Allosterically Activated Protein Self‐Assembly for the Construction of Helical Microfilaments with Tunable Helicity

Protein allostery, a chemical‐to‐mechanical effect that can precisely regulate protein structure, exists in many proteins. Herein, we demonstrate that protein allostery can be used to drive self‐assembly for the construction of tunable protein architectures. Calmodulin (CaM) was chosen as a model allosteric protein. Ca²⁺‐mediated contraction of CaM to a closed state can activate CaM and its ligand to self‐assemble into a 1D protein helical microfilament. Conversely, relaxation of CaM to the open state can unwind and further dissociate the helical assemblies. Fine regulation of the protein conformation by tuning the external Ca²⁺ level allows us to obtain various protein helical nanostructures with tunable helicity. This study offers a new approach toward chemomechanically controlled protein self‐assembly.     

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.     

Enhanced free-energy calculation using multiscale simulation

We propose a multiscale simulation method combining the efficiency of a coarse-grained model (CGM) and the accuracy of an all-atom model (AAM) for free-energy landscape calculation of protein systems. A protein's conformation space is quickly searched first using CGM. Then the obtained information is incorporated into AAM simulations. The free-energy landscape is subsequently obtained from AAM simulations. This method was tested on chignolin folding. The results demonstrated that the computational time was reduced by as much as 90%.     

Molecular dynamics simulation exploration of cooperative migration mechanism of calcium ions in sarcoplasmic reticulum Ca2+‐ATPase

Calcium ATPase is a member of the P‐type ATPase, and it pumps calcium ions from the cytoplasm into the reticulum against a concentration gradient. Several X‐ray structures of different conformations have been solved in recent years, providing basis for elucidating the active transport mechanism of Ca²⁺ ions. In this work, molecular dynamics (MD) simulations were performed at atomic level to investigate the dynamical process of calcium ions moving from the outer mouth of the protein to their binding sites. Five initial locations of Ca²⁺ ions were considered, and the simulations lasted for 2 or 6 ns, respectively. Specific pathways leading to the binding sites and large structural rearrangements around binding sites caused by uptake of calcium ions were identified. A cooperative binding mechanism was observed from our simulation. Firstly, the first Ca²⁺ ion binds to site I , and then, the second Ca²⁺ ion approaches. The interactions between the second Ca²⁺ and the residues around site I disturb the binding state of site I and weaken its binding ability for the first bound Ca²⁺. Because of the electrostatic repulsion of the second Ca²⁺ and the electrostatic attraction of site II , the first bound Ca²⁺ shifts from site I to site II . Concertedly, the second Ca²⁺ binds to site I , forming a binding state with two Ca²⁺ ions, one at site I and the other at site II . Both of Glu908 and Asp800 coordinate with the two Ca²⁺ ions simultaneously during the concerted binding process, which is believed to be the hinge to achieve the concerted binding. In our simulations, four amino acid residues that serve as the channel to link the outer mouth and the binding sites during the binding process were recognized, namely Tyr837, Tyr763, Asn911, and Ser767. The analyses regarding the activity of the proteins via mutations of some key residues also supported our cooperative mechanism. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Do Valine Side Chains Have an Influence on the Folding Behavior of β‐Substituted β‐Peptides?

The influence of valine side chains on the folding/unfolding equilibrium and, in particular, on the 3₁₄‐helical propensity of β³‐peptides were investigated by means of molecular‐dynamics (MD) simulation. To that end, the valine side chains in two different β³‐peptides were substituted by leucine side chains. The resulting four peptides, of which three have never been synthesized, were simulated for 150 to 200 ns at 298 and 340 K, starting from a fully extended conformation. The simulation trajectories obtained were compared with respect to structural preferences and folding behavior. All four peptides showed a similar folding behavior and were found to predominantly adopt 3₁₄‐helical conformations, irrespective of the presence of valine side chains. No other well‐defined conformation was observed at significant population in any of the simulations. Our results imply that β³‐peptides show a structural preference for 3₁₄‐helices independent of the branching nature of the side chains, in contrast to what has been previously proposed on the basis of circular‐dichroism (CD) measurements.     

