation, apoptosis, endocytosis and many other cellular functions. There is great interest in and considerable effort being given to defining the relationships between the structures of polyubiquitin modifications and the fates of the modified proteins. Does each ubiquitin modification achieve a specific effect, much like phosphorylation, or is ubiquitin like glycosylation, where there is heterogeneity and redundancy in the signal? The sensitive analytical tools needed to address such questions readily are not yet mature. To lay the foundation for mass spectrometry (MS)‐based studies of the ubiquitin code, we have assembled seven isomeric diubiquitins with all‐native sequences and isopeptide linkages. Using these compounds as standards enables the development and testing of a new MS‐based strategy tailored specifically to characterize the number and sites of isopeptide linkages in polyubiquitin chains. Here, we report the use of Asp‐selective acid cleavage, separation by reverse phase high‐performance liquid chromatography and characterization by tandem MS to distinguish and characterize all seven isomeric lysine‐linked ubiquitin dimers. Copyright © 2014 John Wiley & Sons, Ltd.     

Targeted mass spectrometric strategy for global mapping of ubiquitination on proteins

Post-translational modifications of proteins including phosphorylation, glycosylation, acetylation and ubiquitination facilitate the regulation of many cellular processes and intracellular signaling events. Ubiquitination plays a key role in the functional regulation and degradation of many classes of proteins, and the study of ubiquitination and poly-ubiquitination has emerged as one of the most active areas in proteomic research. A variety of mass spectrometric methods have been described for the identification of ubiquitination sites, the study of poly-ubiquitin topology and the identification of ubiquitin substrates. The most popular workflow for both ubiquitination site mapping and poly-ubiquitination chain topology characterization is to take advantage of the Gly-Gly signature on the substrate's lysine residue observed after tryptic digestion. Although a number of protocols have been described for the mapping of ubiquitination sites, one major challenge is that ubiquitination is typically heterogeneous, and several lysine residues may be ubiquitinated within a protein. When multiple ubiquitination sites are present, multiple analyses are often required to cover all of the potential modification sites which in turn can necessitate the usage of larger quantities of material. In addition, the level of ubiquitination on endogenous and recombinant proteins may be of low intensity, adding further analytical challenges in the identification of this modification. The use of the multiple reaction monitoring (MRM)-initiated detection and sequencing workflow (MIDAS) for the identification of phosphorylation sites has previously been described. Here, we explore the use of an MRM workflow for ubiquitination site mapping on the substrate protein, receptor interacting protein (RIP).     

Effects of covalent modification by 4‐hydroxy‐2‐nonenal on the noncovalent oligomerization of ubiquitin

When lipid membranes containing ω‐6 polyunsaturated fatty acyl chains are subjected to oxidative stress, one of the reaction products is 4‐hydroxy‐2‐nonenal (HNE)—a chemically reactive short chain alkenal that can covalently modify proteins. The ubiquitin proteasome system is involved in the clearing of proteins modified by oxidation products such as HNE, but the chemical structure, stability and function of ubiquitin may be impaired by HNE modification. To evaluate this possibility, the susceptibility of ubiquitin to modification by HNE has been characterized over a range of concentrations where ubiquitin forms non‐covalent oligomers. Results indicate that HNE modifies ubiquitin at only two of the many possible sites, and that HNE modification at these two sites alters the ubiquitin oligomerization equilibrium. These results suggest that any role ubiquitin may have in clearing proteins damaged by oxidative stress may itself be impaired by oxidative lipid degradation products. Copyright © 2016 John Wiley & Sons, Ltd.     

Conformational Space Sampled by Domain Reorientation of Linear Diubiquitin Reflected in Its Binding Mode for Target Proteins

Linear polyubiquitin chains regulate diverse signaling proteins, in which the chains adopt various conformations to recognize different target proteins. Thus, the structural plasticity of the chains plays an important role in controlling the binding events. Herein, paramagnetic NMR spectroscopy is employed to explore the conformational space sampled by linear diubiquitin, a minimal unit of linear polyubiquitin, in its free state. Rigorous analysis of the data suggests that, regarding the relative positions of the ubiquitin units, particular regions of conformational space are preferentially sampled by the molecule. By combining these results with further data collected for charge-reversal derivatives of linear diubiquitin, structural insights into the factors underlying the binding events of linear diubiquitin are obtained.     

