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R B Freedman

Publications and source records attributed to R B Freedman.

At least 73 records · Page 4Linked to original sources
PubMed1994

High-resolution separation of recombinant human interferon-gamma glycoforms by micellar electrokinetic capillary chromatography.

Recombinant human interferon-gamma (IFN-gamma) glycoform populations produced by Chinese hamster ovary cells have been resolved by micellar electrokinetic capillary chromatography (MECC). Separations were performed in uncoated fused silica capillaries at alkaline pH in the presence of micellar concentrations of the anionic detergent sodium dodecyl sulfate (SDS). Maximum resolution was obtained reproducibly with high-ionic-strength borate/SDS electrophoresis buffer. Under the conditions described, glycoform migration time was inversely related to the amount of carbohydrate associated with the protein. Digestion of IFN-gamma with peptide-N-glycosidase F allowed virtual real-time monitoring of glycosidase digests by capillary electrophoresis. Analysis of other digestions with either neuraminidase or endoglycosidase H (endo H) showed most IFN-gamma glycoforms to be sialylated and a minor proportion of glycoforms to be associated with oligomannose structures. While both bovine pancreas ribonuclease B and horse-radish peroxidase glycoforms were separated by this technique, proteins glycosylated at multiple sites such as bovine serum fetuin and human alpha 1-acid glycoprotein were not well resolved by MECC.

Amidohydrolases↗
PubMed1994

Solution structure of the active domain of tissue inhibitor of metalloproteinases-2. A new member of the OB fold protein family.

Homonuclear two-dimensional and three-dimensional 1H nuclear magnetic resonance spectroscopy has been used to obtain essentially complete sequence-specific assignments for 123 of the 127 amino acid residues present in the truncated form of tissue inhibitor of metalloproteinases-2 (delta TIMP-2), the active N-terminal domain of the protein. Analysis of the through-space nuclear Overhauser effect data obtained for delta TIMP-2 allowed determination of both the secondary structure of the domain and also a low-resolution tertiary structure defining the protein backbone topology. The protein contains a five-stranded antiparallel beta-sheet that is rolled over on itself to form a closed beta-barrel, and two short helices which pack close to one another on the same barrel face. A comparison of the delta TIMP-2 structure with other known protein folds reveals that the beta-barrel topology is homologous to that seen in proteins of the oligosaccharide/oligonucleotide binding (OB) fold family. The common structural features include the number of beta-strands and their arrangement, the beta-barrel shear number, an interstrand hydrogen bond network, the packing of the hydrophobic core, and a conserved beta-bulge. Superpositions of the beta-barrels from delta TIMP-2 and two previously known members of the OB protein fold family (staphylococcal nuclease and Escherichia coli heat-labile enterotoxin) confirmed the similarity in beta-barrel topology. The three-dimensional structure of delta TIMP-2 has allowed a more detailed interpretation than was previously possible of the functional significance of available protein sequence and site-directed mutagenesis data for the TIMP family. Furthermore, the structure has revealed conserved surface regions of potential functional importance.

Amino Acid Sequence↗
PubMed1994

Dissecting the mechanism of protein disulfide isomerase: catalysis of disulfide bond formation in a model peptide.

As a model for understanding how protein disulfide isomerase (PDI) catalyzes disulfide bond formation in proteins, its action on a 28-residue disordered peptide containing only two cysteine residues has been examined. Disulfide formation in the peptide using the chemical reaction with small molecule thiol/disulfide reagents, such as oxidized and reduced glutathione or cystamine and cysteamine, occurs in two steps, via two alternative intermediate mixed disulfides between the reagent and either peptide cysteine residue. All thiol/disulfide forms of the peptide could be trapped and quantified, so the rates of their interconversion could be measured. Catalytic amounts of PDI increased the rates of these reactions. All rate enhancements were independent of the concentration of the peptide, indicating that it bound to PDI with an apparent Km of less than 3 microM. In the presence of glutathione, PDI accelerated the formation of both single mixed disulfide species, plus their subsequent rearrangement to form the peptide disulfide bond, but not interchange of the mixed disulfide glutathione between the two cysteine residues. In contrast, PDI did not catalyze the reaction of the reagent cystamine with the reduced peptide to form the mixed disulfide, nor the interchange of this mixed disulfide between cysteine residues, but did catalyze the subsequent intramolecular step of peptide disulfide bond formation to a similar extent as with the glutathione mixed disulfide. These effects on the two steps involving the mixed disulfides with glutathione or cystamine accounted for much of the overall catalytic effect of PDI on disulfide bond formation in the peptide, indicating that direct transfer of disulfide bonds from PDI to the peptide occurred less frequently. These findings demonstrate the utility of using such peptides as PDI substrates and have implications for the mechanism of action of PDI.

