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PubMed2006

Transition metal catalyzed methods for site-selective protein modification.

The broad utility of protein bioconjugates has created a need for new and diverse strategies for site-selective protein modification. In particular, chemical reactions that target alternative amino acid side chains or unnatural functional groups are emerging as a valuable complement to more commonly used lysine- and cysteine-based strategies. Considering their widespread use in organic synthesis, reactions catalyzed by transition metals could provide a particularly powerful set of transformations for the continued expansion of the bioconjugation toolkit. Recent efforts to apply transition metal catalysis to protein modification have resulted in new methods for protein cross-linking, tryptophan modification, tyrosine modification, reductive amination of protein amines, and unnatural amino acid labeling. These strategies have substantially expanded the synthetic flexibility of protein modification, and thus the range of applications for which bioconjugates can be used in chemical biology and materials science.

Amino Acids↗
PubMed2006

Characterization of histones and their post-translational modifications by mass spectrometry.

Histone proteins and their accompanying post-translational modifications have received much attention for their ability to affect chromatin structure and, hence, regulate gene expression. Recently, mass spectrometry has become an important complementary tool for the analysis of histone variants and modification sites, for determining the degree of occupancy of these modifications and for quantifying differential expression of these modifications from various samples. Additionally, as advancements in mass spectrometry technologies continue, the ability to read entire 'histone codes' across large regions of histone polypeptides or intact protein is possible. As chromatin biology demands, mass spectrometry has adapted and continues as a key technology for the analysis of gene regulation networks involving histone modifications.

Amino Acid Sequence↗
PubMed2005

Oxidative DNA modifications.

Oxidative DNA modifications are frequent in mammalian DNA and have been suggested an important mechanism in carcinogenesis, diabetes and ageing. The foundations for this suggestion are: Evidence for the importance of oxidative DNA modifications in cancer development is: high levels of oxidative lesions in cancer tissue; highly conserved and specific DNA repair systems targeting oxidative lesions; high levels of oxidative DNA lesions in oxidative DNA repair knock-out animals; defective repair of oxidative lesions in cancer-prone progeria syndromes; reduced cancer incidence in populations with high dietary antioxidant intake; and increased oxidative stress to DNA in tobacco smokers. Conflicting evidence for a relation between oxidative stress to DNA and cancer is: disagreement about the true levels and occurrence of the oxidative lesions in vivo; failure to identify the localization of oxidative lesions in important genes, e.g. tumor suppressor and oncogenes; lack of evidence that the oxidative lesions induce mutations in vivo; no cancer development in animals knocked-out for specific DNA repair enzymes in spite of high tissue levels of oxidative lesions; and unchanged cancer rates after antioxidant interventions in large clinical controlled and randomized trials. The rate of DNA oxidation has been estimated from urinary excretion of repair products and it is evident that if these lesions were not repaired, a large part of DNA would be oxidized to a degree not compatible with living. The methodologies by which oxidative DNA modifications are measured cover a wide and different range, advantages and disadvantages will be presented. One particular problem is artificial oxidation, and methods to prevent such artifacts will be presented together with results from a large interlaboratory standardization program. The methodology by which the lesions can be measured is complicated and prone to artifacts during DNA isolation, digestion, derivatization and maybe even during the separation procedure proper prior to detection. A large effort from 20+ laboratories supported by a grant from the EU has reduced artifacts considerably and work towards interlaboratory standardization of the methodology is in progress. The presently agreed "normal" levels of the most frequent known lesion 8-oxodG is about 5 per million dG's in DNA. A comprehensive evaluation of the evidence, from chemistry to clinical and epidemiological trials, linking oxidative modifications to cancer will be given. Finally, an estimate of the quantitative role oxidative DNA modifications play among the multiplicity of other insults is given. While there is no question that all of these oxidative mechanisms do exist, quantitative data on their importance for the human situation do not exist. Prospective human studies that can provide such quantitative data on different mechanisms are underway.

Aging↗
PubMed2005

NAD-, NMN-, and NADP-dependent modification of dinitrogenase reductases from Rhodospirillum rubrum and Azotobacter vinelandii.