Conformational Changes in Calcium‐Sensor Proteins under Molecular Crowding Conditions

Fundamental components of signaling pathways are switch modes in key proteins that control start, duration, and ending of diverse signal transduction events. A large group of switch proteins are Ca²⁺ sensors, which undergo conformational changes in response to oscillating intracellular Ca²⁺ concentrations. Here we use dynamic light scattering and a recently developed approach based on surface plasmon resonance to compare the protein dynamics of a diverse set of prototypical Ca²⁺‐binding proteins including calmodulin, troponin C, recoverin, and guanylate cyclase‐activating protein. Surface plasmon resonance biosensor technology allows monitoring conformational changes under molecular crowding conditions, yielding for each Ca²⁺‐sensor protein a fingerprint profile that reflects different hydrodynamic properties under changing Ca²⁺ conditions and is extremely sensitive to even fine alterations induced by point mutations. We see, for example, a correlation between surface plasmon resonance, dynamic light scattering, and size‐exclusion chromatography data. Thus, changes in protein conformation correlate not only with the hydrodynamic size, but also with a rearrangement of the protein hydration shell and a change of the dielectric constant of water or of the protein–water interface. Our study provides insight into how rather small signaling proteins that have very similar three‐dimensional folding patterns differ in their Ca²⁺‐occupied functional state under crowding conditions.     

Elongated Thrombin Binding Aptamer: A G‐Quadruplex Cation‐Sensitive Conformational Switch

Aptamer‐based biosensors offer promising perspectives for high performance, specific detection of proteins. The thrombin binding aptamer (TBA) is a G‐quadruplex‐forming DNA sequence, which is frequently elongated at one end to increase its analytical performances in a biosensor configuration. Herein, we investigate how the elongation of TBA at its 5′ end affects its structure and stability. Circular dichroism spectroscopy shows that TBA folds in an antiparallel G‐quadruplex conformation with all studied cations (Ba²⁺, Ca²⁺, K⁺, Mg²⁺, Na⁺, NH₄⁺, Sr²⁺ and the [Ru(NH₃)₆]^2+/3+ redox marker) whereas other structures are adopted by the elongated aptamers in the presence of some of these cations. The stability of each structure is evaluated on the basis of UV spectroscopy melting curves. Thermal difference spectra confirm the quadruplex character of all conformations. The elongated sequences can adopt a parallel or an antiparallel structure, depending on the nature of the cation; this can potentially confer an ion‐sensitive switch behavior. This switch property is demonstrated with the frequently employed redox complex [Ru(NH₃)₆]³⁺, which induces the parallel conformation at very low concentrations (10 equiv per strand). The addition of large amounts of K⁺ reverts the conformation to the antiparallel form, and opens interesting perspectives for electrochemical biosensing or redox‐active responsive devices.     

Metal binding discrimination of the calmodulin Q41C/K75C mutant on Ca2+ and La3+

Calmodulin (CaM) is a multifunctional Ca²⁺-binding protein regulating the activity of many enzymes in response to fluctuation of the intracellular Ca²⁺ level. It has been shown that a CaM Q41C/K75C mutant (CaMSS) with a disulfide bond in the N-terminal domain exhibits greatly reduced affinity to Ca²⁺. In the present study, the experimental results revealed a unique metal binding pattern in CaMSS towards La³⁺ and Ca²⁺ separately: the mutant protein binds Ca²⁺ at site I, III and IV; however, it binds La³⁺ at site I, II and IV. A putative mechanism was proposed which is the conformation of site II (or site III) of CaMSS could be altered and thus loses its metal ion affinity in response to metal binding in the opposite terminal domain possibly through the long range domain interaction. The present work may offer new perspectives for understanding the mechanisms of specific metal ion affinity in CaM and for CaM-based protein design.     

