Positions Of Cysteine Residues Research Articles

Cloning of the Amino-terminal and 5′-Flanking Region of the Human MUC5AC Mucin Gene and Transcriptional Up-regulation by Bacterial Exoproducts

To obtain gene regulatory sequence for the mucin gene MUC5AC, we have isolated the MUC5AC amino terminus cDNA and 5'-flanking region. This was possible through the use of rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR) in which the 5' sequence of the human gastric mucin cDNA HGM-1 (1) was used to design the first MUC5AC-specific primer. Primers for subsequent rounds of RACE were designed from the 5'-ends of amplified RACE products. After five rounds of RACE-PCR, we could no longer generate upstream extensions of the cDNA and hypothesized that we had reached the 5'-end. Primer extension and RNase protection analysis confirmed this. Combined nucleotide sequence for the RACE-PCR products was 3.3 kb with an open reading frame encoding 1100 amino acids. A putative translation start site was found at nucleotide +48. This was followed by a 45 nucleotide putative signal sequence. This amino-terminal sequence contains no tandem repeats but is >60% similar to the amino-terminal nucleotide sequence of MUC2. The positions of cysteine residues in this MUC2-similar region are almost 100% conserved between the two genes. Northern analysis showed expression of cognate RNA in the stomach and airway but not muscle and esophagus. This pattern was the same as that obtained using previously reported 3'-MUC5AC sequences. We have cloned approximately 4 kb of genomic DNA upstream of the transcription start site and have sequenced 1366 nucleotides containing a TATA box, a CACCC box, and putative binding sites for NFkappaB and Sp 1. Within 4 kb of the transcription start site are elements mediating transcriptional up-regulation in response to bacterial exoproducts.

Isolation and structural characterization of hepatic metallothionein from the roach (shape Rutilus rutilus L.)

Metallothioneins (MTs), considered as metal biomarkers by many authors, are very conserved proteins that present great interests in phylogenetical studies. This paper reports the purification of the hepatic MT from the roach (Rutilus rutilus). After extensive reverse-phase HPLC, the sequence of the MT was established by a combination of techniques including automated Edman degradation, mass spectrometry and enzymatic treatment. Sequence comparison with other fishes or mammalian MTs showed considerable identities and a high conservation in cysteine residues positions. MTs of roach and goldfish that both belong to the same family (Cyprinidae) share 97% identity. Ninety five% identity were found between roach and stone loach (Cypriniforms, Cobitidae) MTs. Only 77% identity were found with pleuronectiforms or salmoniforms. This sequence brings a new element in the study of the phylogenetical relationships among teleost species.

The Redox State of Cysteines in Human Immunodeficiency Virus Type 1 Vif in Infected Cells and in Virions

HIV-1 Vif has two conserved cysteine residues in positions 114 and 133, both of which were found to be essential for HIV-1 infection and for Vif function in transcomplementation assays (X-Y. Ma, P. Sova, W. Chao, and D. J. Volsky, 1994, J. Virol.68: 1714–1720). We evaluated here the redox status and disulfide bond formation of Vif cysteines inside cells or in virions and tested the role of Vif cysteines in Vif distribution in cells and in virions. Immunoblot analysis of Vif in wild type virus-infected cells and virions under different redox conditions revealed that the cysteine residues are readily accessible to chemical interaction but they do not form intramolecular disulfide bonds either inside cells or in virions, nor do they form covalent bonds with other proteins in either compartment. Cysteine mutants of Vif resembled wildtype Vif in their intracellular and virion distribution, indicating that Vif cysteines do not affect intracellular Vif transport and packaging into virions. We conclude that the cysteines in Vif do not form sulfhydryl bonds either intracellularly or in virions and may contribute to Vif activity rather than structure.