Nitrogenase activity in the photosynthetic bacterium Rhodospirillum rubrum is reversibly regulated by ADP-ribosylation of a specific arginine residue of dinitrogenase reductase based on the cellular nitrogen or energy status. In this paper, we have investigated the ability of nicotinamide adenine dinucleotide, NAD (the physiological ADP-ribose donor), and its analogs to support covalent modification of dinitrogenase reductase in vitro. R. rubrum dinitrogenase reductase can be modified by DRAT in the presence of 2 mM NAD, but not with 2 mM nicotinamide mononucleotide (NMN) or nicotinamide adenine dinucleotide phosphate (NADP). We also found that the apo- and the all-ferrous forms of R. rubrum dinitrogenase reductase are not substrates for covalent modification. In contrast, Azotobacter vinelandii dinitrogenase reductase can be modified by the dinitrogenase reductase ADP-ribosyl transferase (DRAT) in vitro in the presence of either 2 mM NAD, NMN or NADP as nucleotide donors. We found that: (1) a simple ribose sugar in the modification site of the A. vinelandii dinitrogenase reductase is sufficient to inactivate the enzyme, (2) phosphoADP-ribose is the modifying unit in the NADP-modified enzyme, and (3) the NMN-modified enzyme carries two ribose-phosphate units in one modification site. This is the first report of NADP- or NMN-dependent modification of a target protein by an ADP-ribosyl transferase.

Adenosine Diphosphate Ribose↗
PubMed2005

A sensitive method for the quantitative measurement of protein thiol modification in response to oxidative stress.

The combination of proteomics with highly specific and sensitive affinity techniques is important for the identification of posttranslational modifications by reactive oxygen and nitrogen species (ROS/RNS). One of the most pressing problems with this approach is to determine accurately the extent of modification of specific amino acids, such as cysteine residues, in a complex protein sample. A number of techniques relevant to free radical biology use biotin tagging as a method to follow protein modification with high sensitivity and specificity. To realize the potential of this approach to provide quantitative data, we have prepared a series of biotinylated proteins through the modification of lysine residues. These proteins were then used as quantitative standards in electrophoretic separation of protein samples labeled with biotin-conjugated iodoacetamide. The utility of the approach was assessed by measuring modification of thiols in response to exposure to thiol oxidants, as well as the amount of protein adduct formation with a biotin-tagged electrophilic lipid. Furthermore, using a combination of native and biotin-tagged cytochrome c, this method was used to quantitate the amount of thiol relative to the amount of protein in a given spot on a two-dimensional gel. Thus, we have developed a versatile, cost-effective standard that can be used in proteomic methods to quantitate biotin tags in response to oxidative stress.

Animals↗
PubMed2004

Modifications of the inverted T-shaped silicone implant for treatment of temporomandibular joint ankylosis.

PURPOSE: Inverted T-shaped silicone implants have been used for reconstruction of ankylosed temporomandibular joints for 10 years. As the implant is custom made during the operation, dimensional adjustments according to individual need are routine. MATERIAL AND METHOD: A new modification to increase the stability of the inverted T-shaped silicone implant is presented. The modification consists of a middle process on the long arm of the T-shaped silicone implant, the first of which was inserted into the medullary cavity of the mandibular ramus. This modification further stabilizes the implant position and helps prevent its displacement. The modification was used on difficult cases such as bilateral ankylosis, osteotomies below the condylar notch or incompliant patients. This modification was used in six patients. RESULTS: No dislocation, nor extrusion of the implant or re-ankylosis of TMJ was observed.

Adolescent↗
PubMed2004

Regulation of transcription of the steroidogenic acute regulatory protein (StAR) gene: temporal and spatial changes in transcription factor binding and histone modification.

We examined the binding of transcription factors and histone modifications associated with induction of expression of the steroidogenic acute regulatory protein (StAR) gene in MA-10 cells using a quantitative chromatin immunoprecipitation (ChIP) assay. GATA-4, SF-1/Ad4BP, and cyclic AMP response element binding protein binding protein (CBP) bind rapidly to the StAR proximal promoter, but in different patterns following 8-Br-cAMP stimulation. Concomitantly, histone modifications occur in a spatial and temporal sequence including increased association of acetylated histone H3 with the proximal promoter region, increased association of dimethylated lysine 4 histone H3 with exonic sequences, a modification that marks actively transcribed regions, and reduced association of a marker linked to gene silencing (lysine 9 dimethylated histone H3). Our findings demonstrate that transcription factors and coactivators are rapidly associated with the StAR proximal promoter, that the patterns of binding differ which has implications for postulated direct interactions among these factors, and that multiple histone modifications are demonstrable in a spatially- and temporally-specific pattern along the StAR gene. These observations suggest that a combinatorial code of transcription factors including reciprocal changes in histone modifications associated with active transcription and gene silencing control StAR gene expression.