Involvement of Long‐Lived Intermediate States in the Complex Folding Pathway of the Human Telomeric G‐Quadruplex

The energy landscapes of human telomeric G‐quadruplexes are complex, and their folding pathways have remained largely unexplored. By using real‐time NMR spectroscopy, we investigated the K⁺‐induced folding of the human telomeric DNA sequence 5′‐TTGGG(TTAGGG)₃A‐3′. Three long‐lived states were detected during folding: a major conformation (hybrid‐1), a previously structurally uncharacterized minor conformation (hybrid‐2), and a partially unfolded state. The minor hybrid‐2 conformation is formed faster than the more stable hybrid‐1 conformation. Equilibration of the two states is slow and proceeds via a partially unfolded intermediate state, which can be described as an ensemble of hairpin‐like structures.     

Amplified Electrochemical Immunosensor for Calmodulin Detection Based on Gold‐Silver‐Graphene Hybrid Nanomaterials and Enhanced Gold Nanorods Labels

Calmodulin (CaM) is an important intracellular calcium‐binding protein. It plays a critical role in a variety of biological and biochemical processes. In this paper, a new electrochemical immunosensing protocol for sensitive detection of CaM was developed by using gold‐silver‐graphene (AuAgGP) hybrid nanomaterials as protein immobilization matrices and gold nanorods (GNRs) as enhanced electrochemical labels. Electrode was first modified with thionine‐chitosan film to provide an immobilization support for gold‐silver‐graphene hybrid nanomaterials. The hybrid materials formed an effective matrix for binding of CaM with high density and improved the electrochemical responses as well. Gold nanorods were prepared for the fabrication of enhanced labels (HRP‐Ab₂‐GNRs), which provided a large capacity for HRP‐Ab₂ immobilization and a facile pathway for electron transfer. With two‐step immunoassay format, the HRP‐Ab₂‐GNRs labels were introduced onto the electrode surface, and produced electrochemical responses by catalytic reaction of HRP toward enzyme substrate of hydrogen peroxide (H₂O₂) in the presence of thionine. The proposed immunosensor showed an excellent analytical performance for the detection of CaM ranging from 50 pg mL^?1 to 200 ng mL^?1 with a detection limit of 18 pg mL^?1. The immunosensor has also been successfully applied to the CaM analysis in two cancer cells (HepG2 and MCF‐7) with high sensitivity, which has shown great potency for improving clinic diagnosis and treatment for cancer study.     

Development of an Efficient Procedure for Determination of Copper,Zinc and Iron after Solid Phase Extraction on 3‐(1‐(1‐H‐Indol‐3‐yl)‐3‐Phenylallyl)‐1H‐Indole Loaded on Duolite XAD 761

A method for the simultaneous preconcentration of Cu²⁺,Zn²⁺ and Fe³⁺ ions, in some food samples has been reported. The method is based on the adsorption of 3‐(1‐(1‐H‐indol‐3‐yl)‐3‐phenylallyl)‐1H‐indole (IPAI) loaded on Duolite XAD 761. The metal ions adsorbed on the modified solid phase resin are eluted using 6 mL of 4 mol L^?1 nitric acid. The influences of the analytical parameters including pH and amount of ligand and solid phase and type and amount of surfactant and sample volume on the metal ions recoveries were investigated. The effects of matrix ions on the retentions of the analytes were also examined. The recoveries of analytes were generally higher than 95% with a RSD lower than 5%. The method has been successfully applied for these metals content evaluation in some real samples.     

