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PubMed1984

The EcoA restriction and modification system of Escherichia coli 15T-: enzyme structure and DNA recognition sequence.

The EcoA restriction enzyme from Escherichia coli 15T- has been isolated. It proves to be an unusual enzyme, clearly related functionally to the classical type I restriction enzymes. The basic enzyme is a two subunit modification methylase. Another protein species can be purified which by itself has no enzymatic activities but which converts the modification methylase to an ATP and S-adenosylmethionine-dependent restriction endonuclease. The DNA recognition sequence of EcoA has an overall structure that is very similar to previously determined type I sequences. It is: 5'-GAGNNNNNNNGTCA-3' 3'-CTCNNNNNNNCAGT-5' where N can be any nucleotide. Modification methylates the adenosyl residue in the specific trinucleotide and the adenosyl residue in the lower strand of the specific tetranucleotide.

Base Sequence↗
PubMed1984

Development-dependent modification of the extracellular matrix by a sulphated glycoprotein in Volvox carteri.

We report the chemical characterization of the highly sulphated glycoprotein SSG 185 from Volvox carteri. SSG 185 is a hydroxyproline-containing, extracellular glycoprotein. The sulphate residues are clustered within the parent saccharide structure of SSG 185, since on mercaptolysis all the sulphate residues are recovered in a small saccharide fragment containing mannose, arabinose and sulphate (in a molar ratio of 112). SSG 185 is a short-lived molecule, serving as a precursor for a high mol. wt. component of the extracellular matrix. Synthesis of SSG 185 is developmentally controlled. Different SSG 185 variants, with unknown modifications in the sulphated saccharide fragment, are synthesized at different developmental stages or under the influence of the sexual inducer. These modifications remain conserved in the aggregated state of SSG 185, indicating the development-dependent modification of the extracellular matrix.

Journal Article↗
PubMed1989

Modification of nuclear lamin proteins by a mevalonic acid derivative occurs in reticulocyte lysates and requires the cysteine residue of the C-terminal CXXM motif.

The C-terminus of nuclear lamins (CXXM) resembles a C-terminal motif (the CAAX box) of fungal mating factors and ras-related proteins. The CAAX box is subject to different types of post-translational modifications, including proteolytic processing, isoprenylation and carboxyl methylation. By peptide mapping we show that both chicken lamins A and B2 are processed proteolytically in vivo. However, whereas the entire CXXM motif is cleaved from lamin A, at most three C-terminal amino acids are removed from lamin B2. Following translation of cDNA-derived RNAs in reticulocyte lysates, lamin proteins specifically incorporate a derivative of [14C]mevalonic acid (MV), i.e. the precursor of a putative isoprenoid modification. Remarkably, no MV is incorporated into lamin B2 translated from a mutant cDNA encoding alanine instead of cysteine in the C-terminal CXXM motif. These results implicate this particular cysteine residue as the target for modification of lamin proteins by an isoprenoid MV derivative, and they indicate that isoprenylation is amenable to studies in cell-free systems. Moreover, our observations suggest that C-terminal processing of newly synthesized nuclear lamins is a multi-step process highly reminiscent of the pathway elaborated recently for ras-related proteins.

Animals↗
PubMed1995

Rp-phosphorothioate modifications in RNase P RNA that interfere with tRNA binding.

We have used Rp-phosphorothioate modifications and a binding interference assay to analyse the role of phosphate oxygens in tRNA recognition by Escherichia coli ribonuclease P (RNase P) RNA. Total (100%) Rp-phosphorothioate modification at A, C or G positions of RNase P RNA strongly impaired tRNA binding and pre-tRNA processing, while effects were less pronounced at U positions. Partially modified E. coli RNase P RNAs were separated into tRNA binding and non-binding fractions by gel retardation. Rp-phosphorothioate modifications that interfered with tRNA binding were found 5' of nucleotides A67, G68, U69, C70, C71, G72, A130, A132, A248, A249, G300, A317, A330, A352, C353 and C354. Manganese rescue at positions U69, C70, A130 and A132 identified, for the first time, sites of direct metal ion coordination in RNase P RNA. Most sites of interference are at strongly conserved nucleotides and nine reside within a long-range base-pairing interaction present in all known RNase P RNAs. In contrast to RNase P RNA, 100% Rp-phosphorothioate substitutions in tRNA showed only moderate effects on binding to RNase P RNAs from E. coli, Bacillus subtilis and Chromatium vinosum, suggesting that pro-Rp phosphate oxygens of mature tRNA contribute relatively little to the formation of the tRNA-RNase P RNA complex.

