Amino-terminal Methionine Research Articles

Signal recognition particle prevents N-terminal processing of bacterial membrane proteins

Bacterial proteins are synthesized with an N-formylated amino-terminal methionine, and N-formylated peptides elicit innate-immunity responses against bacterial infections. However, the source of these formylated peptides is not clear, as most bacterial proteins are co-translationally deformylated by peptide deformylase. Here we develop a deformylation assay with translating ribosomes as substrates, to show that the binding of the signal recognition particle (SRP) to signal sequences in nascent proteins on the ribosome prevents deformylation, whereas deformylation of nascent proteins without signal sequence is not affected. Deformylation and its inhibition by SRP are not influenced by trigger factor, a chaperone that interacts with nascent chains on the ribosome. We propose that bacterial inner-membrane proteins, in particular those with N-out topology, can retain their N-terminal formyl group during cotranslational membrane insertion and supply formylated peptides during bacterial infections.

Identification of methionine aminopeptidase 2 as a molecular target of the organoselenium drug ebselen and its derivatives/analogues: Synthesis, inhibitory activity and molecular modeling study

A collection of twenty-six organoselenium compounds, ebselen and its structural analogues, provided a novel approach for inhibiting the activity of human methionine aminopeptidase 2 (MetAP2). This metalloprotease, being responsible for the removal of the amino-terminal methionine from newly synthesized proteins, plays a key role in angiogenesis, which is essential for the progression of diseases, including solid tumor cancers. In this work, we discovered that ebselen, a synthetic organoselenium drug molecule with anti-inflammatory, anti-oxidant and cytoprotective activity, inhibits one of the main enzymes in the tumor progression pathway. Using three-step synthesis, we obtained twenty-five ebselen derivatives/analogues, ten of which are new, and tested their inhibitory activity toward three neutral aminopeptidases (MetAP2, alanine and leucine aminopeptidases). All of the tested compounds proved to be selective, slow-binding inhibitors of MetAP2. Similarly to ebselen, most of its analogues exhibited a moderate potency (IC50=1–12μM). Moreover, we identified three strong inhibitors that bind favorably to the enzyme with the half maximal inhibitory concentration in the submicromolar range.

A predicted T4 secretion system and conserved DNA-repeats identified in a subset of related Arthrobacter plasmids

BLAST analysis of pAO1 ORFs of Arthrobacter nicotinovorans revealed 12 ORFs, including the ORF of a transcriptional regulator, predicted to encode the components of a T4-secretion system involved in bacterial conjugation. These ORFs were conserved and showed synteny among 14 Arthrobacter plasmids. A DNA repeat of about 370 nucleotides was found to be present 5' to the pAO1 ORFs of DUF4192-, DprA- and ParB-like proteins. Similar repeats were present in identical positions on 12 additional Arthrobacter plasmids. The DNA repeats on a particular plasmid are highly identical duplications. The DNA repeats contain alternating GC and AT reach sequences, potential protein DNA-binding sites and purine reach stretches. The sequences end with 5′ATG.AAC3′ which results in the amino terminal sequence methionine (M) and asparagine (N) for all predicted DprA, DUF4192 and ParB proteins. The presences of conserved ORFs of a T4-secretion system and of similar DNA repeats suggest that these Arthrobacter plasmids are related and evolved from a common ancestor. The functional significance of the DNA repeats in a coordinated common mechanism of regulation of expression of the dprA-(involved in natural competence), parB- (involved in plasmid partitioning) and duf4192- (unknown function in plasmid life cycle) genes remains to be established.

Decoding the Growth Advantage of Hypoxia-Sensitive Lung Cancer

Decoding the Growth Advantage of Hypoxia-Sensitive Lung Cancer

Biosimilars: the process is the product. The example of recombinant streptokinase

