Protein Modification Reactions Research Articles

Protein interactions in the sumoylation cascade – lessons from X‐ray structures

Sumoylation is a multi-step protein modification reaction in which SUMO (small ubiquitin-like modifier) proteins are covalently attached to lysine residues of substrate proteins. Here, we compare the sequences and structures of modifiers and enzymes involved in sumoylation with those of the related ubiquitination and neddylation cascades. By using available structural data on modifier/enzyme/substrate interactions, we discuss and model sumoylation complexes that include SUMO-1 and the E1 and E2 enzymes Aos1-uba2 and ubc9, or SUMO-1 and E2 together with the E3 ligase RanBP2 and its substrate RanGAP1. Their comparison provides insight into the protein interactions underlying sumoylation, and suggests how SUMO proteins may be translocated between enzymes during the various steps of the protein modification reaction.

Analysis of protein adduction kinetics by quantitative mass spectrometry: Competing adduction reactions of glutathione- S-transferase P1-1 with electrophiles

Defining the mechanisms and consequences of protein adduction is crucial to understanding the toxicity of reactive electrophiles. Application of tandem mass spectrometry and data analysis algorithms enables detection and mapping of chemical adducts at the level of amino acid sequence. Nevertheless, detection of adducts does not indicate relative reactivity of different sites. Here, we describe a method to measure the kinetics of competing adduction reactions at different sites on the same protein. Adducts are formed by electrophiles at Cys14 and Cys47 on the metabolic enzyme glutathione- S-transferase P1-1 and modification is accompanied by a loss of enzymatic activity. Relative quantitation of protein adducts was done by tagging N-termini of peptide digests with isotopically labeled phenyl isocyanate and tracking the ratio of light-tagged peptide adducts to heavy-tagged reference samples in liquid chromatography–tandem mass spectrometry analyses using a multiple reaction monitoring method. This approach was used to measure rate constants for adduction at both positions with two different model electrophiles, N-iodoacetyl- N-biotinylhexylenediamine and 1-biotinamido-4-(4′-[maleimidoethyl-cyclohexane]-carboxamido)butane. The results indicate that Cys47 was approximately two- to three-fold more reactive toward both electrophiles than was Cys14. This result was consistent with the relative reactivity of these electrophiles in a complex proteome system and with previously reported trends in reactivity of these sites. Kinetic analyses of protein modification reactions provide a means of evaluating the selectivity of reactive mediators of chemical toxicity.

The Edinburgh human metabolic network reconstruction and its functional analysis

A better understanding of human metabolism and its relationship with diseases is an important task in human systems biology studies. In this paper, we present a high-quality human metabolic network manually reconstructed by integrating genome annotation information from different databases and metabolic reaction information from literature. The network contains nearly 3000 metabolic reactions, which were reorganized into about 70 human-specific metabolic pathways according to their functional relationships. By analysis of the functional connectivity of the metabolites in the network, the bow-tie structure, which was found previously by structure analysis, is reconfirmed. Furthermore, the distribution of the disease related genes in the network suggests that the IN (substrates) subset of the bow-tie structure has more flexibility than other parts.

An Affinity-Based Method for the Purification of Fluorescently-Labeled Biomolecules

Due to the difficulty of separating mixtures of labeled and unlabeled biomolecules, a general new method for the affinity purification of modified proteins has been developed. A Sepharose-based solid support bearing beta-cyclodextrin groups was used to capture chromophore-modified proteins selectively, while unmodified proteins remained in solution. After isolation of the resin, the modified proteins were released by treating the sample with a competitive cyclodextrin binder, such as adamantane carboxylic acid. This procedure was demonstrated for several dyes displaying a wide range of spectral characteristics and diverse chemical structures. Preliminary studies have shown that this method can also be used to enrich modified peptide fragments present in proteolytic digests. This technique is anticipated to accelerate the development of new protein modification reactions and could provide a useful tool for proteomics applications.

Solution structure and backbone dynamics of an N-terminal ubiquitin-like domain in the GLUT4-regulating protein, TUG.