8-Bromo Cyclic Adenosine Monophosphate↗
PubMed2004

Reversal and consolidation of activity-induced synaptic modifications.

Persistent activity-induced synaptic modification is generally regarded as the cellular basis for developmental refinement of neuronal connections and for learning and memory. It has long been recognized that synaptic modifications can be reversed by subsequent stimuli. Recent in vivo studies indicate that reversal of synaptic modifications is a natural process that can be triggered by physiological activity. Long-term potentiation (LTP) of hippocampal synapses in adult rats was reversed as rats entered a novel environment. LTP of retinotectal synapses in developing Xenopus was also reversed by subsequent spontaneous activity. Repetitive stimulation with spaced patterns, however, can overcome this reversal, leading to stabilized synaptic modifications. The requirement of spaced stimulus patterns for stable synaptic modifications could ensure appropriate refinement of developing connections.

Animals↗
PubMed2004

Chemical modification of arginine residues of Notechis scutatus scutatus notexin.

Notexin, a presynaptic phospholipase A2 (PLA2) neurotoxin isolated from Notechis scutatus scutatus venom, was inactivated by arginine-specific reagents, phenylglyoxal and 1,2-cyclohexanedione. Kinetic analyses of the modification reaction revealed that the inactivation of notexin followed pseudo-first order kinetics and the loss of PLA2 activity was correlated with the incorporation of one molecule of modification reagent per toxin molecule. However, the results of amino acid analysis and sequence determination revealed that two arginine residues at positions 43 and 79 of notexin were modified simultaneously. Modification of the arginine residues was accompanied with a decrease in the ability to inhibit the indirectly evoked contraction of chick biventer cervicis muscle and bind with synaptic membranes. The secondary structure of the toxin molecule did not significantly change after modification with phenylglyoxal as revealed by the CD spectra. The modified derivative retained its affinity for Ca2+, indicating that the modified arginine residues did not participate in Ca2+ -binding. Together with the notion that Arg-43 and Arg-79 of notexin are located in the proximity of its catalytic site and toxic site, respectively, our results suggest that modification of Arg-43 and Arg-79 should differently contribute to the observed decrease in the PLA2 activity and neurotoxic effect of notexin.

Animals↗
PubMed2006

SUMO modification through rapamycin-mediated heterodimerization reveals a dual role for Ubc9 in targeting RanGAP1 to nuclear pore complexes.

SUMOs (small ubiquitin-related modifiers) are eukaryotic proteins that are covalently conjugated to other proteins and thereby regulate a wide range of important cellular processes. The molecular mechanisms by which SUMO modification influences the functions of most target proteins and cellular processes, however, remain poorly defined. A major obstacle to investigating the effects of SUMO modification is the availability of a system for selectively inducing the modification or demodification of an individual protein. To address this problem, we have developed a procedure using the rapamycin heterodimerizer system. This procedure involves co-expression of rapamycin-binding domain fusion proteins of SUMO and candidate SUMO substrates in living cells. Treating cells with rapamycin induces a tight association between SUMO and a single SUMO substrate, thereby allowing specific downstream effects to be analyzed. Using RanGAP1 as a model SUMO substrate, the heterodimerizer system was used to investigate the molecular mechanism by which SUMO modification targets RanGAP1 from the cytoplasm to nuclear pore complexes (NPCs). Our results revealed a dual role for Ubc9 in targeting RanGAP1 to NPCs: In addition to conjugating SUMO-1 to RanGAP1, Ubc9 is also required to form a stable ternary complex with SUMO-1 modified RanGAP1 and Nup358. As illustrated by our studies, the rapamycin heterodimerizer system represents a novel tool for studying the molecular effects of SUMO modification.

Dimerization↗
PubMed2005

Visual monitoring of post-translational lipid modifications using EGFP-GTPase probes in live cells.

Modification of small GTPases by lipids is required for their proper subcellular localization and biological activity. Lipids added post-translationally include both farnesyl and geranylgeranyl isoprenoids and the fatty acid palmitate. Thus, specific small molecule inhibitors of these processes cause mislocalization of small GTPases and impair their biological activity. Common biochemical methods of determining the lipid modification status or inhibitor sensitivity of small GTPases, such as in vitro prenylation assays, SDS-PAGE mobility shifts or metabolic labeling, although highly useful in their own right, cannot distinguish differences among specific subpopulations of cells, link lipid modification status with other properties of interest, or provide spatio-temporal information. An alternative method takes advantage of the tight link between small GTPase lipid modification and subcellular localization. The innate localization pattern of the enhanced green fluorescent protein, a common epitope tag frequently used in live cell imaging, is altered by fusion to modified but not unmodified small GTPases. We describe here a technique that takes advantage of these properties to monitor post-translational modifications of these proteins in a rapid, visual manner in live cells.