Amino Acid Sequence↗
PubMed1994

Protein-S-S-glutathione mixed disulfides as models of unfolded proteins.

Mixed disulfides between glutathione and the reduced forms of disulfide-bonded proteins were generated and characterized to explore their suitability as models of the unfolded state of newly-synthesized secretory proteins. RNase T1 and alpha-lactalbumin were reduced and converted to mixed disulfide derivatives, named GS-RNase T1 and GS-alpha-lactalbumin, in good yield; the molecular masses of the derivatives were confirmed by electrospray mass spectrometry. The intrinsic fluorescence of the derivatives and the binding of the hydrophobic fluorescent dye ANS were characteristic of fully unfolded proteins. Fluorescence studies and enzyme activity data indicated that GS-RNase T1 could be refolded to a nativelike state at NaCl concentrations greater than 1.5 M, as was previously demonstrated for the reduced, carboxymethylated derivative of this protein. The [NaCl]-dependent folding/unfolding equilibrium for GS-RNase T1 was reversible and could be influenced by urea. Fluorescence studies indicated that GS-alpha-lactalbumin showed a [NaCl]-dependent partial shift toward a more nativelike state, which was enhanced by the presence of Ca2+ ions. Both of the GS derivatives stimulated the ATPase activity of BiP, with apparent affinities in the range 0.1-1.0 mM. The results indicate that these GS-S-protein mixed disulfide derivatives are ideal model unfolded proteins that can be used as substrates for detailed studies on secretory protein folding in vitro and on the interactions between unfolded proteins and facilitators of protein folding.

Adenosine Triphosphatases↗
PubMed1994

Peptidyl prolyl cis-trans-isomerase activity associated with the lumen of the endoplasmic reticulum.

Peptidyl prolyl cis-trans-isomerase (PPI) activity was detected in microsomal fractions from bovine and rat liver. Extensive washing, proteinase and sonication treatments indicated that although some of this activity was due to adsorbed cytosolic enzymes, there was also an active but latent microsomal PPI activity. Density-gradient subfractionation indicated that activity was associated with vesicles derived from both the rough and the smooth endoplasmic reticulum (ER), suggesting that the activity was located within the ER lumen. The luminal PPI activity was inhibited by cyclosporin A and was active towards an unfolded protein substrate as well as towards the standard peptide substrate.

Amino Acid Isomerases↗
PubMed1994

The characterization of a cyclophilin-type peptidyl prolyl cis-trans-isomerase from the endoplasmic-reticulum lumen.

A luminally located peptidyl prolyl cis-trans-isomerase (PPI) has been purified from bovine liver microsomes. It has a molecular mass of 20.6 kDa, and N-terminal sequencing demonstrates strong sequence similarity to the sequences of the cyclophilin B family. The enzyme catalyses the isomerization of the standard proline-containing peptide N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide, as well as the refolding of RNAase T1. Kinetic properties, substrate-specificity data and inhibition by cyclosporin A indicate that it is a cyclophilin-type PPI, consistent with the amino-acid-sequence results.

Amino Acid Isomerases↗
PubMed1994

Fluorescence dynamics of staphylococcal nuclease in aqueous solution and reversed micelles.

