Circular dichroism of cysteine proteinases from papaya latex. Evidence of differences in the folding of their polypeptide chains.

Two forms of proteinase omega were isolated from a commercial preparation of chymopapain (EC 3.4.22.6) by means of cation-exchange liquid chromatography. Their circular dichroism (CD) spectra in the 182-320 nm region indicated that the two forms possess closely related structures. For comparison, we also recorded the CD spectra of chromatographically purified samples of papain (EC 3.422.2) and the most abundant form of chymopapain. According to the qualitative criteria proposed by Manavalan and Johnson (1983) Nature 305, 831-832), the spectral characteristics of papain correctly indicate that this protein belongs to the alpha + beta class. Proteinase omega is also placed in the alpha + beta category, while chymopapain seems to be an alpha/beta protein. Quantitative estimation of secondary structures yielded contents of helices and parallel beta-sheet that were higher in the case of chymopapain. Thus, the results of this work suggest that there are some differences in the folding pattern of chymopapain with respect to the other two proteinases. This proposal seems unexpected when the high amino acid sequence identity among these enzymes is considered.     

Structural similarity of chymopapain forms as indicated by circular dichroism.

Four chymopapain forms were isolated by high-resolution liquid chromatography on a cation-exchange column. The three major forms possess nearly identical secondary and tertiary structures, as judged from their c.d. spectra; these components showed similar proteolytic activity and Mr values close to that of papain. The fourth isolated component seems to be a mixture of modified proteins.     

Evidence from two-protonic-state reactivity probe kinetics that chymopapain in fresh nonfruit latex ofCarica papaya consists of multiple forms of chymopapain A. The value of catalytic site characteristics in the identification,classification, and characterization of the papaya cysteine proteinases papain,the chymopapains,and papaya proteinase Ω

Fresh latex ofCarica papaya was collected from the stem, leaves, and petioles of the growing plant and fractionated by ion-exchange chromatography on a column of SP-Sephadex-C50 and by FPLC using a Mono S column. The fractions were examined for catalytic activity using Z-Lys-ONp andl-BAPNA as substrates and the thiol contents and reactivity characteristics were determined by using 2,2′-dipyridyl disulfide as a two-protonic-state thiol titrant and reactivity probe. By these methods the fresh nonfruit latex was shown to contain papain (EC 3.4.22.2), multiple forms of chymopapain, all of which have catalytic site reactivities characteristic of chymopapain A, and papaya proteinase Ω (originally called papaya peptidase A). The necessity now to characterize the catalytic site of a chymopapain in order to identify it is discussed.     

Systematic investigation of interactions between papain and MPA-capped CdTe quantum dots

Fluorescent quantum dots (QDs) have been widely applied in biological and biomedical areas, but relatively little is known about the interaction of QDs with some natural enzymes. Herein, the interactions between 3-mercaptopropionic acid-capped CdTe QDs (MPA-QDs) and papain were systematically investigated by UV–Vis absorption spectra, fluorescence spectra and circular dichroism (CD) spectra under the physiological conditions. The fluorescence spectra results indicated that MPA-QDs quenched the fluorescence intensity of papain. The modified Stern–Volmer quenching constant K _a at different temperatures and the corresponding thermodynamic parameters ΔH, ΔG and ΔS were also calculated. The binding of MPA-QDs and papain is a result of the formation of QDs-papain complex and the electrostatic interactions play a major role in stabilizing the complex. The CD technique was further used to analyze the conformational changes of papain induced by MPA-QDs and the results indicated that the biological activity of papain was affected by MPA-QDs dramatically.     

Circular dichroic spectroscopy of Arg46-nicked ovine lutropin α and derived fragments

Theα subunit of ovine lutropin can be nicked with the endoproteinase Arg-C to give a single cleavage of the Arg⁴⁶-Ser⁴⁷ peptide bond. Following reduction by sulfitolysis, the N-terminal (residues 1–46) and C-terminal (residues 47–96) fragments can be separated and then recombined and reoxidized to yield a reconstituted nickedα that binds to theβ subunit but exhibits only 2–3% of the receptor-binding potency of intact lutropin. We have investigated nickedα, the two separated fragments, and reconstituted nickedα by circular dichroic spectroscopy and compared the spectra with those of intactα and reduced, reoxidized intactα. Between 200 and 225 nm the spectra of the two intact preparations are similar, as are the spectra of the two nicked preparations. However, the extremum negative ellipticities of the nicked preparations are substantially less than those of the intact preparations between 210 and 220 nm, indicating a loss in secondary structure accompanying cleavage of the Arg⁴⁶-Ser⁴⁷ bond. The sum of the spectra of the two fragments is significantly different from that of reconstituted nickedα, showing that the secondary structures in the isolated fragments are quite different from that of the reconstituted nicked protein. Reduced receptor binding by lutropin preparations containing a nickedα subunit may be attributable in part to the loss of secondary structure, probably helicity.     