Dual crosslinked pH‐ and temperature‐sensitive hydrogel beads for intestine‐targeted controlled release

Novel drug‐loaded hydrogel beads for intestine‐targeted controlled release were developed by using pH‐ and temperature‐sensitive carboxymethyl chitosan‐graft‐poly(N,N‐diethylacrylamide) (CMCTS‐g‐PDEA) hydrogel as carriers and vitamin B₂ (VB₂) as a model drug. The hydrogel beads were prepared based on Ca²⁺ ionic crosslinking in acidic solution and formed dual crosslinked network structure. The structure of hydrogel and morphology of drug‐loaded beads were characterized by Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and scanning electron microscopy (SEM). The study about swelling characteristics of hydrogel beads indicated that the beads had obvious pH‐ and temperature‐sensitivity. In vitro release studies of drug‐loaded beads were carried out in pH 1.2 HCl buffer solution and pH 7.4 phosphate buffer solution at 37°C, respectively. The results indicated that the dual crosslinked method could effectively control the drug release rate under gastrointestinal tract (GIT) conditions, which was superior to traditional single crosslinked beads. In addition, the effects of grafting percentage, pH value, and temperature on the release behavior of the VB₂ were investigated. The drug release mechanism of CMCTS‐g‐PDEA drug‐loaded beads was analyzed by Peppa's potential equation. According to this study, the dual crosslinked hydrogel beads based on CMCTS‐g‐PDEA could serve as suitable candidate for drug site‐specific carrier in intestine. Copyright © 2009 John Wiley & Sons, Ltd.     

“Protein‐Like” Copolymers: Effect of Polymer Architecture on the Performance in Bioseparation Process

Recently, a new class of copolymers, so‐called protein‐like copolymers has been predicted theoretically by computer simulation. In these copolymers, the conformation of the copolymer determines the exposure of certain comonomer units to the outer solution. Depending on the conformation, copolymer molecules with essentially the same comonomer composition could have pronouncedly different properties. The authors demonstrated experimentally such behavior in case of poly[(N‐vinylcaprolactam)‐co‐(N‐vinylimidazole)] (Dokl. Chem. 2001 , 375, 637). One more group of copolymers with protein‐like behavior is copolymers of N‐isopropylacrylamide with N‐vinylimidazole. Poly[(N‐isopropylacrylamide)‐co‐(N‐vinylimidazole)] was synthesized by radical polymerization and separated into two fractions using immobilized metal affinity chromatography on Cu²⁺‐loaded iminodiacetic acid sepharose CL 6B (Cu²⁺‐IDA‐sepharose). The unbound fraction which passed through the column and bound fraction eluted with Ethylenediaminetetraacetic acid, disodium salt (EDTA) solution differed significantly in molecular weight, 1.4×10⁶ and 1.35×10⁵, respectively but were very close in comonomer composition, 7.8 and 9.1 mol‐% of imidazole, respectively. The composition of bound fraction was confirmed by titration of imidazole groups. Despite close chemical composition, the bound and unbound fraction behaved differently with respect to temperature‐induced phase separation at different pH values, the dependence of hydrodynamic diameter on pH and concentration of Cu²⁺‐ions, and the coprecipitation of soybean trypsin inhibitor with the copolymer in the presence of Cu²⁺‐ions. The differences in the behavior of copolymer fractions are rationalized assuming that the bound fraction presents a protein‐like copolymer.     

Effect of metal cations [Li+, Na+, K+, Be2+, Mg2+, and Ca2+] on the structure of 2‐(3′‐hydroxy‐2′‐pyridyl)benzoxazole: A theoretical investigation

Density functional theory calculations were performed at the B3LYP/6‐311++G(d,p) level to systematically explore the geometrical multiplicity and binding strength for the complexes formed by alkaline and alkaline earth metal cations, viz. Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ (Mⁿ⁺, hereinafter), with 2‐(3′‐hydroxy‐2′‐pyridyl)benzoxazole. A total of 60 initial structures were designed and optimized, of which 51 optimized structures were found, which could be divided into two different types: monodentate complexes and bidentate complexes. In the cation‐heteroatom complex, bidentate binding is generally stronger than monodentate binding, and of which the bidentate binding with five‐membered ring structure has the strongest interaction. Energy decomposition revealed that the total binding energies mainly come from electrostatic interaction for alkaline metal ion complexes and orbital interaction energy for alkaline earth metal ion complex. In addition, the electron localization function analysis show that only the Be? O and Be? N bond are covalent character, and others are ionic character. © 2012 Wiley Periodicals, Inc.     