The GLUT4-regulating protein, TUG, functions to retain GLUT4-containing membrane vesicles intracellularly and, in response to insulin stimulation, releases these vesicles to the cellular exocytic machinery for translocation to the plasma membrane. As part of our on going effort to describe the molecular basis for TUG function, we have determined the tertiary structure and characterized the backbone dynamics for an N-terminal ubiquitin-like domain (TUG-UBL1) using NMR spectroscopy. A well-ordered conformation is observed for residues 10-83 of full-length TUG, and confirms a beta-grasp or ubiquitin-like topology. Although not required for in vitro association with GLUT4, the functional role of the TUG-UBL1 domain has not yet been described. We undertook a limited literature review of similar N-terminal UBL domains and noted that a majority participate in protein-protein interactions, generally functioning as adaptor modules to physically associate the over all activity of the protein with a specific cellular process, such as the ubiquitin-proteasome pathway. In consistent fashion, TUG-UBL1 is not expected to participate in a covalent protein modification reaction as it lacks the characteristic C-terminal diglycine ("GG") motif required for conjugation to an acceptor lysine, and also lacks the three most common acceptor lysine residues involved in polyubiquitination. Additionally, analysis of the TUG-UBL1 molecular surface reveals a lack of conservation of the "Ile-44 hydrophobic face" typically involved in ubiquitin recognition. Instead, we speculate on the possible significance of a concentrated area of negative electrostatic potential with increased backbone mobility, both of which are features suggestive of a potential protein-protein interaction site.

Asparagine-linked protein glycosylation: from eukaryotic to prokaryotic systems

Asparagine-linked protein glycosylation is a prevalent protein modification reaction in eukaryotic systems. This process involves the co-translational transfer of a pre-assembled tetradecasaccharide from a dolichyl-pyrophosphate donor to the asparagine side chain of nascent proteins at the endoplasmic reticulum (ER) membrane. Recently, the first such system of N-linked glycosylation was discovered in the Gram-negative bacterium, Campylobacter jejuni. Glycosylation in this organism involves the transfer of a heptasaccharide from an undecaprenyl-pyrophosphate donor to the asparagine side chain of proteins at the bacterial periplasmic membrane. Here we provide a detailed comparison of the machinery involved in the N-linked glycosylation systems of eukaryotic organisms, exemplified by the yeast Saccharomyces cerevisiae, with that of the bacterial system in C. jejuni. The two systems display significant similarities and the relative simplicity of the bacterial glycosylation process could provide a model system that can be used to decipher the complex eukaryotic glycosylation machinery.

Tyrosine-Selective Protein Alkylation Using π-Allylpalladium Complexes

A new protein modification reaction has been developed based on a palladium-catalyzed allylic alkylation of tyrosine residues. This technique employs electrophilic pi-allyl intermediates derived from allylic acetate and carbamate precursors and can be used to modify proteins in aqueous solution at room temperature. To facilitate the detection of modified proteins using SDS-PAGE analysis, a fluorescent allyl acetate was synthesized and coupled to chymotrypsinogen A and bacteriophage MS2. The tyrosine selectivity of the reaction was confirmed through trypsin digest analysis. The utility of the reaction was demonstrated by using taurine-derived carbamates as water solubilizing groups that are cleaved upon protein functionalization. This solubility switching technique was used to install hydrophobic farnesyl and C(17) chains on chymotrypsinogen A in water using little or no cosolvent. Following this, the C(17) alkylated proteins were found to associate with lipid vesicles. In addition to providing a new protein modification strategy targeting an under-utilized amino acid side chain, this method provides convenient access to synthetic lipoproteins.

An evolving view of the eukaryotic oligosaccharyltransferase

Asparagine-linked glycosylation (ALG) is one of the most common protein modification reactions in eukaryotic cells, as many proteins that are translocated across or integrated into the rough endoplasmic reticulum (RER) carry N-linked oligosaccharides. Although the primary focus of this review will be the structure and function of the eukaryotic oligosaccharyltransferase (OST), key findings provided by the analysis of the archaebacterial and eubacterial OST homologues will be reviewed, particularly those that provide insight into the recognition of donor and acceptor substrates. Selection of the fully assembled donor substrate will be considered in the context of the family of human diseases known as congenital disorders of glycosylation (CDG). The yeast and vertebrate OST are surprisingly complex hetero-oligomeric proteins consisting of seven or eight subunits (Ost1p, Ost2p, Ost3p/Ost6p, Ost4p, Ost5p, Stt3p, Wbp1p, and Swp1p in yeast; ribophorin I, DAD1, N33/IAP, OST4, STT3A/STT3B, Ost48, and ribophorin II in mammals). Recent findings from several laboratories have provided overwhelming evidence that the STT3 subunit is critical for catalytic activity. Here, we will consider the evolution and assembly of the eukaryotic OST in light of recent genomic evidence concerning the subunit composition of the enzyme in diverse eukaryotes.