Circular dichroism and the secondary structure of the ROF2 protein from Arabidopsis thaliana

The protein ROF2 from the plant Arabidopsis thaliana acts as a heat stress modulator, being involved in the long-term acquired thermotolerance of the plant. Here we investigate the relationship between the biological function and the structure of ROF2, inferred by circular dichroism (CD) spectroscopy. The far-UV CD spectra, analyzed with the CDPro and DICHROWEB program packages, yield the percentages of α-helices, β-sheets, unordered regions, turns and poly(Pro)II-helices in the secondary structure of ROF2. According to the analysis, the percentages of the structural elements of ROF2 are about 40% for β-sheets, 30% for unordered regions, 17% for turns, 10% for poly(Pro)II-helices and 3% for α-helices. The near-UV CD spectra suggest that ROF2 proteins can associate, forming super-secondary structures. Our CD experiments performed at temperatures between 5 °C and 97 °C indicate that the thermal denaturation of ROF2 caused by a raise in temperature up to 55 °C is followed by a thermal refolding of the protein as the temperature is raised further. The new secondary structure, acquired around 65 °C, remains stable up to 97 °C. The structural stability of ROF2 at high temperatures might play an important role in the experimentally observed thermotolerance of Arabidopsis thaliana.     

Eremophilenolides from petasites japonicus

Chemical investigation of the young flower stalks of Petasites japonicus afforded some eremophilenolides, including a mixture of the two new compounds 6β-angeloyloxy-3β,8α-dihydroxyeremophil-7(11)-en-12,8β- olide and 6β-angeloyloxy-3β,8β-dihydroxyeremophil-7(11)-en-12,8α- olide. Their structures were elucidated by chemical and spectroscopic methods. The ¹³C NMR signals for the carbon atoms of the eremophilenolides were assigned with the help of Beierbeck's parameters. The CD spectra of the compounds are briefly discussed.     

Chymopapain A. Purification and investigation by covalent chromatography and characterization by two-protonic-state reactivity-probe kinetics, steady-state kinetics and resonance Raman spectroscopy of some dithioacyl derivatives.

Chymopapain A was isolated from the dried latex of papaya (Carica papaya) by ion-exchange chromatography followed by covalent chromatography by thiol-disulphide interchange. The latter procedure was used to produce fully active enzyme containing one essential thiol group per molecule of protein, to establish that the chymopapain A molecule contains, in addition, one non-essential thiol group per molecule and to recalculate the literature value of epsilon 280 for the enzyme as 36 000 M-1 X cm -1. The Michaelis parameters for the hydrolysis of L-benzoylarginine p-nitroanilide and of benzyloxy-carbonyl-lysine nitrophenyl ester at 25 degrees C, and I 0.1 at several pH values catalysed by chymopapain A, papaya proteinase omega, papain (EC 3.4.22.2) and actinidin (EC 3.4.22.14) were determined. Towards these substrates chymopapain A has kcat./km values similar to those of actinidin and of papaya proteinase omega and significantly lower than those of papain or ficin. The environment of the catalytic site of chymopapain A is markedly different from those of other cysteine proteinases studied to date, as evidenced by the pH-dependence of the second-order rate constant (k) for the reaction of the catalytic-site thiol group with 2,2'-dipyridyl disulphide. The striking bell-shaped component that is a characteristic feature of the reactions of S-/ImH+ (thiolate/imidazolium) ion-pair components of many cysteine-proteinase catalytic sites with the 2,2'-dipyridyl disulphide univalent cation is not present in the pH-k profile for the chymopapain A reaction. The result is consistent with the presence of an additional positive charge in, or near, the catalytic site that repels the cationic form of the probe reagent. Resonance Raman spectra were collected at pH values 2.5, 6.0 and 8.0 for each of the following dithioacyl derivatives of chymopapain A: N-benzoylglycine-, N-(Beta-phenylpropionl)glycine- and N-methoxycarbonylphenylalanylglycine-. The main conclusion of the spectral study is that in each case the acyl group binds as a single population known as conformer B in which the glycinic N atom is in close contact with the thiol S atom of the catalytic-site cysteine residue, as is the case also for papain and other cysteine proteinases studied. Thus the abnormal catalytic-site environment of chymopapain A detected by the reactivity-probe studies, which may have consequences for the acylation step of the catalytic act, does not perturb the conformation of the bound acyl group at the acyl-enzyme-intermediate stage of catalysis.     

