Determination of the accessibility and localization of tryptophan residues in the influenza virus hemagglutinin molecule

The accessibility and localization of tryptophane residues in the influenza viral hemagglutinin molecule have been determined by measuring specific quenching of tryptophane fluorescence by neutral (acrylamide), anionic (I-) and cationic (Cs+) quenchers. It has been shown that acrylamide quenches 64% of tryptophane fluorescence in H3-hemagglutinin whereas I- and Cs+ quench only 34%. The tryptophanyl residues have been assumed to be located in the hemagglutinin molecule both in the cationic and anionic environments. 64% of tryptophanyls have been shown to be located on the surface of the protein globule.     

Hydrogen exchange of the tryptophan residues in bovine alpha-lactalbumin studied by UV spectroscopy

The effect of Ca²⁺ ion on structural fluctuation of a milk Ca²⁺-binding protein, α-lactalbumin, under native conditions was investigated by comparing hydrogen-exchange reactions of tryptophan residues in the apo-form without Ca²⁺ and in the holo-form at 1 mM CaCl₂ at pH 7.0 in the presence of 0.1M Na⁺. The reactions were followed by measuring time-dependent absorption changes at 298–300 nm due to the ²H-¹H exchange of the tryptophan imino protons and were found to be biphasic under all the conditions examined. Two of the four tryptophan protons are insensitive to Ca²⁺ concentration and show a relatively fast exchange rate. The other two protons are much more extensively protected (a protection degree of 10³–10⁵) and are markedly affected by the presence of Ca²⁺. Examinations of the temperature dependence and pH dependence of the individual exchange rates have been utilized for elucidating the exchange mechanism. The fast protons show a low activation energy reaction with so-called EX₂ kinetics. The exchange reaction of the slow protons is accompanied by a high activation energy, and the exchange mechanism of the protons depended on the presence or absence of stabilizing Ca²⁺ ions—the EX₁ kinetics for the apo-protein and the EX₂ kinetics for the holo-protein at 1 mM Ca²⁺. The exchange reaction in the thermally unfolded state was also found to be biphasic, but the fast phase, which has an exchange rate in the fully exposed state, becomes predominant with decreasing temperature. By taking this fact and using a structural unfolding model of hydrogen exchange, the present results are fully consistent with thermodynamic parameters of the thermal transition and kinetic parameters of refolding reactions induced by concentration jumps of guanidine hydrochloride obtained in previous studies. It is demonstrated that the reaction of the slow protons in the native state is mediated by a transient global unfolding equivalent to the “thermal” unfolding under a native condition and that switching of the exchange mechanism from the EX₁ to EX₂ kinetics results from acceleration of the refolding rate with an increase in Ca²⁺ concentration. The transient global unfolding takes place even under a strongly native condition, e.g., at a temperature 20° below the beginning of the thermal transition.     

Fluorescence of tryptophan residues in firefly luciferases and enzyme--substrate complexes

Quenching of tryptophan fluorescence of Luciola mingrelica (single tryptophan residue, Trp-419) and Photinus pyralis (two tryptophan residues, Trp-417 and Trp-426) luciferases with different quenchers (I-, Cs+, acrylamide) was studied. The conserved Trp-417(419) residue was shown to be not accessible to charged particles, and positively and negatively charged amino acid residues are located in close vicinity to it. We found previously unreported effective energy transfer from this tryptophan to luciferin during the quenching of the tryptophan fluorescence. The distance between the luciferin molecule and Trp-417(419) was calculated: 11-15 and 12-17 A for P. pyralis and L. mingrelica luciferases, respectively. The role of the conserved Trp residue in the catalysis is discussed. ATP and AMP are also quenchers of the tryptophan fluorescence of the luciferases. In this case, an allosteric mechanism of the interaction of Trp-417(419) with an excess of ATP (AMP) is proposed.     

Detoxification of castor bean residues and the simultaneous production of tannase and phytase by solid-state fermentation using Paecilomyces variotii

In this work, we introduce a biological detoxification method that converts toxic waste from castor beans into animal feed material. This method simultaneously induces the production of tannase and phytase by Paecilomyces variotii; both enzymes have high levels of activity and have the potential to be used in feedstuffs because they decrease overall anti-nutritional factors. The maximum tannase and phytase activities obtained were 2600 and 260 U/g after 48 and 72 h, respectively. SDS-PAGE electrophoresis of the fermented castor cake extracts revealed a reduction in ricin bands during fermentation, and the bands were no longer visible after 48 h. The cytotoxicity of the extracts was evaluated by MTT testing on RAW cells, and a progressive increase in cellular viability was obtained, reaching almost 100% after 72 h of fermentation.     