Base Sequence↗
PubMed1991

Prevention of bioprosthetic heart valve tissue calcification by charge modification: effects of protamine binding by formaldehyde.

Calcification is the principal cause of the clinical failure of bioprosthetic heart valves (BHV). Calcification occurs through an interaction of host and implant factors, mainly younger age and glutaraldehyde pretreatment, respectively. The hypothesis of this work was that an impaired balance between positively and negatively charged amino acids, due to the reaction with Lys and Hyl tissue-collagen residues, expose affinity sites to Ca++. We further hypothesized that regardless of the cause(s) of BHV calcification, positive charge modification of the tissues will prevent their propensity to calcify. Modification of BHV tissue was obtained by covalently binding protamine sulfate, a polybasic peptide, via formaldehyde and subsequent glutaraldehyde tissue crosslinking. Protamine-bound tissue exhibited stability properties (shrinkage temperature and resistance to collagenase digestion) similar to BHV tissue. Protamine-treated tissue was less permeable to Ca++, and reduced staining was observed with positively charged dyes, indicating the presence of positively charged functional groups in the modified tissue. Significant prevention of calcification was exhibited by the p-bound tissue in comparison to BHV tissue, 30.9 and 109 micrograms/mg calcium, respectively, after 30 days of subdermal implants in rats. The modification procedure resulted in stable, covalent links of approximately 10% w/w protamine with undiminished anticalcification properties, even after 1 year storage. The results support our hypotheses, and orthotopical heart valve replacements are required in order to completely evaluate the treatment efficacy and biocompatibility.

Biocompatible Materials↗
PubMed2005

Effects of surface modification of poly (3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx) on physicochemical properties and on interactions with MC3T3-E1 cells.

As a new member of the polyhydroxyalkanoate (PHA) family, poly (3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx) has better mechanical and processible properties than poly (3-hydroxybutyrate) (PHB). Still, it is difficult to introduce functional groups to the polyester carbon chain of PHBHHx, which restricts the modification of PHBHHx for a wide range. In this study, a procedure for the modification of the surface of PHBHHx films under strongly alkaline conditions was described. Through this kind of modification, carboxyl and hydroxyl groups were introduced to the surface and the total surface free energy was increased, which was mainly due to the increased polar components. Meanwhile, this process makes the surface rougher, resulting in larger total surface areas. After mineralization in simulated body fluids (SBFs), the apatite nucleation and growth on the surface-hydrolyzed PHBHHx films were significantly faster than on the unmodified PHBHHx films. This phenomenon should have a close relationship with the increased carboxyl and hydroxyl groups. The physicochemical properties also influenced the cell response to PHBHHx films. Compared to unmodified PHBHHx, fibronectin adsorption, and MC3T3-E1 cell attachment and proliferation were significantly greater on surface-hydrolyzed PHBHHx, which may be due to the increased surface free energy and rougher surface. Therefore, surface hydrolysis makes PHBHHx more suitable for osteoblast cell response and for application in bone-tissue engineering.

3-Hydroxybutyric Acid↗
PubMed2005

Influence of surface self-modification in Ringer's solution on the passive behavior of titanium.