Studies on the C-24 configurations of Δ7-sterols in theseeds of Cucurbita maxima

Uncertainties surrounding the structures of the Δ⁷-sterols in the seeds of Cucurbita maxima have been resolved. Seven components were found by TLC, GLC, HPLC, mass spectrometry and ¹H NMR. They were 24β-ethyl-5α-cholesta-7,22,25(27)-trien-3β-ol, 24β-ethyl-5α-cholesta-7,25(27)-dien-3gb-ol, avenasterol, spinasterol, 24-dihydrospinasterol, 24ζ-methyllathosterol and 25(27)-dehydrofungisterol. The ¹H NMR spectra indicated that the sterols with an ethyl substituent at C-24 occurred in the absence of their C-24 epimers. This seems to be the first instance of the detection of 25(27)-dehydrofungisterol in a higher plant.     

Activation of the progesterone-signaling pathway by methyl-beta-cyclodextrin or steroid in Xenopus laevis oocytes involves release of 45-kDa Galphas

Treatment of Xenopus laevis oocytes with cholesterol-depleting methyl-β-cyclodextrin (MeβCD) stimulates phosphorylation of mitogen-activated protein kinase (MAPK) and oocyte maturation, as reported previously [Sadler, S.E., Jacobs, N.D., 2004. Stimulation of Xenopus laevis oocyte maturation by methyl-β-cyclodextrin. Biol. Reprod. 70, 1685-1692.]. Here we report that treatment of oocytes with MeβCD increased levels of immunodetectable 39-kDa mos protein. The protein synthesis inhibitor, cycloheximide, blocked the appearance of Mos, blocked MeβCD-stimulated phosphorylation of MAPK, and inhibited MeβCD-induced oocyte maturation. These observations suggest that MeβCD activates the progesterone-signaling pathway. Chemical inhibition of steroid synthesis and mechanical removal of follicle cells were used to verify that MeβCD acts at the level of the oocyte and does not require production of steroid by surrounding follicle cells. Cortical Gα_s is contained in low-density membrane; and treatment of oocytes with progesterone or MeβCD reduced immunodetectable levels of Gα_s protein in cortices and increased internal levels of 45-kDa Gα_s in cortical-free extracts. Dose-dependent increases in internal Gα_s after treatment of oocytes with progesterone correlated with the steroid-induced maturation response, and the increase in internal Gα_s after hormone treatment was comparable to the decrease in cortical Gα_s. These results are consistent with a model in which release of Gα_s from the plasma membrane is involved in activation of the progesterone-signaling pathway that leads to amphibian oocyte maturation.     

The nature of bile salt micelles as studied by deuterium NMR

Deuterium NMR of 3α,12α-dihydroxy-7,7-dideutero-5β-cholanoic acid was studied. Molecular sizes obtained from deuterium spin-lattice relaxation time (T₁) data of 3α,12α-dihydroxy-7,7-dideutero-5β-cholanoic acid in methanol and in water are in accordance with monomeric and tetrameric structures in the two media, respectively. The deuterium T₁ and intensity of 3α,12α-dihydroxy-7,7-dideutero-5β-cholanoic acid in aqueous solution at pH 8.0–8.8 were studied as functions of NaCl and lecithin concentrations. The results indicated that tetramers are in equilibrium with larger aggregates when secondary micelles are formed in the precense of NaCl, and that 3α, 12α-dihydroxy-7,7-dideutero-5β-cholanoic acid forms mixed micelles with lecithin with a molecular ratio of 2 : 3.     

