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Epitope mapping of the Syrian hamster prion protein utilizing chimeric and mutant genes in a vaccinia virus expression system.

The cellular prion protein (PrPc) is a host-encoded sialoglycoprotein bound to the external surface of the cell membrane by a glycosyl phosphatidylinositol anchor. A posttranslationally modified PrP isoform (PrPSc) is a component of the infectious particle causing scrapie and the other prion diseases. mAb have been raised against the protease-resistant core of Syrian hamster (SHa) PrPSc designated PrP 27-30. To map the epitopes within PrP reacting to these antibodies, we have expressed wild-type, chimeric mouse (Mo)/SHa and mutant MoPrP genes using recombinant vaccinia virus systems. The fidelity of the expression of recombinant PrPC was examined using vaccinia viruses expressing SHa-PrPC. It is full length, possesses Asn-linked carbohydrates and is attached to the external surface of the cell membrane by a glycosyl phosphatidylinositol anchor that is sensitive to cleavage by phosphatidylinositol-specific phospholipase C. We have tested 18 mAb for their ability to bind to chimeric prion proteins on immunoblots. Three distinct epitopes were identified that mapped to amino acid differences between SHa and MoPrP sequences. The first epitope, recognized by three of the antibodies tested, was defined by methionines at amino acids 108 and 111 in the mouse protein. The second epitope was dependent upon the presence of asparagines at positions 154 and 174 in MoPrP and was recognized by four of the antibodies tested. The third epitope mapped to a single amino acid substitution at residue 138 in MoPrP. mAb raised against SHaPrP 27-30 specific for this epitope are able to bind MoPrPC which has a single amino acid change (Ile to Met) at position 138. Eleven of the 18 antibodies tested mapped to this immunodominant epitope. It is located within a postulated amphipathic helix, a structure associated with immunodominant Ag. Inasmuch as PrPC, in its native form on the cell surface, is detected by the mAb 13A5 (a prototypic antibody of the immunodominant third epitope class), it is likely that this epitope is accessible in the native conformation of this protein.

Animals↗

Interdomain hydrolysis of a truncated Pseudomonas exotoxin by the human immunodeficiency virus-1 protease.

The specificity of HIV-1 (human immunodeficiency virus-1) protease has been evaluated relative to its ability to cleave the three-domain Pseudomonas exotoxin (PE66) and related proteins in which the first domain has been deleted or replaced by a segment of CD4. Native PE66 is not hydrolyzed by the HIV-1 protease. However, removal of its first domain produces a molecule which is an excellent substrate for the enzyme. The major site of cleavage in this truncated exotoxin, called LysPE40, occurs in a segment that connects its two major domains, the translocation domain (II), and the ADP-ribosyltransferase (III). This interdomain region contains the sequence ...Asn-Tyr-Pro-Thr... which is similar to that surrounding the scissile Tyr-Pro bond in the gag precursor polyprotein, a natural substrate of the HIV-1 protease. Nevertheless, it is not this sequence that is recognized and cleaved by the enzyme, but one 6 residues away, ...Ala-Leu-Leu-Glu... in which the Leu-Leu peptide bond is hydrolyzed. A second, slower cleavage takes place at the Leu-Ala bond 3 residues in from the NH2 terminus of LysPE40. When domain I of PE66 is replaced by a segment comprising the first two domains of CD4, the resulting chimeric protein is hydrolyzed at the same Leu-Leu bond by HIV-1 protease. Enzyme activities toward synthetic peptides modeled after the sequences defined above in LysPE40 are in complete accord, relative to specificity, kinetics, and pH optimum, with results obtained in the hydrolysis of the parent protein. These findings demonstrate that ideas concerning the specificity of the HIV-1 protease that are based solely upon its processing of natural viral polyproteins can be expanded by evaluation of other multidomain proteins as substrates. Moreover, it would appear that it is not a particular conformation, but sequence and accessibility that play the dominant role in defining sites in a protein substrate that are susceptible to hydrolysis by the enzyme.

ADP Ribose Transferases↗

Change of cytokeratin organization during development of Mallory bodies as revealed by a monoclonal antibody.