Cloning, sequencing and analysis of cDNA encoding bovine intercellular adhesion molecule-1 (ICAM-1)

Intercellular adhesion molecule-1 (ICAM-1) is an inducible glycoprotein that interacts with the leukocyte β 2-integrins, LFA-1 and Mac-1. We have isolated and analyzed a cDNA clone coding for the putative bovine ICAM-1 gene and compared it with known comparative sequences from other species as well as bovine ICAM-3. The 3398-bp bovine ICAM-1 cDNA sequence codes for 535 amino acids and shows 57% homology with human ICAM-1 and 47% homology with bovine ICAM-3 at the amino acid levels. The predicted number and positions of cysteine residues in bovine ICAM-1 are all conserved among species including bovine ICAM-3. It has two arginineglycine-aspartate (RGD) sites in the extracellular region and a serine residue in the cytoplasmic tail. Northern blot results show that the bovine ICAM-1 gene is expressed in stimulated leukocytes whereas bovine ICAM-3 is expressed predominantly in resting neutrophils.

Fluorescence study of neurohypophyseal hormones and their analogues. Distance distributions in a series of arginine-vasopressin analogues.

Analogues of arginine-vasopressin (AVP) in which substitution of the proline residue in position 7 (by either sarcosine or N-methylalanine) combined with replacement of the cysteine residue in position 1 were the subject of a fluorescence and molecular mechanics study. We obtained two groups of analogues: selective antidiuretic agonists (cysteine or beta-mercaptopropionic acid in position 1) and pressor and uterotonic antagonists (deaminopenicillamine or beta-mercapto-beta, beta-cyclopentamethylenepropionic acid in position 1). Using frequency-domain measurements of fluorescence resonance energy transfer (FRET) we estimated the distance distribution between the phenolic ring of Tyr2 and the disulphide bridge Cys1-Cys6. We also analyzed acrylamide quenching of tyrosyl fluorescence to determine the exposure of the tyrosyl ring to the solvent. Results from fluorescence experiments were compared with those from Monte Carlo simulation (ECEPP/3 force-field).

Effects of amino acid replacements on cadmium binding of metallothionein alpha-fragment.

To evaluate whether only 20 cysteine residues at invariant positions are needed to bind and coordinate the metals in metallothioneins (MTs), and whether changing the positions of cysteine residues in the sequence affects the metal-binding capacity and the coordination of MTs, we examined the cadmium-binding affinities of seven mutant MT alpha s using an Escherichia coli expression system. Five mutant MT alpha s in which the constitutive amino acid residues other than cysteines of the alpha-fragment were replaced with glycine residues, and the remaining two mutant MT alpha s in which the invariant positions of the cysteine residues of the alpha-fragment were shifted, were analysed for their ability to be expressed as cadmium-binding forms and for their biochemical properties. The results showed that extreme alteration of the constitutive amino acid residues other than cysteines in the MT alpha-fragment leads to disruption of their cadmium-binding abilities and of their structure. However, mutant MT alpha s containing changes of the invariant positions of the cysteine residues were expressed in a cadmium-binding form in Escherichia coli, although the invariant positions of 20 cysteine residues in the MTs are thought to be important for their metal-binding abilities. These results suggest that the position of cysteine residues and the chemical nature of the other amino acids in the amino acid sequence of MTs are less critical than expected.

Mutational analysis of extracellular cysteine residues of rat secretin receptor shows that disulfide bridges are essential for receptor function.

We attempted to express point-mutant secretin receptors where each of the 10 extracellular Cys residues was replaced by a Ser residue, in Chinese hamster ovary (CHO) cells. Six of the point-mutant receptors (C24-->S, C44-->S, C53-->S, C67-->S, C85-->S and C101-->S) could not be detected by binding or functional studies: the mutations resulted in functional inactivation of the receptor. In contrast, the four other point-mutant receptors (C11-->S, C186-->S, C193-->S and C263-->S) were able to bind poorly 125I-secretin, and to activate adenylate cyclase with high secretin EC50 values. These results suggest that cysteine residues 24, 44, 53, 67, 85 and 101 are necessary for receptor function, and that the two putative disulfide bridges formed by cysteine residues 11, 186, 193 and 263 are functionally relevant, but not essential for receptor expression. Secretin activated the adenylate cyclase through the quadruple mutant (C11,186,193,263-->S), the four triple mutants, and through double mutants C186,193-->S and C186,263-->S with a very high (microM) EC50 value, suggesting that, in the wild-type receptor, disulfide bridges are formed between C11-C186, and between C193-C263. Prior treatment with dithiothreitol resulted in a marked EC50 increase of the wild-type receptor and of those receptors with at least the two cysteine residues in positions 11 and 186, suggesting that the C11-C186 (but not the C193-C263) disulfide bridge was accessible to this reducing agent. Several results nevertheless indicated that, in mutant receptors, alternative disulfide bridges can be formed between cysteine 186 and cysteine 193 or 263, suggesting that these three residues are in close spatial proximity in the wild-type receptor.

