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1.
Mercuric ion interacts with indoles, including tryptophan, to produce complexes whose absorption spectra are broader, less structured, and red-shifted as compared with those of the parent compound. Fluorescence and phosphorescence are totally quenched. In a survey of the effect of transition metal ions on tryptophan fluorescence, the strong quenching by Hg2+ was unique among the uncolored ions. Mercuric nitrate quenched the fluorescence of practically every protein tested, but the sensitivity to quenching varied with the protein. Ovalbumin was the most sensitive to quenching by Hg2+, over 70% of the intrinsic fluorescence being quenched by 2 moles of mercuric ion. Difference absorption spectra show that sulfhydryl groups are attacked by these reagents and Hg2+ is, in addition, perturbing the environment near some tryptophans. In contrast to Hg2+, Zn2+ had negligible effect on protein fluorescence. The emission spectra of proteins which were partly quenched by mercuric ion showed shifts in their maxima to higher or lower wavelengths. This suggests that mercuric ion quenched certain tryptophans more than others, and supports the idea that protein fluorescence is heterogeneous and arises from tryptophans in different microenvironments.  相似文献   

2.
Annexin A5 (AnxA5) binds to negatively charged phospholipid membranes in a Ca2+ dependent manner. Several studies already demonstrate that Mg2+ ions cannot induce the binding. In this paper, quartz crystal microbalance with dissipation monitoring (QCM-D), Brewster angle microscopy (BAM), polarization modulation infrared reflection absorption spectroscopy (PMIRRAS) and molecular dynamics (MD) were performed to elucidate the high specificity of Ca2+ versus Mg2+ on AnxA5 binding to membrane models. In the presence of Ca2+, AnxA5 showed a strong interaction with lipids, the protein is adsorbed mainly in α-helix under the DMPS monolayer, with an orientation of the α-helices axes slightly tilted with respect to the normal of the phospholipid monolayer as revealed by PMIRRAS. The Ca2+ ions interact strongly with the phosphate group of the phospholipid monolayer. In the presence of Mg2+, instead of Ca2+, no interaction of AnxA5 with lipids was detected. Molecular dynamics simulations allow us to explain the high specificity of calcium. Ca2+ ions are well exposed and surrounded by labile water molecules at the surface of the protein, which then favour their binding to the phosphate group of the membrane, explaining their specificity. To the contrary, Mg2+ ions are embedded in the protein structure, with a smaller number of water molecules strongly bound. We conclude that the embedded Mg2+ ions inside the AnxA5 structure are not able to link the protein to the phosphate group of the phospholipids for this reason.  相似文献   

3.
A fluorescence and absorption chemosensor (SAAT) based on 5-(hydroxymethyl)-salicylaldehyde (SA) and o-aminothiophenol (AT) was designed and synthesized. SAAT in DMSO–HEPES (20.0 mM, v/v, 1:99, pH = 7.0) solution shows a highly selective and sensitive absorption and an ‘on–off’ fluorescence response to Cu2+ ions in aqueous solutions over all other competitive metal ions including Na+, Ag+, Ba2+, Ca2+, Cd2+, Mg2+, Zn2+, Cr3+, Al3+, Hg2+, K+, Mn2+, Ni2+, Sr2+, Tb3+ and Co2+. SAAT exhibits ratiometric absorption sensing ability for Cu2+ ions. Importantly, SAAT also can sense Cu2+ ions using fluorescence quenching, the fluorescence intensity of SAAT showed a good linear relationship with Cu2+ concentration, and the detection limit of Cu2+ was 0.34 μM. The results of Job's plot, Benesi–Hildebrand plot, mass spectra, and density functional theory calculations confirmed that the selective absorption and fluorescence response were attributed to the formation of a 1:1 complex between SAAT and Cu2+. SAAT in test film could identify Cu2+ in water samples using the intuitive fluorescence colour change under a UV lamp. SAAT has great application value as a selective and sensitive chemosensor to discriminate and detect Cu2+ ions.  相似文献   