The dynamical fluorescence properties of the sole tryptophan residue (Trp-140) in Staphylococcus aureus nuclease (EC 3.1.31.1) have been investigated in aqueous solution and reversed micelles composed of either sodium bis(2-ethylhexyl)sulfosuccinate (AOT) in isooctane or cetyltrimethylammonium chloride (CTAC) in isooctane/hexanol (12:1 by volume). The fluorescence decay of nuclease in the different environments can be described by a trimodal distribution of fluorescence lifetimes at approx. 0.5, 1.5 and 5.0 ns. The relative amplitudes depend on the environment. For pH 9.0 solutions the contribution of the two shortest lifetime components in the distribution is largest for AOT and smallest for CTAC reversed micelles. There is reasonable agreement between the average fluorescence lifetime and the fluorescence quantum efficiency confirming a significant fluorescence quenching in AOT reversed micelles. Fluorescence anisotropy decay revealed that the tryptophan environment in aqueous nuclease solutions is rigid on a nanosecond timescale. When nuclease was entrapped into reversed micelles the tryptophan gained some internal flexibility as judged from the distinct presence of a shorter correlation time. The longer correlation time reflected the rotational properties of the protein-micellar system. Modulation of the overall charge of nuclease (isoelectric point pH 9.6) by using buffer of pH 9.0 and pH 10.4, respectively, and of the size of empty micelles by selecting two values of the water to surfactant molar ratio, had only a minor effect on the rotational properties of nuclease in the positively charged reversed micelles. Encapsulation of nuclease in anionic reversed micelles resulted in the development of protein bound to aggregated structures which are immobilised on a nanosecond timescale. According to far UV circular dichroism results the secondary structure of nuclease only followed the already published pH-dependent changes. Encapsulation had no major effect on the overall secondary structure.

Cetrimonium↗
PubMed1994

A single purification procedure for the major resident proteins of the ER lumen: endoplasmin, BiP, calreticulin and protein disulfide isomerase.

We have developed a single purification procedure for the four major resident endoplasmic reticulum (ER) proteins: protein disulfide isomerase (PDI), BiP, endoplasmin, and calreticulin. Three of these proteins are thought to play a role in protein folding in vivo, whereas calreticulin is thought to be the major calcium binding protein in the ER. The proteins were purified from fresh bovine liver by taking advantage of individual characteristics of the proteins. Liver microsomes were prepared and then premeabilized to release the lumenal contents. After ammonium sulfate precipitation, the proteins were purified by chromatography; BiP was purified by affinity chromatography on ATP-agarose, and both endoplasmin and calreticulin were purified by affinity chromatography on Con A-Sepharose. PDI was purified by anionic ion exchange chromatography.

Amino Acid Sequence↗
PubMed1994

Protein disulphide isomerase: building bridges in protein folding.

Protein disulphide isomerase (PDI) has been known for many years to assist in the folding of proteins containing disulphide bonds, but the exact mechanism by which it achieves this is only now becoming clear. The active site of PDI closely resembles that of the redox protein thioredoxin, and cDNA cloning has revealed a superfamily of proteins with related active-site sequences, in organisms ranging from bacteria to higher animals and plants. Recent mutagenesis studies are now helping to unravel the catalytic mechanism of PDI, and work in yeast and other systems is clarifying the physiological roles of the multiple PDI-related proteins.

Amino Acid Sequence↗
PubMed1994

Folding and stability of the active N-terminal domain of tissue inhibitor of metalloproteinases-1 and -2.

The truncated forms of tissue inhibitor of metalloproteinase-1 and -2 (delta TIMP-1 and -2), comprising the N-terminal active domain, are ideal molecules for structural analysis by intrinsic fluorescence as each contains a single conserved tryptophan residue. In this paper we describe studies on their conformational stability, unfolding/refolding kinetics and the environment of the unique tryptophan as judged by its fluorescence properties in the native state and exposure to an external quencher, acrylamide. Two forms of delta TIMP-2 were studied: delta TIMP-2 T21 derived from the full-length cDNA clone isolated from a mixed-tumour library, and delta TIMP-2 A21 containing the highly conserved V18IRAK22 sequence. In all three delta TIMP proteins the tryptophan environments in the native state appeared to be similar, but substantial differences were seen in their conformational stabilities and refolding kinetics. delta TIMP-1 was approximately twice as stable as delta TIMP-2 T21 and 1.4-fold more stable than delta TIMP-2 A21. This stability difference between delta TIMP-1 and delta TIMP-2 was shown to be independent of N-linked glycosylation. delta TIMP-1 and delta TIMP-2 A21 both showed simple two-state refolding kinetics, whereas delta TIMP-2 T21 refolding was more complex and biphasic in character. These differences between delta TIMP-2 T21 and A21 suggest that residue 21 is a structurally important site in the TIMP protein. All three truncated molecules can be considered as stable independent folding domains ideally suited for further structural analysis.

Base Sequence↗
PubMed1993

Chemical modification of tissue inhibitor of metalloproteinases-1 and its inactivation by diethyl pyrocarbonate.