The influence of the spontaneous surface modification of titanium by exposure to Ringer's solution at open-circuit conditions on the passive behavior was studied. The electrochemical behavior of Ti was compared in a simple NaCl and in Ringer's physiological solution. Potentiodynamic polarization curves show significantly higher passive current densities in Ringer's solution as compared with the simple saline solution. Furthermore, impedance spectra measured at the open-circuit potential as a function of time indicate that in saline solution a long-term exposure over some days leads to a strong increase of the protectiveness of the passive film. This improvement of the passive behavior cannot be observed in Ringer's solution, but a strong modification of the passive film/electrolyte interface can be seen in the impedance spectra. The changes in the impedance spectra can be correlated with the results observed by surface characterization regarding the morphology (scanning electron microscopy) and chemical composition of the surface (X-ray photoelectron spectroscopy). In agreement with previous work by others, a spontaneous modification of the surface of Ti by Ca and P species was observed. The composition of the Ca/P precipitates changes as a function of time, indicating a slow formation of a hydroxyapatite-like deposit layer on the surface. The results of the present work indicate that the formation of the outer Ca-P deposit layer on the passive Ti surface (which is beneficial for the biological performance) hinders the normal aging of the passive TiO(2). Even though the protectiveness of the passive film can be considered as high also in Ringer's solution, significantly higher passive dissolution rates (i.e., higher metal-ion release) for Ti exposed to Ringer's solution can be expected as compared with a simple saline solution.

Electrochemistry↗
PubMed2005

A COMPASS in the voyage of defining the role of trithorax/MLL-containing complexes: linking leukemogensis to covalent modifications of chromatin.

Chromosomal rearrangements and translocations play a major role in the pathogenesis of hematological malignancies. The trithorax-related mixed lineage leukemia (Mll) gene located on chromosome 11 is rearranged in a variety of aggressive human B and T lymphoid tumors as well as acute myeloid leukemia (AML) in both children and adults. It was first demonstrated for the yeast MLL homolog complex, Set1/COMPASS, and now for the MLL complex itself, that these complexes are histone methyltransferases capable of methylating the fourth lysine of histone H3. The post-translational modifications of histones by methylation have emerged as a key regulatory mechanism for both repression and activation of gene expression. Studies from several laboratories during the past few years have brought about a watershed of information defining the molecular machinery and factors involved in the recognition and modification of nucleosomal histones by methylation. In this review, we will discuss the recent findings regarding the molecular mechanism and consequences of histone modification by the MLL related protein containing complex COMPASS.

Adult↗
PubMed2006

Effect of methylglyoxal modification and phosphorylation on the chaperone and anti-apoptotic properties of heat shock protein 27.

Heat shock protein 27 (Hsp27) is a stress-inducible protein in cells that functions as a molecular chaperone and also as an anti-apoptotic protein. Methylglyoxal (MGO) is a reactive dicarbonyl compound produced from cellular glycolytic intermediates that reacts non-enzymatically with proteins to form products such as argpyrimidine. We found considerable amount of Hsp27 in phosphorylated form (pHsp27) in human cataractous lenses. pHsp27 was the major argpyrimidine-modified protein in brunescent cataractous lenses. Modification by MGO enhanced the chaperone function of both pHsp27 and native Hsp27, but the effect on Hsp27 was at least three-times greater than on pHsp27. Phosphorylation of Hsp27 abolished its chaperone function. Transfer of Hsp27 using a cationic lipid inhibited staurosporine (SP)-induced apoptotic cell death by 53% in a human lens epithelial cell line (HLE B-3). MGO-modified Hsp27 had an even greater effect (62% inhibition). SP-induced reactive oxygen species in HLE-B3 cells was significantly lower in cells transferred with MGO-modified Hsp27 when compared to native Hsp27. In vitro incubation experiments showed that MGO-modified Hsp27 reduced the activity of caspase-9, and MGO-modified pHsp27 reduced activities of both caspase-9 and caspase-3. Based on these results, we propose that Hsp27 becomes a better anti-apoptotic protein after modification by MGO, which may be due to multiple mechanisms that include enhancement of chaperone function, reduction in oxidative stress, and inhibition of activity of caspases. Our results suggest that MGO modification and phosphorylation of Hsp27 may have important consequences for lens transparency and cataract development.