4.
F Mazzei  G Onori 《Biopolymers》1984,23(4):759-766
The uv absorption spectra and melting profiles of an initially ion-free solution of E. coli unfractionated tRNA are significantly modified by the addition of either Na+, Mg2+, or Mn2+ or of other first-series transition-metal ions such as Ni2+, Co2+, and Zn2+. The main effect of the addition of all monovalent or divalent cations examined is an increase of the ordered and stacking stabilized tRNA structure, as revealed by a drop in the absorption near 260 nm, as well as in the 4-TU absorption region. Sharp differences have, however, been detected in the 290–305-nm range in the presence of the various ions studied. When transition-metal ions were added to a tRNA solution, an absorption peak appeared at 294 nm. This effect is interpreted as a perturbation of the electronic structure of the bases due to direct binding of metal ions to the bases. An analysis of the variation in the spectrum as a function of metal concentration and of the thermal melting reversibility in the presence of various metal ions supports the conclusion that while all ions investigated are involved in binding to the phosphate groups of tRNA, transition-metal ions are also able to bind directly to the bases.  相似文献   

5.
A new rhodamine–ethylenediamine–nitrothiourea conjugate (RT) was synthesized and its sensing property as a fluorescent chemodosimeter toward metal ions was explored in water media. Analytical results from absorption and fluorescence spectra revealed that the addition of Hg2+ ions to the aqueous solution of the chemodosimeter RT caused a distinct fluorescence OFF–ON response with a remarkable visual color change from colorless to pink; however, no clear spectral and color changes were observed from other metal ions including: Zn2+, Cu2+, Cd2+, Pb2+, Ag+, Fe2+, Cr3+, Co3+, Ni2+, Ca2+, Mg2+, K+ and Na+. The sensing results and the molecular structure suggested that a Hg2+‐induced a desulfurization reaction and cyclic guanylation of the thiourea moiety followed by ring‐opening of the rhodamine spirolactam in RT are responsible for a distinct fluorescence turn‐on signal, indicating that RT is a remarkably sensitive and selective chemodosimeter for Hg2+ ions in aqueous solution. Hg2+ within a concentration range from 0.1 to 25 μM can be determined using RT as a chemodosimeter and a detection limit of 0.04 μM is achieved. Copyright © 2014 John Wiley & Sons, Ltd.  相似文献   

6.
Heavy metal pollutants such as Cd, Hg, Pb, As, and Se are considered as both a global problem and a growing threat to the humanity. Being strongly poisonous to the metal-sensitive enzymes and leading to the growth inhibition and death of organisms, these metals have a toxic impact on the plants and animals. Inducing the metal-binding cysteine-rich peptides such as metallothioneins, phytochelatins, and defensins, higher organisms like plants and animals usually react to the heavy metal stress. In this study, a recombinant defensin protein was expressed in bean and its ability in the cadmium absorption was determined. Experimental studies revealed that this protein was able to absorb cadmium ions in reduced form more than oxide one. Molecular dynamics simulations were carried out in order to evaluation of experimental studies, using a model of Cd2+ or Na+ and Cl ions enclosed in a fully hydrated simulation box with the recombinant defensin. The theoretical results also suggested that the reduced recombinant defensin was more powerful in the absorption of Cd2+ than its oxide form. The present study is the first report of Cd2+ absorption potential of this new reduced recombinant defensin. The results unraveled that this recombinant defensin can be adopted as a molecular switch in the cadmium pollution of the environment and also the important role of sulfur groups in the absorption of cadmium ions.  相似文献   

