A differential scanning calorimetric study of Newcastle disease virus: identification of proteins involved in thermal transitions

Study of rabies virus by Differential Scanning Calorimetry

Differential Scanning Calorimetry (DSC) has been used in the past to study the thermal unfolding of many different viruses. Here we present the first DSC analysis of rabies virus. We show that non-inactivated, purified rabies virus unfolds cooperatively in two events centered at approximately 62 and 73 °C. Beta-propiolactone (BPL) treatment does not alter significantly viral unfolding behavior, indicating that viral inactivation does not alter protein structure significantly. The first unfolding event was absent in bromelain treated samples, causing an elimination of the G-protein ectodomain, suggesting that this event corresponds to G-protein unfolding. This hypothesis was confirmed by the observation that this first event was shifted to higher temperatures in the presence of three monoclonal, G-protein specific antibodies. We show that dithiothreitol treatment of the virus abolishes the first unfolding event, indicating that the reduction of G-protein disulfide bonds causes dramatic alterations to protein structure. Inactivated virus samples heated up to 70 °C also showed abolished recognition of conformational G-protein specific antibodies by Surface Plasmon Resonance analysis. The sharpness of unfolding transitions and the low standard deviations of the Tm values as derived from multiple analysis offers the possibility of using this analytical tool for efficient monitoring of the vaccine production process and lot to lot consistency.

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Differential Scanning Calorimetry analysis of rabies virus.

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Rabies virus unfolds in two thermal events.

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The first event corresponds to G-protein.

Spectrum of Newcastle disease virus stability in gradients of temperature and pH

Newcastle disease (ND) is one of the highly pathogenic viral diseases of avian species. The disease is endemic in many developing countries where agriculture serves as the primary source of national income. Newcastle disease virus (NDV) belongs to the family Paramyxoviridae and is well characterized member among the avian paramyxovirus serotypes. The failure of vaccination is one of the major causes of NDV outbreaks in field condition. The present study gives a brief picture about the biology of NDV genome and its proteins under different conditions of temperature and pH. Our results indicate that the NDV is non-infective above 42 °C and unstable above 72 °C. The study will be useful in defining an optimum storage condition for NDV without causing any deterioration in its viability.

Between-species variation in the kinetic stability of TIM proteins linked to solvation-barrier free energies

Theoretical, computational, and experimental studies have suggested the existence of solvation barriers in protein unfolding and denaturation processes. These barriers are related to the finite size of water molecules and can be envisioned as arising from the asynchrony between water penetration and breakup of internal interactions. Solvation barriers have been proposed to play roles in protein cooperativity and kinetic stability; therefore, they may be expected to be subject to natural selection. We study the thermal denaturation, in the presence and in the absence of chemical denaturants, of triosephosphate isomerases (TIMs) from three different species: Trypanosoma cruzi, Trypanosoma brucei, and Leishmania mexicana. In all cases, denaturation was irreversible and kinetically controlled. Surprisingly, however, we found large differences between the kinetic denaturation parameters, with T. cruzi TIM showing a much larger activation energy value (and, consequently, much lower room-temperature, extrapolated denaturation rates). This disparity cannot be accounted for by variations in the degree of exposure to solvent in transition states (as measured by kinetic urea m values) and is, therefore, to be attributed mainly to differences in solvation-barrier contributions. This was supported by structure-energetics analyses of the transition states and by application of a novel procedure to estimate from experimental data the solvation-barrier impact at the entropy and free-energy levels. These analyses were actually performed with an extended protein set (including six small proteins plus seven variants of lipase from Thermomyces lanuginosus and spanning a wide range of activation parameters), allowing us to delineate the general trends of the solvation-barrier contributions. Overall, this work supports that proteins sharing the same structure and function but belonging to different organisms may show widely different solvation barriers, possibly as a result of different levels of the selection pressure associated with cooperativity, kinetic stability, and related factors.

Natural selection for kinetic stability is a likely origin of correlations between mutational effects on protein energetics and frequencies of amino acid occurrences in sequence alignments