High-performance liquid chromatography/tandem mass spectrometry identification of salmon calcitonin degradation products in aqueous solution preparations.

Degradation impurities have been investigated, by means of high-performance liquid chromatography (HPLC)/ mass spectrometry, in commercial ampoules of salmon calcitonin, aqueous solution, stored for up to 2 years. Oxidation derivatives of the cysteine residues in positions 1 and 7, with cleavage of the disulfide bridge, were observed in all samples. Using our reversed-phase separation, these oxidation derivatives coeluted and presented an HPLC behavior identical to the derivative of salmon calcitonin with the disulfide bridge reduced. In a previous study this last compound was tentatively identified, without confirmation by mass spectrometry, as a major degradation product of salmon calcitonin in aqueous solution.

Coordination of the [2Fe-2S] cluster in wild type and molecular variants of Clostridium pasteurianum ferredoxin, investigated by ESEEM spectroscopy.

The [2Fe-2S] ferredoxin from Clostridium pasteurianum contains five cysteine residues in positions 11, 14, 24, 56, and 60. This pattern is unique, and a combination of site-directed mutagenesis and spectroscopy is therefore being implemented to identify the ligands of the [2Fe-2S] cluster. The possible involvement of ligands other than cysteine in some molecular variants of this ferredoxin has been considered, histidines being likely candidates. Therefore, the three histidine residues in positions 6, 7, and 90 of the amino acid sequence have been individually and collectively replaced by alanine or valine. The mutated ferredoxins have been purified and were all found to contain [2Fe-2S] clusters of which the UV-visible absorption spectra were identical to that of the wild-type protein. The H6A/H7A/ H90A triply mutated ferredoxin was further characterized by EPR and by ESEEM spectroscopy and was found to differ only marginally from the wild-type protein. The ESEEM spectra of wild-type ferredoxin displayed weak 14N hyperfine interactions at the three principal g-factors of the [2Fe-2S] center. The estimated 14N coupling constants (Aiso = 0.6 MHz; e2qQ approximately 3.3 MHz) indicate that the ESEEM effect is most likely due to 14N from the polypeptide backbone. 2H2O ESEEM spectra showed that the [2Fe-2S] cluster is accessible for exchange with solvent deuterons. ESEEM spectra of the previously characterized C24A and C14A/C24A variants have been recorded and were also found to be very similar to those of the wild-type protein. There was no evidence for coordination of the [2Fe-2S] cluster by [14N]histidine or other 14N nuclei, in either wild-type or mutant forms of the ferredoxin. By these criteria, the environment of the [2Fe-2S] center is not distinguishable from those in plant-type ferredoxins. Non-cysteinyl coordination most probably occurs only in the C14A/C24A variant, which contains no more than three cysteine residues. The data shown here indicate that the fourth ligand of the [2Fe-2S] cluster is neither a histidine residue nor another nitrogenous ligand. The possibility of oxygenic coordination for this molecular variant is discussed.

S-pyridylethylation of intact polyacrylamide gels and in situ digestion of electrophoretically separated proteins: a rapid mass spectrometric method for identifying cysteine-containing peptides.