Synthesis and properties of some O-(2,2-dialkoxyethyl)glycolaldehydes

β-d-Mannosidase (β-d-mannoside mannohydrolase EC 3.2.1.25) was purified 160-fold from crude gut-solution of Helix pomatia by three chromatographic steps and then gave a single protein band (mol. wt. 94,000) on SDS-gel electrophoresis, and three protein bands (of almost identical isoelectric points) on thin-layer iso-electric focusing. Each of these protein bands had enzyme activity. The specific activity of the purified enzyme on p-nitrophenyl β-d-mannopyranoside was 1694 nkat/mg at 40° and it was devoid of α-d-mannosidase, β-d-galactosidase, 2-acet-amido-2-deoxy-d-glucosidase, (1→4)-β-d-mannanase, and (1→4)-β-d-glucanase activities, almost devoid of α-d-galactosidase activity, and contaminated with <0.02% of β-d-glucosidase activity. The purified enzyme had the same K_m for borohydride-reduced β-d-manno-oligosaccharides of d.p. 3–5 (12.5mm). The initial rate of hydrolysis of (1→4)-linked β-d-manno-oligosaccharides of d.p. 2–5 and of reduced β-d-manno-oligosaccharides of d.p. 3–5 was the same, and o-nitrophenyl, methylumbelliferyl, and naphthyl β-d-mannopyranosides were readily hydrolysed. β-d-Mannobiose was hydrolysed at a rate ～25 times that of 6¹-α-d-galactosyl-β-d-mannobiose and 6³-α-d-galactosyl-β-d-mannotetraose, and at ～90 times the rate for β-d-mannobi-itol.     

Stabilization of neurotoxic soluble beta-sheet-rich conformations of the Alzheimer's disease amyloid-beta peptide

An emerging paradigm for degenerative diseases associated with protein misfolding, such as Alzheimer's disease, is the formation of a toxic species due to structural transitions accompanied by oligomerization. Increasingly, the focus in Alzheimer's disease is on soluble oligomeric forms of the amyloid-β peptide (Aβ) as the potential toxic species. Using a variety of methods, we have analyzed how sodium dodecyl sulphate (SDS) modulates the folding of Aβ40 and 42 and found that submicellar concentrations of SDS solubilize Aβ and induce structural transitions. Under these conditions, Aβ40 and 42 are interconverting oligomeric ensembles with a predominantly β-sheet structure. The Aβ42 soluble oligomers form β-sheet structures more readily and have increased stability compared with Aβ40 under identical conditions. The presence of added Cu²⁺ significantly promotes and stabilizes the formation of the soluble oligomeric β-sheet structures but these structures are nonamyloidogenic. In contrast, in the absence of added Cu²⁺, these β-sheet oligomers possess the hallmarks of amyloidogenic structures. These SDS-induced β-sheet forms of Aβ, both in the presence and absence of Cu²⁺, are toxic to neuronal cells.     

Dynameomics: A Consensus View of the Protein Unfolding/Folding Transition State Ensemble across a Diverse Set of Protein Folds

The Dynameomics project aims to simulate a representative sample of all globular protein metafolds under both native and unfolding conditions. We have identified protein unfolding transition state (TS) ensembles from multiple molecular dynamics simulations of high-temperature unfolding in 183 structurally distinct proteins. These data can be used to study individual proteins and individual protein metafolds and to mine for TS structural features common across all proteins. Separating the TS structures into four different fold classes (all proteins, all-α, all-β, and mixed α/β and α + β) resulted in no significant difference in the overall protein properties. The residues with the most contacts in the native state lost the most contacts in the TS ensemble. On average, residues beginning in an α-helix maintained more structure in the TS ensemble than did residues starting in β-strands or any other conformation. The metafolds studied here represent 67% of all known protein structures, and this is, to our knowledge, the largest, most comprehensive study of the protein folding/unfolding TS ensemble to date. One might have expected broad distributions in the average global properties of the TS relative to the native state, indicating variability in the amount of structure present in the TS. Instead, the average global properties converged with low standard deviations across metafolds, suggesting that there are general rules governing the structure and properties of the TS.     

Thiophosphate analogs of ADP and ATP as substrates in partial reactions of energy conversion in chloroplasts

