Infrared studies of interaction between metal ions and Ca(2+)-binding proteins. Marker bands for identifying the types of coordination of the side-chain COO- groups to metal ions in pike parvalbumin (pI = 4.10)

Genome and pan-genome analysis of a new exopolysaccharide-producing bacterium Pyschrobacillus sp. isolated from iron ores deposit and insights into iron uptake

Bacterial exopolysaccharides (EPS) have emerged as one of the key players in the field of heavy metal-contaminated environmental bioremediation. This study aimed to characterize and evaluate the metal biosorption potential of EPS produced by a novel Psychrobacillus strain, NEAU-3TGS, isolated from an iron ore deposit at Tamra iron mine, northern Tunisia. Genomic and pan-genomic analysis of NEAU-3TGS bacterium with nine validated published Psychrobacillus species was also performed. The results showed that the NEAU-3TGS genome (4.48 Mb) had a mean GC content of 36%, 4,243 coding sequences and 14 RNA genes. Phylogenomic analysis and calculation of nucleotide identity (ANI) values (less than 95% for new species with all strains) confirmed that NEAU-3TGS represents a potential new species. Pangenomic analysis revealed that Psychrobacillus genomic diversity represents an "open" pangenome model with 33,091 homologous genes, including 65 core, 3,738 shell, and 29,288 cloud genes. Structural EPS characterization by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy showed uronic acid and α-1,4-glycosidic bonds as dominant components of the EPS. X-ray diffraction (XRD) analysis revealed the presence of chitin, chitosan, and calcite CaCO3 and confirmed the amorphous nature of the EPS. Heavy metal bioabsorption assessment showed that iron and lead were more adsorbed than copper and cadmium. Notably, the optimum activity was observed at 37°C, pH=7 and after 3 h contact of EPS with each metal. Genomic insights on iron acquisition and metabolism in Psychrobacillus sp. NEAU-3TGS suggested that no genes involved in siderophore biosynthesis were found, and only the gene cluster FeuABCD and trilactone hydrolase genes involved in the uptake of siderophores, iron transporter and exporter are present. Molecular modelling and docking of FeuA (protein peptidoglycan siderophore-binding protein) and siderophores ferrienterobactine [Fe+3 (ENT)]-3 and ferribacillibactine [Fe+3 (BB)]-3 ligand revealed that [Fe+3 (ENT)]-3 binds to Phe122, Lys127, Ile100, Gln314, Arg215, Arg217, and Gln252. Almost the same for [Fe+3 (ENT)]-3 in addition to Cys222 and Tyr229, but not Ile100.To the best of our knowledge, this is the first report on the characterization of EPS and the adsorption of heavy metals by Psychrobacillus species. The heavy metal removal capabilities may be advantageous for using these organisms in metal remediation.

Metallic nanoparticle actions on the outer layer structure and properties of Bacillus cereus and Staphylococcus epidermidis

Although the antimicrobial activity of nanoparticles (NPs) penetrating inside the cell is widely recognised, the toxicity of large NPs (>10 nm) that cannot be translocated across bacterial membranes remains unclear. Therefore, this study was performed to elucidate the direct effects of Ag-NPs, Cu-NPs, ZnO-NPs and TiO2-NPs on relative membrane potential, permeability, hydrophobicity, structural changes within chemical compounds at the molecular level and the distribution of NPs on the surfaces of the bacteria Bacillus cereus and Staphylococcus epidermidis. Overall analysis of the results indicated the different impacts of individual NPs on the measured parameters in both strains depending on their type and concentration. B. cereus proved to be more resistant to the action of NPs than S. epidermidis. Generally, Cu-NPs showed the most substantial toxic effect on both strains; however, Ag-NPs exhibited negligible toxicity. All NPs had a strong affinity for cell surfaces and showed strain-dependent characteristic dispersion. ATR-FTIR analysis explained the distinctive interactions of NPs with bacterial functional groups, leading to macromolecular structural modifications. The results presented provide new and solid evidence for the current understanding of the interactions of metallic NPs with bacterial membranes.

Simultaneous Identification and Species Differentiation of Major Allergen Tropomyosin in Crustacean and Shellfish by Infrared Spectroscopic Chemometrics

To solve the lack of rapid and accurate methods for allergen identification and traceability, an infrared spectroscopic chemometric analytical model (IR-CAM) was established by combining infrared spectroscopy with principal component and cluster analysis. By comparing the second derivative infrared (SD-IR) spectra of 5 proteins and 14 crustaceans and shellfish tropomyosin (TM), 8 shared peaks and unique fingerprint peaks in the amide III region were found for crabs, shrimps, and shellfish. Based on the unique fingerprint peaks coexisting with shared peaks, allergen TM in crustaceans and shellfish could be identified within 10 min (cf. ELISA ∼ 4 h). Concurrently, the species differentiation of TM at the Class/Family level was achieved based on IR-CAM. Validation by fermented aquatic products TM (n = 60) demonstrated that the developed IR-CAM could simultaneously identify and differentiate TM in crustaceans and shellfish accurately. It could be applied for allergen detection and traceability of aquatic products on an antibody-free basis.