In-gel proteolytic digestion of acrylamide-gel separated proteins is a method widely used for generating peptide fragments for the purpose of identifying proteins by Edman degratation, tandem mass spectrometry, and peptide-mass fingerprinting. However, it is well recognised for disulfide-bonded proteins electrophoresed under reducing conditions that if no precautions are taken to minimise disulfide bond formation during protein digestion or peptide isolation, complex peptide maps can result. Here, we describe an improved method for in-gel protein digestion. It consists of first reducing and S-pyridylethylating Coomassie Brilliant Blue R-250-stained proteins immobilised in the whole gel slab with dithiothreitol and 4-vinylpyridine, excising the individual stained and alkylated proteins, and then digesting them in situ in the gel matrix with trypsin or Achromobacter lyticus protease I. Peptide fragments generated in this manner are extracted from the gel piece and purified to homogeneity by a rapid (< or = 12 min) reversed-phase high performance liquid chromatography (HPLC) procedure, based upon conventional silica supports. Recoveries of peptides are increased by S-pyridylethylation of acrylamide-immobilised proteins prior to in-gel digestion. Further, the levels of gel-related contaminants, which otherwise result in suppression of sample signals during electrosprayionisation mass spectrometry, are greatly reduced by the reduction/alkylation step. Additionally, we demonstrate that S-beta-(4-pyridylethyl)-cysteine containing peptides can be readily identified during reversed-phase HPLC by absorbance at 254 nm, and during electrospray ionisation tandem mass spectrometry by the appearance of a characteristic-pyridylethyl fragment ion of 106 Da. The position of cysteine residues in a sequence can be determined as phenylthiohydantoin S-beta-(4-pyridylethyl)-cysteine during Edman degradation, and by tandem mass spectrometry.

CDNA cloning of porcine granulocyte‐macrophage colony‐stimulating factor

Porcine granulocyte-macrophage colony-stimulating factor (GM-CSF) cDNA was cloned by using polymerase chain reaction (PCR) and sequenced. A coding sequence of the porcine GM-CSF precursor protein, including the signal peptide sequence and stop codon, is 435 bp in length. The identities of the porcine GM-CSF coding sequence when compared to ovine, bovine, human and murine sequences were 89, 86, 83 and 70% at the nucleotide level, and 80, 74, 73, and 56% at the amino acid level. The hydrophobicity profiles, putative glycosylation sites and positions of cysteine residues were highly conserved in porcine, ovine, bovine and human GM-CSF but not murine. This is the first report of the porcine GM-CSF cDNA cloning and sequence.

Biochemical Characterization of a Palmitoyl Acyltransferase Activity That Palmitoylates Myristoylated Proteins

Dynamic regulation of signal transduction by reversible palmitoylation-depalmitoylation cycles has been recently described. However, further understanding of fatty acylation reactions has been hampered by our lack of knowledge about the specific transferases and thioesterases involved. Here, we describe an assay for the palmitoyl acyltransferase (PAT) that palmitoylates "myrGlyCys" containing members of the Src family of protein tyrosine kinases (PTKs). Since N-myristoylation of Fyn PTK, a member of the Src family, has been shown to be a prerequisite for palmitolylation, a new single plasmid vector that allows overexpression of myristoylated Fyn substrate in Escherichia coli was developed. Purified myristoylated protein substrates were incubated with [125I]iodopalmitoyl CoA, a palmitoyl CoA analog, in the presence of bovine brain lysates. Transfer of radiolabel to the Fyn substrate was detected by SDS-polyacrylamide gel electrophoresis and autoradiography. This assay was used to partially purify and characterize PAT activity from bovine brain. Here, we demonstrate that PAT is a membrane-bound enzyme, which palmitoylates myristoylated Fyn substrates containing a cysteine residue in position three. The PAT activity attached palmitate to Fyn proteins via a thioester linkage and exhibited a fatty acyl CoA preference for long chain fatty acids. It is likely that palmitoylation of Fyn and other Src family members by PAT regulates PTK localization and signaling functions.

Characterization of in vitro oxidized barstar

The polypeptide inhibitor of the ribonuclease barnase, barstar, has two cysteine residues in positions 40 and 82. These have been proposed to form a disulfide bridge leading to an increase in stability without changing the inhibitory activity of the protein. Barstar and a mutant (E80A) were oxidized in vitro and the biochemical and physico-chemical properties of the oxidized monomers were analysed. The oxidized proteins show no inhibition of barnase using a plate assay and are significantly destabilized. CD spectra indicate a loss of secondary structure. The amino acid substitution E80 → A stabilizes the oxidized barstar to about the same extent as it does the reduced protein, indicating, however, that the helical region which it is in is intact.