A monoclonal murine antibody (KM 54-5) was produced against Mallory body (MB) material isolated from liver tissue of griseofulvin treated mice. The antigen was identified by positive immunofluroescence microscopy of MBs and by the immunoblotting technique on polypeptides separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis. In immunoblotting experiments, antibody KM 54-5 reacted with cytokeratins A (human no. 8) and D (human no. 18) of murine, bovine, and human hepatocytes as well as with cytokeratin A (no. 8) and its degradation products present in isolated murine MB. In immunofluorescence microscopy the antibody did not react with cytokeratin filaments of normal liver but showed a positive reaction with MBs after a certain stage in MB development had been reached. In a dot blot assay, using individual cytokeratin polypeptides isolated from murine liver and purified by ion exchange chromatography in pH 8 buffer containing 8 M urea, the antibody reacted with the individual polypeptides A (no. 8) and D (no. 18) but not with the heterotypic tetramer (A2D2) reconstituted from these polypeptides in 4 M urea. These findings confirm the cytokeratin nature of MB filaments. In addition, they show that the pathologic process of MB formation involves changes in cytokeratin organization and conformation, resulting in the accessibility of a specific antigenic determinant which is inaccessible ("masked") in the heterotypic tetramer subunit and in the cytokeratin filaments of normal cells. Hence this study presents an example of a pathological change of cytokeratin filaments and illustrates the value of monoclonal antibodies in the detection of such changes.

Animals↗

Production and characterization of monoclonal antibodies to the N-terminal domain of lambda repressor.

Monoclonal antibodies reactive with distinct regions of the N-terminal domain of the lambda repressor protein have been isolated. By comparing the affinities of these antibodies for mutant repressors with increased and decreased thermal stabilities, each of the antibodies can be shown to bind to epitopes accessible in the native conformation of the N-terminal domain. Experiments probing antibody binding to protein fragments, mutant variants, and peptides have also been used to define likely regions of contact between the antibodies and the N-terminal domain.

Amino Acid Sequence↗

[Luminescence study of the spatial organization of protein-lipid complexes of mitochondrial membranes in different functional states].

Molecular organization of protein-lipid complexes of membranes in different functional states of mitochondria was studied from luminescence of pyrene and pyrene-butyrate which quenched the luminescence of mitochondrial membrane proteins. Maximum quenching was about 30 per cent. This value is found to be constant for a given type of membranes. Mitochondrial membrane proteins are organized into bulk assemblies hardly accessible for quenchers. Essential conformational changes in protein assemblies on functioning of the respiratory chain were not revealed. Changes in epimerization of pyrene in different states of the mitochondria may point to changes in viscosity of hydrophobic regions of membranes.

Animals↗

The nature of information used in making clinical decisions in general practice.

This preliminary study indicates that in general practice:(1) Acquisition of appropriate clinical information is more often than not dependent on prior information of a highly selected kind available economically only to a personal doctor.(2) The amount of previous information which could be stored outside the brains of a personal doctor and his patient is relatively enormous and almost unlimited.(3) But, the amount of this externally stored previous information which will ever be used, referred to, or be clinically useful is minimal.(4) Logic branching systems for obtaining this essential clinical information for each episode are of two kinds. There is first the system which is universally appropriate to all patients and all diseases as a whole, a field in which the computer is becoming pre-eminent, but which also has its limitations. Secondly there is the highly personalised system, constituted by the clinical dialogue of the patient and his personal doctor, the structure of which, at present, defies any simplification and which we abandon at our peril.(5) Continuing care by group-practice teams operating under one roof eliminates the need for fragmentation of primary clinical records.(6) A simple up-dated manually-prepared paper summary of clinical problems encountered and therapeutic activity taken, may well be the essential core of this shared record. This would be backed up by the ad hoc clinical records of each health care professional as accessible, second level archives, conforming to some simple, systematic and universally accepted structure (Bjorn and Cross, 1970).It would be of great interest to know whether or not the same conclusions would be drawn from a similar study of the selected clinical problems which are dealt with by the hospital-based specialist services.

Decision Making↗

NMR investigations of protein-carbohydrate interactions: insights into the topology of the bound conformation of a lactose isomer and beta-galactosyl xyloses to mistletoe lectin and galectin-1.