Anaerobic stress in germinating castor bean, ethanol metabolism, and effects on subcellular organelles

Endosperms from castor beans (Ricinus communis) germinated for 0 to 6 days were exposed to anoxia for 0 to 15 hours. Ethanol, the only alcohol detected by gas chromatography in the tissue, accumulates to a concentration of 15 millimolar during the first 2 to 4 hours of anoxia and subsequently decreases. The absolute amount of ethanol varies from 10 micromoles per 5-day endosperm after 4 hours anoxia to less than 1 micromole in 2-day endosperm after 4 hours. Lactate content is 2 micromoles or less per endosperm. Alcohol dehydrogenase and pyruvate decarboxylase activities, which are localized in cytosolic fractions, are not greatly affected by anoxia. The recoveries of the marker enzymes and protein in endoplasmic reticulum (ER) and mitochondrial fractions decrease during anoxia. After 15 hours, the recovery of NADPH cytochrome c reductase is 15% of that in controls, fumarase is 50%, and catalase is 75%.

Glyoxysomes and ER are capable of converting ethanol to acetaldehyde which was measured using the fluorogenic reagent, 5,5-dimethyl-1,3-cyclohexanedione. The glyoxysomal activity is dependent on a hydrogen peroxide-generating substrate and the ER is dependent on NADPH. However, these activities are less than 3% of the alcohol dehydrogenase activity.

     

Accessibility of tryptophan residues in immunoglobulin M as an index of its conformational changeability

Demonstrated herein is the possibility of using the accessibility of tryptophan (Trp) residues in immunoglobulin M (IgM) upon modification with Koshland reagent (2-hydroxy-5-nitrobenzyl bromide) as an index of the conformational changeability of IgM. Of fourteen Trp's in the native IgM (per HL-region) only one appeared to be most accessible, evidently Trp312 in the mu-chain. Irreversible acidic and thermal conformational transitions in IgM increase the number of accessible Trp's approximately two-fold. Following partial enzymatic deglycosylation of IgM, deep scission of mannose in particular, all Trp's become inaccessible. Modification of the most accessible Trp increases 2-3 fold the number of tyrosine residues readily accessible upon nitration with tetranitromethane. Modification of four trp's using spin-label method data causes a sharp reduction of the mobility of the C mu 3 domain and a simultaneous decrease in the solubility of modified IgM.     

The tryptophan residues of aspartate transcarbamylase: site-directed mutagenesis and time-resolved fluorescence spectroscopy.

Aspartate transcarbamylase (EC 2.1.3.2) contains two tryptophan residues in position 209 and 284 of the catalytic chains (c) and no such chromophore in the regulatory chains (r). Thus, as a dodecamer [(c3)2(r2)3] the native enzyme molecule contains 12 tryptophan residues. The present study of the regulatory conformational changes in this enzyme is based on the fluorescence properties of these intrinsic probes. Site-directed mutagenesis was used in order to differentiate the respective contributions of the two tryptophans to the fluorescence properties of the enzyme and to identify the mobility of their environment in the course of the different regulatory processes. Each of these tryptophan residues gives two independent fluorescence decays, suggesting that the catalytic subunit exists in two slightly different conformational states. The binding of the substrate analog N-phosphonacetyl-L-aspartate promotes the same fluorescence signal whether or not the catalytic subunits are associated with the regulatory subunits, suggesting that the substrate-induced conformational change of the catalytic subunit is the essential trigger for the quaternary structure transition involved in cooperativity. The binding of the substrate analog affects mostly the environment of tryptophan 284, while the binding of the activator ATP affects mostly the environment of tryptophan 209, confirming that this activator acts through a mechanism different from that involved in homotropic cooperativity.     