Age Factors↗
PubMed1991

A combination of posttranslational modifications is responsible for the production of neuronal alpha-tubulin heterogeneity.

We describe the presence of alpha-tubulin and MAP2 acetyltransferase activities in mouse brain. The enzyme(s) copurified with microtubules through two cycles of assembly-disassembly. Incubation of microtubule proteins with [3H]acetyl CoA resulted in a strong labeling of both alpha-tubulin and MAP2. To determine the site of the modification, tubulin was purified and digested with Glu-C endoproteinase. A unique radioactive peptide was detected and purified by HPLC. Edman degradation sequencing showed that this peptide contained epsilon N-acetyllysine at position 40 of the alpha-tubulin molecule. This result demonstrates that mouse brain alpha-tubulin was acetylated at the same site as in Chlamydomonas. Isoelectric focusing analysis showed that acetylated alpha-tubulin was resolved into five isoelectric variants, denoted alpha 3 and alpha 5 to alpha 8. This heterogeneity is not due to acetylation of other sites but results from a single acetylation of Lys40 of an heterogeneous population of alpha-tubulin isoforms. These isoforms are produced by posttranslational addition of one to five glutamyl units. Thus, neuronal alpha-tubulin is extensively modified by a combination of modifications including acetylation, glutamylation, tyrosylation, and other yet unknown modifications.

Acetylation↗
PubMed1990

Amino acid modification of proteins in regenerating sciatic nerves of rats.

Recent experiments have shown that Arg, Lys, and Leu can be incorporated posttranslationally into proteins of regenerating sciatic nerves of rats. The present experiments investigate a mixture of 15 radioactive amino acids to determine if additional amino acids can be conjugated posttranslationally to proteins of regenerating nerves. Proteins of regenerating sciatic nerves of rats were able to incorporate Arg, Lys, Leu, Pro, Val, Ala, Phe, and Ser in relatively large amounts and Asp, Glu, Thr, Gly, Ile, His, and Tyr in relatively low or undetectable amounts, in the most advanced portion of the regenerating nerves. Two-dimensional SDS PAGE showed incorporation of the amino acid mixture into distinct radioactive peaks with molecular weights in the 80-90 kD, 53-66 kD, 22-46 kD, and 17 kD ranges with isoelectric points between 5.0 and 7.9. Most of the amino acids were incorporated into proteins in all of the molecular weight ranges. But Ser was incorporated in highest amounts in the 17 kD range, and Val was most abundant in the 22-46 kD range. In some cases results indicated that single proteins were modified by several amino acids. While we do not yet know which amino acids modify specific nerve proteins or the function of the modifications in nerve regeneration, these studies demonstrate the participation of some but not all amino acids in posttranslational modification reactions and the selective modification of specific groups of nerve proteins by these amino acids.

Amino Acids↗
PubMed2005

Supercritical fluid crystallization of griseofulvin: crystal habit modification with a selective growth inhibitor.

Poly (sebacic anhydride) (PSA) was used as a growth inhibitor to selectively modify habit of griseofulvin crystals formed via the Precipitation with a compressed-fluid antisolvent (PCA) process. PSA and griseofulvin were coprecipitated within a PCA injector, which provided efficient mixing between the solution and compressed antisolvent process streams. Griseofulvin crystal habit was modified from acicular to bipyramidal when the mass ratio of PSA/griseofulvin in the solution feed stream was <or=1:1. The habit modification was attributed to the preferential adsorption of PSA to the fastest growing crystal face of the acicular crystal form, which inhibited growth. Scanning electron microscopy (SEM) was used to characterize the griseofulvin and PSA particles, and gave results consistent with a selective growth inhibition mechanism. SEM micrographs showed regions on griseofulvin crystals where PSA microparticles had preferentially adsorbed. X-ray powder diffraction (XRPD) and differential scanning calorimetry (DSC) analysis of the griseofulvin crystals indicated no changes in the crystalline form after the habit modification. Powder compressibility decreased from 49 +/- 3% to 28 +/- 7% with the modification in crystal habit. No change in the physical stability of the processed powder was observed after being stored at 25 degrees C/60% RH and 40 degrees C/70% RH for 23 days. Despite the change in crystal habit, griseofulvin crystals achieved 100% dissolution within 60 min in a simulated gastric fluid.