Construction of a competitive electrochemical immunosensor based on sacrifice of Prussian blue and its ultrasensitive detection of alpha-fetoprotein

Effective signal amplification is a prerequisite for ultrasensitive detection by electrochemical immunosensors. For quantitative and ultrasensitive detection of alpha-fetoprotein (AFP), we designed a competitive electrochemical immunosensor and transferred the immunoreactivity from the electrode surface to the cuvette. AFP antigen was captured using AFP primary antibody (Ab₁) immobilized on magnetic nanobeads (MBs), and ZIF-8 nanomaterials attached to secondary antibody (Ab₂) were used as probes. MBs helped retain the sandwich structure in the test tube through incubation and washing steps. Then, an appropriately fixed excess of sodium ethylenediaminetetraacetic acid (EDTA) solution was added to the cuvettes, resulting in etching of Zn ions from ZIF-8 and formation of Zn-EDTA complexes. After magnetic separation, a certain amount of supernatant is added dropwise to the Prussian blue (PB)-modified electrode (GCE), and Fe ions (from PB) complex with the remaining EDTA in the supernatant, thus reducing the signal response value of PB. The higher the AFP concentration, the lower the amount of free EDTA in the supernatant, the less the destruction of PB, and therefore the higher the current. Under optimal conditions, the immunosensor achieved ultra-sensitive detection of AFP in the range of 10^-4 ng/mL-100 ng/mL with a limit of detection (LOD) as low as 0.032 pg/mL (S/N = 3). The excellent performance provides an important tool for the early screening and detection of AFP.

Dewatering municipal wastewater sludge using electro-coagulation combined with added free nitrous acid

An electro-coagulation (EC) process combined with added free nitrous acid (FNA) improves sludge dewaterability. Under optimal conditions(EC voltage of 25 V, EC process time of 60 min, FNA dosage of 1.13 mg/L, pH value of 4.5), specific resistance to filtration (SRF) and water content (WC) was decreased by 89.57%, and 18.90%respectively. The EC process disrupted the sludge structure, reducing sludge particles' size (D50) from 59.5 to 50.5 μm. After adding FNA, the sludge cells lysed, and the DNA concentrations and soluble chemical oxygen demand (SCOD) increased from 6.07 μg/ml and 29 mg/L to 364 μg/ml and 588 mg/L, respectively. The conversion of Fe(II) to Fe(III) was enhanced. The addition of FNA after EC further improved the sludge dewaterability. Combined conditioning using EC and FNA can effectively destroy tightly bound extracellular polymeric substances (TB-EPS) and release bound water. In addition, the pH value is kept low, which benefits sludge dewaterability and the removal of heavy metals. The concentrations of Zn and Mn in the sludge cake were reduced by 92.3% and 69.0%, respectively. The Bureau of Reference (BCR) sequential extraction method showed increases in the percentages of the residual fractions of Zn and Mn, showing that EC combined with FNA is an efficient and versatile means of sludge conditioning.

Bioactive, Degradable and Tough Hybrids Through Calcium and Phosphate Incorporation

We report the first inorganic/organic hybrids that show outstanding mechanical properties (withstanding cyclic loading) and bone bioactivity. This new hybrid material may fulfil the unmet clinical need for bioactive synthetic bone grafts that can withstand cyclic loading. A SiO2/PTHF/PCL-diCOOH sol-gel hybrid system, that combined inorganic and organic conetworks at the molecular level, previously demonstrated unprecedented synergy of properties, with excellent flexibility and promoted formation of articular cartilage matrix in vitro. Here, for the first time, calcium and phosphate ions were incorporated into the inorganic component of the hybrid network, to impart osteogenic properties. Calcium methoxyethoxide and triethyl phosphate were the calcium and phosphate precursors because they allow for incorporation into the silicate network at low temperature. The hybrid network was characterised with ATR-FTIR, XRD and solid-state Nuclear Magnetic Resonance, which proved calcium and phosphate incorporation and suggested the Ca2+ ions also interacted with PCL-diCOOH through ionic bonds. This resulted in an increased strength (17-64 MPa) and modulus of toughness (2.5-14 MPa) compared to the original SiO2/PTHF/PCL-diCOOH hybrid material (which showed strength of ~3 MPa and modulus of toughness of ~0.35 MPa), while also maintaining the ability to withstand cyclic loading. The presence of calcium and phosphates in the silicate network resulted in a more congruent dissolution of the inorganic and organic co-networks in TRIS buffer. This was shown by the presence of silicon, calcium and phosphate ions along with PCL in the TRIS buffer after 1 week, whereas Ca-free hybrids mainly released PCL with negligible Si dissolution. The presence of calcium and phosphates also enabled deposition of hydroxycarbonate apatite following immersion in simulated body fluid, which was not seen on Ca-free hybrid. All hybrids passed cell cytotoxicity tests and supported preosteoblast cell attachment. The phosphate-free hybrid showed the best mechanical behaviour and supported better cell attachment, spreading and potentially differentiation of cells. Therefore, the SiO2-CaO/PTHF/PCL-diCOOH hybrid represents a promising biomaterial for use in bone regeneration.

