Effect of aminoacylation on tRNA conformation

Translational diffusion coefficients have been simulated for various conformations of tRNA^Phe (yeast) by bead models, in order to analyze data obtained by dynamic light scattering on the free and the aminoacylated form. The 18% increase of the translational diffusion coefficient upon deacylation, reported by Potts et al. (1981), could not be represented by any change of the L-hinge angle, but could only be simulated by a conformation change to an extended form with extensive dissociation of base pairs. Since extensive unpairing is not consistent with evidence accumulated in the literature, the change of the diffusion coefficient must be mainly due to processes other than intramolecular conformational changes.     

The conformation of single-stranded nucleic acids tDNA versus tRNA

Conformational analyses using the single-strand-specific nuclease from mung bean and restriction endonucleases have been performed on a series of DNA fragments related to the sequence of the yeast initiator tRNA(Met). Mung bean nuclease cleaves DNA fragments exclusively in some, but not all, single-stranded regions as predicted by RNA secondary structural rules. Comparison of cleavage patterns of yeast initiator tRNA(Met), tDNA(Met) (a DNA oligomer having the sequence of tRNA(Met] and the anti-tDNA(Met) (the complement of tDNA(Met] suggests that the conformation of the three molecules is very similar. Furthermore, both tDNA and anti-tDNA are cleaved by HhaI and CfoI restriction endonucleases at two GCG/C sites which would be in double-stranded regions (the acceptor and dihydrouridine stem), if the two molecules adopt the tRNA cloverleaf structure. On the other hand, minor cleavage products show that the core region, i.e. the extra loop area, is slightly more exposed in tDNA and in anti-tDNA than in tRNA. Therefore, we submit that the global conformation of nucleic acids is primarily dictated by the interaction of purine and pyrimidine bases with atoms and functional groups common to both RNA and DNA. In this view the 2'-hydroxyl group, in tRNA at least, is an auxiliary structural feature whose role is limited to fostering local interactions, which increase the stability of a given conformation.     

Effect of G-1 on histidine tRNA microhelix conformation

Histidine tRNAs (tRNA^His) are unique in that they possess an extra 5′-base (G-1) not found in other tRNAs. Deletion of G-1 results in at least a 250-fold reduction in the rate of histidine charging in vitro. To better understand the role of the G-1 nucleotide in defining the structure of tRNA^His, and to correlate structure with cognate amino acid charging, NMR and molecular dynamics (MD) studies were performed on the wild-type and a ΔG-1 mutant Escherichia coli histidine tRNA acceptor stem microhelix. Using NMR-derived distance restraints, global structural characteristics are described and interpreted to rationalize experimental observations with respect to aminoacylation activity. The quality of the NMR-derived solution conformations of the wild-type and ΔG-1 histidine microhelices (micro helix^His) is assessed using a variety of MD-based computational protocols. Most of the duplex regions of the acceptor stem and the UUCG tetraloop are well defined and effectively superimposable for the wild-type and ΔG-1 mutant microhelix^His. Differences, however, are observed at the end of the helix and in the single-stranded CCCA-3′ tail. The wild-type microhelix^His structure is more well defined than the mutant and folds into a ‘stacked fold-back’ conformation. In contrast, we observe fraying of the first two base pairs and looping back of the single-stranded region in the ΔG-1 mutant resulting in a much less well defined conformation. Thus the role of the extra G-1 base of the unique G-1:C73 base pair in tRNA^His may be to prevent end-fraying and stabilize the stacked fold-back conformation of the CCCA-3′ region.     

RNase A - tRNA binding alters protein conformation.

