Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit

In bacteria, the binding between the riboswitch aptamer domain and ligand is regulated by environmental cues, such as low Mg²⁺ in macrophages during pathogenesis to ensure spatiotemporal expression of virulence genes. Binding was investigated between the flavin mononucleotide (FMN) riboswitch aptamer and its anionic ligand in the presence of molecular crowding agent without Mg²⁺ ion, which mimics pathogenic conditions. Structural, kinetic, and thermodynamic analyses under the crowding revealed more dynamic conformational rearrangements of the FMN riboswitch aptamer compared to dilute Mg²⁺‐containing solution. It is hypothesized that under crowding conditions FMN binds through an induced fit mechanism in contrast to the conformational selection mechanism previously demonstrated in dilute Mg²⁺solution. Since these two mechanisms involve different conformational intermediates and rate constants, these findings have practical significance in areas such as drug design and RNA engineering.     

Direct Observation of Ca2+‐Induced Calmodulin Conformational Transitions in Intact Xenopus laevis Oocytes by 19F NMR Spectroscopy

The Ca²⁺‐mediated conformational transition of the protein calmodulin (CaM) is essential to a variety of signal transduction pathways. Whether the transition in living cells is similar to that observed in buffer is not known. Here, we report the direct observation by ¹⁹F NMR spectroscopy of the transition of the Ca²⁺‐free and ‐bound forms in Xenopus laevis oocytes at different Ca²⁺ levels. We find that the Ca²⁺‐bound CaM population increased greatly upon binding the target protein myosin light‐chain kinase (MLCK) at the same Ca²⁺ level. Paramagnetic NMR spectroscopy was also exploited for the first time to obtain long‐range structural constraints in cells. Our study shows that ¹⁹F NMR spectroscopy can be used to obtain long‐range structural constraints in living eukaryotic cells and paves the way for quantification of protein binding constants.     

Mobility Study of Individual Residue Sites in the Carbohydrate Recognition Domain of LSECtin Using SDSL–EPR Technique

Conformational changes in proteins profoundly influence their functional profiles. With site-directed spin labeling (SDSL)?Celectron paramagnetic resonance (EPR) spectroscopy, we investigated the mobility features of individual residue sites in the carbohydrate recognition domain (CRD) of LSECtin, a type II integral membrane protein. The mobility of six different residue sites scatting around the Ca²⁺-1-binding site were investigated by comparing their EPR spectra rotational correlation time ?? _c in order to obtain the information of conformational changes of relevant region. The results showed that the overall mobility of LSECtin-CRD increased after addition of Ca²⁺ and N-acetylglucosamine, but different sites in the CRD exhibited different mobility features, suggesting that these sites may have different functional profiles. The preliminary observations thus demonstrated that SDSL?CEPR spectroscopy is not only an effective technique to reveal the mobility of single residue sites in LSECtin-CRD but also that the functions of single residue sites may be indicated by their conformational dynamics.     

Removing coordinated metal ions from proteins: a fast and mild method in aqueous solution

Thermodynamic and kinetic studies of metal binding to proteins require the investigation of metal-free proteins, which are often difficult to obtain. We have developed a very fast and mild method to eliminate metal ions from proteins by column chromatography using a commercially available Ni-NTA-type stationary phase. This material, initially designed for protein purification purposes in biotechnology, acts as a strong cation chelator when Ni²⁺ ions are removed. We have tested this new method with Ca-ATPase, an integral membrane protein exhibiting a strong affinity for Ca²⁺. By eluting the protein over the Ni²⁺-free NTA gel, we could remove 95% of the total Ca²⁺ and obtain an essentially Ca²⁺-free protein. This method is efficient with only a small amount of NTA gel, and we suggest that it can be applied in general for removal of metal ions from proteins. Moreover, as this procedure can be carried out under mild conditions, the chosen protein kept its enzymatic activity.     

Metal‐Mediated Self‐Assembly of a β‐Sandwich Protein

The β‐sandwich cupredoxin Plastocyanin (Pc) was found to self‐assemble in the presence of Zn²⁺, a known mediator of protein–protein interfaces. Diffraction‐quality crystals of Pc grew from solutions containing zinc acetate as the sole precipitant. Di‐ and trinuclear zinc sites contribute to the crystal contacts in this structure. A different crystal form, also involving numerous zinc bridging ions, was obtained in the presence of poly(ethylene glycol) 8 000. Comparison of the two crystal forms reveals the effect of macromolecular crowding on self‐assembly. Solution‐state structural characterisation of the Zn²⁺‐mediated Pc oligomers was performed by using a combination of chemical shift perturbation mapping and small‐angle X‐ray scattering. The data indicate the formation of dimers in solution. The implications for metal‐mediated assembly and crystallisation are discussed.     