Loss of slc39a14 causes simultaneous manganese hypersensitivity and deficiency in zebrafish

Manganese neurotoxicity is a hallmark of hypermanganesemia with dystonia 2, an inherited manganese transporter defect caused by mutations in SLC39A14. To identify novel potential targets of manganese neurotoxicity, we performed transcriptome analysis of slc39a14-/- mutant zebrafish that were exposed to MnCl2. Differentially expressed genes mapped to the central nervous system and eye, and pathway analysis suggested that Ca2+ dyshomeostasis and activation of the unfolded protein response are key features of manganese neurotoxicity. Consistent with this interpretation, MnCl2 exposure led to decreased whole-animal Ca2+ levels, locomotor defects and changes in neuronal activity within the telencephalon and optic tectum. In accordance with reduced tectal activity, slc39a14-/- zebrafish showed changes in visual phototransduction gene expression, absence of visual background adaptation and a diminished optokinetic reflex. Finally, numerous differentially expressed genes in mutant larvae normalised upon MnCl2 treatment indicating that, in addition to neurotoxicity, manganese deficiency is present either subcellularly or in specific cells or tissues. Overall, we assembled a comprehensive set of genes that mediate manganese-systemic responses and found a highly correlated and modulated network associated with Ca2+ dyshomeostasis and cellular stress. This article has an associated First Person interview with the first author of the paper.

What Is Parvalbumin for?

Parvalbumin (PA) is a small, acidic, mostly cytosolic Ca2+-binding protein of the EF-hand superfamily. Structural and physical properties of PA are well studied but recently two highly conserved structural motifs consisting of three amino acids each (clusters I and II), which contribute to the hydrophobic core of the EF-hand domains, have been revealed. Despite several decades of studies, physiological functions of PA are still poorly known. Since no target proteins have been revealed for PA so far, it is believed that PA acts as a slow calcium buffer. Numerous experiments on various muscle systems have shown that PA accelerates the relaxation of fast skeletal muscles. It has been found that oxidation of PA by reactive oxygen species (ROS) is conformation-dependent and one more physiological function of PA in fast muscles could be a protection of these cells from ROS. PA is thought to regulate calcium-dependent metabolic and electric processes within the population of gamma-aminobutyric acid (GABA) neurons. Genetic elimination of PA results in changes in GABAergic synaptic transmission. Mammalian oncomodulin (OM), the β isoform of PA, is expressed mostly in cochlear outer hair cells and in vestibular hair cells. OM knockout mice lose their hearing after 3–4 months. It was suggested that, in sensory cells, OM maintains auditory function, most likely affecting outer hair cells’ motility mechanisms.

Synthesis, Characterization, and Cellular Uptake of Magnesium Maltol and Ethylmaltol Complexes

Magnesium deficiency and/or deficit (hypomagnesemia, <0.75 mmol/L in the blood) has become a recognized problem in healthcare and clinical settings. Concomitantly, supplementation has become recognized as the primary means of mitigating such deficiencies. Common magnesium supplements typically suffer from shortcomings: rapid dissociation and subsequent laxation (magnesium salts: e.g., magnesium chloride), poor water solubility (magnesium oxides and hydroxides), poor characterizability (magnesium chelates), and are/or use of non-natural ligands. To this end, there is a need for the development of fully characterized, water-soluble, all-natural magnesium compounds. Herein, we discuss the synthesis, solution and solid-state characterization, aqueous solubility, and cellular uptake of magnesium complexes of maltol and ethylmaltol, ligands whose magnesium complexes have yet to be fully explored.

Lanthanide-dependent coordination interactions in lanmodulin: a 2D IR and molecular dynamics simulations study

The biological importance of lanthanides, and the early lanthanides (La³⁺-Nd³⁺) in particular, has only recently been recognized, and the structural principles underlying selective binding of lanthanide ions in biology are not yet well established. Lanmodulin (LanM) is a novel protein that displays unprecedented affinity and selectivity for lanthanides over most other metal ions, with an uncommon preference for the early lanthanides. Its utilization of EF-hand motifs to bind lanthanides, rather than the Ca²⁺ typically recognized by these motifs in other proteins, has led it to be used as a model system to understand selective lanthanide recognition. Two-dimensional infrared (2D IR) spectroscopy combined with molecular dynamics simulations were used to investigate LanM's selectivity mechanisms by characterizing local binding site geometries upon coordination of early and late lanthanides as well as calcium. These studies focused on the protein's uniquely conserved proline residues in the second position of each EF-hand binding loop. We found that these prolines constrain the EF-hands for strong coordination of early lanthanides. Substitution of this proline results in a more flexible binding site to accommodate a larger range of ions but also results in less compact coordination geometries and greater disorder within the binding site. Finally, we identify the conserved glycine in the sixth position of each EF-hand as a mediator of local binding site conformation and global secondary structure. Uncovering fundamental structure-function relationships in LanM informs the development of synthetic biology technologies targeting lanthanides in industrial applications.