Anhydrides↗
PubMed1983

Kinetics of the rapid modification of human serum albumin with trinitrobenzenesulfonate and localization of its site.

The rapid reaction of human serum albumin with trinitrobenzenesulfonate (I) and the location of the reactive site were investigated to characterize the chemical modification of albumin by I. The modification proceeds through trinitrophenylation of a lysine residue of albumin and monoaddition of the byproduct, sulfite ion, to the trinitrophenylalbumin, as reported previously. The individual kinetic parameters for both reactions were determined at various pH values and 25 degrees. The epsilon-amino group of the lysine residue which has a pKa value of approximately 8.9 was the reactive group involved in the trinitrophenylation. The dissociation constant of the sulfite monoadduct was about 10-fold smaller than that of the monoadduct of the model compound trinitrophenyl alpha-acetyllysine. The modification of albumin by I reduced the fluorescence intensity of the tryptophan-214 residue in the albumin amino acid sequence. Acetylation of the lysine-199 residue with aspirin and 5-nitroaspirin decreased the trinitrophenylation rate of albumin with I. These results on the fluorescence spectroscopy and the effect of the acetylation suggest that the reactive group for I is the lysine-199 residue located near the tryptophan-214 residue.

Acetylation↗
PubMed1978

Direct modification of the glycocalyx of a cultured muscle cell line by incorporation of foreign gangliosides and an integral membrane glycoprotein.

As part of a program to better understand the cause-or-effect nature of the relationship between cell surface carbohydrate and cell properties and behaviour, experiments have been carried out on direct modification of the glycocalyx of cultured cells. Modification was by incorporation of gangliosides and an integral membrane glycoprotein chosen to be dissimilar to species occurring naturally in the cell line. Two methods of incorporation were investigated: simple addition of the new components to the culture medium for various times, or assembly of the components into the walls of lipid vesicles which were subsequently fused with cells. Gangliosides from beef brain and glycophorin, the major human erythrocyte sialoglycoprotein, were successfully added to the surface of myoblasts in quantities sufficient to represent a significant perturbation. Changes in cell adhesion, morphology, and viability were observed which seem to be a direct result of glycocalyx modification.

Animals↗
PubMed2006

Posttranslational modifications of collagen studied by off-line coupling of HPLC and CE.

A typical example of non-enzymatic change of collagen is glycation (the Maillard reaction, formation of advanced glycation end products) resulting from the reaction of sugars with the epsilon-amino group of lysine. Posttranslational non-enzymatic modifications of collagen by sugars were studied. Collagenous tissues were incubated as a test protein separately with both glucose and ribose. The collagen mixture was digested by bacterial collagenase and separated by reversed-phase HPLC (in a Jupiter Proteo 90 A column). The eluate from this HPLC separation was collected as seven fractions and consecutively analysed by CE in a bare fused silica capillary (57/50 cm x 75 mm id) using 100 mM sodium 1-heptanesulfonate in 100 mM phosphate buffer, pH 2.5 (NaH2PO4 adjusted to pH by phosphoric acid). The chromatographic and electromigration behaviour of individual peptides varied considerably. This off-line HPLC-CE coupling made it possible to discover minor changes in the structure of collagen caused by posttranslational modifications. A new HPLC-CE technique for peptide analysis was developed, and applied to the identification of posttranslational modifications in slowly metabolised test proteins.

Animals↗
PubMed1989

Proteins of the acrosomal region in mouse sperm: immunological probes reveal post-testicular modifications.