Animals↗
PubMed2006

Accelerated nuclei preparation and methods for analysis of histone modifications in yeast.

The continuing identification of new histone post-translational modifications and ongoing discovery of their roles in nuclear processes has increased the demand for quick, efficient, and precise methods for their analysis. In the budding yeast Saccharomyces cerevisiae, a variety of methods exist for the characterization of histone modifications on a global scale. However, a wide gap in preparation time and histone purity exists between the most widely used extraction methods, which include a simple whole cell extraction (WCE) and an intensive histone extraction. In this work we evaluate various published WCE buffers for their relative effectiveness in the detection of histone modifications by Western blot analysis. We also present a precise, yet time-efficient method for the detection of subtle changes in histone modification levels. Lastly, we present a protocol for the rapid small-scale purification of nuclei that improves the performance of antibodies that do not work efficiently in WCE. These new methods are ideal for the analysis of histone modifications and could be applied to the analysis and improved detection of other nuclear proteins.

Buffers↗
PubMed1998

Oxidative modification of HDL3 in vitro and its effect on PLTP-mediated phospholipid transfer.

The oxidation of HDL3 by Cu(II) and its effect on the ability of these particles to act as phospholipid acceptors in human plasma phospholipid transfer protein (PLTP)-mediated lipid transfer were investigated. Oxidation of HDL3 was monitored by measuring the following parameters: (i) formation of conjugated dienes, (ii) production of thiobarbituric acid reactive substances (TBARS), (iii) decrease in reactive lysine and (iv) tryptophan residues, (v) change in particle charge and (vi) diameter, and (vii) oligomerisation of apoA-I and apoA-II. Formation of conjugated dienes was the parameter responding to the oxidative treatment with the fastest kinetics. The appearance of TBARS and modification of apolipoprotein tryptophan residues were detected simultaneously but required higher Cu(II) concentrations for maximal kinetics. Cross-linking of the major protein constituents of HDL3, apoA-I and apoA-II, represented later steps of the oxidation process. Further, the oxidative modification was accompanied by a progressive change in HDL3 particle charge and a minor increase in particle diameter. PLTP-mediated phospholipid transfer to the oxidized particles was investigated using an assay measuring the transfer of fluorescent, pyrene-labeled PC. The transfer was significantly inhibited, but only after extensive modification of the HDL proteins, suggesting that the HDL oxidative modifications occurring in vivo do not essentially impair its phospholipid acceptor function. A similar but less pronounced inhibition was observed when two other phospholipid transfer proteins, the nonspecific lipid transfer protein (ns-LTP) and the phosphatidylcholine transfer protein (PC-TP), were studied in parallel. This indicates that the inhibition was partly due to unspecific effects of the modification on acceptor particle surface properties, but included an aspect specific for PLTP.

Animals↗
PubMed2003

O-GlcNAc: a regulatory post-translational modification.

Beta-N-acetylglucosamine (O-GlcNAc) is a regulatory post-translational modification of nuclear and cytosolic proteins. The enzymes for its addition and removal have recently been cloned and partially characterized. While only about 80 mammalian proteins have been identified to date that carry this modification, it is clear that this represents just a small percentage of the modified proteins. O-GlcNAc has all the properties of a regulatory modification including being dynamic and inducible. The modification appears to modulate transcriptional and signal transduction events. There are also accruing data that O-GlcNAc plays a role in apoptosis and neurodegeneration. A working model is emerging that O-GlcNAc serves as a metabolic sensor that attenuates a cell's response to extracellular stimuli based on the energy state of the cell. In this review, we will focus on the enzymes that add/remove O-GlcNAc, the functional impact of O-GlcNAc modification, and the current working model for O-GlcNAc as a nutrient sensor.

Acetylglucosamine↗
PubMed1999

Short term modification of disparity vergence eye movements.

