Amino acid screening based on structural modeling identifies critical residues for the function, ion selectivity and structure of Arabidopsis MTP1

Arabidopsis thaliana MTP1 is a vacuolar membrane Zn(2+)/H(+) antiporter of the cation diffusion facilitator family. Here we present a structure-function analysis of AtMTP1-mediated transport and its remarkable Zn(2+) selectivity by functional complementation tests of more than 50 mutant variants in metal-sensitive yeast strains. This was combined with homology modeling of AtMTP1 based on the crystal structure of the Escherichia coli broad-specificity divalent cation transporter YiiP. The Zn(2+)-binding sites of EcYiiP in the cytoplasmic C-terminus, and the pore formed by transmembrane helices TM2 and TM5, are conserved in AtMTP1. Although absent in EcYiiP, Cys31 and Cys36 in the extended N-terminal cytosolic domain of AtMTP1 are necessary for complementation of a Zn-sensitive yeast strain. On the cytosolic side of the active Zn(2+)-binding site inside the transmembrane pore, Ala substitution of either Asn258 in TM5 or Ser101 in TM2 non-selectively enhanced the metal tolerance conferred by AtMTP1. Modeling predicts that these residues obstruct the movement of cytosolic Zn(2+) into the intra-membrane Zn(2+)-binding site of AtMTP1. A conformational change in the immediately preceding His-rich cytosolic loop may displace Asn258 and permit Zn(2+) entry into the pore. This would allow dynamic coupling of Zn(2+) transport to the His-rich loop, thus acting as selectivity filter or sensor of cytoplasmic Zn(2+) levels. Individual mutations at diverse sites within AtMTP1 conferred Co and Cd tolerance in yeast, and included deletions in N-terminal and His-rich intra-molecular cytosolic domains, and mutations of single residues flanking the transmembrane pore or participating in intra- or inter-molecular domain interactions, all of which are not conserved in the non-selective EcYiiP.     

Anti-hypertensive activity of genetically modified soybean seeds accumulating novokinin

Novokinin (Arg-Pro-Leu-Lys-Pro-Trp), which has been designed based on the structure of ovokinin (2-7), significantly reduces the systolic blood pressure at a dose of 100 microg/kg after oral administration in spontaneously hypertensive rats (SHRs). In this study, we generated a transgenic soybean which accumulates novokinin. A vector encoding a modified beta-conglycinin alpha' subunit (4novokinin-alpha') in which four novokinin sequences have been incorporated by site-directed mutagenesis was introduced into somatic embryos by whisker-mediated gene transformation to produce a transgenic soybean. The 4novokinin-alpha' occupied 0.5% of total soluble protein and 5% of the beta-conglycinin alpha' subunit in the transgenic soybean seeds. Protein extracted from the transgenic soybean reduced systolic blood pressure after single oral administration in SHRs at a dose of 0.15 g/kg. Defatted flour from the transgenic soybean also reduced the systolic blood pressure at a dose of 0.25 g/kg. Thus, the 4novokinin-alpha' produced in soybean exhibited an anti-hypertensive activity in SHRs after oral administration.     

Demethylthiolating Agents for Ribonucleoside 5′-S-Methyl Phosphorothiolates

Several oxidizing agents were examined for their ability to demethylthiolate adenosine- and cytidine 5′-S-methyl phosphorothiolates.

Iodine dissolved in an aqueous potassium iodide solution or in dimethyl sulfoxide (DMSO) was the most effective demethylthiolating agent of those tested in the present study, rapidly giving the demethylthiolated products in quantitative yields. The iodine-DMSO solution demethyl-thiolated the ribonucleoside 5′-S-methyl phosphorothiolates to give ribonucleoside 5′-monophosphates even under anhydrous conditions, DMSO acting as an oxygen donor in this reaction.

Hydrogen peroxide has high demethylthiolating ability in spite of its low reaction rate. Isoamyl nitrite, an effective demethylthiolating agent for O-alkyl S-methyl phosphorothiolates, was not effective for the demethylthiolation of ribonucleoside 5′-S-methyl phosphorothiolates, because the unprotected amino groups of the S-methyl nucleotides were attacked by the reagent to give deaminated products. N-Chlorosuccinimide had no effect on the demethylthiolation of S-methyl phosphorothiolates.     