Double Metal Ions Competitively Control the Guest‐Sensing Process: A Facile Approach to Stimuli‐Responsive Supramolecular Gels

A facile approach to the design of stimuli‐responsive supramolecular gels (SRSGs) termed double‐metal‐ion competitive coordination control is reported. By this means, the fluorescence signals and guest‐selective responsiveness of the SRSGs are controlled by the competitive coordination of two different metal ions with the gelators and the target guest. To demonstrate this approach, a gelator G2 based on multiple self‐assembly driving forces was synthesized. G2 could form Ca²⁺‐coordinated metallogel CaG with strong aggregation‐induced emission (AIE). Doping of CaG with Cu²⁺ results in AIE quenching of CaG and formation of Ca²⁺‐ and Cu²⁺‐based metallogel CaCuG. CaCuG could fluorescently detect CN^? with specific selectivity through the competitive coordination of CN^? with the Cu²⁺ and the coordination of Ca²⁺ with G2 again. This approach may open up routes to novel stimuli‐responsive supramolecular materials.     

Selective separation of strontium by multitopic ion‐pair receptor: A DFT exploration

Selective extraction of a radionuclide in the presence of other interfering ions is one of the vital steps in the back‐end‐of‐the‐nuclear fuel cycle. The presence of interfering cations (such as Ca²⁺) in the radioactive waste and involvement of multiple separation steps are known to be bottlenecks in the efficient Sr²⁺ extraction. Here, using free energy corrected density functional theory, we have proposed a two‐step Sr²⁺ extraction methodology in nitrate media in the presence of interfering Ca²⁺ ion using a multitopic ion‐pair receptor, which was earlier reported to be strongly selective for K⁺ (Kim et al. J. Am. Chem. Soc. 2012, 134 , 1782–1792). To depict the correct free energy trend in the proposed extraction processes, the most probable binding mode of the metal (Sr²⁺, Ca²⁺, and K⁺) nitrates in the host are identified. In excellent agreement with the previously reported experiment, Crown/Pyrrole (C/P) binding is noted to be the most preferable mode for KNO₃, where K⁺ and occupied the Crown (C) and Pyrrole (P) site, respectively. However, the divalent metal ions (Ca²⁺ and Sr²⁺) are noted to marginally prefer Crown/Crown‐Pyrrole (C/CP) mode, in which metal reside at the C site while two nitrates occupy the P site and also simultaneously bind at the outer sphere of C site to coordinate with the metal via monodentate motif. Based on the free energy of extraction, we predict that the selective separation of chemically alike Ca²⁺/Sr²⁺ pair is indeed achievable using this receptor. We propose that once [Sr(NO₃)₂] is extracted in organic media, the receptor's high affinity toward K⁺ in nitrate media can be used to back strip Sr²⁺ to the aqueous phase.     

9‐Benzylidene‐9H‐fluorene Derivatives Linked to Monoaza‐15‐crown‐5: Synthesis and Metal Ion Sensing

Two kinds of novel styryl chemosensory 2‐FMNC and 3‐FMNC, were designed and synthesized by an apporiate introduction of 9‐benzylidene‐9H‐fluorene group as fluorophore with the aim at avoiding photoisomerisation. These 9‐benzylidene‐9H‐fluorene derivatives showed the similar selectivity and sensitivity upon addition of metal ions. The sensitivity of FMNC to alkaline earth metal ions was Ba²⁺>Sr²⁺>Ca²⁺≈Mg²⁺.     