W2466.48 Opens a Gate for a Continuous Intrinsic Water Pathway during Activation of the Adenosine A2A Receptor

The question how G‐protein‐coupled receptors transduce an extracellular signal by a sequence of transmembrane conformational transitions into an intracellular response remains to be solved at molecular detail. Herein, we use molecular dynamics simulations to reveal distinct conformational transitions of the adenosine A_2A receptor, and we found that the conserved W246^6.48 residue in transmembrane helix TM6 performs a key rotamer toggle switch. Agonist binding induces the sidechain of W246^6.48 to fluctuate between two distinct conformations enabling the diffusion of water molecules from the bulk into the center of the receptor. After passing the W246^6.48 gate, the internal water molecules induce another conserved residue, Y288^7.53, to switch to a distinct rotamer conformation establishing a continuous transmembrane water pathway. Further, structural changes of TM6 and TM7 induce local structural changes of the adjacent lipid bilayer.     

Exposure of hydrophobic sites in CA2+-binding proteins: Influence on chromatographic properties and structure-function relationships

Calmodulin and related Ca²⁺ -binding proteins were characterized using different labeling, chromatographic and spectroscopic techniques. Ca²⁺-binding to members of the so-called “EF-hand”- or “helix-loop-helix”-model protein family induced conformational changes, thereby exposing hydrophobic sites in some of them. These sites were identified using the photoreactive, carbene-generating, radioactive probe 3-(trifluoromethyl)-3-(m-[¹²⁵1]iodophenyl)diazirine, and characterized using different high performance liquid chromatography techniques. The influence of chemical modification of some of the amino acid residues on the properties of calmodulin were characterized using circular dichroism. A correlation between an increase of oxidized methionine residues of calmodulin and a decrease of Ca²⁺-induced helical content was observed.     

Gold Nanorods as Contrast Agents for Biological Imaging: Optical Properties,Surface Conjugation and Photothermal Effects†

Gold nanorods (NRs) have plasmon‐resonant absorption and scattering in the near‐infrared (NIR) region, making them attractive probes for in vitro and in vivo imaging. In the cellular environment, NRs can provide scattering contrast for darkfield microscopy, or emit a strong two‐photon luminescence due to plasmon‐enhanced two‐photon absorption. NRs have also been employed in biomedical imaging modalities such as optical coherence tomography or photoacoustic tomography. Careful control over surface chemistry enhances the capacity of NRs as biological imaging agents by enabling cell‐specific targeting, and by increasing their dispersion stability and circulation lifetimes. NRs can also efficiently convert optical energy into heat, and inflict localized damage to tumor cells. Laser‐induced heating of NRs can disrupt cell membrane integrity and homeostasis, resulting in Ca²⁺ influx and the depolymerization of the intracellular actin network. The combination of plasmon‐resonant optical properties, intense local photothermal effects and robust surface chemistry render gold NRs as promising theragnostic agents.     

Mercuric ions induced aggregation of gold nanoparticles as investigated by localized surface plasmon resonance light scattering and dynamic light scattering techniques

With the development of nanosciences, both localized surface plasmon resonance light scattering (LSPR-LS) and dynamic light scattering (DLS) techniques have been widely used for quantitative purposes with high sensitivity. In this contribution, we make a comparison of the two light scattering techniques by employing gold nanoparticles (AuNPs) aggregation induced by mercuric ions. It was found that citrate-stabilized AuNPs got aggregated in aqueous medium in the presence of mercuric ions through a chelation process, resulting in greatly enhanced LSPR-LS signals and increased hydrodynamic diameter. The enhanced LSPR-LS intensity ( I) is proportional to the concentration of mercuric ions in the range of 0.4-2.5 M following the linear regression equation of I = 84.7+516.4c, with the correlation coefficient of 0.983 (n = 6) and the limit of determination (3 ) about 0.10 M. On the other hand, the increased hydrodynamic diameter can be identified by the DLS signals only with a concentration of Hg 2+ in the range of 1.0-2.5 M, and a linear relationship between the average hydrodynamic diameters of the resulted aggregates and the concentration of Hg 2+ can be expressed as d = 6.16 + 45.9c with the correlation coefficient of 0.994. In such case, LSPR-LS signals were further applied to the selective determination of mercuric ions in lake water samples with high sensitivity and simple operation.     