CH Mode Mixing Determines the Band Shape of the Carboxylate Symmetric Stretch in Apo-EDTA, Ca2+-EDTA, and Mg2+-EDTA

The infrared spectra of EDTA complexed with Ca²⁺ and Mg²⁺ contain, to date, unidentified vibrational bands. This study assigns the peaks in the linear and two-dimensional infrared spectra of EDTA, with and without either Ca²⁺ or Mg²⁺ ions. Two-dimensional infrared spectroscopy and DFT calculations reveal that, in both the presence and absence of ions, the carboxylate symmetric stretch and the terminal CH bending vibrations mix. We introduce a method to calculate participation coefficients that quantify the contribution of the carboxylate symmetric stretch, CH wag, CH twist, and CH scissor in the 1400-1550 cm^-1 region. With the help of participation coefficients, we assign the 1400-1430 cm^-1 region to the carboxylate symmetric stretch, which can mix with CH modes. We assign the 1000-1380 cm^-1 region to CH twist modes, the 1380-1430 cm^-1 region to wag modes, and the 1420-1650 cm^-1 region to scissor modes. The difference in binding geometry between the carboxylate-Ca²⁺ and carboxylate-Mg²⁺ complex manifests as new diagonal and cross-peaks between the mixed modes in the two complexes. The small Mg²⁺ ion binds EDTA tighter than the Ca²⁺ ion, which causes a redshift of the COO symmetric stretches of the sagittal carboxylates. Energy decomposition analysis further characterizes the importance of electrostatics and deformation energy in the bound complexes.

Infrared spectroscopy probes ion binding geometries

Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.

Deciphering calcium-binding behaviors of casein phosphopeptides by experimental approaches and molecular simulation

Casein phosphopeptides (CPPs) as premium additives in functional foods can facilitate the transport and adsorption of calcium. The atomic resolution decipherment of calcium-CPP binding behaviors is critical for understanding the calcium bioavailability enhancement potential of CPPs. In the present study, the experimental methods (UV-vis, FTIR and isothermal titration calorimetry) and molecular dynamics simulation were combined to reveal the calcium-binding behaviors of β-casein phosphopeptides (1-25) (P5) with the best capability in carrying calcium ions. We found that it could carry approximately six calcium ions, and the calcium-binding sites were primarily located at the carbonyl group of Glu-2 and the phosphate group of phosphorylated Ser-15, Ser-18, and Ser-19. An interesting finding was that calcium ions could be bound by three coordinated modes, including unidentate, bidentate and tridentate geometries, resulting in the strong binding abilities. The binding process of calcium ions to P5 was spontaneous with the binding free energies of -5.2 kcal mol-1. Hydrophobic interactions were considered to be the major driving force for the calcium ion binding. The present study provides novel molecular insights into the binding process between Ca2+ and calcium-binding peptides.

Non-Additive Effects of Binding Site Mutations in Calmodulin

Despite decades of research on ion-sensing proteins, gaps persist in the understanding of ion binding affinity and selectivity even in well-studied proteins such as calmodulin. Site-directed mutagenesis is a powerful and popular tool for addressing outstanding questions about biological ion binding and is employed to selectively deactivate binding sites and insert chromophores at advantageous positions within ion binding structures. However, even apparently nonperturbative mutations can distort the binding dynamics they are employed to measure. We use Fourier transform infrared (FTIR) and ultrafast two-dimensional infrared (2D IR) spectroscopy of the carboxylate asymmetric stretching mode in calmodulin as a mutation- and label-independent probe of the conformational perturbations induced in calmodulin's binding sites by two classes of mutation, tryptophan insertion and carboxylate side-chain deletion, commonly used to study ion binding in proteins. Our results show that these mutations not only affect ion binding but also induce changes in calmodulin's conformational landscape along coordinates not probed by vibrational spectroscopy, remaining invisible without additional perturbation of binding site structure. Comparison of FTIR line shapes with 2D IR diagonal slices provides a clear example of how nonlinear spectroscopy produces well-resolved line shapes, refining otherwise featureless spectral envelopes into more informative vibrational spectra of proteins.

Bioinspired Design and Fabrication of Polymer Composite Films Consisting of a Strong and Stiff Organic Matrix and Microsized Inorganic Platelets

Intensive studies on nacre-inspired composites with exceptional mechanical properties based on an organic/inorganic hierarchical layered structure have been conducted; however, integrating high strength, stiffness, and toughness for engineering materials still remains a challenge. We herein report the design and fabrication of polymer composites through a hydrogel-film casting method that allow for building uniformly layered organic/inorganic microstructure. Alginate (Alg) was used for an organic matrix, whose mechanical properties were controlled by Ca²⁺ cross-linking toward the simultaneously strong, stiff, and tough resultant composite. Alumina (Alu) microplatelets were used for horizontally aligned inorganic phase, and their alignment and interactions with the organic matrix were improved by polyvinylpyrrolidone (PVP) coating on the platelet. The composite film exhibits well-balanced elastic and plastic deformation under tensile stress, leading to high stiffness and toughness, which have not been generally achieved in microplatelet-based composite films developed in previous studies. The synergistic effect of Ca²⁺ cross-linking and PVP-coated Alu platelets on the mechanical properties improved polymer-platelet interfacial interactions, and platelet alignment is clearly demonstrated through mechanical tests and Fourier transform infrared and X-ray diffraction analyses. We further demonstrate that the reinforcing effect of the Alu platelet and PVP-coated platelet on the mechanical properties is dependent on humidity. Such effects are maximized at highly dry conditions, which is consistent with the model estimation. Furthermore, a thick bulk composite was produced by laminating thin films and showed high mechanical properties under flexural stress. Our design and fabrication strategies combined with the understanding of their mechanism yield an alternative approach to produce engineered composite materials.

