Confined dynamics of a ribosome‐bound nascent globin: Cone angle analysis of fluorescence depolarization decays in the presence of two local motions

We still know very little about how proteins achieve their native three‐dimensional structure in vitro and in the cell. Folding studies as proteins emerge from the mega Dalton‐sized ribosome pose special challenges due to the large size and complicated nature of the ribosome‐nascent chain complex. This work introduces a combination of three‐component analysis of fluorescence depolarization decays (including the presence of two local motions) and in‐cone analysis of diffusive local dynamics to investigate the spatial constraints experienced by a protein emerging from the ribosomal tunnel. We focus on E. coli ribosomes and an all‐α‐helical nascent globin in the presence and absence of the cotranslationally active chaperones DnaK and trigger factor. The data provide insights on the dynamic nature and structural plasticity of ribosome‐nascent chain complexes. We find that the sub‐ns motions of the N‐terminal fluorophore, reporting on the globin dynamics in the vicinity of the N terminus, are highly constrained both inside and outside the ribosomal tunnel, resulting in high‐order parameters (>0.85) and small cone semiangles (<30°). The shorter globin chains buried inside the tunnel are less spatially constrained than those of a reference sequence from a natively unfolded protein, suggesting either that the two nascent chain sequences have a different secondary structure and therefore sample different regions of the tunnel or that the tunnel undergoes local structural adjustments to accommodate the globin sequence. Longer globins emerging out of the ribosomal tunnel are also found to have highly spatially constrained slow (ns) motions. There are no observable spectroscopic changes in the absence of bound chaperones.     

IMPROVED METHODS FOR THE ISOLATION OF CYANOBACTERIAL DNA FROM ENVIRONMENTAL SAMPLES1

DNA isolated from environmental samples often contains enzyme inhibitors disruptive to downstream molecular applications. Most of the existing methods of cyanobacterial DNA isolation do not effectively eliminate these inhibitors from sediment samples or cells collected from freshwater ecosystems. We describe improved methods based on the xanthogenate‐SDS nucleic acid isolation (XS) method of Tillett and Neilan (2000) . Our improved methods provided high‐quality cyanobacterial DNA that could be amplified in PCR and digested with a restriction enzyme. Results were superior to several commercial kits. The DNA yield was also similar to that obtained via the standard XS method. These methods should provide valuable new tools for the expanded application of molecular genetics to limnological and oceanographic research.     

Distinct conformational changes in activated agonist-bound and agonist-free glycine receptor subunits

Ligand binding to Cys-loop receptors produces either global conformational changes that lead to activation or local conformational changes that do not. We found that the fluorescence of a fluorophore tethered to R271C in the extracellular M2 region of the α1 glycine receptor increases during glycine activation but not during ivermectin activation. This prompted the hypothesis that this signal reports a glycine-mediated conformational change not essential for activation. We tested this by investigating whether the fluorescence signal depended on whether the fluorophore was attached to a glycine-free or a glycine-bound subunit. Agonist-free subunits were created by incorporating T204A and R65K mutations, which disrupted glycine binding to both (+) and (−) subunit interfaces. In heteromeric receptors comprising wild-type and R65K,T204A,R271C triple-mutant subunits, the fluorescence response exhibited a drastically reduced glycine sensitivity relative to the current response. Two conclusions can be drawn from this. First, because the labeled glycine-free subunits were activated by glycine binding to neighboring wild-type subunits, our results provide evidence for a cooperative activation mechanism. However, because the fluorescent label on glycine-free subunits does not reflect movements at the channel gate, we conclude that glycine binding also produces a local non-concerted conformational change that is not essential for receptor activation.     