BackgroundWorldwide, streptokinase remains the most used thrombolytic agent for the treatment of myocardial infarction. Recombinant streptokinase, from E. coli, is increasingly used in developing countries as a biosimilar of native streptokinase; however, potency assignments relative to the WHO International Standard (IS) are highly variable with potentially dangerous consequences. A proportion of recombinant streptokinase appears to be incompletely processed, retaining the amino-terminal methionine engineered for intracellular expression.ObjectivesTo investigate and quantify the impact of an amino-terminal methionine on streptokinase activity.MethodsMature native streptokinase (rSK) was cloned and a novel variant constructed to include an amino-terminal methionine (rSK-Met) that is not susceptible to processing during expression. Potencies of rSK and rSK-Met were determined relative to the WHO IS using a chromogenic solution (European Pharmacopoeia) assay, and fibrin-based assays.ResultsIn the chromogenic solution assay there was no measurable difference between rSK and rSK-Met activities. In the fibrin-based methods, however, potency estimates for rSK-Met were greatly reduced compared with rSK, and fibrinolytic activity for rSK-Met was shown to increase over time with methionine aminopeptidase treatment. This apparent difference in activity and fibrin selectivity was consistent with potency estimates for several different batches of commercial recombinant streptokinase products also tested; consequently, different potencies would be assigned to therapeutic recombinant streptokinase products depending on the degree of amino-terminal methionine processing, and on the pharmacopoeial assay method used, affecting the dosage patients receive. This has serious health implications and provides an example of the danger in the unregulated clinical use of biosimilars.

Ubiquitin code assembly and disassembly

Ubiquitin, a 76 amino-acid polypeptide, presents a compact three-dimensional structure, utilising a fold that recurs within larger polypeptides and in other protein modifiers, such as NEDD8 and SUMO. Ubiquitylation was initially recognised as a signal for proteasome-mediated degradation. We shall consider here how this view has evolved to appreciate that the dynamic appendage of different types of ubiquitin chains represents a versatile, three-dimensional code, fundamental to the control of many cellular processes.

Getting Connected

Acetylation of an amino-terminal methionine is important for mediating specific protein-protein interactions.

N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex.

Although many eukaryotic proteins are amino (N)-terminally acetylated, structural mechanisms by which N-terminal acetylation mediates protein interactions are largely unknown. Here, we found that N-terminal acetylation of the E2 enzyme, Ubc12, dictates distinctive E3-dependent ligation of the ubiquitin-like protein Nedd8 to Cul1. Structural, biochemical, biophysical, and genetic analyses revealed how complete burial of Ubc12's N-acetyl-methionine in a hydrophobic pocket in the E3, Dcn1, promotes cullin neddylation. The results suggest that the N-terminal acetyl both directs Ubc12's interactions with Dcn1 and prevents repulsion of a charged N terminus. Our data provide a link between acetylation and ubiquitin-like protein conjugation and define a mechanism for N-terminal acetylation-dependent recognition.

β-Glycosidase of Thermus thermophilus KNOUC202: Gene and biochemical properties of the enzyme expressed in Escherichia coli

The beta-glycosidase gene of Thermus thermophilus KNOUC202 was cloned, expressed in Escherichia coli JM109(DE3), and the enzyme was purified and characterized. The gene (KNOUC202/beta-gly) was composed of 1296 bp encoding a beta-glycosidase (KNOUC202beta-glycosidase) of 431 a.a., belonging to the family 1 of glycosyl hydrolase. The gene was expressed as monomer of 430 a.a. with amino terminal methionine excised in E. coli JM109(DE3). The enzyme hydrolyzed beta-glycosides whose glycone are galactose, glucose and fucose well, however showed no or very low activity on beta-D-glycosides whose glycone are disaccharides and xylose. kcat of the enzyme for the hydrolysis of p-Nph-beta-D-Glcp was lower than those for p-Nph-beta-D-Galp and ONPG, however K(m) for p-Nph-beta-D-Glcp was highly lower than those for p-Nph-beta-D-Galp and ONPG resulting in the catalytic efficiency(k(cat)/K(m)) for the hydrolysis of p-Nph-beta-D-Glcp much higher than those for p-Nph-beta-D-Galp and ONPG. Optimum pH and optimum temperature of the enzyme were pH 5.4 and 90 degrees C. The enzyme has high thermostability, not losing its activity at 80 degrees C for 2 h in 0.05 M Na-phosphate buffer of pH 6.8 with T(m) of 100.0 +/- 0.031 degrees C in 0.02 M Tris-HCl buffer of pH 8.2. The beta-glycosidase produced a disaccharide composed of galactose as transglycosylation byproduct during hydrolysis of lactose.