7.
The improved Cd2+ surface affinity characteristics of a mutated cyanobacterial metallothionein SmtA (K45C) were investigated via experimental and theoretical methods. Molecular dynamics simulations were carried out using a model of Cd2+ and other ions enclosed in a fully hydrated simulation box with the wild-type or mutated SmtA protein. The theoretical results suggested that mutated SmtA was more powerful in absorption of Cd2+ than the wild-type protein. Then, the mutated smtA gene (from Synechococcus PCC 7942) was synthesized by simplified gene synthesis method and expressed on isopropyl-beta-d-thiogalactopyranoside induction. The protein expression was investigated by SDS-PAGE and verified by Western blotting. Finally, cadmium uptake ratio of mutant protein toward wild type was analyzed by atomic absorption. This study is the first example of cytoplasmic expression of a mutant protein. Experimental results also verified that the mutation intensifies uptake of Cd2+ ions.  相似文献   

8.
《Biophysical journal》2021,120(23):5322-5332
The electrostatic interaction of RNA with its aqueous environment is most relevant for defining macromolecular structure and biological function. The attractive interaction of phosphate groups in the RNA backbone with ions in the water environment leads to the accumulation of positively charged ions in the first few hydration layers around RNA. Electrostatics of this ion atmosphere and the resulting ion concentration profiles have been described by solutions of the nonlinear Poisson-Boltzmann equation and atomistic molecular dynamics (MD) simulations. Much less is known on contact pairs of RNA phosphate groups with ions at the RNA surface, regarding their abundance, molecular geometry, and role in defining RNA structure. Here, we present a combined theoretical and experimental study of interactions of a short RNA duplex with magnesium (Mg2+) ions. MD simulations covering a microsecond time range give detailed hydration geometries as well as electrostatics and spatial arrangements of phosphate-Mg2+ pairs, including both pairs in direct contact and separated by a single water layer. The theoretical predictions are benchmarked by linear infrared absorption and nonlinear two-dimensional infrared spectra of the asymmetric phosphate stretch vibration which probes both local interaction geometries and electric fields. Contact pairs of phosphate groups and Mg2+ ions are identified via their impact on the vibrational frequency position and line shape. A quantitative analysis of infrared spectra for a range of Mg2+-excess concentrations and comparison with fluorescence titration measurements shows that on average 20–30% of the Mg2+ ions interacting with the RNA duplex form contact pairs. The experimental and MD results are in good agreement. In contrast, calculations based on the nonlinear Poisson-Boltzmann equation fail in describing the ion arrangement, molecular electrostatic potential, and local electric field strengths correctly. Our results underline the importance of local electric field mapping and molecular-level simulations to correctly account for the electrostatics at the RNA-water interface.  相似文献   

9.
The alkaline phosphatase (EC 3.1.3.1.) from Rhizobium leguminosarum WU235 has been purified. The enzyme is a non-specific phosphomonoesterase, has a molecular weight of 78,500 and a sub-unit molecular weight of 39,400. Magnesium and zinc ions are implicated in the structure of the enzyme; atomic absorption analysis gave 1.9 g-atoms Mg2+ and 1.9–5.1 g-atoms Zn2+ per mole of enzyme. In addition high concentrations of Mg2+ markedly stimulate the enzyme. The phosphatase is inhibited by Li+ and Na+ and stimulated by K+, Rb+ and Cs+, which suggests that the enzyme is K+ activated.  相似文献   

10.
We study numerically the local dynamics of the intracellular calcium concentration in the vicinity of a voltage- and calcium-dependent plasma membrane L-type calcium channel. To account for the low number of Ca2+ ions and buffer molecules present in sub-femtoliter volumes, we use an exact stochastic simulation algorithm including diffusion. We present a novel, unified simulation method that implements reaction-diffusion events of Ca2+ ions and buffer molecules, stochastic ion channel gating and channel conductance as a multivariate Markov process. For fixed-voltage dynamics, e.g. under voltage-clamp conditions, it is shown that voltage-sensitive channel-gating steps can be incorporated exactly. We compare multi- and single-voxel geometries and show that the single-voxel approach leads to almost identical first- and second-order moments, at much lower computation time. Numerical examples illustrate the variability in local Ca2+ fluctuations as induced by bursts of channel openings in response to membrane depolarisations. Finally, by introducing calmodulin as a link, it is shown how this variability is passed on to downstream signalling pathways. The method may prove useful to study calcium microdomains and calcium-regulated processes triggered by membrane depolarisations as evoked by, e.g., viral channel-forming proteins during virus-host cell interactions.  相似文献   