Role of ADP-ribosylation in wound repair. The contributions of Thomas K. Hunt, MD.

Nearly 36 years ago Thomas K. Hunt, with Patrick Twomey, was the first to report that the level of lactate significantly increases in healing wounds. This observation convinced him that lactate, besides being the by-product of glycolysis, must have a regulatory role in the healing process. He set out to investigate this observation and found it to be so. This article is written in recognition of his foresight. It summarizes the salient findings emanating from this fundamental observation and describes the biochemical principles by which most of the lactate action may be explained. Down-regulation of the ubiquitous protein modification reaction called ADP-ribosylation turned out to be a basic signal behind the role of lactate in wound healing.

Biases and complex patterns in the residues flanking protein N-glycosylation sites.

N-Glycosylation, the most common and most versatile protein modification reaction, occurs at the beta-amide of the aspargine of the Asn-Xaa-Ser/Thr sequon. For reasons that are unclear, not all such sequons are glycosylated. To find patterns that affect glycosylation, we examined the amino acid residues from the 20th preceding the sequon to the 20th residue following it, using bioinformatics tools. A clean data set of annotated, experimentally verified, glycosylated and nonglycosylated sequons derived from 617 well-defined nonredundant N- and N-,O-glycoproteins listed in SWISS-PROT (June 2002) was used. NXS and NXT sequons were analyzed separately. Although no overt patterns were found to explain sequon occupancy or nonoccupancy, trends for over- or underrepresentation of certain amino acids at particular positions were statistically significant and different in NXS and NXT sequons. In extension of earlier reports, none of the 80 Asn-Pro-Ser/Thr found were glycosylated, and a markedly low level of glycosylation was seen in sequons with Pro at the position following the Ser/Thr. In addition, a general observation was made that the considerable number of glycosylated sequons in the C-terminal 10 residues of glycoproteins suggests that N-glycosylation in these cases may be posttranslational and not cotranslational, as widely accepted.

Protein thioacylation: 2. Reagent stability in aqueous media and thioacylation kinetics.

Several thioacylating reagents have been tested toward hydrolysis under conditions suitable for protein modifications: 20-35 degrees C and buffered solutions at pH 7.5-8.5. Aliphatic dithioesters are sufficiently stable in aqueous media at room temperature (or below) if protein modification reaction time does not exceed 24 h, whereas at 35 degrees C reaction times must be limited to a few hours. Kinetic data obtained in gelatin thioacylation at room temperature using aliphatic dithioesters and dithio acid are consistent with a second-order reaction rate with respect to amine concentration. The pH dependence of the second-order reaction rate constants indicate that dithioester reacts exclusively with the free amine form of lysine residue, whereas dithiocarboxylate ion reacts with both amine and ammonium ion, probably through a more complex mechanism. Interestingly thioacylation using dithio acids may be obtained in pH near neutrality or in slightly acidic media, thus offering protein modification possibilities at pH 5-9. Thioacylation reaction rates may be expressed as R = -(dAt/dt) = k[H3O+](-b)At2[thioacylating agent] in which At is the amine concentration at time t, constants k and b depending on the reagent nature.

δ-N-Methylarginine Is a Novel Posttranslational Modification of Arginine Residues in Yeast Proteins

We have found a novel modification of protein arginine residues in the yeast Saccharomyces cerevisiae. Intact yeast cells lacking RMT1, the gene encoding the protein omega-NG-arginine methyltransferase, were labeled with the methyl donor S-adenosyl-L-[methyl-3H]methionine. The protein fraction was acid-hydrolyzed to free amino acids, which were then fractionated on a high resolution sulfonated polystyrene cation exchange column at pH 5.27 and 55 degreesC. In the absence of the omega-NG, NG-[3H]dimethylarginine product of the RMT1 methyltransferase, we were able to detect a previously obscured 3H-methylated species that migrated in the region of methylated arginine derivatives. The [3H]methyl group(s) of this unknown species were not volatilized by treatment with 2 M NaOH at 55 degreesC for up to 48 h, suggesting that they were not modifications of the terminal omega-guanidino nitrogen atoms. However, this base treatment did result in the formation of a new 3H-methylated derivative that co-chromatographed with delta-N-methylornithine on high resolution cation exchange chromatography, on reverse phase high pressure liquid chromatography, and on thin layer chromatography. From these data, we suggest that the identity of the original unknown methylated residue is delta-N-monomethylarginine. The presence of this methylated residue in yeast cells defines a novel type of protein modification reaction in eukaryotes.