Purification and Characterization,of Rice Bran Lipase II

A species of rice bran lipase (lipase II) was purified by ammonium sulfate precipitation, followed by successive chromatographies on DEAE-cellulose, Sephadex G–75 and CH-Sephadex C–50. Both polyacrylamide disc electrophoresis and ultracentrifugation demonstrated that the enzyme protein is homogeneous. The isoelectric point of the enzyme was 9.10 by ampholine electrophoresis. The sedimentation coefficient of the enzyme was evaluated to be 2.60 S, and the molecular weight to be 33,300 according to Archbald’s method. The enzyme showed the optimum pH between 7.5 and 8.0, and the optimum temperature at about 27°C. It was stable over the pH range from 5 to 9.5 and below 30°C. In substrate specificity, the enzyme exhibited a high specificity toward triglycerides having short-carbon chain fatty acids, although it was capable of hydrolyzing the ester bonds in the rice and olive oil.     

Backbone resonance assignment for the outer membrane lipoprotein receptor LolB from Escherichia coli

LolB, which is anchored to the outer membrane of Gram-negative bacteria, receives outer-membrane-directed lipoproteins from LolA, and incorporates them into the outer membrane. We established backbone resonance assignments of ²H/¹³C/¹⁵N labeled LolB from Escherichia coli.     

Adductor muscles of the thigh of crab-eating monkeys (Macaca fascicularis)

On the basis of 44 hindlimbs of 14 male and 14 female crab-eating monkeys (Macaca fascicularis), the morphology of the adductor muscles of the thigh was described and some functional indices were calculated. The results obtained from this study agreed generally with those of otherMacaca species reported by various authors. For the classification and nomenclature of the adductors, the criteria proposed byUhlmann (1967, 1968) was well adapted to the crab-eating monkey. The adductors comprise the m. gracilis, m. pectineus, m. adductor longus, pars longa and pars brevis of m. adductor brevis, pars lata and pars minima of m. adductor magnus and m. obturatorius externus. In males, the adductors are generally inserted further down the femur, and the insertions of pars brevis of the m. adductor brevis and pars minima of the m. adductor magnus have longer attachments to the femur than in females. The arrangement of each adductor muscle and of each fasciculus of a thigh muscle may invoke a principle of organization.     

An NMR method for the determination of protein binding interfaces using TEMPOL-induced chemical shift perturbations

Background

The determination of protein–protein interfaces is of crucial importance to understand protein function and to guide the design of compounds. To identify protein–protein interface by NMR spectroscopy, ¹³C NMR paramagnetic shifts induced by freely diffusing 4-hydroxy-2, 2, 6, 6-tetramethyl-piperidine-1-oxyl (TEMPOL) are promising, because TEMPOL affects distinct ¹³C NMR chemical shifts of the solvent accessible nuclei belonging to proteins of interest, while ¹³C nuclei within the interior of the proteins may be distinguished by a lack of such shifts.

Method

We measured the ¹³C NMR paramagnetic shifts induced by TEMPOL by recording ¹³C–¹³C TOCSY spectra for ubiquitin in the free state and the complex state with yeast ubiquitin hydrolase1 (YUH1).

Results

Upon complexation of ubiquitin with YUH1, ¹³C NMR paramagnetic shifts associated with the protein binding interface were reduced by 0.05 ppm or more. The identified interfacial atoms agreed with the prior X-ray crystallographic data.

Conclusions

The TEMPOL-induced ¹³C chemical shift perturbation is useful to determine precise protein–protein interfaces.

General significance

The present method is a useful method to determine protein–protein interface by NMR, because it has advantages in easy sample preparations, simple data analyses, and wide applicabilities.     