Poly(arginine)‐Selective Coprecipitation Properties of Self‐Assembling Apoferritin and Its Tb3+ Complex: A New Luminescent Biotool for Sensing of Poly(arginine) and Its Protein Conjugates

The apoferritin protein and apoferritin–Tb³⁺ complex were demonstrated to form oligomeric and polymeric self‐assemblies in neutral aqueous solutions, based on characterization by using luminescence and UV/Vis spectroscopy, dynamic light scattering, and transmission electron microscopy. Addition of a 20‐mer or higher poly(arginine) to the solution resulted in coprecipitation through nanoscale interactions, while biological proteins and other poly(amino acids) rarely yielded precipitates under the conditions employed. The apoferritin–Tb³⁺ complex assembly exhibited a particularly long‐lived green luminescence in aqueous solution, and its poly(arginine)‐selective precipitation behavior was followed by monitoring the changes in luminescence. The poly(arginine)‐tagged albumin precipitated selectively and quantitatively, so that the apoferritin–Tb³⁺ complex can function as a new luminescent biotool for the sensing of poly(arginine) and its protein conjugates.     

Ultrasensitive Measurement of Ca2+ Influx into Lipid Vesicles Induced by Protein Aggregates

To quantify and characterize the potentially toxic protein aggregates associated with neurodegenerative diseases, a high‐throughput assay based on measuring the extent of aggregate‐induced Ca²⁺ entry into individual lipid vesicles has been developed. This approach was implemented by tethering vesicles containing a Ca²⁺ sensitive fluorescent dye to a passivated surface and measuring changes in the fluorescence as a result of membrane disruption using total internal reflection microscopy. Picomolar concentrations of Aβ42 oligomers could be observed to induce Ca²⁺ influx, which could be inhibited by the addition of a naturally occurring chaperone and a nanobody designed to bind to the Aβ peptide. We show that the assay can be used to study aggregates from other proteins, such as α‐synuclein, and to probe the effects of complex biofluids, such as cerebrospinal fluid, and thus has wide applicability.     

Unraveling Ultrafast Photoinduced Proton Transfer Dynamics in a Fluorescent Protein Biosensor for Ca2+ Imaging

Imaging Ca²⁺ dynamics in living systems holds great potential to advance neuroscience and cellular biology. G‐GECO1.1 is an intensiometric fluorescent protein Ca²⁺ biosensor with a Thr‐Tyr‐Gly chromophore. The protonated chromophore emits green upon photoexcitation via excited‐state proton transfer (ESPT). Upon Ca²⁺ binding, a significant population of the chromophores becomes deprotonated. It remains elusive how the chromophore structurally evolves prior to and during ESPT, and how it is affected by Ca²⁺. We use femtosecond stimulated Raman spectroscopy to dissect ESPT in both the Ca²⁺‐free and bound states. The protein chromophores exhibit a sub‐200 fs vibrational frequency shift due to coherent small‐scale proton motions. After wavepackets move out of the Franck–Condon region, ESPT gets faster in the Ca²⁺‐bound protein, indicative of the formation of a more hydrophilic environment. These results reveal the governing structure–function relationship of Ca²⁺‐sensing protein biosensors.     

A calcium-modulated plasmonic switch

A plasmonic switch based on the calcium-induced conformational changes of calmodulin is shown to exhibit reversible wavelength modulations in response to changing calcium concentration. The extinction maximum (lambdamax) of a localized surface plasmon resonance (LSPR) sensor functionalized with a novel calmodulin construct, cutinase-calmodulin-cutinase (CutCaMCut), reversibly shifts by 2-3 nm. A high-resolution (HR) LSPR spectrometer with a wavelength resolution (3sigma) of 1.5 x 10-2 nm was developed to detect these wavelength modulations in real-time, providing information about the dynamics and structure of the protein. The rate of conversion from open (Ca2+-bound) to closed (Ca2+-free) calmodulin is shown to be 4-fold faster than the reverse process, with a closing rate of 0.127 s-1 and opening rate of 0.034 s-1. As far as we are aware, this plasmonic switch marks the first use of LSPR spectroscopy to detect reversible conformational changes in an unlabeled protein.     