A hallmark of oligosaccharides is their often limited spatial flexibility, allowing them to access a distinct set of conformers in solution. Viewing each individual or even the complete ensemble of conformations as potential binding partner(s) for lectins in protein-carbohydrate interactions, it is pertinent to address the question on the characteristics of bound state conformation(s) in solution. Also, it is possible that entering the lectin's binding site distorts the low-energy topology of a glycosidic linkage. As a step to delineate the strategy of ligand selection for galactosides, a common physiological docking point, we have performed a NMR study on two non-homologous lectins showing identical monosaccharide specificity. Thus, the conformation of lactose analogues bound to bovine heart galectin-1 and to mistletoe lectin in solution has been determined by transferred nuclear Overhauser effect measurements. It is demonstrated that the lectins select the syn conformation of lactose and various structural analogues (Galbeta(1-->4)Xyl, Galbeta(1-->3)Xyl, Galbeta(1-->2)Xyl, and Galbeta(1-->3)Glc) from the ensemble of presented conformations. No evidence for conformational distortion was obtained. Docking of the analogues to the modeled binding sites furnishes explanations, in structural terms, for exclusive recognition of the syn conformer despite the non-homologous design of the binding sites.

Binding Sites↗

The voltage-activated hydrogen ion conductance in rat alveolar epithelial cells is determined by the pH gradient.

Voltage-activated H+ currents were studied in rat alveolar epithelial cells using tight-seal whole-cell voltage clamp recording and highly buffered, EGTA-containing solutions. Under these conditions, the tail current reversal potential, Vrev, was close to the Nernst potential, EH, varying 52 mV/U pH over four delta pH units (delta pH = pHo - pHi). This result indicates that H+ channels are extremely selective, PH/PTMA > 10(7), and that both internal and external pH, pHi, and pHo, were well controlled. The H+ current amplitude was practically constant at any fixed delta pH, in spite of up to 100-fold symmetrical changes in H+ concentration. Thus, the rate-limiting step in H+ permeation is pH independent, must be localized to the channel (entry, permeation, or exit), and is not bulk diffusion limitation. The instantaneous current-voltage relationship exhibited distinct outward rectification at symmetrical pH, suggesting asymmetry in the permeation pathway. Sigmoid activation kinetics and biexponential decay of tail currents near threshold potentials indicate that H+ channels pass through at least two closed states before opening. The steady state H+ conductance, gH, as well as activation and deactivation kinetic parameters were all shifted along the voltage axis by approximately 40 mV/U pH by changes in pHi or pHo, with the exception of the fast component of tail currents which was shifted less if at all. The threshold potential at which H+ currents were detectably activated can be described empirically as approximately 20-40(pHo-pHi) mV. If internal and external protons regulate the voltage dependence of gH gating at separate sites, then they must be equally effective. A simpler interpretation is that gating is controlled by the pH gradient, delta pH. We propose a simple general model to account for the observed delta pH dependence. Protonation at an externally accessible site stabilizes the closed channel conformation. Deprotonation of this site permits a conformational change resulting in the appearance of a protonation site, possibly the same one, which is accessible via the internal solution. Protonation of the internal site stabilizes the open conformation of the channel. In summary, within the physiological range of pH, the voltage dependence of H+ channel gating depends on delta pH and not on the absolute pH.

Animals↗

The resolution of heterogeneous fluorescence of multitryptophan-containing proteins studied by a fluorescence-quenching method.

From acrylamide quenching results, analyzed by an itterative non-linear least-squares method, we have shown that the fluorescence of multitryptophan-containing proteins, such as horse-liver alcohol dehydrogenase, 3-phosphoglycerate kinase and lysozyme, can be resolved for different segmental contributions, each characterized by collisional (Ki) and static (Vi) quenching constants. The ability to resolve the heterogeneous fluorescence of proteins makes it possible to follow changes in dynamics of the individual residues. In yeast 3-phosphoglycerate kinase, which contains only two tryptophan residues, three fluorescent fractions, characterized by different accessibility to the quencher, were observed. Two of them are assigned to one of the tryptophan residue. This may be interpreted in terms of conformational fluctuations, which facilitate the access of acrylamide molecules to the buried tryptophan residues.

Acrylamide↗

Catalytic implications from the Drosophila protein L-isoaspartyl methyltransferase structure and site-directed mutagenesis.