Inhibition of photosystem II photochemistry by Cr is caused by the alteration of both D1 protein and oxygen evolving complex

The effect of chromium (Cr) on photosystem II (PSII) electron transport and the change of proteins content within PSII complex were investigated. When Lemna gibba was exposed to Cr during 96 h, growth inhibition was found to be associated with an alteration of the PSII electron transport at both PSII oxidizing and reducing sides. Investigation of fluorescence yields at transients K, J, I, and P suggested for Cr inhibitory effect to be located at the oxygen-evolving complex and Q_A reduction. Those Cr-inhibitory effects were related to the change of the turnover of PSII D1 protein and the alteration of 24 and 33 kDa proteins of the oxygen-evolving complex. The inhibition of the PSII electron transport and the formation of reactive oxygen species induced by Cr were highly correlated with the decrease in the content of D1 protein and the amount of 24 and 33 kDa proteins. Therefore, functional alteration of PSII activity by Cr was closely related with the structural change within PSII complex.     

In situ measured seasonal variations in F v/F m of two common Red Sea corals

Pulse amplitude modulated (PAM) fluorometry has been suggested as a tool for estimating environmental stresses on corals. However, information regarding natural changes in maximal quantum yields (F _v/F _m) of corals during “normal” (i.e. non-bleaching) years has been limited. In this study, seasonal variations in F _v/F _m for Stylophora pistillata and Favia favus, measured in situ, correlated with seasonal changes in solar irradiance but not in sea temperature. Interactions between sea temperature and irradiance were further studied by growing these corals and Pocillopora damicornis under controlled conditions. Exposure to high light with normal or high temperatures resulted in lower F _v/F _m values than exposure to low light at both temperatures. Thus, high irradiances may cause decreased F _v/F _m values in corals at least as much as, if not more than, high temperatures. Such seasonal variations should be taken into account when using PAM fluorometry as a diagnostic tool for predicting coral bleaching.     

Ozone foliar symptoms in woody plant species assessed with ultrastructural and fluorescence analysis

This paper compares the responses to ozone in five woody species: Fagus sylvatica (FS), Acer pseudoplatanus (AP), Fraxinus excelsior (FE), Viburnum lantana (VL) and Ailanthus altissima (AA). The hypothesis being tested was that the strategies that plants adopt to resist oxidative pressure are species-specific. The study was carried out on field grown plants in an area in Northern Italy characterized by elevated levels of ozone pollution. The observations were made both at ultrastructural (using light and electronic microscopy) and physiological (using chlorophyll a transient fluorescence and microspectral fluorometry) level. Common responses were: the hypersensitive response (i.e. the death of palisade mesophyll cells) and the formation of callose layers separating injured from healthy cells. FS and AP were capable of thickening the palisade mesophyll cell walls. This thickening process involved changes in cell wall chemical structure, evidenced by the accumulation of yellow autofluorescence compounds. Species-specific behaviours were observed with the fluorescence analysis, with special reference to the photochemical de-excitation constant (Kp). This value increased in FE and AP, and decreased in AA. The observed responses are interpreted as adaptative strategies against the ozone stress. The increase of Kp indicates that the reaction centres were working as more effective quenchers.     

Protective effects of antioxidative serotonin derivatives isolated from safflower against postischemic myocardial dysfunction

N-(p-Coumaroyl)serotonin (C) and N-feruroylserotonin (F) with antioxidative activity are present in safflower oil. The protective effects of C and F were investigated in perfused guinea-pig Langendorff hearts subjected to ischemia and reperfusion. Changes in cellular levels of high phosphorous energy, NO and Ca²⁺ in the heart together with simultaneous recordings of left ventricular developed pressure (LVDP) were monitored by an nitric oxide (NO) electrode, fluorometry and ³¹P-NMR. The rate of recovery of LVDP from ischemia by reperfusion was 30.8% in the control, while in the presence of C or F a gradual increase to 63.2 or 61.0% was observed. Changes of transient NO signals (T_NO) released from heart tissue in one contraction (LVDP) were observed to be upside-down with respect to transient fura-2-Ca²⁺ signals (T_Ca) and transient O₂ signals detected with a pO₂ electrode. At the final stage of ischemia, the intracellular concentration of Ca²⁺ ([Ca²⁺]_i) and the release of NO increased with no twitching and remained at a high steady level. The addition of C increased the NO level at the end of ischemia compared with the control, but [Ca²⁺]_i during ischemia decreased. On reperfusion, the increased diastolic level of T_Ca and T_NO returned rapidly to the control level with the recovery of LVDP. By in vitro EPR, C and F were found to directly quench the activity of active radicals. Therefore, it is concluded that the antioxidant effects of two derivatives isolated from safflower play an important role in ischemia-reperfusion hearts in close relation with NO.     