亲和分离在蛋白质泛素化修饰研究中的应用进展

蛋白质泛素化是真核生物最普遍、最复杂的翻译后修饰方式之一,在细胞的信号转导、生长、发育、代谢等生命过程中发挥着重要作用。泛素化过程的失调则与神经退行性疾病、炎症反应、癌症等重大疾病的发生发展密切相关。分析和研究蛋白质泛素化的结构与功能,可望为认识生命、探索疾病调控内在规律和发现新的诊断策略提供重要信息。生命体系的高度复杂性,泛素化修饰位点、结构类型的多变和多样性,时空动态变化等特点给蛋白质泛素化分析研究带来了巨大的挑战。亲和分离以其高选择性成为泛素化蛋白质结构与功能研究的有力工具。免疫亲和分离法基于抗原-抗体相互作用,是最为经典的分离分析方法,已广泛应用于泛素化蛋白质或肽段的富集分离。源于天然泛素受体的泛素结合结构域(ubiquitin binding domains, UBDs)可与泛素或多聚泛素链相互作用。UBDs和基于此发展起来的串联泛素结合实体(tandem ubiquitin-binding entities, TUBEs)已成为蛋白质泛素化功能研究的热门识别分子。各种多肽类化合物的发展也为蛋白质泛素化的结构和功能解析提供新工具。此外,多种亲和识别配基的联合使用,在蛋白质泛素化修饰的高特异性、高灵敏度分析中展现了独特的优势,为认识生命体内的泛素化修饰提供了重要保障。该文对亲和分离方法在蛋白质泛素化修饰分析中的应用及进展进行了综述。     

Catalytic proficiency of ubiquitin conjugation enzymes: balancing pK(a) suppression, entropy, and electrostatics

Biological organisms orchestrate coordinated responses to external stimuli through temporal fluctuations in protein-protein interaction networks using molecular mechanisms such as the synthesis and recognition of polyubiquitin (polyUb) chains on signaling adaptor proteins. One of the pivotal chemical steps in ubiquitination involves reaction of a lysine amino group with a thioester group on an activated E2, or ubiquitin conjugation enzyme, to form an amide bond between Ub and a target protein. In this study, we demonstrate a nominal 14-fold range for the rate of the chemical step, k(cat), catalyzed by different E2 enzymes using non-steady-state, single-turnover assays. However, the observed range for k(cat) is as large as ～100-fold for steady-state, single-turnover assays. Biochemical assays were used in combination with measurement of the underlying protein-protein interaction kinetics using NMR line-shape and ZZ-exchange analyses to determine the rate of polyUb chain synthesis catalyzed by the heterodimeric E2 enzyme Ubc13-Mms2. Modest variations in substrate affinity and k(cat) can achieve functional diversity in E2 mechanism, thereby influencing the biological outcomes of polyubiquitination. E2 enzymes achieve reaction rate enhancements through electrostatic effects such as suppression of substrate lysine pK(a) and stabilization of transition states by the preorganized, polar enzyme active site as well as the entropic effects of binding. Importantly, modestly proficient enzymes such as E2s maintain the ability to tune reaction rates; this may confer a biological advantage for achieving specificity in the diverse cellular roles for which these enzymes are involved.     

Self assembled monolayers on silicon for molecular electronics

We present an overview of various aspects of the self-assembly of organic monolayers on silicon substrates for molecular electronics applications. Different chemical strategies employed for grafting the self-assembled monolayers (SAMs) of alkanes having different chain lengths on native oxide of Si or on bare Si have been reviewed. The utility of different characterization techniques in determination of the thickness, molecular ordering and orientation, surface coverage, growth kinetics and chemical composition of the SAMs has been discussed by choosing appropriate examples. The metal counterelectrodes are an integral part of SAMs for measuring their electrical properties as well as using them for molecular electronic devices. A brief discussion on the variety of options available for the deposition of metal counterelectrodes, that is, soft metal contacts, vapor deposition and soft lithography, has been presented. Various theoretical models, namely, tunneling (direct and Fowler-Nordheim), thermionic emission, Poole-Frenkel emission and hopping conduction, used for explaining the electronic transport in dielectric SAMs have been outlined and, some experimental data on alkane SAMs have been analyzed using these models. It has been found that short alkyl chains show excellent agreement with tunneling models; while more experimental data on long alkyl chains are required to understand their transport mechanism(s). Finally, the concepts and realization of various molecular electronic components, that is, diodes, resonant tunnel diodes, memories and transistors, based on appropriate architecture of SAMs comprising of alkyl chains (sigma- molecule) and conjugated molecules (pi-molecule) have been presented.     

Comparison of CID versus ETD based MS/MS fragmentation for the analysis of protein ubiquitination

Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(ε) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins.     