Accessibility of tryptophan residues in immunoglobulin M molecule as an indicator of its conformational variability

The accessibility of tryptophan residues in immunoglobulin M to modification with the Koshland reagent (2-hydroxy-5-nitrobenzyl bromide) was used as an indicator of its conformational variability. Of 14 tryptophan residues (per HL-fragment) in the native IgM, only one (presumably Trp312 in the mu-chain) was the most accessible. Irreversible acid- or temperature-induced conformational changes of IgM increased almost 2-fold the number of accessible tryptophan residues. After partial enzymatic deglycosylation of IgM (especially by an intense splitting of mannose), all tryptophan residues became inaccessible. Modification of the most accessible tryptophan residue increased 2- to 3-fold the number of tyrosine residues accessible to nitration with tetranitromethane. Using the spin label method, it was demonstrated that modification of four tryptophan residues in IgM considerably decreased the mobility of the Cmu 3 domain together with an essential drop in. the solubility of the modified IgM.     

Modification of tryptophan and tryptophan residues in proteins by reactive nitrogen species.

Formation of 3-nitrotyrosine by the reaction between reactive nitrogen species (RNS) and tyrosine residues in proteins has been analyzed extensively and it is used widely as a biomarker of pathophysiological and physiological conditions mediated by RNS. In contrast, few studies on the nitration of tryptophan have been reported. This review provides an overview of the studies on tryptophan modifications by RNS and points out the possible importance of its modification in pathophysiological and physiological conditions. Free tryptophan can be modified to several nitrated products (1-, 4-, 5-, 6-, and 7-), 1-N-nitroso product, and several oxidized products by reaction with various RNS, depending on the conditions used. Among them, 1-N-nitrosotryptophan and 6-nitrotryptophan (6-NO(2)Trp) have been found as the abundant products in the reaction with peroxynitrite, and 6-NO(2)Trp has been the most abundant product in the reaction with the peroxidase/hydrogen peroxide/nitrite systems. 6-NO(2)Trp has also been observed as the most abundant nitrated product of the reactions between peroxynitrite or myeloperoxidase/hydrogen peroxide/nitrite and tryptophan residues both in human Cu,Zn-superoxide dismutase and in bovine serum albumin, as well as the reaction of peroxynitrite with myoglobin and hemoglobin. Several oxidized products have also been identified in the modified Cu,Zn-SOD. However, no 1-N-nitrosotryptophan and 1-N-nitrotryptophan has been observed in the proteins reacted with peroxynitrite or the myeloperoxidase/H(2)O(2)/nitrite system. The modification of tryptophan residues in proteins may occur at a more limited number of sites in vivo than that of tyrosine residues, since tryptophan residues are more buried inside proteins and exist less frequently in proteins, generally. However, surface-exposed tryptophan residues tend to participate in the interaction with the other molecules, therefore the modification of those tryptophans may result in modulation of the specific interaction of proteins and enzymes with other molecules.     

我国优势油脂类生物柴油植物蓖麻的种质资源发掘和生物柴油利用

发展可再生生物质能源是解决人类能源危机和环境污染的重要途径。利用边际土地发展油脂类生物质能是生物质能的重要组成部分。蓖麻因为适应性强和油脂成份独特被誉为"理想的生物柴油植物"。蓖麻是我国优势油脂类能源植物,利用边际土地,发展蓖麻产业为我国生物柴油产业化提供原料,是我国现阶段生物柴油产业化发展的相对理想而又现实的选择,而且具有重要的发展前景和巨大的发掘潜力。立足我国现阶段生物柴油产业化的瓶颈问题,着重阐述了蓖麻种质资源发掘的现状、优良品种培育的途径和发展前景,以及利用蓖麻种子油生产商业化生物柴油的现状,以期推动我国利用边际土地发展蓖麻产业以及生物柴油商业化生产。     

Gluconeogenesis from amino acids in germinating castor bean endosperm and its role in transport to the embryo

During germination of the castor bean all of the contents of the endosperm are ultimately transported to the embryo through the cotyledon or respired. A net loss of nitrogen from the endosperm begins about the fourth day, i.e. at the time when embryo growth and fat breakdown are also beginning. Amino acid analysis of the exudate from the cotyledons, still enclosed in the endosperm, showed that the amounts of aspartate, glutamate, glycine, and alanine were very low and that glutamine made up 40% of the amino acids in the exudate.

Amino acids labeled with ¹⁴C were applied to intact excised endosperms to follow utilization. Aspartate, glutamate, alanine, glycine, serine, and leucine were converted to sugar to varying extents. Proline, arginine, valine, and phenylalanine were not appreciably converted to sugars. Proline and glutamate were converted to glutamine. When ¹⁴C-glutamate, aspartate, and alanine were added to the outer endosperm of intact seedlings, only sugars and glutamine contained appreciable label in the exudate. When ¹⁴C-valine was added, it was virtually the only labeled compound in the exudate.