Bovine pancreatic ribonuclease A (RNase A) catalyzes the cleavage of P-O5' bonds in RNA on the 3' side of pyrimidine to form cyclic 2',5'-phosphates. Even though extensive structural information is available on RNase A complexes with mononucleotides and oligonucleotides, the interaction of RNase A with tRNA has not been fully investigated. We report the complexation of tRNA with RNase A in aqueous solution under physiological conditions, using a constant RNA concentration and various amounts of RNase A. Fourier transform infrared, UV-visible, and circular dichroism spectroscopic methods were used to determine the RNase binding mode, binding constant, sequence preference, and biopolymer secondary structural changes in the RNase-tRNA complexes. Spectroscopic results showed 2 major binding sites for RNase A on tRNA, with an overall binding constant of K = 4.0 x 105 (mol/L)-1. The 2 binding sites were located at the G-C base pairs and the backbone PO2 group. Protein-RNA interaction alters RNase secondary structure, with a major reduction in alpha helix and beta sheets and an increase in the turn and random coil structures, while tRNA remains in the A conformation upon protein interaction. No tRNA digestion was observed upon RNase A complexation.     

Features of cardiovascular functioning during different phases of the menstrual cycle

The purpose of the present study was to determine whether there is a menstrual cycle effect on heart rate, blood pressure and heart rate variability. 10 healthy regularly cycling females (age 19-23 years) were studied during the follicular phase and luteal phase over two month. We found significant changes in heart rate, AMo and stress index during the menstrual cycle with a minimum in the follicular phase and maximum in the luteal phase. The HF and LF components decreased more during the luteal phase than during the follicular phase (p < 0.05), whereas a tendency for increase LF/HF was observed in the luteal phase. In the follicular phase SDNN, pNN50, Mo, MxDMn were significantly higher than in the luteal phase. Furthermore, the VIK was higher in the luteal phase compared to the follicular phase (p = 0.003). Blood pressure did not show any significant change during both these phases of the menstrual cycle. These findings indicate that sympathetic nervous activity in the luteal phase is greater than in the follicular phase, whereas parasympathetic nervous activity is predominant in the follicular phase. A difference of the balance of ovarian hormones may be responsible for these changes of autonomic functions during the menstrual cycle.     

Induced Cotton effects of tRNA-acridine orange complex and tRNA conformation

Circular dichroism spectra of acridine orange bound to E. coli tRNA were studied at varying tRNA phosphate-to-dye (P/D) ratios for both unfractionated and purified materials in the absence of Mg⁺⁺. From the rather discrete features exhibited in the circular dichroism spectra three types of interactions were observed: (1) A high P/D ratio such as 75.2 or 49.8 indicates the interaction between the nucleotide base and dye molecule. The spectra with a large positive peak at 515 mμ are, however, quite different from that of DNA–AO complex under similar conditions. (2) With an intermediate P/D ratio (26.5 to 9.6) dye molecules bound strongly to the polynucleotide chain. (3) With low P/D ratios (≤7.5) the interaction appears to be due to the stacked dye molecules in the single-stranded part of tRNA. The spectra of the third group have an isobestic point at 477 mμ. Below a P/D ratio of 4 the spectrum shows one positive and two negative bands which may be the characteristics of circular dichroism of stacked dyes in polynucleotide chain. Although no drastic change in the conformation of tRNA itself was detectable in the presence of Mg⁺⁺ in the ultraviolet region, a dramatic change was observed in the circular dichroism of tRNA–acridine orange complex when Mg⁺⁺ concentration was increased to 10^?3M. It was inferred that certain conformational changes other than simple hydrogen bond formation occured in tRNA molecules at this high Mg⁺⁺ concentration, so that the amount of bound dye in the stacking condition was increased through the transition.     

Comparison of activity and conformation changes during refolding of urea-denatured creatine kinase

The course of the recovery of the enzymatic activity and the native conformation during the renaturation of urea-denatured creatine kinase (ATP:creatine N-phosphotransferase, EC 2.7.3.2) has been studied. Under suitable conditions, an activity recovery of 95% can be obtained and the reactivation follows a triphasic course. The initial two phases are relatively fast, whereas the slow phase takes some 24 h to reach completion. The recovery of the native conformation has been followed by changes in fluorescence, ultraviolet absorption and in exposed SH groups and has been shown to be a biphasic process. Both the reactivation and the refolding processes are independent of protein concentrations within a certain range, showing that the dimerization of the enzyme molecule is not rate-limiting. A comparison of the rate constants for the refolding of the molecule with those for the recovery of its catalytic activity shows that these are not synchronized and the activity recovery approaches completion after the refolding and dimerization of the subunits so far as can be detected by the methods employed. The final stage of refolding with complete activity recovery probably involves subtle conformational changes of the dimeric enzyme molecule not detectable by the physiochemical methods used in the present study.     