New Calcium‐Selective Smart Contrast Agents for Magnetic Resonance Imaging

Calcium plays a vital role in the human body and especially in the central nervous system. Precise maintenance of Ca²⁺ levels is very crucial for normal cell physiology and health. The deregulation of calcium homeostasis can lead to neuronal cell death and brain damage. To study this functional role played by Ca²⁺ in the brain noninvasively by using magnetic resonance imaging, we have synthesized a new set of Ca²⁺‐sensitive smart contrast agents (CAs). The agents were found to be highly selective to Ca²⁺ in the presence of other competitive anions and cations in buffer and in physiological fluids. The structure of CAs comprises Gd³⁺‐DO3A (DO3A=1,4,7‐tris(carboxymethyl)‐1,4,7,10‐tetraazacyclododecane) coupled to a Ca²⁺ chelator o‐amino phenol‐N,N,O‐triacetate (APTRA). The agents are designed to sense Ca²⁺ present in extracellular fluid of the brain where its concentration is relatively high, that is, 1.2–0.8 mM . The determined dissociation constant of the CAs to Ca²⁺ falls in the range required to sense and report changes in extracellular Ca²⁺ levels followed by an increase in neural activity. In buffer, with the addition of Ca²⁺ the increase in relaxivity ranged from 100–157 %, the highest ever known for any T₁‐based Ca²⁺‐sensitive smart CA. The CAs were analyzed extensively by the measurement of luminescence lifetime measurement on Tb³⁺ analogues, nuclear magnetic relaxation dispersion (NMRD), and ¹⁷O NMR transverse relaxation and shift experiments. The results obtained confirmed that the large relaxivity enhancement observed upon Ca²⁺ addition is due to the increase of the hydration state of the complexes together with the slowing down of the molecular rotation and the retention of a significant contribution of the water molecules of the second sphere of hydration.     

Live‐Cell Quantitative Imaging of Proteome Degradation by Stimulated Raman Scattering

Protein degradation is a regulatory process essential to cell viability and its dysfunction is implicated in many diseases, such as aging and neurodegeneration. In this report, stimulated Raman scattering microscopy coupled with metabolic labeling with ¹³C‐phenylalanine is used to visualize protein degradation in living cells with subcellular resolution. We choose the ring breathing modes of endogenous ¹²C‐phenylalanine and incorporated ¹³C‐phenylalanine as protein markers for the original and nascent proteomes, respectively, and the decay of the former wasquantified through ¹²C/(¹²C+¹³C) ratio maps. We demonstrate time‐dependent imaging of proteomic degradation in mammalian cells under steady‐state conditions and various perturbations, including oxidative stress, cell differentiation, and huntingtin protein aggregation.     

Highly selective light scattering imaging of chromium (III) in living cells with silver nanoparticles

In this contribution, we present a highly selective chromium ion (Cr³⁺)-induced aggregation of citrate-capped silver nanoparticles, which could be applied for the imaging of the distribution of Cr³⁺ in cells. It was found that selective aggregation of citrate-capped silver nanoparticles occurs at room temperature in the presence of Cr³⁺ in aqueous medium of pH 6.8, resulting in color change from yellow to pink in 10 min and enhanced localized surface plasmon resonance (LSPR) scattering signals. Tenfold of other metal ions including Al³⁺, Ca²⁺, Co²⁺, Cu²⁺, Fe²⁺, Fe³⁺, Hg²⁺, La³⁺, Mg²⁺, Ni²⁺, Pb²⁺, Tb³⁺ and Zn²⁺ had no response. Mechanism analysis showed that the aggregation is mainly dependent on the chelation of Cr³⁺ ion with the citrate ion capped on silver nanoparticles, forming crosslinking aggregates of silver nanoparticles. With the Cr³⁺-induced enhancement of LSPR scattering signals, Cr³⁺ in cytoplasm of human bone marrow neuroblastoma cells could be imaged with dark-field light scattering imaging technique.     

Purification of Biliary Protein and Its Effect on Calcium Carbonate Mineralization

The biliary protein (BP) was isolated from pig bile by gel filtration. The interaction between Ca²⁺ and protein was measured by fluorescence spectra. The result showed that there was a strong coordination between biliary protein and Ca²⁺. The CaCO₃ crystals obtained in systems with and without BP were characterized by scanning electron microscopy, Fourier transform infrared spectrography and powder X‐ray diffractometry. The possible formation mechanism of CaCO₃ in biliary protein solution was discussed.     