The results show that amino acids which on deamination can give rise to intermediates in the pathway of conversion of fat to sucrose are largely converted to sucrose and the nitrogen transported as glutamine. Other amino acids released from the endosperm protein are transported intact into the seedling axis. Some carbon from the gluconeogenic amino acids is also transported as glutamine.

     

Characterization of the tryptophan residues of Escherechia coli alkaline phosphatase by phosphorescence and optically detected magnetic resonance spectroscopy.

The phosphorescence and zero field optically detected magnetic resonance (ODMR) of the tryptophan (Trp) residues of alkaline phosphatase from Escherechia coli are examined. Each Trp is resolved optically and identified with the aid of the W220Y mutant and the terbium complex of the apoenzyme. Trp(109), known from earlier work to be the source of room-temperature phosphorescence (RTP), emits a highly resolved low-temperature phosphorescence (LTP) spectrum and has the narrowest ODMR bands observed thus far from any protein site, revealing a uniquely homogeneous local environment. The decay kinetics of Trp(109) at 1.2 K reveals that the major triplet population (70%) undergoes inefficient crystallike spin-lattice relaxation by direct interaction with lattice phonons, the remainder being relaxed efficiently by local disorder modes. The latter population is smaller than is typical for protein sites, suggesting an unusual degree of local rigidity and order consistent with the long-lived RTP. Trp(220) emits a broader LTP spectrum originating to the blue of Trp(109). It has typically broad ODMR bands consistent with local heterogeneity. The LTP of Trp(268) has an ill-defined origin blue shifted relative to Trp(220) and ODMR frequencies consistent with a greater degree of solvent exposure. Trp(268) has noticeable dispersion of its decay kinetics, consistent with quenching at the triplet level by a nearby disulfide residue.     

Growth,carbohydrates and associated invertase and amylase activities in castor bean and maize as affected by metribuzin and NaCl

Growth parameters (leaf area, length of shoot and root, water content and dry matter accumulation), contents of reducing sugars and saccharose as well as activities of α- and β-amylases of castor bean and maize seedlings and adult plants supplemented with 0.5 μg g^?1 and 2.5 μg g^?1 of metribuzin either alone or in combination with 50 μg g^?1 NaCl, were increased significantly whereas at high concentrations (5 and 10 μg g^?1) of herbicide, an opposite response was apparent. On the other hand, polysaccharide content and invertase activity of castor bean and maize seedlings and adult plants were significantly decreased in response to low concentrations (0.5 and 2.5 μg g^?1) of metribuzin and increased significantly at high concentrations (5 and 10 μg g^?1) of the herbicide either alone or in combination with 50 μg g^?1 NaCl. Total carbohydrate contents of castor bean and maize seedlings and whole plants treated with herbicide either alone or in combination with NaCl did not change significantly. Growth parameters, carbohydrate fractions contents and activities of enzymes in both castor bean and maize seedlings and whole plants treated with herbicide alone were consistently higher than those values detected in plants treated with herbicide in combination with NaCl.     

Impact of the tryptophan residues of Humicola lanuginosa lipase on its thermal stability.

Thermal stability of wild type Humicola lanuginosa lipase (wt HLL) and its two mutants, W89L and the single Trp mutant W89m (W117F, W221H, and W260H), were compared. Differential scanning calorimetry revealed unfolding of HLL at T(d)=74.4 degrees C whereas for W89L and W89m this endotherm was decreased to 68.6 and 62 degrees C, respectively, demonstrating significant contribution of the above Trp residues to the structural stability of HLL. Fluorescence emission spectra revealed the average microenvironment of Trps of wt HLL and W89L to become more hydrophilic at elevated temperatures whereas the opposite was true for W89m. These changes in steady-state emission were sharp, with midpoints (T(m)) at approx. 70.5, 61.0, and 65.5 degrees C for wt HLL, W89L, and W89m, respectively. Both steady-state and time resolved fluorescence spectroscopy further indicated that upon increasing temperature, the local movements of tryptophan(s) in these lipases were first attenuated. However, faster mobilities became evident when the unfolding temperatures (T(m)) were exceeded, and the lipases became less compact as indicated by the increased hydrodynamic radii. Even at high temperatures (up to 85 degrees C) a significant extent of tertiary and secondary structure was revealed by circular dichroism. Activity measurements are in agreement with increased amplitudes of conformational fluctuations of HLL with temperature. Our results also indicate that the thermal unfolding of these lipases is not a two-state process but involves intermediate states. Interestingly, a heating and cooling cycle enhanced the activity of the lipases, suggesting the protein to be trapped in an intermediate, higher energy state. The present data show that the mutations, especially W89L in the lid, contribute significantly to the stability, structure and activity of HLL.     