It appears plausible that natural selection constrains, to some extent at least, the stability in many natural proteins. If, during protein evolution, stability fluctuates within a comparatively narrow range, then mutations are expected to be fixed with frequencies that reflect mutational effects on stability. Indeed, we recently reported a robust correlation between the effect of 27 conservative mutations on the thermodynamic stability (unfolding free energy) of Escherichia coli thioredoxin and the frequencies of residues occurrences in sequence alignments. We show here that this correlation likely implies a lower limit to thermodynamic stability of only a few kJ/mol below the unfolding free energy of the wild-type (WT) protein. We suggest, therefore, that the correlation does not reflect natural selection of thermodynamic stability by itself, but of some other factor which is linked to thermodynamic stability for the mutations under study. We propose that this other factor is the kinetic stability of thioredoxin in vivo, since( i) kinetic stability relates to irreversible denaturation, (ii) the rate of irreversible denaturation in a crowded cellular environment (or in a harsh extracellular environment) is probably determined by the rate of unfolding, and (iii) the half-life for unfolding changes in an exponential manner with activation free energy and, consequently, comparatively small free energy effects can have deleterious consequences for kinetic stability. This proposal is supported by the results of a kinetic study of the WT form and the 27 single-mutant variants of E. coli thioredoxin based on the global analyses of chevron plots and equilibrium unfolding profiles determined from double-jump unfolding assays. This kinetic study suggests, furthermore, one of the factors that may contribute to the high activation free energy for unfolding in thioredoxin (required for kinetic stability), namely the energetic optimization of native-state residue environments in regions, which become disrupted in the transition state for unfolding.

Role of solvation barriers in protein kinetic stability

The stability of several protein systems of interest has been shown to have a kinetic basis. Besides the obvious biotechnological implications, the general interest of understanding protein kinetic stability is emphasized by the fact that some emerging molecular approaches to the inhibition of amyloidogenesis focus on the increase of the kinetic stability of protein native states. Lipases are among the most important industrial enzymes. Here, we have studied the thermal denaturation of the wild-type form, four single-mutant variants and two highly stable, multiple-mutant variants of lipase from Thermomyces lanuginosa. In all cases, thermal denaturation was irreversible, kinetically controlled and conformed to the two-state irreversible model. This result supports that the novel molecular-dynamics-focused, directed-evolution approach involved in the preparation of the highly stable variants is successful likely because it addresses kinetic stability and, in particular, because heated molecular dynamics simulations possibly identify regions of disrupted native interactions in the transition state for irreversible denaturation. Furthermore, we find very large mutation effects on activation enthalpy and entropy, which were not accompanied by similarly large changes in kinetic urea m-value. From this we are led to conclude that these mutation effects are associated to some structural feature of the transition state for the irreversible denaturation process that is not linked to large changes in solvent accessibility. Recent computational studies have suggested the existence of solvation/desolvation barriers in at least some protein folding/unfolding processes. We thus propose that a solvation barrier (arising from the asynchrony between breaking of internal contacts and water penetration) may contribute to the kinetic stability of lipase from T. lanuginosa (and, possibly, to the kinetic stability of other proteins as well).

Alterations in erythrocyte membrane protein composition in advanced non-small cell lung cancer

Cancer can be associated with hematological complications related to red blood cell (RBC) function, whose physiological roles have now been expanded since it is now known that RBC are also signalling cells. The aim of this study was to explore the alterations occurring in the protein composition of RBC in advanced non-small cell lung cancer (NSCLC). Blood samples from 21 patients with advanced (stages III-IV) NSCLC (16 squamous cell carcinomas and 5 adenocarcinomas), and from 21 healthy volunteers were used. Samples from 6 randomly selected patients and 6 controls were used for the screening of erythrocyte ghost alterations by Differential Scanning Calorimetry (DSC). Samples from 15 patients and 15 controls, different from those used in the DSC measurements, were randomly selected for analysis of the expression of glycophorin (GP) species, band 3, and glycoproteins by SDS-PAGE and Western blotting or lectin enzyme immunoassays. Additionally, 5 patients with chronic obstructive pulmonary disease (COPD) were used as a control group representative of a benign inflammatory disease. Blood samples from the COPD patients were used to analyze the expression of GPs, band 3 and syaloglycoproteins. We observed the following in NSCLC: (a) changes in GP expression levels, mainly decreases in the GPA and GPC monomers, and in the GPAB dimers; (b) a decrease in the band 3 protein level, and (c) alterations in the expression of different sialoglycoproteins. RBC from the COPD patients also showed protein abnormalities, some of them, especially at the level of band 3 and the syaloglycoproteins, being similar to those in NSCLC.

Thermal stability of the hemagglutinin-neuraminidase from Sendai virus evidences two folding domains

The domain structure of hemagglutinin-neuraminidase from Sendai virus (cHN) was investigated by studying the thermal stability in the 20-100 degrees C range. Differential scanning calorimetry evidences two conformational transitions. The first transition is apparently a reversible two-state process, with Tm 48.3 degrees C, and is shifted to 50.1 degrees C in the presence of the substrate analogue 2,3-dehydro-2-deoxy-N-acetyl neuraminic acid, meaning that the substrate binding domain is involved in the transition. The second transition, with apparent Tm 53.2 degrees C, is accompanied by irreversible loss of enzymatic activity of the protein, and the presence of the substrate analogue does not affect the Tm. The data indicate that cHN is composed of two independent folding domains, and that only one domain is involved in the binding of the substrate. Our results suggest that the paramyxovirus neuraminidases have the folding properties of a two-domain protein.