Synthesis of defined ubiquitin dimers

Many proteins are post-translationally modified by the attachment of poly-ubiquitin (Ub) chains. Notably, the biological function of the attached Ub chain depends on the specific lysine residue used for conjugate formation. Here, we report an easy and efficient method to synthesize site-specifically linked Ub dimers by click reaction between two artificial amino acids. In fact, we were able to synthesize all seven naturally occurring Ub connectivities, providing the first example of a method that gives access to all Ub dimers. Furthermore, these synthetic Ub dimers are recognized by the natural ubiquitination machinery and are proteolytically stable, making them optimal candidates to further investigate the function of differently linked Ub chains.     

Dissecting Ubiquitin Signaling with Linkage‐Defined and Protease Resistant Ubiquitin Chains

Ubiquitylation is a complex posttranslational protein modification and deregulation of this pathway has been associated with different human disorders. Ubiquitylation comes in different flavors: Besides mono‐ubiquitylation, ubiquitin chains of various topologies are formed on substrate proteins. The fate of ubiquitylated proteins is determined by the linkage‐type of the attached ubiquitin chains, however, the underlying mechanism is poorly characterized. Herein, we describe a new method based on codon expansion and click‐chemistry‐based polymerization to generate linkage‐defined ubiquitin chains that are resistant to ubiquitin‐specific proteases and adopt native‐like functions. The potential of these artificial chains for analyzing ubiquitin signaling is demonstrated by linkage‐specific effects on cell‐cycle progression.     

Structure-activity studies of ferroelectric and antiferroelectric imine ligands and their square-planar complexes

The synthesis and characterization of the mesomorphic and dielectric properties of a series of new imine-based liquid crystalline compounds that exhibit tilted SmC* phases is reported. The presence of an imino linkage within the mesogenic nucleus of these compounds is significant due to the ability of salicylaldimines to coordinate to metals. Structure-activity studies have also been carried out by varying the structural elements in the ligands. The structural variations include changing the length of the chiral chain and incorporating fluorocarbon segments in the achiral terminal chain.     

The Length of a Ubiquitin Chain: A General Factor for Selective Recognition by Ubiquitin‐Binding Proteins

The attachment of ubiquitin (Ub) chains of various length to proteins is a prevalent posttranslational modification in eukaryotes. The fate of a modified protein is determined by Ub‐binding proteins (UBPs), which interact with Ub chains in a linkage‐selective manner. However, the impact and functional consequences of chain length on the binding selectivity of UBPs remain mostly elusive. We have generated Ub chains of defined length and linkage by using click chemistry and GELFrEE fractionation. These defined polymers were used in affinity‐based enrichment assays to identify length‐ and linkage‐selective interaction partners on a proteome‐wide scale. For the first time, it is revealed that the length of a Ub chain generally has a major impact on its ability to be selectively recognized by UBPs.     

Probing affinity and ubiquitin linkage selectivity of ubiquitin-binding domains using mass spectrometry

Non-covalent interactions between ubiquitin (Ub)-modified substrates and Ub-binding domains (UBDs) are fundamental to signal transduction by Ub receptor proteins. Poly-Ub chains, linked through isopeptide bonds between internal Lys residues and the C-terminus of Ub, can be assembled with varied topologies to mediate different cellular processes. We have developed and applied a rapid and sensitive electrospray ionization-mass spectrometry (ESI-MS) method to determine isopeptide linkage-selectivity and affinity of poly-Ub·UBD interactions. We demonstrate the technique using mono-Ub and poly-Ub complexes with a number of α-helical and zinc-finger (ZnF) UBDs from proteins with roles in neurodegenerative diseases and cancer. Affinities in the 2-200 μM range were determined to be in excellent agreement with data derived from other biophysical techniques, where available. Application of the methodology provided further insights into the poly-Ub linkage specificity of the hHR23A-UBA2 domain, confirming its role in Lys48-linked poly-Ub signaling. The ZnF UBP domain of isopeptidase-T showed no linkage specificity for poly-Ub chains, and the Rabex-5 MIU also exhibited little or no specificity. The discovery that a number of domains are able to bind cyclic Lys48 di-Ub with affinities similar to those for the acyclic form indicates that cyclic poly-Ub may be capable of playing a role in Ub-signaling. Detection of a ternary complex involving Ub interacting simultaneously with two different UBDs demonstrated the co-existence of multi-site interactions, opening the way for the study of crosstalk between individual Ub-signaling pathways.     