Protein L-isoaspartyl methyltransferases (PIMT; EC 2.1.1.77) catalyze the S-adenosylmethionine-dependent methylation of L-isoaspartyl residues that arise spontaneously in proteins with age, thereby initiating a repair process that restores the normal backbone configuration to the damaged polypeptide. In Drosophila melanogaster, overexpression of PIMT in transgenic flies extends the normal life span, suggesting that protein damage can be a limiting factor in longevity. To understand structural features of the Drosophila PIMT (dPIMT) important for catalysis, the crystal structure of dPIMT was determined at a resolution of 2.2 A, and site-directed mutagenesis was used to identify the role of Ser-60 in catalysis. The core structure of dPIMT is similar to the modified nucleotide-binding fold observed in PIMTs from extreme thermophiles and humans. A striking difference of the dPIMT structure is the rotation of the C-terminal residues by 90 degrees relative to the homologous structures. Effectively, this displacement generates a more open conformation that allows greater solvent access to S-adenosylhomocysteine, which is almost completely buried in other PIMT structures. The enzyme may alternate between the open conformation found for dPIMT and the more closed conformations described for other PIMTs during its catalytic cycle, thereby allowing the exchange of substrates and products. Catalysis by dPIMT requires the side chain of the conserved, active site residue Ser-60, since substitution of this residue with Thr, Gln, or Ala reduces or abolishes the methylation of both protein and isoaspartyl peptide substrates.

Amino Acid Sequence↗

Splice site consensus sequences are preferentially accessible to nucleases in isolated adenovirus RNA.

The conformation of RNA sequences spanning five 3' splice sites and two 5' splice sites in adenovirus mRNA was probed by partial digestion with single-strand specific nucleases. Although cleavage of nucleotides near both 3' and 5' splice sites was observed, most striking was the preferential digestion of sequences near the 3' splice site. At each 3' splice site a region of very strong cleavage is observed at low concentrations of enzyme near the splice site consensus sequence or the upstream branch point consensus sequence. Additional sites of moderately strong cutting near the branch point consensus sequence were observed in those sequences where the splice site was the preferred target. Since recognition of the 3' splice site and branch site appear to be early events in mRNA splicing these observations may indicate that the local conformation of the splice site sequences may play a direct or indirect role in enhancing the accessibility of sequences important for splicing.

Adenovirus Early Proteins↗

Thermodynamic characterization of ligand-induced conformational changes in UDP-N-acetylglucosamine enolpyruvyl transferase.

The binding of UDP-N-acetylglucosamine (UDPNAG) to the enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) was studied in the absence and presence of the antibiotic fosfomycin by isothermal titration calorimetry. Fosfomycin binds covalently to MurA in the presence of UDPNAG and also in its absence as demonstrated by MALDI mass spectrometry. The covalent attachment of fosfomycin affects the thermodynamic parameters of UDPNAG binding significantly: In the absence of fosfomycin the binding of UDPNAG is enthalpically driven (DeltaH = -35.5 kJ mol(-1) at 15 degrees C) and opposed by an unfavorable entropy change (DeltaS = -25 J mol(-1) K(-1)). In the presence of covalently attached fosfomycin the binding of UDPNAG is entropically driven (DeltaS = 187 J mol(-1)K(-1) at 15 degrees C) and associated with unfavorable changes in enthalpy (DeltaH = 28.8 kJ mol(-1)). Heat capacities for UDPNAG binding in the absence or presence of fosfomycin were -1.87 and -2.74 kJ mol(-1) K(-1), respectively, indicating that most ( approximately 70%) of the conformational changes take place upon formation of the UDPNAG-MurA binary complex. The major contribution to the heat capacity of ligand binding is thought to be due to changes in the solvent-accessible surface area. However, associated conformational changes, if any, also contribute to the experimentally measured magnitude of the heat capacity. The changes in solvent-accessible surface area were calculated from available 3D structures, yielding a DeltaC(p) of -1.3 kJ mol(-1) K(-1); i.e., the experimentally determined heat capacity exceeds the calculated one. This implies that other thermodynamic factors exert a large influence on the heat capacity of protein-ligand interactions.