Comparison of different tomato puree production phases from an environmental point of view

The International Journal of Life Cycle Assessment - Agro-food systems are involved with considerable environmental impacts. Tomato as an important vegetable crop is processed into some products...     

Antibodies specific for 1-methylguanosine as a probe of tRNA conformation

Antibodies specific for 1-methylguanosine (m1G) were produced by immunization of rabbits with a bovine serum albumin conjugate of m1G. Antibodies specificity was determined by measuring the inhibition of binding of 3H-m1G trialcohol by various nucleosides or related derivatives. The relative affinities of the unpurified antibodies for various nucleosides showed that m1G trialcohol had an 8-fold higher affinity than m1G; further, guanosine and 2'-O-methylguanosine had at least a 500-fold lower affinity than m1G. The antibodies were purified on m1G-AH-Sepharose column and subsequently immobilized to Sepharose. Immobilized m1G antibodies quantitatively and exclusively retained m1G-containing oligonucleotides derived from ribonuclease A digests of 32P-labeled phage T4 tRNAPro. On the other hand, intact 32P-labeled T4 tRNAPro or its precursor RNA(s) did not bind to the same column. These findings indicate that at least a portion of m1G adjacent to the 3' end of the anticodon in intact T4 tRNAPro is not accessible for antibody binding.     

Intensity-fluctuation spectroscopy and tRNA conformation. II. Changes of size and shape of tRNA in the melting process

We have measured the translational (D^T) and rotational (D^R) diffusion coefficients of bulk tRNA from baker's yeast during the thermal unfolding process by means of photon-correlation spectroscopy. It should be noted that our estimate of the rotational diffusion coefficient represented, for the first time, measurements on a small macromolecule in solution by the photoelectron time-of-arrival technique with a delay-time resolution of 1 nsec. The melting curves expressed in terms of δD^T vs temperature were consistent with the literature data in revealing the melting steps and their dependence on NaCl concentration. Additionally, it was possible to prove the existence of an intermediate, more compact structure during the initial steps of the thermal unfolding process. We found that the temperature ranges over which this intermediate structure appears depend strongly on salt concentration. By utilizing both translational and rotational diffusion coefficients and Perrin's equations for ellipsoids of revolution, we have computed the values of the equivalent length and width of tRNA molecules in solution at four different temperatures for NaCl concentrations of 0.2, 0.5, and 1M. The approximate model of ellipsoids of revolution also permits us to obtain an estimate of the radius of gyration, which is in very good agreement with literature data measured by means of small-angle x-ray scattering. Furthermore, we have measured the shape and size changes of tRNA with varying NaCl concentrations at room temperatures (25°C). The molecule becomes smaller and more spherical when NaCl concentration increases. As a result of partial melting at 70°C, the macromolecule is surprisingly elongated with an approximate axial ratio of 8:1 and has dimensions of about 180/22Å. Such information on conformational changes by a simultaneous determination of rotational and translational diffusion coefficients illustrates the potential of this approach, not available by other methods.     

Cytological and immunocytochemical studies of the anterior pituitary gland of the beagle bitch during various reproduction phases]