Tissue inhibitor of metalloproteinases-1 (TIMP-1) was treated with a range of chemical modification reagents in order to identify amino acid residues essential for inhibitory activity. Diethyl pyrocarbonate (DEPC) was found to be a potent inactivator at low reagent/TIMP molar concentrations. The extent of modification at 50% inactivation was determined as 1.5 sites/molecule. The DEPC-modified inhibitor did not form stable complexes with stromelysin, but was shown to retain native structure as judged by conformational stability to denaturation by guanidine hydrochloride. Peptide mapping experiments were used to find the sites of DEPC incorporation within the primary structure of TIMP and three residues were identified (His-95, His-144 and His-164). Mutant TIMPs in which histidine residues have been substituted or deleted retain inhibitory activity and were found to be equally as sensitive to DEPC inactivation as the wild-type. No new sites of DEPC modification in the mutant proteins were detected. The possible contribution made by His residues 95, 144 and 164 to the inhibitory activity of TIMP is discussed.

Amino Acid Sequence↗
PubMed1993

Peptide binding to protein disulfide isomerase occurs at a site distinct from the active sites.

Protein disulfide isomerase (PDI) is a multifunctional protein resident in the lumen of the rough endoplasmic reticulum that facilitates protein folding via disulfide bond isomerization. Previously we determined that PDI binds a variety of peptides that can be covalently attached to this protein via a photoreactive cross-linker. We have now investigated the relationship between the peptide binding site and the ability of PDI to catalyze disulfide bond isomerization. PDI has two identical sequences, -WCGHCK-, that have been demonstrated to be important in PDI-catalyzed disulfide isomerization. We have found that other proteins containing these thioredoxin-like active site sequences do not bind the photoreactive peptide probes. Moreover, although chemical modification of the 2 cysteines within the thioredoxin-like active site regions completely inhibits PDI-catalyzed disulfide isomerization, these modifications do not affect peptide binding by PDI. Both of these observations suggest that peptide binding occurs at a site other than the putative PDI active sites. To localize the site in PDI at which binding occurs, we used a radiolabeled peptide photoaffinity probe. Peptide fragments generated by cleavage of 125I-peptide-labeled PDI with cyanogen bromide yielded a single 8-kDa polypeptide fragment containing the 125I-labeled peptide site, but neither of the putative catalytic sites of PDI. An 125I-labeled tryptic peptide was generated from this cyanogen bromide fragment and determined by microsequencing to contain residues 451-476 of PDI; this 26-residue peptide is noteworthy because of its extremely high content of acidic amino acids. Based on these findings we conclude that the peptide binding site is located in the COOH-terminal domain of the protein, and it is distinct from the two active sites for PDI-catalyzed disulfide isomerization and from the region of PDI that has estrogen receptor sequence similarity.

Amino Acid Sequence↗
PubMed1993

On the biosynthesis of bovine pancreatic trypsin inhibitor (BPTI). Structure, processing, folding and disulphide bond formation of the precursor in vitro and in microsomes.

The natural gene for bovine pancreatic trypsin inhibitor (BPTI) was expressed by in vitro transcription/translation systems as the 100-residue pre-proBPTI, with a signal peptide for translocation into the endoplasmic reticulum. Expression in the presence of microsomes defined the site of co-translational cleavage of the signal peptide. The resulting proBPTI in the microsomes consists of the 58 residues of mature BPTI, plus an additional 13 residues at the N terminus, including a cysteine residue at position -10, and seven residues at the C terminus. ProBPTI remained in the unfolded, reduced form within microsomes when synthesized under reducing conditions, but folded and formed disulphide bonds rapidly when the disulphide form of glutathione was added. Complete folding could occur within about one minute, even when residue Cys10 was replaced by Ser. The structure of proBPTI was determined by circular dichroism and two-dimensional NMR and found to be that of mature BPTI with flexible extensions on both termini. Its inhibition of the activity of alpha-chymotrypsin was indistinguishable from that of the mature protein. The extensions of the precursor appeared to play only very minor roles in refolding in vitro under conditions where folding and disulphide bond formation are coupled. Under pH and redox conditions thought to reflect those in vivo, complete folding and disulphide bond formation required several hours. Addition of protein disulphide isomerase to in vitro folding experiments caused substantial and similar increases in the rate of formation of the fully folded state for both mature BPTI and proBPTI; the half time for folding to the native state was reduced to approximately two minutes, which is comparable to that occurring in microsomes. The absence of substantial effects of the N and C-terminal extensions on the protein structure, inhibitor activity and refolding leaves their functional roles to be discovered.

Amino Acid Sequence↗