Characterization of the Ca2+-coordination structures of L- and T-plastins in combination with their synthetic peptide analogs by FTIR spectroscopy

FTIR spectroscopy was employed to characterize the coordination structures of divalent cations (M2+ = Ca2+ or Mg2+) bound by L- and T-plastins, which contain two EF-hand motifs. We focused on the N-terminal headpieces in the L- and T-plastins to analyze the regions of COO- stretching and amide-I in solution. The spectral profiles indicated that these headpieces have EF-hand calcium-binding sites because bands at 1551 cm-1 and 1555 cm-1 were observed for the bidentate coordination mode of Glu at the 12th position of the Ca2+-binding site of Ca2+-loaded L-plastin and T-plastin, respectively. The amide-I profile of the Mg2+-loaded L-plastin headpiece was identical with that of the apo L-plastin headpiece, meaning that L-plastin has a lower affinity for Mg2+. The amide-I profiles for apo, Mg2+-loaded and Ca2+-loaded T-plastin suggested that aggregation was generated in protein solution at a concentration of 1 mM. The implications of the FTIR spectral data for these plastin headpieces are discussed on the basis of data obtained for synthetic peptide analogs corresponding to the Ca2+-binding site.

Coordination to lanthanide ions distorts binding site conformation in calmodulin

The Ca²⁺-sensing protein calmodulin (CaM) is a popular model of biological ion binding since it is both experimentally tractable and essential to survival in all eukaryotic cells. CaM modulates hundreds of target proteins and is sensitive to complex patterns of Ca²⁺ exposure, indicating that it functions as a sophisticated dynamic transducer rather than a simple on/off switch. Many details of this transduction function are not well understood. Fourier transform infrared (FTIR) spectroscopy, ultrafast 2D infrared (2D IR) spectroscopy, and electronic structure calculations were used to probe interactions between bound metal ions (Ca²⁺ and several trivalent lanthanide ions) and the carboxylate groups in CaM's EF-hand ion-coordinating sites. Since Tb³⁺ is commonly used as a luminescent Ca²⁺ analog in studies of protein-ion binding, it is important to characterize distinctions between the coordination of Ca²⁺ and the lanthanides in CaM. Although functional assays indicate that Tb³⁺ fully activates many Ca²⁺-dependent proteins, our FTIR spectra indicate that Tb³⁺, La³⁺, and Lu³⁺ disrupt the bidentate coordination geometry characteristic of the CaM binding sites' strongly conserved position 12 glutamate residue. The 2D IR spectra indicate that, relative to the Ca²⁺-bound form, lanthanide-bound CaM exhibits greater conformational flexibility and larger structural fluctuations within its binding sites. Time-dependent 2D IR lineshapes indicate that binding sites in Ca²⁺-CaM occupy well-defined configurations, whereas binding sites in lanthanide-bound-CaM are more disordered. Overall, the results show that binding to lanthanide ions significantly alters the conformation and dynamics of CaM's binding sites.

Sorption behavior of tetracyclines on suspended organic matters originating from swine wastewater

Tetracyclines (TCs) discharged from livestock wastewater have aroused public concerns due to their pharmacological threats to ecosystems and human health. As an important medium in the wastewater, suspended organic matters (SOMs) play vital roles in antibiotics transport and degradation. However, limited information has been reported in the relevant literature. This study investigated TCs sorption behavior on SOM, withdrawn from swine wastewater. High TCs sorption capacities were detected, with the maximum values ranging from 0.337 to 0.679mg/g. Increasing pH and temperature led to the decline of sorption capacity. Results from three-dimensional excitation-emission matrix fluorescence spectroscopy and Fourier transform infrared spectrometry revealed that amide and carboxyl groups were the main functional groups for TCs adsorption. The interactions between SOM and TCs were clarified as predominated by hydrogen-bonding and cation-exchange in acid conditions, and electrostatic repulsion in neutral or alkaline conditions. Adsorption kinetics modeling was conducted, and a satisfactory fitting was achieved with the Freundlich equation. These results indicated that the adsorption process was a rather complex process, involving a combination of cation-exchange and hydrogen-bonding. The results will provide a better understanding of the capability of SOM for TCs transport and abatement in the wastewater treatment process.

Infrared study of synthetic peptide analogues of the calcium-binding site III of troponin C: The role of helix F of an EF-hand motif

The EF-hand motif (helix-loop-helix) is a Ca(2+)-binding domain that is common among many intracellular Ca(2+)-binding proteins. We applied Fourier-transform infrared spectroscopy to study the synthetic peptide analogues of site III of rabbit skeletal muscle troponin C (helix E-loop-helix F). The 17-residue peptides corresponding to loop-helix F (DRDADGYIDAEELAEIF), where one residue is substituted by the D-type amino acid, were investigated to disturb the α-helical conformation of helix F systematically. These D-type-substituted peptides showed no band at about 1555 cm(-1) even in the Ca(2+)-loaded state although the native peptide (L-type only) showed a band at about 1555 cm(-1) in the Ca(2+)-loaded state, which is assigned to the side-chain COO(-) group of Glu at the 12th position, serving as the ligand for Ca(2+) in the bidentate coordination mode. Therefore, helix F is vital to the interaction between the Ca(2+) and the side-chain COO(-) group of Glu at the 12th position. Implications of the COO(-) antisymmetric stretch and the amide-I' of the synthetic peptide analogues of the Ca(2+)-binding sites are discussed.