DAD1 Is Required for the Function and the Structural Integrity of the Oligosaccharyltransferase Complex

Asparagine-linked glycosylation is a highly conserved protein modification reaction that occurs in all eukaryotic organisms. The oligosaccharyltransferase (OST), which has its active site exposed on the luminal face of the endoplasmic reticulum (ER), catalyzes the transfer of preassembled high mannose oligosaccharides onto certain asparagine residues of nascent polypeptides. The mammalian OST complex was initially thought to be composed of three transmembrane proteins, ribophorin I (RI), ribophorin II (RII), and OST48. Most recently, a small integral membrane protein of 12 kDa called DAD1 has been identified as an additional member of the mammalian OST complex. A point mutation in the DAD1 gene is responsible for the temperature-sensitive phenotype of a baby hamster kidney-derived cell line (tsBN7) that undergoes apoptosis at the non-permissive temperature. Furthermore, the mutant protein DAD1 is not detectable in tsBN7 cells 6 h after shifting the cells to the non-permissive temperature. This temperature-sensitive cell line offered unique opportunities to study the effects caused by the loss of one OST subunit on the other three subunits and also on N-linked glycosylation. Western blot analysis of cell lysates showed that after 6 h at the non-permissive temperature, steady-state levels of the ribophorins were reduced by about 50%, and OST48 was barely detectable. On the other hand, steady-state levels of other components of the rough ER, such as the alpha-subunits of the TRAP (translocon-associated membrane protein) and the Sec61 complex, which are components of the translocation apparatus, are not affected by the instability of the OST subunits. Furthermore, N-glycosylation of the ribophorins was seriously affected 6 h after shifting the cells to the non-permissive temperature, and after 12 h they were synthesized only in the non-glycosylated form. As may be expected, this defect in the OST complex at the non-permissive temperature caused also the underglycosylation of a secretory glycoprotein. We concluded that degradation of DAD1 at the non-permissive temperature not only affects the stability of OST48 and the ribophorins but also results in the functional inactivation of the OST complex.

Carbon Dioxide Enhancement of Peroxynitrite-Mediated Protein Tyrosine Nitration

Production of reactive species has been associated with tissue injury in diverse human disorders and experimental models of disease. Peroxynitrite is a strong oxidant with multiple pathways of reactivity. One protein modification reaction that may be specific to peroxynitrite is the nitration of the ortho position of tyrosine residues and nitrotyrosine has been used as a marker for peroxynitrite-mediated oxidative stress. Nitrotyrosine was formed when peroxynitrite was reacted at physiological pH with fatty acid-free bovine serum albumin or with human plasma proteins. Nitrotyrosine was not formed when proteins were incubated with nitric oxide, nitrogen dioxide, or nitric oxide plus hydrogen peroxide in the presence of ferrous iron or ferrihorseradish peroxidase. Low-molecular-weight molecules such as uric acid, ascorbate, and sulfhydryls inhibited protein tyrosine nitration in the absence of bicarbonate. Addition of bicarbonate catalytically enhanced the yield of nitration and overcame the inhibition of these antioxidants. Bicarbonate/CO2enhanced the yield of protein nitrotyrosine in a concentration-dependent manner. Catalysis of nitration is achieved by the interaction of CO2with the peroxynitrite anion. A mechanism is proposed involving an ONOO(O)CO−intermediate, which readily nitrates tyrosine residues in a non-radical-dependent manner. Thus, peroxynitrite nitrates tyrosine residues by a mechanism that is catalyzed by CO2under normal physiological conditions.

Biochemistry, molecular biology, and genetics of the oligosaccharyltransferase

Asparagine-linked glycosylation is a highly conserved protein modification reaction that occurs in all eukaryotes. The initial stage in the biosynthesis of N-linked glycoproteins, catalyzed by the enzyme oligosaccharyltransferase (OST), involves the transfer of a preassembled high-mannose oligosaccharide from a dolichol-linked oligosaccharide donor onto asparagine acceptor sites in nascent proteins in the lumen of the rough endoplasmic reticulum. Biochemical, molecular biological, and genetic studies conducted during the past 5 years have resulted in an explosive growth in our knowledge concerning the OST. Although the basic biochemical properties of the enzyme were determined more than a decade ago using intact microsomal membranes, recent studies provide novel insight into the catalytic mechanism of the enzyme. The OST was recently purified as a large heteroligomeric membrane protein complex; the sequences of many of the subunits have been determined from both fungal and vertebrate sources. Consistent with the evolutionary conservation of N-linked glycosylation, protein sequence comparisons reveal significant homologies between vertebrate, invertebrate, plant, and fungal OST subunits. Yeast molecular genetic methods have been instrumental in the functional characterization of the OST subunits, and have proven to be powerful tools for the identification of novel gene products that influence oligosaccharide transfer in vivo.