Thiophosphate analogs of ADP and ATP have been employed in partial reactions of photosynthetic energy conversion in chloroplasts. Substitution of oxygen by sulfur at the α-phosphate yields a pair of diastereomers (ADPαS, ATPαS, A and B forms). Two diastereomeric compounds are also obtained by replacement of oxygen by sulfur in the β-phosphate group of ATP (ATPβS, A and B form) (Eckstein, F. and Goody, R.S. (1976) Biochemistry 15, 1685–1691).The A form of ADPαS is phosphorylated by chloroplasts with a K_m comparable to that of ADP but with a lower V. The B form of ADPαS as well as ADPβS is not a substrate in photophosphorylation and only weakly competes with ADP.The A forms of ADPαS and ATPαS strongly compete with ADP for the tight nucleotide binding site of CF₁ in the light-induced exchange reaction, whereas the B forms display a much smaller competitive effect. The efficiencies of ADPβS and the A isomer of ATPβS are intermediate, and the B form of ATPβS is a weaker competitor.The A forms of ATPαS and ATPβS are hydrolyzed by light-triggered ATPase, whereas the B forms are not. The efficiency of the A isomer of ATPαS is comparable to that of normal ATP, and the A form of ATPβS is cleaved at a lower rate. In trypsin-activated Ca²⁺-dependent ATPase the A form of ATPαS is the only thiophosphate analog to be hydrolyzed.The results indicate a stereospecific interaction of ADP and ATP at the catalytic sites as well as the tight nucleotide binding site of coupling ATPase of chloroplasts.     

Chromatographic and electrophoretic analyses of papaya proteinases

Although it is known that unripe fruit from Carica papaya contains several proteinase enzymes which are used industrially, only one of these, papain, has been extensively characterized. Recently, the separate use of other enzymes of the family has been considered but information on their hydrodynamic properties is contradictory. The use of newer methods of separation has enabled us to separate a proteinase which runs slowly on acidic polyacrylamide gels (papain) from the four other proteinases. The proteinase which runs fastest on acidic polyacrylamide gels has an M, of 25 k and a pI of 11.0. This latter pI is the same as that of a proteinase which has an M, of 28 k and runs more quickly than papain but more slowly than chymopapain on acidic gels. We therefore have data showing that the proteinase enzymes from papaya can be classified by pI and M, into papain (pI 8.75, M, 23 k), chymopapains A and B (pI 10.3–10.4 or 10.6–10.7 and M, 24 k), papaya proteinase A (Ω) (pI 11.0, M, 24 k) and papaya proteinase β (pI 11.0, M, 28 K).     

A 13c-n.m.r. study of a di- and a tri-saccharide containing the α-d-galactopyranosyl group

The ¹³C-n.m.r. spectra of methyl 4-O-α-d-galactopyranosyl-α-d-galactopyranoside (1) and methyl 4-O-[4-O-(α-d-galactopyranosyl)-β-d-galactopyranosyl]-β-d-glucopyranoside (2) in D₂O were recorded. Comparison of these spectra with the spectra of methyl α-d-galactopyranoside (4) and methyl β-lactoside (5) provided substantial confirmation of the structures of 1 and 2.     

Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations

Mounting spectroscopic evidence indicates that alanine predominantly adopts extended polyproline II (PPII) conformations in short polypeptides. Here we analyze Raman optical activity (ROA) spectra of N-acetylalanine-N′-methylamide (Ala dipeptide) in H₂O and D₂O using density functional theory on Monte Carlo (MC) sampled geometries to examine the propensity of Ala dipeptide to adopt compact right-handed (α_R) and left-handed (α_L) helical conformations. The computed ROA spectra based on MC-sampled α_R and PPII peptide conformations contain all the key spectral features found in the measured spectra. However, there is no significant similarity between the measured and computed ROA spectra based on the α_L- and β-conformations sampled by the MC methods. This analysis suggests that Ala dipeptide populates the α_R and PPII conformations but no substantial population of α_L- or β-structures, despite sampling α_L- and β-structures in our MC simulations. Thus, ROA spectra combined with the theoretical analysis allow us to determine the dominant populated structures. Including explicit solute-solvent interactions in the theoretical analysis is essential for the success of this approach.     

Estrogenic activity of constituents from the rhizomes of Rheum undulatum Linné

Stilbenes have been reported to be phytoestrogen compounds owing to its structural similarity to the estrogenic agent diethylstilbestrol. To find new stilbene-derivative phytoestrogens, isolation of stilbene-rich R. undulatum was performed and led to identify six new compounds (1–5 and 28), one newly determined absolute configurations compound (27) together with 21 previously reported compounds (6–26). The structures of compounds were determined on the basis of extensive spectroscopic methods including 1D and 2D NMR and CD spectra data. All the isolated compounds were tested for their estrogenic activities in HepG2 cells transiently transfected with ERα, ERβ and ERE-reporter plasmid. Among them, stilbene-derivatives, piceatannol 3′-O-β-d-xylopyranoside (12), cis-rhaponticin (16) and rhapontigenin 3′-O-β-d-glucopyranoside (17), showed the more potent binding affinity for estrogen receptors than 17β-estrodiol.