Precise Modulation of Tropomyosin Polymer Length is Crucial for its Association with Actin and Ability to Regulate Myosin Function

Tropomyosin (Tm) is an evolutionarily conserved dimeric α-helical coiled-coil protein, which interacts end to end to form polymers capable of associating with and stabilising actin-filaments and thereby regulate myosin function. The fission yeast Schizosaccharomyces pombe possesses a single Tm, known as Cdc8. Cdc8 is an essential protein, which can be acetylated on its amino terminal methionine in vivo. This acetylation increases the affinity of Cdc8 for actin, and also enhances its ability to regulate myosin function (J. Cell Sci. 120: 1635-1645). We have recently undertaken an extensive analysis on the physical properties of acetylated and unacetylated Cdc8 together with a series of novel amino terminal Cdc8 mutants, in an attempt to explore the effect acetylation has upon the regulatory function of the Cdc8 protein. By correlating the stability of each protein and its propensity to form polymers with its ability to associate with actin and regulate myosin, it has been possible to establish that precise modulation of Tm-polymer length is crucial for its function. Cdc8 mutants capable of forming Tm-polymers significantly longer than the wild-type protein had a reduced affinity for actin, and in contrast to both wild type forms of the protein were unable to regulate myosin. The longer Tm-polymers are unable to efficiently coil around the already formed actin filament, and together our data are consistent with a mechanism by which acetylation regulates the formation of short Tm-polymers (normally up of ∼2 Cdc8 dimers) which associate with actin-filaments and are subsequently stabilised by electrostatic interactions with actin.

Tropomyosin Specifically Regulates Type II Myosin In Yeast

Tropomyosin (Tm) is an evolutionarily conserved α-helical coiled-coil protein that forms polymers which coil around actin filaments to regulate their integrity and function within cells. In yeast, tropomyosin stabilised actin filaments are used by molecular motors to transport cargoes or generate motile forces. Acetylation of the amino terminal methionine of mammalian Tms is required for these proteins to associate with actin and is also crucial in regulating the formation of the actomyosin complex, however it is unclear whether this post-translational modification affects myosin regulation.The fission yeast, Schizosaccharomyces pombe, contains a single Tm isoform, Cdc8, which localises to the cytokinetic actomyosin ring and is absolutely required for its formation and function during cell division. Our previous work has revealed that both acetylated and unacetylated forms of Cdc8 are present within fission yeast cells, and whilst we have shown that acetylated Cdc8 is capable of regulating myosin function in vitro, the role of the unacetylated form remains unresolved.S. pombe possesses five myosin's representing 3 individual myosin classes, Class I (Myo1), II (Myo2 & Myp2) and V (Myo51 and Myo52). We have examined the role that acetylated and non-acetylated Cdc8 play in regulating each class of myosin within the cell. Myo2 is found localised exclusively to the cytokinetic actomyosin ring and its function is to facilitate cell division, whilst Myo1, and Myo52 are associated with actin polymers throughout the cell cycle. In this study we show that acetylated Cdc8 specifically affects Myo2 function, but does not affect the motor activity of Myo1 or Myo52. This is not only consistent with the fact that acetylated Cdc8 is found associated predominantly with actin filaments within the cytokinetic ring, but also with the cytokinetic defects observed in cells lacking acetylated Cdc8.

Purification and Biochemical Characterization of Methionine Aminopeptidase (MetAP) from Mycobacterium smegmatis mc2155

The methionine aminopeptidase (MetAP) catalyzes the removal of amino terminal methionine from newly synthesized polypeptide. MetAP from Mycobacterium smegmatis mc(2) 155 was purified from the culture lysate in four sequential steps to obtain a final purification fold of 22. The purified enzyme exhibited a molecular weight of approximately 37 kDa on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Activity staining was performed to detect the methionine aminopeptidase activity on native polyacrylamide gel. The enzyme was characterized biochemically, using L-methionine p-nitroanilide as substrate. The enzyme was found to have a temperature and pH optimum of 50 degrees C and 8.5, respectively, and was found to be stable at 50 degrees C with half-life more than 8 h. The enzyme activity was enhanced by Mg(2+) and Co(2+) and was inhibited by Fe(2+) and Cu(2+). The enzyme activity inhibited by EDTA is restored in presence of Mg(2+) suggesting the possible role of Mg(2+) as metal cofactor of the enzyme in vitro.