Electrospray-Ionization Mass-Spectrometry of Molecular Variants of a (2Fe-2S) Ferredoxin

The [2Fe-2S] ferredoxin from Clostridium pasteurianum is a homodimeric protein of which each subunit contains one [2Fe-2S] cluster. In previous investigations, the five cysteine residues in positions 11, 14, 24, 56 and 60 had been mutated into serine or alanine. The wild type ferredoxin and several of its molecular variants have now been analyzed by electrospray-ionization mass spectrometry. In the negative-ion detection mode, depending on the infusion solvent used, molecular peaks attributable to the apoprotein, to the monomeric holoprotein, and to the dimeric holoprotein were detected in all cases. The data confirmed the presence of the expected mutations, showed that all of these proteins contain one [2Fe-2S] cluster per subunit, and indicated that the dimeric structure of these ferredoxins could be retained in the conditions of the electrospray ionization. This investigation establishes the power of electrospray-ionization mass spectrometry for the analysis of oligomeric proteins containing labile metal clusters.

Chemokines, a family of chemotactic cytokines.

Chemokines are low-molecular-weight proteins that stimulate recruitment of leukocytes. They are secondary pro-inflammatory mediators that are induced by primary pro-inflammatory mediators such as interleukin-1 (IL-1) or tumor necrosis factor (TNF). The physiologic importance of this family of mediators is derived from their specificity. Unlike the classic leukocyte chemo-attractants, which have little specificity, members of the chemokine family induce recruitment of well-defined leukocyte subsets. Thus, chemokine expression can account for the presence of different types of leukocytes observed in various normal or pathologic states. There are two major chemokine sub-families based upon the position of cysteine residues, i.e., CXC and CC. All members of the CXC chemokine sub-family have an intervening amino acid between the first two cysteines; members of the CC chemokine sub-family have two adjacent cysteines. As a general rule (with some notable exceptions), members of the CXC chemokines are chemotactic for neutrophils, and CC chemokines are chemotactic for monocytes and a small sub-set of lymphocytes. This review discusses the potential role of chemokines in inflammation and focuses on the two best-characterized chemokines, monocyte chemoattractant protein-1 (MCP-1), a CC chemokine, and interleukin-8 (IL-8), a member of the CXC chemokine sub-family.

Extensive Sequence Variation in the Attachment (G) Protein Gene of Avian Pneumovirus: Evidence for Two Distinct Subgroups

The putative attachment protein of the avian pneumovirus that causes turkey rhinotracheitis is, by analogy with mammalian pneumoviruses, expected to be the major antigenic determinant. We report the nucleotide sequence of the attachment (G) protein genes of five different continental European isolates and compare them with the previously published sequence of the G gene for the focal variant of a U.K. isolate. The nucleotide sequences and the predicted amino acid sequences indicate that there are at least two distinct subgroups, similar to the grouping described for human respiratory syncytial (RS) virus. The U.K. and French isolates form one group and the isolates from Spain, Italy and Hungary form a second. The two subgroups can be easily distinguished on the basis of restriction enzyme digestion of PCR-generated products representing the full-length gene. Within the subgroups the predicted G proteins were highly conserved (98.5 to 99.7% amino acid identity) compared to the levels of identity of RS virus G proteins in the same subgroup (80 to 95%). Between the avian pneumovirus subgroups described here there was an unexpected degree of divergence, the average amino acid identity between members of the two groups being only 38%. This compares with the 53% conservation seen between members of the RS virus subgroups A and B. Comparison of the predicted amino acid sequences showed that the G proteins of members of the two avian pneumovirus subgroups had similar structural features. All proteins had an amino-terminal membrane anchor and the positions of cysteine residues were highly conserved. The potential importance of the high level of variation between the two subgroups in terms of epidemiology of the disease is discussed.

Cloning and sequence analysis of a cdna encoding bovine cytosolic aspartate aminotransferase

1. 1. Complementary DNA encoding cytosolic aspartate aminotransferase was isolated from an adult bovine heart library. 2. 2. The amino add sequence deduced for the protein (412 amino acids) is extremely similar (> 94% identity) to that of porcine cytosolic aspartate aminotransferase but interesting differences were noticed comparing the position of cysteine residues.