The changes in anterior pituitary (AP) of pregnant and lactating dogs as compared with pituitary of animals in metestrus-anestrus phase are described with special reference to the relative proportion, topography and morphology of prolactin cells, somatotrophs, corticotrophs, thyrotrophs and gonadotrophs. For demonstration of these cells, suitable histological, histochemical and immunoenzyme cytochemical methods are used. The prolactin cells show progressive hyperplasia during pregnancy, so that at the end of this phase and during lactation, they comprise the most predominant glandular cells in AP. At the same time, they reveal massive hypertrophy with marked morphological features of high secretory activity, After transient or continous interruption of the suckling stimulus they show signs of functional inhibition on involution. The corticotrophs appear at 20. and 30. days of pregnancy to be relatively increased in number. While in the last third of pregnancy and during lactation, they only seem to be more active than those in pituitary of metestrus-anestrus dogs. The somatotrophs appear to be progressively reduced in relative number during pregnancy and lactation. However, they show some morphological signs of active secretion. The thyrotrophs did not show any morphological alterations during the different reproductive phases. The gonadotrophs reveal during pregnancy, especially at 30. day morphological signs of stimulation. On the contrary they appear atrophied during lactation. This may be a result of suckling stimulus and morphological expression of the inverse relationship in the secretion pattern of gonadotrophins and prolactin in dogs during suckling. The estrogen and progesterone levels in plasma as well as the changes in their relative concentrations may largely account for the structural changes on AP of pregnant dogs. However, neuroendocrine reflexes (e.g. suckling stimulus) seem to be of a great importance for the maintainance of stimulation of prolactin cells during lactation.     

月经周期对女性睡眠-觉醒和静息-活动的影响

目前有关月经周期对睡眠影响的研究结果并不一致,而对月经周期中昼夜睡眠-觉醒及静息-活动节律尚缺乏系统性的研究.本研究旨在观察正常育龄期女性月经周期中睡眠-觉醒及静息-活动昼夜节律的变化.我们采用静息-活动监测仪(actigraphy)和睡眠日志,调查了12个自然生活状态下健康育龄期妇女在月经周期不同阶段,即行经期、围排卵期、黄体早期及黄体晚期中睡眠与活动节律的变化.结果显示,睡眠-觉醒节律参数在四期之间无统计学显著差异;而静息-活动节律方面,所有受试女性静息-活动节律的平均日周期长度为(24.01±0.29)h,并且四期之间无显著性差异.行经期日间稳定系数(interdaily stability,IS)比黄体早期显著增加(P＜0.05).黄体早期日间活动开始时间明显较黄体晚期提前(P＜0.05);黄体早期的活动峰值时相比围排卵期显著提前(P＜0.05).月经周期可以影响静息-活动昼夜节律时相.而总体静息-活动数量与质量未发生显著变化;健康育龄期妇女在月经周期的各阶段中睡眠-觉醒节律亦无明显变异.     

Adrenal catecholamines and related changes during different phases of morphine administration--a histochemical study

(1) Acute morphine treatment of rats reduced the total catecholamine content as well as the noradrenaline content of the adrenal gland. This was accompanied by increased ATPase activity and increased calcium content of the medullary cells. (2) After chronic morphine treatment, the total catecholamine content remained more or less unaltered, but the noradrenaline content was markedly increased together with the noradrenaline-containing areas, in comparison with what was observed in control animals. The ATPase activity of the medullary cells was found to be diminished along with the decreased calcium content. (3) In nalorphine-induced abstinence, a decrease in total catecholamine content together with a reduction of noradrenaline content and of noradrenaline-containing areas were observed. ATPase activity was also found to be increased with increased calcium content.     

The side-by-side model of two tRNA molecules allowing the alpha-helical conformation of the nascent polypeptide during the ribosomal transpeptidation.

Lim and Spirin [25] proposed a preferable conformation of the nascent peptide during the ribosomal transpeptidation. Spirin and Lim [26] excluded the possibilities of the side-by-side model proposed by Johnson et al [13] and the three-tRNA binding model (A, P and E sites) of Rheinberger and Nierhaus [3]. However, a slight conformational change at the 3' end regions of both A and P site tRNA molecules can enable the three different tRNA binding models to converge. With a modification of the angles of the ribose rings of both anticodon and mRNA this model can also be related to the model of Sundaralingam et al [19]. In this model of E coli rRNA the 3' end sequence ACCA76 or GCCA76 of P site tRNA is base-paired to UGGU810 of 23S rRNA, while the ACC75 or GCC75 of A site tRNA are base-paired to GGU1621 23S rRNA. The conformation of the A76 of A site tRNA is necessarily different from that of P site tRNA, at least during the course of the transpeptidation. The A76 of A site tRNA overlaps the binding region of puromycin. The C1400 of 16S rRNA in this model is located at a distance of 4 A from the 5' end of the anticodon of P site tRNA [14] and 17 A from the 5' end of the anticodon of A site tRNA [15]. It is also shown that a considerable but reasonable modification in the conformation of the anticodon loops could lead to accommodation of three deacylated tRNA(Phe) molecules at a time on 70S ribosome in the presence of poly(U) as observed experimentally [6]. A sterochemical explanation for the negatively-linked allosteric interactions between the A and E sites is also shown in the present model.     