Role of protein modification reactions in programming interactions between ras-related GTPases and cell membranes.

INTRODUCTION . . . . . ... . .... . . . . . . . . . . . . . . . ... . ..... . . . . ... 1 8 1 MODIFICATIONS O F THE N O R C -TERMINI O F RAS-RELATED GTPASES . . . . 182 FUNCTIONAL SIGNIFICANCE OF THE MODIFICATIONS . . . . . . . . . . . . . . . . . . . . 187 ARF Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 87 Ras Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188 Rap Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193 Rho-related Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194 Rab Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195 CONCLUSIONSIFUTURE DIRECTIONS 197

Utilization of the free energy of the reversible binding of protein and modifying agent towards the rate-enhancement of protein covalent modification

An analysis is presented of the catalytic factors responsible for the rate-enhancement that may be observed when a protein modification reaction is compared with a reaction of the same modifying agent with a model micromolecular compound exhibiting the same reactive group as the protein under study. It is seen that affinity-mediated rate-enhancement of protein modification is realized by the loss of activation entropy. On the assumption that attainment of maximal affinity-mediated rate-enhancement presents with an activation entropy of the protein modification reaction equal to zero, whereas the activation enthalpy of the reaction remains unchanged, it is shown that the value for maximal affinity-mediated rate-enhancement is equal to e-delta s++/R. Accordingly, protein modification reactions may be differentiated into (i) reactions the rate-enhancement of which (relative to the reaction of the same modifying agent with a model compound) is primarily entropy-controlled and (ii) reactions the rate-enhancement of which is primarily enthalpy-controlled. It is seen that modifying agents of low reactivity towards model compounds, but with a high, i.e. highly negative, activation entropy are better suited as prospective affinity-based protein-modifying agents, since the potential affinity-mediated rate-enhancement, and hence the selectivity, of these compounds is necessarily high. Kinetic and thermodynamic constants of the reaction of modifying agents with proteins, and with model compounds, and values of maximal affinity-mediated rate-enhancement, based on published data of the reaction of several modifying agents with model compounds, are presented and discussed.

Interpretation of Biphasic Protein Modification and Modification-Induced Enzyme Inactivation Reaction Plots

(1990). Interpretation of Biphasic Protein Modification and Modification-Induced Enzyme Inactivation Reaction Plots. Journal of Enzyme Inhibition: Vol. 4, No. 1, pp. 57-62.

Kinetic analysis of protein modification reactions at equilibrium.

A kinetic analysis is presented of reactions of protein modification, and/or of modification-induced enzyme inactivation, which can formally be described by a single exponential function, or by a summation of two exponential functions, of reaction time plus a constant term. The reaction schemes compatible with the kinetic formalism of these cases are given, and a simple kinetic criterion is described whereby the identification of one of these cases, strong negative protein modification co-operativity, may be carried out. The treatment outlined in this paper is applied to a case from the literature, the inactivation of glyceraldehyde-3-phosphate dehydrogenase by butane-2,3-dione [Asriyants, Benkevich & Nagradova (1983) Biokhimiya (Engl. Transl.) 48, 164-171].

Phosphorylation of an N-terminal Regulatory Domain Activates the CheB Methylesterase in Bacterial Chemotaxis

Two types of reversible protein modification reactions have been identified in bacterial chemotaxis, methylation of membrane receptor-transducer proteins at glutamate side chains and phosphorylation of cytoplasmic signal transduction proteins at histidine and aspartate side chains. CheB is a bifunctional enzyme that is involved in both these modification processes. Its C-terminal domain is a methylesterase that catalyzes the hydrolysis of gamma-carboxyl glutamyl methyl esters in the cytoplasmic domain of chemoreceptor proteins. Its N-terminal domain is a phosphatase that catalyzes the hydrolysis of phospho-CheA, the central response regulator of bacterial chemotaxis. Phospho-CheB, produced as an intermediate in the phosphatase reaction, has dramatically increased methylesterase activity. The interplay between the methylesterase and phosphatase activities of CheB may provide a crucial link between adaptation and excitation in stimulus-response coupling.