Molecular level structures of poly(n-alkyl methacrylate)s with different side chain lengths at the polymer/air and polymer/water interfaces

Sum frequency generation (SFG) vibrational spectroscopy has been successfully applied to study molecular structures of several poly(n-alkyl methacrylate)s (PAMAs) with different side chain lengths at the PAMA/air and PAMA/water interfaces. We have observed that the ester side chains from all PAMAs always dominate the interface, but the orientation information of the methyl end group on the side chains varies, depending on the length of the side chain. The contributions from methylene groups on the side chains have been evaluated, and the surface structures have been related to the surface tension of these polymers. Different water restructuring behaviors have been observed for different PAMAs. This phenomenon and its reversibility are strongly dependent on the glass transition temperature of each polymer, which is influenced by the side chain length. Detailed data fitting and analysis has been discussed.     

Effect of preferential solvation of polymer chains on vapor-pressure osmometry results: Computer simulation study

Preferential solvation of polymer chains by molecules of the thermodynamically better component of the solvent mixture is a general phenomenon which affects properties of dissolved chains and has to be taken into account in the interpretation of results of methods for analysis and characterization of polymers. We have investigated (i) the effect of preferential solvation on vapor-pressure osmometry results in mixed solvents close to θ-conditions and (ii) the danger of formation of associates by coarse-grained computer simulations. The study shows that both effects are negligible and the measurements in mixed solvents can be safely performed.     

Phenyl- and cyclopentylimino derivatization for double bond location in unsaturated C<Subscript>37</Subscript>-C<Subscript>40</Subscript> alkenones by GC-MS

A method for the identification of double bond locations in polyunsaturated long chain alkenones adapted to nanogram amounts as currently analyzed by gas chromatography coupled to mass spectrometry (GC-MS) has been developed. The method is based on interpretation of the electron impact mass spectra of the imino derivatives of the carbonyl groups using either cyclopentyl or phenyl substitutents. Other complementary derivatization methods such as elaidization and hydrogenation have also been used for structural characterization of these compounds. This application has led to the identification of a novel homologous series of di-, tri-, and tetraunsaturated ketones with carbon number chain lengths between 37 and 40 in coastal hypersaline sediments. The novel series identified shows a distribution in which the double bond position between different homologs is established by reference to the distance from the carbonyl group whereas the previously known alkenones were constituted by unsaturated homologs with double bonds located at defined distances of the terminal methyl. This difference points out to a dissimilar, but still unknown, biogenic precursor of these novel alkenones.     

Practical guidelines for characterization of O‐diglycosyl flavonoid isomers by triple quadrupole MS and their applications for identification of some fruit juices flavonoids

Fifteen flavonoid O‐diglycosides with different interglycosidic linkage isomery and glycosylation position have been studied in order to analyze their fragmentation patterns. Initial separation was carried out using high performance liquid chromatography with diode array detection (HPLC/DAD) coupled to an electrospray ionization (ESI) interface and a triple quadrupole mass spectrometer. Some useful differences in their MS spectra have been found and discussed. As it has already been reported, [Y*]⁺/[Y₀]⁺ ratio for flavanones and [Y₁]⁺/[Y₀]⁺ ratio for other flavonoids is specific for each isomeric interglycosidic linkage. In this work it has also been observed that the abundance of these ions is dependent on the position of glycosylation. On the basis of these differences, systematic guidelines for our experimental conditions have been proposed for the differentiation of not only isomeric interglycosidic linkage but also glycosylation position using collision‐induced dissociation MS/MS (CID‐MS/MS) spectra in positive mode. These results have been successfully applied for the characterization of three diglycosyl flavonoids found in Citrus fruit juices and these conclusions have also been extrapolated for characterizing two triglycosides in the same fruits. Copyright © 2009 John Wiley & Sons, Ltd.     

An homologous series of 6-O-n-alkyl-alpha-D-galactopyranoses: synthesis and thermotropic mesomorphic properties

An homologous series of 6- O - n -alkyl- alpha -D-galactopyranoses has been prepared. The length of the terminal chains has been varied systematically and the effect on the liquid crystal transition temperatures studied. Most homologues of the series exhibit enantiotropic smectic A* phases. X-ray analysis indicates a lamellar structure for the smectic A* phase with hydrogen-bonded carbohydrate cores at the layer centre, either with no interdigitation of the tilted terminal alkyl chains but with a high degree of chain melting, or with some degree of chain intercalation. The 6- O - n -alkyl- alpha -D-galactopyranoses possess clearing points at higher temperatures than those of the corresponding n -alkyl alpha -D-galactopyranosides. The introduction of a higher degree of hydrogen bonding by the replacement of the oxygen atom in the ether linkage between the chain and the carbohydrate ring by an amide linkage leads to higher transition temperatures. The dependence of the liquid crystalline behaviour on the position of the same alkyl substituent and the nature of the sugar in the pyranose form, as well as on the anomeric configuration of the liquid crystalline carbohydrates with four hydroxy groups, is reported.