Differential Subcellular Localization of RIC-3 Isoforms and Their Role in Determining 5-HT3 Receptor Composition

RIC-3 has been identified as a chaperone molecule involved in promoting the functional expression of nicotinic acetylcholine and 5-HT(3) receptors in mammalian cells. In this study, we examined the effects of RIC-3a (isoform a) and a truncated isoform (isoform d) on RIC-3 localization, mobility, and aggregation and its effect on 5-HT3 receptor composition in mammalian cells. Human RIC-3a possesses an amino-terminal signal sequence that targets it to the endoplasmic reticulum where it is distributed within the reticular network, often forming large diffuse "slicks" and bright "halo" structures. RIC-3a is highly mobile within and between these compartments. Despite the propensity for RIC-3a to aggregate, its expression enhances the level of surface 5-HT3A (homomeric) receptors. In contrast, RIC-3a exerts an inhibitory action on the surface expression of heteromeric 5-HT3A/B receptors. RIC-3d exhibits an altered subcellular distribution, being localized to the endoplasmic reticulum, large diffuse slicks, tubulo-vesicular structures, and the Golgi. Bidirectional trafficking between the endoplasmic reticulum and Golgi suggests that RIC-3d constitutively cycles between these two compartments. In support of the large coiled-coil domain of RIC-3a being responsible for protein aggregation, RIC-3d, lacking this cytoplasmic domain, does not aggregate or induce the formation of bright aggregates. Regardless of these differences, isoform d is still capable of enhancing homomeric, and inhibiting heteromeric, 5-HT3 receptor expression. Thus, both isoforms of RIC-3 play a role in determining 5-HT3 receptor composition.

Structural basis of catalysis by monometalated methionine aminopeptidase.

Methionine aminopeptidase (MetAP) removes the amino-terminal methionine residue from newly synthesized proteins, and it is a target for the development of antibacterial and anticancer agents. Available x-ray structures of MetAP, as well as other metalloaminopeptidases, show an active site containing two adjacent divalent metal ions bridged by a water molecule or hydroxide ion. The predominance of dimetalated structures leads naturally to proposed mechanisms of catalysis involving both metal ions. However, kinetic studies indicate that in many cases, only a single metal ion is required for full activity. By limiting the amount of metal ion present during crystal growth, we have now obtained a crystal structure for a complex of Escherichia coli MetAP with norleucine phosphonate, a transition-state analog, and only a single Mn(II) ion bound at the active site in the position designated M1, and three related structures of the same complex that show the transition from the mono-Mn(II) form to the di-Mn(II) form. An unliganded structure was also solved. In view of the full kinetic competence of the monometalated MetAP, the much weaker binding constant for occupancy of the M2 site compared with the M1 site, and the newly determined structures, we propose a revised mechanism of peptide bond hydrolysis by E. coli MetAP. We also suggest that the crystallization of dimetalated forms of metallohydrolases may, in some cases, be a misleading experimental artifact, and caution must be taken when structures are generated to aid in elucidation of reaction mechanisms or to support structure-aided drug design efforts.

Micro Arrayed Compound Screening (μARCS) for Inhibitors of Methionine Aminopeptidase Type 2

Methionine aminopeptidase type 2 catalyzes the removal of the amino-terminal methionine from newly translated polypeptides and has been shown to be a promising target for anti-angiogenesis and anticancer drugs. We describe a novel μARCS HTS method to identify inhibitors of this target utilizing porous matrices to introduce reagents throughout the assay. A library of 250,000 compounds was screened and compounds with IC50 values of less than 10μM were identified. These compounds may serve as initial lead molecules for further medicinal chemistry optimization.

Cell-Free Synthesis of Polypeptides Lacking an Amino-Terminal Methionine by Using a Dicistroviral Intergenic Internal Ribosome Entry Site

An amino-terminal methionine corresponding to a recombinant AUG initiation codon sometimes affects the functions of proteins. To test the performance of translation mediated by a dicistroviral internal ribosome entry site (IRES), which initiates protein synthesis with elongator tRNAs, we optimized the conditions for cell-free translation. Although the IRES is 188 nucleotides long, a further 50 nucleotides of the upstream sequence stabilized translation efficiency. Optimal ion concentrations were affected by the sequences of the constructs. In a wheat-germ system, IRES-mediated translation produced 78 microg/ml of firefly luciferase from the AUG-deleted sequence, suggesting that dicistroviral IRESs will be able to yield polypeptides with a specific N-terminal amino acid other than methionine.