Stimulatory effect of regucalcin on proteolytic activity is impaired in the kidney cortex cytosol of rats with saline ingestion

The effect of regucalcin (RC) on neutral proteolytic activity in the cytosol of rat kidney cortex was investigated. Proteolytic activity was significantly increased by the presence of RC (0.01 + 0.10 M) in the enzyme reaction mixture. This increase was completely abolished by the addition of anti-RC monoclonal antibody (150 ng/ml). When the renal cortex cytosol was incubated without RC addition, the degradation of globin of substrate was demonstrated by sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. This degradation was clearly inhibited by the addition of anti-RC antibody (150 ng/ml), indicating that protein degradation results partly from the cytosolic endogenous RC. Meanwhile, proteolytic activity was significantly decreased in the renal cortex cytosol of rats with saline ingestion for 2, 7, and 14 days. The effect of RC (0.1 M) in increasing proteolytic activity was weakened in the kidney cortex cytosol of saline-ingested rats. The present study suggests that endogenous RC plays a role in the activation of proteases in the renal cortex cytosol, and that the RC effect is impaired in saline-ingested rats.     

Role of proline residues in conferring thermostability on aqualysin I

To understand the molecular basis of the thermostability of a thermophilic serine protease aqualysin I from Thermus aquaticus YT-1, we introduced mutations at Pro5, Pro7, Pro240 and Pro268, which are located on the surface loops of aqualysin I, by changing these amino acid residues into those found at the corresponding locations in VPR, a psychrophilic serine protease from Vibrio sp. PA-44. All mutants were expressed stably and exhibited essentially the same specific activity as wild-type aqualysin I at 40 degrees C. The P240N mutant protein had similar thermostability to wild-type aqualysin I, but P5N and P268T showed lower thermostability, with a half-life at 90 degrees C of 15 and 30 min, respectively, as compared to 45 min for the wild-type enzyme. The thermostability of P7I was decreased even more markedly, and the mutant protein was rapidly inactivated at 80 degrees C and even at 70 degrees C, with half-lives of 10 and 60 min, respectively. Differential scanning calorimetry analysis showed that the transition temperatures of wild-type enzyme, P5N, P7I, P240N and P268T were 93.99 degrees C, 83.45 degrees C, 75.66 degrees C, 91.78 degrees C and 86.49 degrees C, respectively. These results underscore the importance of the proline residues in the N- and C-terminal regions of aqualysin I in maintaining the integrity of the overall protein structure at elevated temperatures.     

Inhibitory effects of sesquiterpene lactones isolated from Eupatorium chinense L. on IgE-mediated degranulation in rat basophilic leukemia RBL-2H3 cells and passive cutaneous anaphylaxis reaction in mice

Sesquiterpene lactones (SQTLs) have been shown to suppress the degranulation as inferred by histamine release in rat basophilic leukemia RBL-2H3 cells. In this study, we isolated the 9 kinds of SQTLs from Eupatorium chinense L. and examined the effects of these SQTLs on the degranulation in RBL-2H3 cells. The chemical structures of two novel compounds (SQTL-3 and 8) were determined. All the SQTLs suppressed the degranulation from Ag-stimulated RBL-2H3 cells. To disclose the inhibitory mechanism of degranulation by SQTLs, we examined the activation of intracellular signaling molecules such as Lyn, Syk, and PLCγs and intracellular free Ca²⁺ concentration ([Ca²⁺]i). None of these SQTLs showed the activation of Syk and PLCγs. The intracellular free Ca²⁺ concentration ([Ca²⁺]i) was elevated by FcεRI activation, but SQTLs treatment reduced the elevation of [Ca²⁺]i by suppressing Ca²⁺ influx. Thus, it was suggested that the suppression of Ag-stimulated degranulation by these SQTLs is mainly due to the decreased Ca²⁺ influx.Furthermore, in order to clarify the in vivo effect of SQTL-rich extract, we administered SQTL-rich extract to the type I allergic model mice and measured the passive cutaneous anaphylaxis (PCA) reaction induced by IgE-antigen complex. The SQTLs remarkably suppressed PCA reaction in a dose-dependent manner. Thus, it was suggested that SQTLs would be a candidate as an anti-allergic agent.