Mutated Forms of a [2Fe-2S] Ferredoxin with Serine Ligands to the Iron-Sulfur Cluster

The [2Fe-2S] ferredoxin from Clostridium pasteurianum contains five cysteine residues in positions 11, 14, 24, 56 and 60. Residues 24, 56 and 60 have been separately mutated into serine. The modified ferredoxins have been purified and were all found to contain a [2Fe-2S]-type cluster. The electronic absorption and EPR spectra of the C24S protein were only slightly different from those of the native one. In contrast, the C56S and C60S ferredoxins displayed spectroscopic features witnessing the presence of an oxygen ligand to the iron-sulfur cluster: the UV-visible absorption bands were shifted to higher energy by ca. 20 nm, and the high field components of the EPR spectra were shifted from g x=1.92 and g y=1.95 to g x=1.88 and g y=1.92, respectively.

Cysteine to serine replacements in 6-hydroxy-D-nicotine oxidase. Consequences for enzyme activity, cofactor incorporation, and formation of high molecular weight protein complexes with molecular chaperones (GroEL)

6-Hydroxy-D-nicotine oxidase, an enzyme with FAD covalently attached to the protein, contains 6 cysteine residues in positions 45 (Cys1), 59 (Cys2), 136 (Cys3), 173 (Cys4), 260 (Cys5) and 433 (Cys6). Cys2, 3, 5, and 6 were replaced with serine by site-directed mutagenesis. The effects of these exchanges on enzyme activity, the autocatalytic incorporation of the cofactor, and the interaction of the mutant proteins with molecular chaperones were analyzed. The flavinylation of 6-hydroxy-D-nicotine oxidase is dependent on the presence of allosteric effectors, e.g. glycerol 3-phosphate or other phosphorylated tricarbon compounds. Replacement of Cys2 or Cys5 abolished this dependence. Covalent incorporation of FAD was reduced to an undetectable level in the Cys3 and Cys5 mutants. Replacement of Cys6 by Ser had no significant effect on enzyme activity and cofactor attachment. Deletion of two amino acids, Phe and Arg, situated 12 and 11 amino acid residues, respectively, from the carboxyl terminus of the protein, resulted in an inactive enzyme with no covalently bound FAD. This result indicates that almost the entire protein chain has to be synthesized before the cofactor can be incorporated, making a cotranslational flavinylation step rather unlikely. The distribution of the 6-hydroxy-D-nicotine oxidase polypeptide between the high molecular weight complexes and the free soluble form was analyzed by gel filtration on Sephacryl S-200. The wild-type holoenzyme as well as the wild-type apoenzyme were recovered in the eluent fraction of the column while the mutant proteins were retained in high molecular weight complexes, predominantly in those associated with GroEL, as revealed by immunoprecipitation. The extent of complex formation with this molecular chaperone depended on the position of the mutated Cys residue within the protein. Complex formation was highest with protein from the mutants Cys2 and Cys3, less with the Cys5, and absent with the Cys6 mutant protein. Thus, alterations in the amino-terminal part of the 6-hydroxy-D-nicotine oxidase appear more important for the interaction with molecular chaperones than alterations situated in the carboxyl-terminal part of the protein.

Endothelin derivatives showing potent effects in the guinea pig trachea

Endothelin (ET-1) was synthesized by solid-phase peptide synthesis. To prevent side reactions with tryptophan residue, a formyl group was used to protect the β-indole moiety. The two disulfide bridges were formed selectively using S- methylbenzyl for the cysteine residues in positions 3 and 11, and S- acetamidomethyl for positions 1 and 15. Crude synthetic ET-1 was obtained after deprotection and cleavage from the resin by HF, followed respectively by potassium ferricyanide and iodine oxidations, in order to generate sequentially the monocyclic and bicyclic forms of the peptide. Finally, Trp(For) was deprotected by a treatment with piperidine. After each step, a sample of peptide was isolated and purified by RP-HPLC. The biological activity of these synthetic peptides was evaluated on guinea pig tracheal strips. The results suggest that oxidation of Met-7 and/or formylation of Trp-21 do not affect the biological activity of ET-1 in the guinea pig trachea. Moreover, although a decrease of potency and intrinsic activity was observed, the monocyclic analog containing Cys(Acm) residues at positions 1 and 15 exhibited substantial constrictor activity. This result, contrasting with that observed with several vascular preparations, suggests that the guinea pig trachea contains a distinct ET receptor population.