Due to the central role the acrosomal region plays in sperm-egg interactions, monoclonal antibodies (mAbs) were used to identify components of this domain in mouse sperm. Several sperm proteins that localize specifically to the anterior acrosomal region are described here in terms of electrophoretic mobility, susceptibility to proteolytic degradation, and post-translational modification during epididymal transit. Six different mAbs were used, each recognizing a distinctive antigen (Ag) or set of Ags in cauda epididymal mouse sperm: a doublet of 185/200 Kd (M42 mAb); 150-160 Kd (M5 mAb); 105 Kd (W71 mAb); 21, 35, and 60 Kd (M41 mAb); 27 and 33 Kd (W33 mAb); and 57 and 86 Kd (W108 mAb). Previously reported work implicates two of these, M42 Ag and M5 Ag, as participants in sperm-zona interaction (Saling and Lakoski: Biol Reprod 33:527-536, 1985; Saling: Dev Biol 117:511-519, 1986; and Lakoski et al.: Biol Reprod 38:221-233, 1988). Recognition of some (M42, M5, W108), but not all (W33), of the Ags by their corresponding mAbs was affected by sperm incubation with proteases (trypsin or collagenase). Evidence of post-translational modification during epididymal maturation was suggested by altered electrophoretic mobility of several of the Ags (M42, M5, W33, and W108) accompanying sperm transit from proximal to distal epididymis. Retention of sperm within the caput epididymis prevented structural alterations for the four proteins examined, indicating that spatial rather than temporal factors are critical for Ag modification in maturing mouse sperm.

Acrosome↗
PubMed2006

Insights into different results from different causal contrasts in the presence of effect-measure modification.

PURPOSE: Both propensity score (PS) matching and inverse probability of treatment weighting (IPTW) allow causal contrasts, albeit different ones. In the presence of effect-measure modification, different analytic approaches produce different summary estimates. METHODS: We present a spreadsheet example that assumes a dichotomous exposure, covariate, and outcome. The covariate can be a confounder or not and a modifier of the relative risk (RR) or not. Based on expected cell counts, we calculate RR estimates using five summary estimators: Mantel-Haenszel (MH), maximum likelihood (ML), the standardized mortality ratio (SMR), PS matching, and a common implementation of IPTW. RESULTS: Without effect-measure modification, all approaches produce identical results. In the presence of effect-measure modification and regardless of the presence of confounding, results from the SMR and PS are identical, but IPTW can produce strikingly different results (e.g., RR = 0.83 vs. RR = 1.50). In such settings, MH and ML do not estimate a population parameter and results for those measures fall between PS and IPTW. CONCLUSIONS: Discrepancies between PS and IPTW reflect different weighting of stratum-specific effect estimates. SMR and PS matching assign weights according to the distribution of the effect-measure modifier in the exposed subpopulation, whereas IPTW assigns weights according to the distribution of the entire study population. In pharmacoepidemiology, contraindications to treatment that also modify the effect might be prevalent in the population, but would be rare among the exposed. In such settings, estimating the effect of exposure in the exposed rather than the whole population is preferable.

Bias↗
PubMed2004

Characterization and location of post-translational modifications on chromogranin B from bovine adrenal medullary chromaffin granules.

Bovine chromoganin B (CGB)/secretogranin I, an acidic protein with a sequence of 626 residues and an isoelectric point of 5.2 is a major member of the chromogranin/secretogranin (CG/Sg) family. The difference between the theoretical molecular mass (76 kDa) and the value estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis results from post-translational modifications (glycosylation, phosphorylation and sulfation) and from the abundance of acidic residues (D 4.6%, and E 16.5%). Although the sequence of CGB is known, the structural analyses of the post-translational modifications have so far not been carried out. In the present study, using a combination of proteomic techniques including two-dimensional gel electrophoresis, Western blot, high-performance liquid chromatography purification, enzymatic digestion, sequencing, carbohydrate analysis, matrix-assisted laser desorption/ionization-time of flight and liquid chromatography mass spectrometry analysis, we have located 18 post-translational modifications on bovine CGB, isolated from adrenal medulla chromaffin granules. Furthermore, we have identified at the molecular level the presence of a mutation M/V on position 577 of natural CGB. All together these data reflect the complex structure of this protein marker of the neuroendocrine system.

Adrenal Medulla↗