New approach of modifying the anatase to rutile transition temperature in TiO2 photocatalysts

In pure synthetic titanium dioxide, the anatase to rutile phase transition usually occurs between the temperatures of 600 °C and 700 °C.

Role of extracellular polymeric substance in determining the high aggregation ability of anammox sludge

The high aggregation ability of anammox sludge has been extensively observed, but the cause for their aggregation is challenging. Here the structure and composition of extracellular polymeric substance (EPS) excreted from anammox sludge were systematically investigated to interpret the high aggregation ability. We combine results of contact angle, zeta potential and surface thermodynamics analysis as well as the following DLVO theory to address this issue. The results show that hydrophobic interaction is the main force determining the aggregation of anammox sludge. To go insight into inherent mechanism, Fourier transform infrared (FTIR) and x-ray photoelectron (XPS) spectroscopy were conducted and demonstrated there were comparatively few hydrophilic functional groups in the EPS of anammox sludge, compared to that of activated sludge, nitrifying and denitrifying sludge. Further, amino acid composition and secondary structure analyses of protein indicated that large amounts of hydrophobic amino acids and high level of protein loose structure for exposing inner hydrophobic groups of protein in EPS significantly contributed to the hydrophobic interaction and further to the high aggregation ability of anammox sludge, which is the critical finding of this work. This investigation is useful for understanding anammox bacteria and then for accelerating the application of the anammox process in wastewater treatment.

Investigation of the structure of alpha-lactalbumin protein nanotubes using optical spectroscopy

Alpha-lactalbumin (α-la) is one of the major proteins in whey. When partially hydrolysed with Bacillus licheniformis protease, it produces nanotubular structures in the presence of calcium ions by a self-assembly process. This study presents investigation of α-la protein structure during hydrolysis and nanotube formation using optical spectroscopy. Before spectroscopic measurements, nanotubes were examined with microscopy. The observed α-la nanotubes (α-LaNTs) were in the form of regular hollow strands with a diameter of about 20 nm and the average length of 1 μm. Amide and backbone vibration bands of the Raman spectra displayed remarkable conformational changes in α and β domains in the protein structure during nanotube growth. This was confirmed by the Fourier-transform infrared (FTIR) spectroscopy data. Also, FTIR analysis revealed certain bands at calcium (Ca++) binding sites of COO− groups in hydrolysed protein. These sites might be critical in nanotube elongation.

Hydration interactions and stability of soluble microbial products in aqueous solutions

Soluble microbial products (SMP) are organic compounds excreted by microorganisms in their metabolism and decay and the main constituents in effluent from biological wastewater treatment systems. They also have an important contribution to the dissolved organic matters in natural aqueous systems. So far the interactions between SMP colloids have not been well explored. In this work, the interactions between SMP colloids in water and salt solutions were studied by using a combination of static and dynamic light scattering, Fourier transform infrared spectra, Zeta potential and acid-base titration techniques. The second osmotic virial coefficient had a larger value in a 750-mM salt solution than that in a 50-mM solution, indicating that repulsion between SMP colloids increased with an increase in salt concentration, which is contrary with the classic Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory. Such a repulsion was attributed to water structuring and enhanced by the accumulation of hydrophilic counter ions around SMP colloids and the formed hydration force. The repulsion and hydration effect led to the dispersing and deeper draining structure, accompanied by a decreased hydrodynamic radius and increased diffusion coefficient. This hydration force was related to so-called ion specific effect, and electrolyte sodium chloride had a more substantial effect on hydration force than KCl, CsCl, NaBr and NaI. Our results provide an experimental approach to explore the SMP structures, inter-colloid interactions and confirm the non-DLVO forces.

Coordination structures of Mg2+ and Ca2+ in three types of tobacco calmodulins in solution: Fourier-transform infrared spectroscopic studies of side-chain COO- groups

Calmodulin (CaM) is a Ca(2+)-binding protein that regulates a number of fundamental cellular activities. Nicotiana tabacum CaM (NtCaM) comprises 13 genes classified into three types, among which gene expression and target enzyme activation differ. We performed Fourier-transform infrared spectroscopy to compare the secondary and coordination structures of Mg(2+) and Ca(2+) among NtCaM1, NtCaM3, and NtCaM13 as representatives of the three types of NtCaMs. Data suggested that NtCaM13 has a different secondary structure due to the weak β-strand bands and the weak 1661 cm(-1) band. Coordination structures of Mg(2+) of NtCaM3 and NtCaM13 were similar but different from that of NtCaM1, while the Ca(2+)-binding manner was similar among the three CaMs. The amplitude differences of the band at 1554-1550 cm(-1) obtained by second-derivative spectra indicated that the intensity change of the band of NtCaM13 was smaller in response to [Ca(2+)] increases under low [Ca(2+)] conditions than were those of NtCaM1 and NtCaM3, while the intensity reached the same level under high [Ca(2+)]. Therefore, NtCaM13 has a characteristic secondary structure and specific Mg(2+)-binding manner and needs higher [Ca(2+)] for bidentate Ca(2+) coordination of 12th Glu in EF-hand motifs. The Ca(2+)-binding mechanisms of the EF-hand motifs of the three CaMs are similar; however, the cation-dependent conformational change in NtCaM13 is unique among the three NtCaMs.