Alkyl and Aryl Transferases↗

Conformational changes in the alpha- and beta-subunits of the insulin receptor identified by anti-peptide antibodies.

The structure of the insulin receptor was studied with polyclonal antibodies obtained from rabbits which were immunized with synthetic peptides having a sequence identity to three regions of the alpha-subunit and five regions of the beta-subunit. None of the alpha-subunit antibodies including alpha-Pep8 (residues 40-49 (Ullrich, A., Bell, J.R., Chen, E.Y., Herrera, R., Petruzzelli, L.M., Dull, T.J., Gray, A., Coussens, L., Liao, Y.-C., Tsubokawa, M., Mason, A., Seeburg, P.H., Grunfeld, C., Rosen, O.M., and Ramachandran, J. (1985) Nature 313, 756-761), alpha-Pep7 (12 amino acid C-terminal extension (Ebina, Y., Ellis, L., Jarnagin, K., Ederly, M., Graf, L., Clauser, E., Ou, J.-H., Masiar, F., Kan, Y.W., Goldfine, I.D., Roth, R.A., and Rutter, W.J. (1985) Cell 313, 747-758], or alpha-Pep6 (residues 1-7, 9) immunoprecipitated the human insulin receptor solubilized from IM-9 lymphocytes; however, alpha-Pep8 immunoprecipitated the dithiothreitol-reduced receptor. Antibodies prepared against the N terminus of the beta-subunit (alpha-Pep5, residues 780-790) and the ATP binding site (alpha-Pep3, residues 1013-1022) did not react with the intact receptor under any conditions; however, antibodies to the C terminus of the beta-subunit (alpha-Pep1, residues 1314-1324) and to the juxta-membrane region (alpha-Pep3, residues 952-962) immunoprecipitated the solubilized receptor in both its phosphorylated and nonphosphorylated forms. In contrast, the antibody reactive with the regulatory region of the beta-subunit which contains the major autophosphorylation sites (alpha-Pep2, residues 1143-1154) only precipitated the phosphorylated form. Thus the conformation of the extracellular domain of the receptor is rigid and stabilized by disulfide bonds, whereas several regions of the intracellular domain are accessible to antibodies and undergo conformational changes during autophosphorylation.

Amino Acid Sequence↗

Accessibility of aminoglycosides, isolated and in interaction with phosphatidylinositol, to water. A conformational analysis using the concept of molecular hydrophobicity potential.

The mode of interaction between aminoglycosides and negatively charged phospholipids plays a critical role in the inhibition of lysosomal phospholipases induced by these antibiotics and therefore in their nephrotoxicity. Previous works suggested that accessibility of the drug interacting with phospholipids to water could be crucial in this respect. We have used the concept of molecular hydrophobicity potential described by Brasseur [J Med Chem 266: 16120-16127, 1991] to visualize the hydrophobic and hydrophilic envelopes around aminoglycosides assembled with phosphatidylinositol molecules, and to obtain a three-dimensional representation of the complex formed. Using a series of different aminoglycosides, we showed that molecules with a lower inhibitory potential (gentamicin B, amikacin and isepamicin) are surrounded by both hydrophobic and hydrophilic envelopes whereas aminoglycosides which are more inhibitory are enveloped primarily by either hydrophilic (kanamycin A or B) or hydrophobic (gentamicin C1a) envelopes. This approach, which is here for the first time applied to the study of drug-lipid complexes, could help in the better understanding of the molecular mechanism of lysosomal phospholipase inhibition induced by aminoglycosides.

Aminoglycosides↗

Evidence for the involvement of Ala 166 in coupling Na(+) to sugar transport through the human Na(+)/glucose cotransporter.