Dynamics of disparity vergence eye movements can be modified by adaptive stimuli that generate large transient disparities. These modifications were observed for convergence as well as divergence eye movements. After modification, the peak velocities of the step responses for convergence and divergence were substantially higher than in normal baseline responses, a change observed in all four subjects studied. The change in peak velocity of a step response occurred very rapidly after presentation of the adaptive stimuli. Main sequence plots showed that first-order dynamic characteristics increased for post-adaptive responses with respect to normal step responses. Hence, response modification could be quantified as a change in gain accompanied with an increase in the effective response time constant. The adaptive responses to convergent and divergent 'disappearing' step stimuli revealed that the adaptation process modifies the high-velocity component of both disparity convergence and divergence eye movements. Moreover, a gain change in this component alone could account for both the gain and the time constant modifications seen in the overall response. A process of recovery or de-adaptation was also observed for both convergence and divergence eye movements. This observed short-term modification demonstrates a unique control mechanism for vergence eye movements that is effective in either direction.

Adaptation, Ocular↗
PubMed2000

Covalent modification regulates ligand binding to receptor complexes in the chemosensory system of Escherichia coli.

In the Escherichia coli chemosensory pathway, receptor modification mediates adaptation to ligand. Evidence is presented that covalent modification influences ligand binding to receptors in complexes with CheW and the kinase CheA. Kinase inhibition was measured with serine receptor complexes in different modification levels; Ki for serine-mediated inhibition increased 10,000-fold from the lowest to the highest level. Without CheA and CheW, ligand binding is unaffected by covalent modification; thus, the influence of covalent modification is mediated only in the receptor complex, a conclusion supported by an analogy to allosteric enzymes and the observation of cooperative kinase inhibition. Also, the finding that a subsaturating serine concentration accelerates active receptor-kinase complex assembly implies that the assembly/disassembly process may also contribute to kinase regulation.

Allosteric Regulation↗
PubMed2002

Hydrothermal modification of titanium surface in calcium solutions.

Hydrothermal modification of a titanium surface in calcium solutions was performed. The apatite precipitation on the modified surface in Hanks' solution, as a simulated body fluid, was evaluated and the surface microstructure changes after the modification were characterized by thin-film X-ray diffractometry (TF-XRD) and X-ray photoelectron spectroscopy (XPS). Hydrothermal modification in CaO solution enhanced the precipitation of apatite on the titanium surface. High pH, high pressure and high temperature of the CaO solution increased the thickness of the surface-modified layer and enhanced the synthesis of calcium titanate which possibly promoted the precipitation of apatite in Hanks' solution. Hydrothermal modification in CaCl2 solution, on the other hand, showed reverse effects. The modification of titanium in CaO solution with hydrothermal treatment is expected to result in excellent osteointegration and can be easily performed by using an autoclave, a clinical apparatus widely used.

Apatites↗
PubMed1998

Functional and morphological evaluation of different polypropylene-mesh modifications for abdominal wall repair.

Modern surgical hernia repair depends increasingly on synthetic meshes for the reconstruction of the abdominal wall. Despite the undisputed advantages of the polypropylene (PP) meshes currently available (Marlex, Prolene), reports of complications after implantation are increasing. Although, serious complications such as perforation and fistula formation are rare, minor and local complaints such as seromas, misfeelings and a decreased abdominal wall mobility are observed in about one-half of the patients. In regard to the exaggerated strength of the currently available mesh modifications a reduction of the material should improve the integration of the meshes into the artificial abdominal wall. In the present study, the commercially available basic mesh Prolene has been compared to two newly constructed PP-mesh modifications with reduced amounts of PP. The modifications have gradually been adopted to the physiological requirements of abdominal wall stability and mobility by reducing the amount of PP to 64% (E-BLUE) and 24% (variant A) of the Prolene mesh (developed by ETHICON, Norderstedt, Germany). All PP-mesh variants have been implanted in a rat model and studied by 3D-photogrammetry, tensiometry, light- and electron microscopy, as well as morphometry over implantation intervals of 3, 7, 14, 21 and 90 days. The data show that current constructions of PP-meshes are oversized and definitely restrict abdominal wall mobility in the present model. Sufficient stability of the artificial abdominal wall is even guaranteed by PP-mesh modifications with a reduction of PP-quantity to about 25% of the Prolene mesh. The degree of fibrosis directly correlated with abdominal wall restriction, whereas the formation of connective tissue in the interface PP-fibre/host-issue depends on the amount and activity of the inflammatory reaction. The quantity and quality of inflammation, again, directly relies to the amount of PP and to the surface area in contact with the recipient tissues. Altogether, the present study suggests that a modification of the PP-meshes could be helpful to prevent major and minor complications of surgical PP-meshes.

Abdominal Muscles↗