Coordination to divalent cations by calcium-binding proteins studied by FTIR spectroscopy

We review the Fourier-transform infrared (FTIR) spectroscopy of side-chain COO(-) groups of Ca(2+)-binding proteins: parvalbumins, bovine calmodulin, akazara scallop troponin C and related calcium binding proteins and peptide analogues. The COO(-) stretching vibration modes can be used to identify the coordination modes of COO(-) groups of Ca(2+)-binding proteins to metal ions: bidentate, unidentate, and pseudo-bridging. FTIR spectroscopy demonstrates that the coordination structure of Mg(2+) is distinctly different from that of Ca(2+) in the Ca(2+)-binding site in solution. The interpretation of COO(-) stretches is ensured on the basis of the spectra of calcium-binding peptide analogues. The implication of COO(-) stretches is discussed for Ca(2+)-binding proteins. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.

pH dependence of structure and surface properties of microbial EPS

The flocculation of microorganisms plays a crucial role in bioreactors, and is substantially affected by pH. However, the mechanism for such an effect remains unclear. In this work, with an integrated approach, the pH dependence of structure and surface property of microbial extracellular polymeric substances (EPS), excreted from Bacillus megaterium TF10, and accordingly its flocculation is elucidated. From the Fourier transform infrared spectra and acid-base titration test results, the main functional groups and buffering zones in the EPS responsible for the microbial flocculation are indentified. The laser light scattering analysis reveals that the deprotonated or protonated states of these functional groups in EPS result in more dense and compact structure at a lower pH because of hydrophobicity and intermolecular hydrogen bonds. The zeta potential measurements identify the isoelectric point and indicate that the electrostatic repulsion action of EPS is controlled by pH. The highest flocculation efficiency is achieved near the isoelectric point (pH 4.8). These results clearly demonstrate that the EPS structure, surface properties, and accordingly the microbial flocculation are dependent heavily on pH in solution.

Alginate ion adsorption on a TiO2 particle film and interactions of adsorbed alginate with calcium ions investigated by attenuated total reflection infrared (ATR-IR) spectroscopy

The adsorption of alginic acid on a TiO(2) particle film from aqueous solution was investigated by attenuated total reflection infrared (ATR-IR) spectroscopy. ATR-IR spectra recorded at different pHs confirmed that alginate adsorption to TiO(2) is favored at pH 3.0 and no significant adsorption occurs above pH 5.0. Upon adsorption the carboxylic acid groups of alginic acid are converted to the carboxylate form and bind to surface Ti(IV) ions via bridging bidentate structures. Spectral analyses of the carboxylic acid and carboxylate stretching vibrations indicated that about three in four -COOH groups are converted to -COO(-) groups as they bind coordinately to TiO(2). Additionally, the spectral data at pH 8.0 showed specific interactions of Ca(2+) ions with the free COO(-) groups of the polysaccharide backbone of adsorbed alginic acid.

Silk-based delivery systems of bioactive molecules

Silks are biodegradable, biocompatible, self-assembling proteins that can also be tailored via genetic engineering to contain specific chemical features, offering utility for drug and gene delivery. Silkworm silk has been used in biomedical sutures for decades and has recently achieved Food and Drug Administration approval for expanded biomaterials device utility. With the diversity and control of size, structure and chemistry, modified or recombinant silk proteins can be designed and utilized in various biomedical application, such as for the delivery of bioactive molecules. This review focuses on the biosynthesis and applications of silk-based multi-block copolymer systems and related silk protein drug delivery systems. The utility of these systems for the delivery of small molecule drugs, proteins and genes is reviewed.

Metal-controlled interdomain cooperativity in parvalbumins

Conformational behavior of five homologous proteins, parvalbumins (PAs) from northern pike (alpha and beta isoforms), Baltic cod, and rat (alpha and beta isoforms), was studied by scanning calorimetry, circular dichroism, and bis-ANS fluorescence. The mechanism of the temperature-induced denaturation of these proteins depends dramatically on both the peculiarities of their amino acid sequences and on their interaction with metal ions. For example, the pike alpha-PA melting can be described by two successive two-state transitions with mid-temperatures of 90 and 120 degrees C, suggesting the presence of two thermodynamic domains. The intermediate state populated at the end of the first transition was shown to bind Ca(2+) ions, and was characterized by the largely preserved secondary structure and increased solvent exposure of hydrophobic groups. Mg(2+)- and Na(+)-loaded forms of pike alpha-PA demonstrated a single two-state transition. Therefore, the mechanism of the PA thermal denaturation is controlled by metal binding. It ranged from the absence of detectable first-order transition (apo-form of pike PA), to the two-state transition (e.g., Mg(2+)- and Na(+)-loaded forms of pike alpha-PA), to the more complex mechanisms (Ca(2+)-loaded PAs) involving at least one partially folded intermediate. Analysis of isolated cavities in the protein structures revealed that the interface between the CD and EF subdomains of Ca(2+)-loaded pike alpha-PA is much more loosely packed compared with PAs manifesting single heat-sorption peak. The impairment of interactions between CD and EF subdomains may cause a loss of structural cooperativity and appearance of two separate thermodynamic domains. One more peculiar feature of pike alpha-PA is that depending on its interactions with metal ions, it can be an intrinsically disordered protein (apo-form), an ordered protein of mesophilic (Na(+)-bound state), thermophilic (Mg(2+)-form), or even of the hyperthermophilic origin (Ca(2+)-form).