11.
Ca2+-ATPases are membrane pumps that transport calcium ions across the cell membrane and are dependent on ATP. The mechanism of Listeria monocytogenes Ca2+-ATPase (LMCA1) in its native environment remains incompletely understood. LMCA1 has been investigated biochemically and biophysically with detergents in the past. This study characterizes LMCA1 using the detergent-free Native Cell Membrane Nanoparticles (NCMNP) system. As demonstrated by ATPase activity assays, the NCMNP7-25 polymer is compatible with a broad pH range and Ca2+ ions. This result suggests that NCMNP7-25 may have a wider array of applications in membrane protein research.  相似文献   

12.
About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. In this study, we used molecular dynamics (MD) simulations to investigate whether a cognate metal (bound to the structure) can be replaced with other similar metal ions. We have chosen seven different proteins (phospholipase A2, sucrose phosphatase, pyrazinamidase, cysteine dioxygenase (CDO), plastocyanin, monoclonal anti-CD4 antibody Q425, and synaptotagmin 1 C2B domain) bound to seven different divalent metal ions (Ca2+, Mg2+, Zn2+, Fe2+, Cu2+, Ba2+, and Sr2+, respectively). In total, 49 MD simulations each of 50 ns were performed and each trajectory was analyzed independently. Results demonstrate that in some cases, cognate metal ions can be exchanged with similar metal ions. On the contrary, some proteins show binding affinity specifically to their cognate metal ions. Surprisingly, two proteins CDO and plastocyanin which are known to bind Fe2+ and Cu2+, respectively, do not exhibit binding affinity to any metal ion. Furthermore, the study reveals that in some cases, the active site topology remains rigid even without cognate metals, whereas, some require them for their active site stability. Thus, it will be interesting to experimentally verify the accuracy of these observations obtained computationally. Moreover, the study can help in designing novel active sites for proteins to sequester metal ions particularly of toxic nature.  相似文献   

13.
The stability of RNA tertiary structures depends heavily on Mg2+. The Mg2+-RNA interaction free energy that stabilizes an RNA structure can be computed experimentally through fluorescence-based assays that measure Γ2+, the number of excess Mg2+ associated with an RNA molecule. Previous explicit-solvent simulations predict that the majority of excess Mg2+ ions interact closely and strongly with the RNA, unlike monovalent ions such as K+, suggesting that an explicit treatment of Mg2+ is important for capturing RNA dynamics. Here we present a reduced model that accurately reproduces the thermodynamics of Mg2+-RNA interactions. This model is able to characterize long-timescale RNA dynamics coupled to Mg2+ through the explicit representation of Mg2+ ions. KCl is described by Debye-Hückel screening and a Manning condensation parameter, which represents condensed K+ and models its competition with condensed Mg2+. The model contains one fitted parameter, the number of condensed K+ ions in the absence of Mg2+. Values of Γ2+ computed from molecular dynamics simulations using the model show excellent agreement with both experimental data on the adenine riboswitch and previous explicit-solvent simulations of the SAM-I riboswitch. This agreement confirms the thermodynamic accuracy of the model via the direct relation of Γ2+ to the Mg2+-RNA interaction free energy, and provides further support for the predictions from explicit-solvent calculations. This reduced model will be useful for future studies of the interplay between Mg2+ and RNA dynamics.  相似文献   