Directed Supramolecular Surface Assembly of SNAP‐tag Fusion Proteins

Supramolecular assembly of proteins on surfaces and vesicles was investigated by site‐selective incorporation of a supramolecular guest element on proteins. Fluorescent proteins were site‐selectively labeled with bisadamantane by SNAP‐tag technology. The assembly of the bisadamantane functionalized SNAP‐fusion proteins on cyclodextrin‐coated surfaces yielded stable monolayers. The binding of the fusion proteins is specific and occurs with an affinity in the order of 10⁶ M ^?1 as determined by surface plasmon resonance. Reversible micropatterns of the fusion proteins on micropatterned cyclodextrin surfaces were visualized by using fluorescence microscopy. Furthermore, the guest‐functionalized proteins could be assembled out of solution specifically onto the surface of cyclodextrin vesicles. The SNAP‐tag labeling of proteins thus allows for assembly of modified proteins through a host–guest interaction on different surfaces. This provides a new strategy in fabricating protein patterns on surfaces and takes advantage of the high labeling efficiency of the SNAP‐tag with designed supramolecular elements.     

Transglutaminase 2 inhibits apoptosis induced by calciumoverload through down-regulation of Bax

An abrupt increase of intracellular Ca²⁺ is observed in cells under hypoxic or oxidatively stressed conditions. The dysregulated increase of cytosolic Ca²⁺ triggers apoptotic cell death through mitochondrial swelling and activation of Ca²⁺-dependent enzymes. Transglutaminase 2 (TG2) is a Ca²⁺-dependent enzyme that catalyzes transamidation reaction producing cross-linked and polyaminated proteins. TG2 activity is known to be involved in the apoptotic process. However, the pro-apoptotic role of TG2 is still controversial. In this study, we investigate the role of TG2 in apoptosis induced by Ca²⁺-overload. Overexpression of TG2 inhibited the {"type":"entrez-nucleotide","attrs":{"text":"A23187","term_id":"833253","term_text":"A23187"}}A23187-induced apoptosis through suppression of caspase-3 and -9 activities, cytochrome c release into cytosol, and mitochondria membrane depolarization. Conversely, down-regulation of TG2 caused the increases of cell death, caspase-3 activity and cytochrome c in cytosol in response to Ca²⁺-overload. Western blot analysis of Bcl-2 family proteins showed that TG2 reduced the expression level of Bax protein. Moreover, overexpression of Bax abrogated the anti-apoptotic effect of TG2, indicating that TG2-mediated suppression of Bax is responsible for inhibiting cell death under Ca²⁺-overloaded conditions. Our findings revealed a novel anti-apoptotic pathway involving TG2, and suggested the induction of TG2 as a novel strategy for promoting cell survival in diseases such as ischemia and neurodegeneration.     

Interaction of trialkyltin(IV) chlorides with sarcoplasmic reticulum calcium ATPase

The interaction of the organotin compounds trimethyltin(IV) and tributyltin(IV) chlorides with the calcium pump from sarcoplasmic reticulum membranes was studied. It was found that the presence of calcium fully protects against the inhibitory effect of both organotin compounds. However, the apparent affinity of the protein for tributyltin chloride is two orders of magnitude higher than for trimethyltin chloride (K_0.5 values of 14 µ m and 1.4 m m , respectively). Studies of intrinsic fluorescence of the Ca²⁺‐ATPase and enzyme phosphorylation by ATP and Pi support the hypothesis that the inhibitory properties of trialkyltin compounds are due to the inhibition of calcium binding to the high‐affinity binding sites of the Ca²⁺‐ATPase. This suggests that there is a specific interaction between the trialkyltin compounds and the calcium binding sites of the protein. The effect of trialkyltin compounds on Ca²⁺‐ATPase was also addressed by differential scanning calorimetry to assess the thermal transition of the protein denaturation, and by infrared spectroscopy in the absorption region corresponding to the amide I band (1600–1700 cm^?1) to observe changes in the secondary structure of the protein. We conclude that the interaction of trialkyltin compounds with Ca²⁺‐ATPase reduces the affinity and cooperativity for calcium binding and, consequently, the inhibition of ATPase activity. These events are accompanied by changes in the secondary structure of the protein, including loss of α‐helix structure and a concomitant increase in protein aggregation or unfolding. The activity of trialkyltin compounds on the Ca²⁺‐ATPase is discussed in relation to their solubility in water and in the lipid phase. Copyright © 2012 John Wiley & Sons, Ltd.