Properties of spreading depression during different phases of cyclic excitation of the rat neocortex

Properties of cortical spreading depression were studied during different phases of cyclic excitation developing in the neocortex of rats under the influence of low-frequency electrical stimulation. Waves of spreading depression appeared in the cortex spontaneously or after microinjection of potassium chloride. During each excitation cycle a state preventing the passage and appearance of these waves developed in the region of electrical stimulation. The degree of blocking in other areas of the cortex outside the region of stimulation depended on the distance from the site of electrical stimulation and on generalization of excitatation over the cortex. After the end of the excitation phase, while the current continued to act, the ability of the cortex to conduct the depression wave was restored. In intervals of cyclic excitation the duration of the waves of spreading depression remained on average only half its duration in the absence of stimulation. The time course of development and the character of recovery of depression during the intervals confirm the hypothesis that activation of the potassium-sodium pump may have a role in the blocking mechanism and enable the temporal parameters of this process to be estimated.     

Flow cytometric analysis of the localization of Helicobacter pylori antigens during different growth phases

Previous studies on the localization of several different Helicobacter pylori antigens have been contradictory. We have therefore examined by using both one- and two-color flow cytometry (FCM), immunofluorescence (IF), and immunoelectron microscopy (IEM), the possible surface localization of some H. pylori antigens that may be important virulence factors. All four methods detected the lipopolysaccharide and the N-acetyl-neuroaminyllactose-binding hemagglutinin protein (HpaA) as surface-exposed, while the urease enzyme was not detected at all and the neutrophil activating protein only in low concentration on the surface of the H. pylori bacteria during culture of H. pylori in liquid broth for 11 days. The FCM analysis was found to be quite sensitive and specific and also extremely fast compared with IF and IEM, and therefore the preferred method for detection of surface-localized antigens of H. pylori.     

Conservation of bone marrow CFUc in different phases of the cell cycle during cryopreservation

The effect of low temperature (-196 degrees C) preservation on the recovery of colon-forming units (CFUs) of bone marrow at different phases of the cell cycle before cryopreservation is dealt with. The intact bone marrow "enriched" with CFUs in S phase of the cell cycle and the bone marrow without colony-forming units in S phase were exposed to cryopreservation. After cryopreservation of the bone marrow enriched with CFUs in S phase and th bone marrow without colony-forming units in S phase the number of CFUs decreases by the same value as in the cryopreserved bone marrow obtained from intact mice.     

月经周期不同阶段游离皮质醇昼夜节律的变化

为了研究皮质醇分泌的昼夜节律在月经周期中的变化,实验对15位月经周期正常的育龄期健康妇女,在月经周期的不同阶段分别于24h内每隔两小时采样,检测唾液昼夜游离皮质醇水平。采用非线性回归分析模型分析皮质醇昼夜节律。结果显示,皮质醇昼夜节律在整个月经周期都具有复杂的明显受到亚节律(ultradian)影响的分泌形式;与月经期相比,围排卵期和黄体晚期昼夜节律波峰宽度(peak-width)明显减低(P=0．005与0．031),而昼夜节律波谷(trough)有抬高趋势(P=0．0622与0．066);黄体晚期的亚节律波幅(ultradian amplitude)与月经期相比显著减低(P=0．002)而与围排卵期相比有减低趋势(P=0．05)。这些结果提示月经周期的不同阶段对皮质醇分泌的昼夜节律有影响。