14.
The stability of RNA tertiary structures depends heavily on Mg2+. The Mg2+-RNA interaction free energy that stabilizes an RNA structure can be computed experimentally through fluorescence-based assays that measure Γ2+, the number of excess Mg2+ associated with an RNA molecule. Previous explicit-solvent simulations predict that the majority of excess Mg2+ ions interact closely and strongly with the RNA, unlike monovalent ions such as K+, suggesting that an explicit treatment of Mg2+ is important for capturing RNA dynamics. Here we present a reduced model that accurately reproduces the thermodynamics of Mg2+-RNA interactions. This model is able to characterize long-timescale RNA dynamics coupled to Mg2+ through the explicit representation of Mg2+ ions. KCl is described by Debye-Hückel screening and a Manning condensation parameter, which represents condensed K+ and models its competition with condensed Mg2+. The model contains one fitted parameter, the number of condensed K+ ions in the absence of Mg2+. Values of Γ2+ computed from molecular dynamics simulations using the model show excellent agreement with both experimental data on the adenine riboswitch and previous explicit-solvent simulations of the SAM-I riboswitch. This agreement confirms the thermodynamic accuracy of the model via the direct relation of Γ2+ to the Mg2+-RNA interaction free energy, and provides further support for the predictions from explicit-solvent calculations. This reduced model will be useful for future studies of the interplay between Mg2+ and RNA dynamics.  相似文献   

15.
The current work presents a conformational evaluation of heparinase II (hepII) from Pedobacter heparinus, employing molecular dynamics (MD) simulations, in order to characterize the main features of the enzyme dynamics, as well as the role of the glycan and metal components on the protein scaffold. Accordingly, four systems were simulated, encompassing nonglycosylated hepII without structural ions, nonglycosylated hepII with Zn2+, nonglycosylated hepII with Ca2+, and glycosylated hepII with Zn2+. The obtained data suggest a role for Zn2+ in modulating the protein flexibility at specific loop regions. Such flexibility pattern is not properly maintained in the absence of such structural ion or when the ion is replaced by Ca2+. Still, semiempirical calculations suggest more favorable interactions with Zn2+. These events correlate with the experimentally reported inhibitory effect of calcium over hepII. Additionally, the glycan chain seems able to promote an additional stabilization on hepII dynamics. Taken together, these results improve our understanding of the structural and dynamical features of hepII, as well as atomic-level comprehension of previous experimental data.  相似文献   

16.
Emission Mössbauer spectra and Perturbed Angular Correlation measurements have been performed on samples of mineral bone powder labelled with 161Tb ou 3+ or 133Ba2+ ions after either in vitro absorption or uptake by metabolic pathway. The study of these hyperfine spectra, compared with those carried out when 161Tb or 133Ba are situated in either hydroxyde lattice or phosphate one, shows that the uptake modes of rare-and alkaline-earth ions on the bone matrix are different. The rare earth ion seems to be adsorbed on the surface bone in an environment of hydroxyl groups similar to the structure of a rare earth hydroxyde. The alkaline earth ion bone uptake appears more complicated and would make according to the following process: at first, surface adsorption on the hydroxylapatite in a hydroxyde environment and then cationic exchange with the calcium phosphate groups into bone crystals.  相似文献   

17.
The effect of equimolar concentrations of Hg2+ and Cd2+ on the whole cell absorption spectra, absorption spectra of the extracted phycocyanin (PC) and fluorescence emission spectra of phycobilisomes (PBS) was investigated in the cells of Anabaena flos-aquae. The PC component of the PBS was found to be extremely sensitive to the Hg2+ rather than the Cd2+ ions. Further, the results showed that Hg2+ and Cd2+ induced decrease in the rate of Hill activity (H2O - DCPIP) was partially restored by the electron donor NH2OH, not by the diphenyl carbazide. Similarly, chlorophyll a fluorescence emission in the presence of metals showed that addition of NH2OH could effectively reverse the metal induced alterations in the fluorescence emission intensity. These results, together, suggested that Hg2+ and Cd2+ caused damage to the photosystems (PS) II reaction center. However, a relatively higher stimulation of the chlorophyll a emission at 695 nm with a red shift of 4.0 nm in the presence of Hg2+, and Cd2+ induced preferential decrease in the emission intensity at 676 nm as compared with the peak at 695 nm were indicative of the differential action of Hg2+ and Cd2+ on the PS II.  相似文献   