Interaction of the mycobacterial heparin-binding hemagglutinin with actin, as evidenced by single-molecule force spectroscopy

Although Mycobacterium tuberculosis and related species are considered to be typical endosomal pathogens, recent studies have suggested that mycobacteria can be present in the cytoplasm of infected cells and cause cytoskeleton rearrangements, the mechanisms of which remain unknown. Here, we used single-molecule force spectroscopy to demonstrate that the heparin-binding hemagglutinin (HBHA), a surface adhesin from Mycobacterium tuberculosis displaying sequence similarities with actin-binding proteins, is able to bind to actin. Force curves recorded between actin and the coiled-coil, N-terminal domain of HBHA showed a bimodal distribution of binding forces reflecting the detection of single and double HBHA-actin interactions. Force curves obtained between actin and the lysine-rich C-terminal domain of HBHA showed a broader distribution of binding events, suggesting they originate primarily from intermolecular electrostatic bridges between cationic HBHA domains and anionic actin residues. We also explored the dynamics of the HBHA-actin interaction, showing that the binding force and binding frequency increased with the pulling speed and contact time, respectively. Taken together, our data indicate that HBHA is able to specifically bind actin, via both its N-terminal and C-terminal domains, strongly suggesting a role of the HBHA-actin interaction in the pathogenesis of mycobacterial diseases.     

Phosphatidylcholine synthesis in castor bean endosperm: characteristics and reversibility of the choline kinase reaction

Choline kinase (EC 2.7.1.32) was measured in concentrated 100,000gav supernatants from castor bean endosperm (Ricinus communis L. var. Hale). Initial velocity analysis, along with competitive inhibitor (hemicholinium-3) and product inhibition (ADPMg2+) studies suggested that the forward reaction followed a sequentially ordered mechanism with ATPMg2+ binding to the enzyme first, followed by choline and then activation of the ternary complex by free Mg2+. The kinetic constants of the forward reaction are reported. A reverse reaction was measured which had a pH optimum of 6.5 and produced 1 mol of ATP for every mole of choline phosphate. The estimated maximum possible Keq at 7.25 was 5 X 10(-3) which suggested that this reaction is highly reversible in this tissue. The possible physiological significance of this is discussed.     

The role of conserved tryptophan and acidic residues in the human dopamine transporter as characterized by site-directed mutagenesis

The human dopamine (DA) transporter (hDAT) contains multiple tryptophans and acidic residues that are completely or highly conserved among Na(+)/Cl(-)-dependent transporters. We have explored the roles of these residues using non-conservative substitution. Four of 17 mutants (E117Q, W132L, W177L and W184L) lacked plasma membrane immunostaining and were not functional. Both DA uptake and cocaine analog (i.e. 2beta-carbomethoxy-3beta-(4-fluorophenyl)tropane, CFT) binding were abolished in W63L and severely damaged in W311L. Four of five aspartate mutations (D68N, D313N, D345N and D436N) shifted the relative selectivity of the hDAT for cocaine analogs and DA by 10-24-fold. In particular, mutation of D345 in the third intracellular loop still allowed considerable [(3)H]DA uptake, but caused undetectable [(3)H]CFT binding. Upon anti-C-terminal-hDAT immunoblotting, D345N appeared as broad bands of 66-97 kDa, but this band could not be photoaffinity labeled with cocaine analog [(125)I]-3beta-(p-chlorophenyl)tropane-2beta-carboxylic acid ([(125)I]RTI-82). Unexpectedly, in this mutant, cocaine-like drugs remained potent inhibitors of [(3)H]DA uptake. CFT solely raised the K(m) of [(3)H]DA uptake in wild-type hDAT, but increased K(m) and decreased V(max) in D345N, suggesting different mechanisms of inhibition. The data taken together indicate that mutation of conserved tryptophans or acidic residues in the hDAT greatly impacts ligand recognition and substrate transport. Additionally, binding of cocaine to the transporter may not be the only way by which cocaine analogs inhibit DA uptake.