Interspecific differences in the response of juvenile stages to physical stress: fluorometric responses of fucoid embryos to variation in meteorological conditions1

Chl fluorescence during and immediately after low tide under four meteorological conditions was measured in embryos of three fucoid algae [Ascophyllum nodosum (L.) Le Jol., Fucus vesiculosus L., and Fucus distichus subsp. edentatus Bach. (Pyl.) H. T. Powell] vertically distributed in the intertidal zone in Québec, Canada. Artificial substrata with attached embryos of each species were outplanted into each zone and into two different microhabitats: under and outside an adult canopy. Several fluorescence measurements were made using pulse‐amplitude‐modulated (PAM) fluorometry, from which maximum quantum yield (F_v/F_m), effective quantum yield (φ_PSII), relative electron transport rate (rETR), and nonphotochemical quenching (NPQ) were calculated. F_v/F_m, φ_PSII, and rETR decreased, and NPQ increased during low tide, most rapidly under the most desiccating meteorological conditions (i.e., sunny‐windy weather). The species occurring lowest in the vertical distribution, F. distichus subsp. edentatus, was the most affected, and the two highest species, A. nodosum and F. vesiculosus, only rarely differed. Tidal height itself also influenced the decline in fluorescence parameters, with more gradual declines in lower zones, except under the least desiccating conditions (i.e., cloudy‐calm weather). Recovery upon reimmersion was rapid in all circumstances. Under a canopy, decreases in maximum and effective quantum yields were more gradual than in exposed locations. Although the young stages of these species were affected by physical conditions experienced during low tide and their exact response depended on the precise meteorological conditions, differences in responses among species were surprisingly small. The abilities of young stages to withstand aerial conditions were, however, consistent with the zonation patterns of adults, and conditions under an adult canopy offered some protection.     

Influence of linker unit on performance of palladium(II) coproporphyrin labelling reagent and its bioconjugates

In this paper we describe the preparation of a series of new phosphorescent labelling reagents, based on monosubstituted palladium(II) coproporphyrin‐I and the isothiocyanato reactive group. The labelling reagents differ with respect to the chemical composition of the linker unit that combines the reactive group and the porphyrin chromophore. Altogether, seven different labelling reagents are prepared. The new labelling reagents are conjugated with monoclonal mouse IgG to yield label conjugates with variable degrees of conjugation. The effect is studied of linker unit on: (a) the conjugation reaction kinetics; (b) the biological activity of the resulting IgG conjugates; and (c) the efficiency of phosphorescence emission. The results show that an increase in the length of the linker unit has a positive effect on both the reactivity of the label and the biological activity of the resulting conjugates. In addition, the results indicate that the labels with the most hydrophilic linker units exhibit the highest phosphorescence emission efficiencies. Copyright © 2003 John Wiley & Sons, Ltd.     

荧光膜片钳新技术的应用及进展

荧光膜片钳(patch-clamp fluorometry,PCF)是将离子通道蛋白局部的构象变化和门控紧密结合,实时记录同一膜片上离子通道的荧光和电流信号的创新型生物物理学技术,其特点是将经典的膜片钳和现代光学记录结合起来,实时同步完美呈现离子通道执行其功能时的蛋白质构象信息.与研究结构的X射线和冰冻电镜不同,荧光膜片钳提供离子通道处于真实细胞膜生理环境并执行功能的实时动态结构信息.随着新的光学技术、显微成像技术、图像分析技术等的进步,大大地扩展了荧光膜片钳技术的记录范围、分辨精度及敏感度,使研究者以前所未有的时空分辨率来实时观察和记录离子通道蛋白的结构变化.