18.
In this study, we numerically analyzed the nonlinear Ca2+-dependent gating dynamics of a single, nonconducting inositol 1,4,5-trisphosphate receptor (IP3R) channel, using an exact and fully stochastic simulation algorithm that includes channel gating, Ca2+ buffering, and Ca2+ diffusion. The IP3R is a ubiquitous intracellular Ca2+ release channel that plays an important role in the formation of complex spatiotemporal Ca2+ signals such as waves and oscillations. Dynamic subfemtoliter Ca2+ microdomains reveal low copy numbers of Ca2+ ions, buffer molecules, and IP3Rs, and stochastic fluctuations arising from molecular interactions and diffusion do not average out. In contrast to models treating calcium dynamics deterministically, the stochastic approach accounts for this molecular noise. We varied Ca2+ diffusion coefficients and buffer reaction rates to tune the autocorrelation properties of Ca2+ noise and found a distinct relation between the autocorrelation time τac, the mean channel open and close times, and the resulting IP3R open probability PO. We observed an increased PO for shorter noise autocorrelation times, caused by increasing channel open times and decreasing close times. In a pure diffusion model the effects become apparent at elevated calcium concentrations, e.g., at [Ca2+] = 25 μM, τac = 0.082 ms, the IP3R open probability increased by ≈20% and mean open times increased by ≈4 ms, compared to a zero noise model. We identified the inactivating Ca2+ binding site of IP3R subunits as the primarily noise-susceptible element of the De Young and Keizer model. Short Ca2+ noise autocorrelation times decrease the probability of Ca2+ association and consequently increase IP3R activity. These results suggest a functional role of local calcium noise properties on calcium-regulated target molecules such as the ubiquitous IP3R. This finding may stimulate novel experimental approaches analyzing the role of calcium noise properties on microdomain behavior.  相似文献   

19.
This pilot study presents preliminary results on interrelations between alkali and alkaline earth elements during their transfer to mycelium and fruitbodies of saprophytic fungi. The accumulation and distribution of four elements (cesium, potassium, sodium, and calcium) was evaluated in king oyster mushroom (Pleurotus eryngii) cultivated under controlled conditions. Elemental composition of caps, stipes, and the substrate was analyzed by atomic absorption/emission spectroscopy to evaluate discrimination, concentration, and transfer factors. The transfer factors determined for all the investigated elements were different and can be put in the following order: Cs > K > Na > Ca. There has been a higher accumulation of cesium in caps than in stipes. Distribution of cesium in fruitbodies depended on the presence of other ions in the substrate. The addition of Ca2+ limited the transport of cesium and potassium from stipes to caps. Sodium and calcium were mainly accumulated in the stipes. In a control experiment, without supplementation with K+, Na+, and Ca2+, ~ 62% of the cesium present in the substrate was extracted by mycelium and transported to the fruitbodies. Possible applications of fruiting saprophytic fungi in bioremediation are discussed.  相似文献   

20.
《Plant science》1986,43(1):51-56
Analysis of the pH 8.3 electrophoresis of the Phaseolus vulgaris seed lectins suggests that each of the five isolectins exists in five different forms. Incubations of the lectins in the presence of EDTA or of metal ions such as Mn2+, Mg2+, Co2+ and Ni2+ shows that their different electrophoretic behaviours are related to the binding of metal ions to the molecules.Determinations of the isolectin metal content by atomic absorption measurements demonstrate that at pH 8.3 their five electrophoretic forms are related to the number of subunits (0, 1, 2, 3 or 4) which contain metal ions in the tetrameric molecules.  相似文献   

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