Synthesis and characterization of L‐leucine containing chiral vinyl monomer and its polymer,poly(2‐(methacryloyloxyamino)‐4‐methyl pentanoic acid)

A chiral monomer containing L ‐leucine as a pendant group was synthesized from methacryloyl chloride and L ‐leucine in presence of sodium hydroxide at 4 °C. The monomer was polymerized by free radical polymerization in propan‐2‐ol at 60 °C using 2,2′‐azobis isobutyronitrile (AIBN) as an initiator under nitrogen atmosphere. The polymer, poly(2‐(Methacryloyloxyamino)‐4‐methyl pentanoic acid) is thus obtained. The molecular weight of the polymer was determined to be: M_w is 6.9 × 10³ and M_n is 5.6 × 10³. The optical rotation of both chiral monomer and its polymer varies with the solvent polarity. The amplification of optical rotation due to transformation of monomer to polymer is associated with the ordered conformation of chiral monomer unit in the polymeric chain due to some secondary interactions like H‐bonding. The synthesized monomer and polymer exhibit intense Cotton effect at 220 nm. The conformation of the chain segments is sensitive to external stimuli, particularly the pH of the medium. In alkaline medium, the ordered chain conformation is destroyed resulting disordered random coils. The ordered coiling conformation is more firmly present on addition of HCl. The polymer exhibits swelling‐deswelling characteristics with the change of pH of the medium, which is reversible. The Cotton effect decreases linearly with the increase of temperature which is reversible on cooling. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2228–2242, 2009     

ESI‐MS studies of the non‐covalent interactions between biologically important metal ions and N‐sulfonylcytosine derivatives

The aim of this report is to present the electrospray ionization mass spectrometry results of the non‐covalent interaction of two biologically active ligands, N‐1 ‐ (p‐toluenesulfonyl)cytosine, 1‐TsC, 1 and N‐1 ‐ methanesulfonylcytosine, 1‐MsC, 2 and their Cu(II) complexes Cu(1‐TsC‐N3)₂Cl₂, 3 and Cu(1‐MsC‐N3)₂Cl₂ and 4 with biologically important cations: Na⁺, K⁺, Ca²⁺, Mg²⁺ and Zn²⁺. The formation of various complex metal ions was observed. The alkali metals Na⁺ and K⁺ formed clusters because of electrostatic interactions. Ca²⁺ and Mg²⁺ salts produced the tris ligand and mixed ligand complexes. The interaction of Zn²⁺ with 1–4 produced monometal and dimetal Zn²⁺ complexes as a result of the affinity of Zn²⁺ ions toward both O and N atoms. Copyright © 2016 John Wiley & Sons, Ltd.     

Luminescence Properties of Ca2Ga2SiO7:RE Phosphors for UV White‐Light‐Emitting Diodes

A series of Eu²⁺‐, Ce³⁺‐, and Tb³⁺‐doped Ca₂Ga₂SiO₇ phosphors is synthesized by using a high‐temperature solid‐state reaction. The powder X‐ray diffraction and structure refinement data indicate that our prepared phosphors are single phased and the phosphor crystalizes in a tetrahedral system with the ${P\bar 42m}$ (113) space group. The Eu²⁺‐ and Ce³⁺‐doped phosphors both have broad excitation bands, which match well with the UV light‐emitting diodes chips. Under irradiation of λ=350 nm, Ca₂Ga₂SiO₇:Eu²⁺ and Ca₂Ga₂SiO₇:Ce³⁺, Li⁺ have green and blue emissions, respectively. Luminescence of Ca₂Ga₂SiO₇:Tb³⁺, Li⁺ phosphor varies with the different Tb³⁺ contents. The thermal stability and energy‐migration mechanism of Ca₂Ga₂SiO₇:Eu²⁺ are also studied. The investigation results indicate that the prepared Ca₂Ga₂SiO₇:Eu²⁺ and Ca₂Ga₂SiO₇:Ce³⁺, Li⁺ samples show potential as green and blue phosphors, respectively, for UV‐excited white‐light‐emitting diodes.