We mutated residue 166, located in the putative Na(+) transport pathway between transmembrane segments 4 and 5 of human Na(+)/glucose cotransporter (hSGLT1), from alanine to cysteine (A166C). A166C was expressed in Xenopus laevis oocytes, and electrophysiological methods were used to assay function. The affinity for Na(+) was unchanged compared to that of hSGLT1, whereas the sugar affinity was reduced and sugar specificity was altered. There was a reduction in the turnover rate of the transporter, and in contrast to that of hSGLT1, the turnover rate depended on the sugar molecule. Exposure of A166C to MTSEA and MTSET, but not MTSES, abolished sugar transport. Accessibility of A166C to alkylating reagents was independent of protein conformation, indicating that the residue is always accessible from the extracellular surface. Sugar and phlorizin did not protect the residue from being alkylated, suggesting that residue 166 is not located in the sugar pathway. MTSEA, MTSET, and MTSES all changed the pre-steady-state kinetics of A166C, independent of pH, and sugars altered these kinetics. The inability of MTSEA-labeled A166C to transport sugar was reversed (with no major change in Na(+) and sugar affinity) if the positive charge on MTSEA was neutralized by increasing the external pH to 9.0. These studies suggest that the residue at position 166 is involved in the interaction between the Na(+) and sugar transport pathways.

Alanine↗

The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource.

BACKGROUND: Tissue Microarrays (TMAs) have emerged as a powerful tool for examining the distribution of marker molecules in hundreds of different tissues displayed on a single slide. TMAs have been used successfully to validate candidate molecules discovered in gene array experiments. Like gene expression studies, TMA experiments are data intensive, requiring substantial information to interpret, replicate or validate. Recently, an open access Tissue Microarray Data Exchange Specification has been released that allows TMA data to be organized in a self-describing XML document annotated with well-defined common data elements. While this specification provides sufficient information for the reproduction of the experiment by outside research groups, its initial description did not contain instructions or examples of actual implementations, and no implementation studies have been published. The purpose of this paper is to demonstrate how the TMA Data Exchange Specification is implemented in a prostate cancer TMA. RESULTS: The Cooperative Prostate Cancer Tissue Resource (CPCTR) is funded by the National Cancer Institute to provide researchers with samples of prostate cancer annotated with demographic and clinical data. The CPCTR now offers prostate cancer TMAs and has implemented a TMA database conforming to the new open access Tissue Microarray Data Exchange Specification. The bulk of the TMA database consists of clinical and demographic data elements for 299 patient samples. These data elements were extracted from an Excel database using a transformative Perl script. The Perl script and the TMA database are open access documents distributed with this manuscript. CONCLUSIONS: TMA databases conforming to the Tissue Microarray Data Exchange Specification can be merged with other TMA files, expanded through the addition of data elements, or linked to data contained in external biological databases. This article describes an open access implementation of the TMA Data Exchange Specification and provides detailed guidance to researchers who wish to use the Specification.

Confidentiality↗

High-performance liquid chromatography of insulin. Accessibility and flexibility.

Current ideas suggest that a conformational change in the insulin monomer may play an important part in its interaction with the insulin receptor. An investigation is reported in which analytical reversed-phase high-performance liquid chromatography of insulin analogues was used to investigate the solution conformation of the insulin monomer. The results are interpreted in terms of elution coefficients modified by the calculated surface accessibilities of individual residues. The results suggest a partial unfolding of the insulin monomer under the experimental conditions used, which is consistent with current ideas on the biologically active conformation of insulin.

Animals↗

Fluorometric measurements of conformational changes in glutamate transporters.

Glutamate transporters remove glutamate from the synaptic cleft to maintain efficient synaptic communication between neurons and to prevent extracellular glutamate concentrations from reaching neurotoxic levels (1). It is thought that glutamate transporters mediate glutamate transport through a reaction cycle with conformational changes between the two major access states that alternatively expose glutamate-binding sites to the extracellular or to the intracellular solution. However, there is no direct real-time evidence for the conformational changes predicted to occur during the transport cycle. In the present study, we used voltage-clamp fluorometry to measure conformational changes in the neuronal excitatory amino acid transporter (EAAT) 3 glutamate transporter covalently labeled with a fluorescent reporter group. Alterations in glutamate and cotransported ion concentrations or in the membrane voltage induced changes in the fluorescence that allowed detection of conformational rearrangements occurring during forward and reverse transport. In addition to the transition between the two major access states, our results show that there are significant Na(+)-dependent conformational changes preceding glutamate binding. We furthermore show that Na(+) and H(+) are cotransported with glutamate in the forward part of the transport cycle. The data further suggest that an increase in proton concentrations slows the reverse transport of glutamate, which may play a neuro-protective role during ischemia.

Amino Acid Transport System X-AG↗