Membrane glycoproteins of Newcastle disease virus: nucleotide sequence of the hemagglutinin-neuraminidase cloned gene and structure/function relationship of predicted amino acid sequence

The nucleotide sequence of the glycoprotein hemagglutinin-neuraminidase (HN) gene of the Newcastle disease virus (NDV) strain Clone-30 has been determined. The open reading frame of the HN gene contains 1731 nucleotides and encodes a protein of 577 amino acids. Three highly conserved patterns among all paramyxovirus HN glycoproteins, and one additional conserved species-specific region are present. The protein contains five potential N-glycosylation sites, all but one located in the C-terminal external domain. The secondary structure prediction shows that the C-terminal external domain is mostly arranged in beta-sheets, while alpha-helices are predominantly located in the N-terminal domain. The nucleotide sequence data of the HN gene reported in this paper has been deposited in the GenBank database, under accession number AF098289.

Lower kinetic limit to protein thermal stability: a proposal regarding protein stability in vivo and its relation with misfolding diseases

In vitro thermal denaturation experiments suggest that, because of the possibility of irreversible alterations, thermodynamic stability (i.e., a positive value for the unfolding Gibbs energy) does not guarantee that a protein will remain in the native state during a given timescale. Furthermore, irreversible alterations are more likely to occur in vivo than in vitro because (a) some irreversible processes (e.g., aggregation, "undesirable" interactions with other macromolecular components, and proteolysis) are expected to be fast in the "crowded" cellular environment and (b) in many cases, the relevant timescale in vivo (probably related to the half-life for protein degradation) is expected to be longer than the timescale of the usual in vitro experiments (of the order of minutes). We propose, therefore, that many proteins (in particular, thermophilic proteins and "complex" proteins systems) are designed (by evolution) to have significant kinetic stability when confronted with the destabilizing effect of irreversible alterations. We show that, as long as these alterations occur mainly from non-native states (a Lumry-Eyring scenario), the required kinetic stability may be achieved through the design of a sufficiently high activation barrier for unfolding, which we define as the Gibbs energy barrier that separates the native state from the non-native ensemble (unfolded, partially folded, and misfolded states) in the following generalized Lumry-Eyring model: Native State <--> Non-Native Ensemble --> Irreversibly Denatured Protein. Finally, using familial amyloid polyneuropathy (FAP) as an illustrative example, we discuss the relation between stability and amyloid fibril formation in terms of the above viewpoint, which leads us to the two following tentative suggestions: (a) the hot spot defined by the FAP-associated amyloidogenic mutations of transthyretin reflects the structure of the transition state for unfolding and (b) substances that decrease the in vitro rate of transthyretin unfolding could also be inhibitors of amyloid fibril formation.

Temperature dependence of fusion by sendai virus

Studies of the temperature dependence of liposome fusion by Sendai virus indicate that fusion occurs maximally at 55 degrees C. The fusion capacity of the virus is also inactivated maximally by preincubation at this temperature and, under the same conditions, the F glycoprotein becomes resistant to proteolysis. By analogy with the activation at elevated temperatures of fusion by influenza virus our results suggest that temperature is also a variable in the activation of fusion by paramyxoviruses and possibly in the activation of other members of the group of viruses that includes myxo-, paramyxo-, retro-, and filoviruses, which all contain cleaved, trimeric fusion glycoproteins.

Acidic pH enhancement of the fusion of Newcastle disease virus with cultured cells

Fusion of the lentogenic strain "Clone 30" of Newcastle disease virus (NDV) with the cell line COS-7 has been studied. Fusion was monitored using the octadecylrhodamine B chloride dequenching assay [Hoekstra, D., de Boer, T., Klappe, K. and Wilschut, J. (1984). Biochemistry 23, 5675-5681]. In the present work, fusion of NDV with COS-7 cells was found to occur in a time- and temperature-dependent fashion. Significant dequenching of the probe occurred at temperatures higher than 28 degrees C. A 20-fold excess of unlabeled virus inhibited fusion by about 53% compared with the control, whereas 62% inhibition of fusion was obtained after digestion of viral glycoproteins with trypsin. The data are discussed in terms of the nonfusion transfer of the probe. In addition, preincubation of cells with 50 mM ammonium chloride or 0.1% sodium azide prevented NDV from fusing with COS-7 cells by about 30% in comparison with the control. The cytopathic effect of NDV infection in cell culture in the presence of ammonium chloride was reduced compared with control. Moreover, viral preincubation at pH 5 yielded a mild inhibition of fusogenic activity. Our results suggest that NDV may use the endocytic pathway as a complementary way of entering cells by direct fusion with the plasma membrane.