Identification of Methionine-rich Clusters That Regulate Copper-stimulated Endocytosis of the Human Ctr1 Copper Transporter

Copper uptake and subsequent delivery to copper-dependent enzymes are essential for many cellular processes. However, the intracellular levels of this nutrient must be controlled because of its potential toxicity. The hCtr1 protein functions in high affinity copper uptake at the plasma membrane of human cells. Recent studies have shown that elevated copper stimulates the endocytosis and degradation of the hCtr1 protein, and this response is likely an important homeostatic mechanism that prevents the overaccumulation of copper. The domains of hCtr1 involved in copper-stimulated endocytosis and degradation are unknown. In this study we examined the importance of potential copper-binding sequences in the extracellular domain and a conserved transmembrane (150)MXXXM(154) motif for copper-stimulated endocytosis and degradation of hCtr1. The endocytic response of hCtr1 to low copper concentrations required an amino-terminal methionine cluster ((40)MMMMPM(45)) closest to the transmembrane region. However, this cluster was not required for the endocytic response to higher copper levels, suggesting this motif may function as a high affinity copper-sensing domain. Moreover, the transmembrane (150)MXXXM(154) motif was absolutely required for copper-stimulated endocytosis and degradation of hCtr1 even under high copper concentrations. Together with previous studies demonstrating a role for these motifs in high affinity copper transport activity, our findings suggest common biochemical mechanisms regulate both transport and trafficking functions of hCtr1.

Functional expression and characterization of a bacterial light-harvesting membrane protein in Escherichia coli and cell-free synthesis systems.

Heterologous expression of a bacterial light-harvesting (LH) integral membrane protein was attempted using Escherichia coli cells and cell-free synthesis systems prepared from E. coli extracts. The alpha-apoprotein of LH1 complex from purple photosynthetic bacterium Rhodospirillum rubrum was overexpressed as a recombinant protein with a histidine (His6) tag added to the carboxyl terminus. Both of the expression systems produced alpha-apoprotein in a fully functional form as can judged by its ability to form a structural subunit with native beta-apoprotein and the pigment molecule bacteriochlorophyll a. The expression product in E. coli appears to be located in the inner cell membrane and can be almost completely extracted by 0.5% (w/v) Triton X-100. Circular dichroism measurement indicated that the expressed alpha-apoproteins from both systems had alpha-helical contents essentially identical with that of the native one. About two thirds of the alpha-apoprotein expressed in E. coli was found to have the amino terminal methionine residue modified by a formyl group. About one third of the alpha-apoprotein expressed in the cell-free system was found to be oxidized at the side chain of the amino terminal methionine residue. Functional expression of the alpha-apoprotein using the cell-free system provides an useful example for producing highly hydrophobic integral membrane proteins with relatively large quantities sufficient for biophysical and structural analysis.

Proteomics-based Target Identification: BENGAMIDES AS A NEW CLASS OF METHIONINE AMINOPEPTIDASE INHIBITORS

LAF389 is a synthetic analogue of bengamides, a class of marine natural products that produce inhibitory effects on tumor growth in vitro and in vivo. A proteomics-based approach has been used to identify signaling pathways affected by bengamides. LAF389 treatment of cells resulted in altered mobility of a subset of proteins on two-dimensional gel electrophoresis. Detailed analysis of one of the proteins, 14-3-3gamma, showed that bengamide treatment resulted in retention of the amino-terminal methionine, suggesting that bengamides directly or indirectly inhibited methionine aminopeptidases (MetAps). Both known MetAps are inhibited by LAF389. Short interfering RNA suppression of MetAp2 also altered amino-terminal processing of 14-3-3gamma. A high resolution structure of human MetAp2 co-crystallized with a bengamide shows that the compound binds in a manner that mimics peptide substrates. Additionally, the structure reveals that three key hydroxyl groups on the inhibitor coordinate the di-cobalt center in the enzyme active site.

Mammalian reovirus core protein micro 2 initiates at the first start codon and is acetylated.

Mammalian reovirus is an enteric virus that contains a double-stranded RNA genome. The genome consists of ten RNA segments that encode eight structural and three non-structural proteins. The structural proteins form a double-layered structure. The innermost layer, called the core, consists of five proteins (lambda1, lambda2, lambda3, micro 2, and sigma2). Protein lambda3 is the RNA-dependent RNA polymerase (RdRp) and micro 2 is thought to be an RdRp cofactor. Translation of most reovirus proteins is known to commence at the first start codon. However, the translation initiation site of the viral core protein micro 2, encoded by the M1 RNA segment, has been in dispute. Although the theoretical molecular weight of micro 2 is 83 267 Da the actual molecular weight is unknown because micro 2 runs aberrantly in SDS-PAGE and has resisted characterization by Edman degradation, indicating that the amino terminus is post-translationally modified. In this study, we used proteolysis coupled with MALDI-Qq-TOFMS to determine that translation of micro 2 initiates at the first AUG codon, that its actual molecular weight approximates the theoretical value of 83 kDa, that the amino terminal methionine residue is removed, and that the next amino acid (alanine) is post-translationally acetylated.