An altered mode of calcium coordination in methionine-oxidized calmodulin

Oxidation of methionine residues in calmodulin (CaM) lowers the affinity for calcium and results in an inability to activate target proteins fully. To evaluate the structural consequences of CaM oxidation, we used infrared difference spectroscopy to identify oxidation-dependent effects on protein conformation and calcium liganding. Oxidation-induced changes include an increase in hydration of alpha-helices, as indicated in the downshift of the amide I' band of both apo-CaM and Ca(2+)-CaM, and a modification of calcium liganding by carboxylate side chains, reflected in antisymmetric carboxylate band shifts. Changes in carboxylate ligands are consistent with the model we propose: an Asp at position 1 of the EF-loop experiences diminished hydrogen bonding with the polypeptide backbone, an Asp at position 3 forms a bidentate coordination of calcium, and an Asp at position 5 forms a pseudobridging coordination with a calcium-bound water molecule. The bidentate coordination of calcium by conserved glutamates is unaffected by oxidation. The observed changes in calcium ligation are discussed in terms of the placement of methionine side chains relative to the calcium-binding sites, suggesting that varying sensitivities of binding sites to oxidation may underlie the loss of CaM function upon oxidation.

Infrared spectroscopic study of the metal-coordination structures of calcium-binding proteins

Carboxylate (COO(-)) groups can coordinate to metal ions in of the following four modes: 'unidentate', 'bidentate', 'bridging' and 'pseudo-bridging' modes. COO(-) stretching frequencies provide information about the coordination modes of COO(-) groups to metal ions. We review the Fourier-transform infrared spectroscopy (FTIR) of side-chain COO(-) groups of Ca(2+)-binding proteins: pike parvalbumin pI 4.10, bovine calmodulin and Akazara scallop troponin C. FTIR spectroscopy of Akazara scallop troponin C has demonstrated that the coordination structure of Mg(2+) is distinctly different from that of Ca(2+) in the Ca(2+)-binding site. The assignments of the COO(-) antisymmetric stretch have been ensured on the basis of the spectra of calcium-binding peptide analogues. The downshift of the COO(-) antisymmetric stretching mode from 1565 cm(-1) to 1555-1540 cm(-1) upon Ca(2+) binding is a commonly observed feature of FTIR spectra for EF-hand proteins.

Infrared spectroscopy of proteins

This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.

Correlation of infrared spectra of zinc(II) carboxylates with their structures

The correlation of the infrared spectra of zinc(II) carboxylates with their structures was investigated in the paper. The complexes with different modes of the carboxylate binding, from chelating, through bridging (syn-syn, syn-anti, monatomic), ionic to monodentate were used for the study, namely [Zn(C6H5CHCHCOO)2(H2O)2] (I) with chelating carboxylate group (C6H5CHCHCOO=cinnamate), [Zn2(C6H5COO)4(pap)2] (II) with syn-syn bridging carboxylate (C6H5COO=benzoate; pap=papaverine), [Zn(C6H5CHCHCOO)2(mpcm)]n (III) with syn-anti carboxylate bridge (mpcm=methyl-3-pyridylcarbamate), [Zn(C5H4NCOO)2(H2O)4] (IV) with ionic carboxylate group (C5H4NCOO=nicotinate), [Zn(C6H5COO)2(pcb)2]n (V) with monodentate carboxylate coordination (pcb=3-pyridylcarbinol) and [Zn3(C6H5COO)6(nia)2] (VI) with syn-syn and monatomic carboxylate bridges (nia=nicotinamide). First, the mode of the carboxylate binding was assigned from the infrared spectra using the magnitude of the separation between the carboxylate stretches, Deltaexp=nuas(COO-)-nus(COO-). Then the values Deltaexp were compared with those calculated from structural data of the carboxylate anion (Deltacalc). The conclusions about the carboxylate binding which resulted from the Delta values, were confronted with the crystal structure of the complexes. The limitations and recommendations were formulated to assign the mode of the carboxylate binding from the infrared spectra. The dependence of the Deltaexp values on the magnitudes of Zn-O-C angles in bidentate carboxylate coordination was observed.

Changes in secondary structures and acidic side chains of melibiose permease upon cosubstrates binding

Infrared difference spectroscopy analysis of the purified melibiose permease of Escherichia coli reconstituted into liposomes was carried out as a function of the presence of the two symporter substrates (Na(+), melibiose) in either H(2)O or in D(2)O media. Essentially, the data first show that addition of Na(+) induces appearance of peaks assigned to changes in the environment and/or orientation of alpha-helical domains of purified melibiose permease. Likewise, melibiose addition in the presence of Na(+) produces peaks corresponding to additional changes of alpha-helix environment or tilt. In addition to these changes, a pair of peaks (1599 (+) cm(-1)/1576 (-) cm(-1)) appearing in the Na(+)-induced difference spectrum is assigned to the antisymmetric stretching of COO(-) groups, since they show practically no shift upon H/D exchange. It is proposed that these acidic groups participate in Na(+) co-ordination. A corresponding pair of peaks, again fairly insensitive to H/D substitution (1591 (-) cm(-1)/1567 (+) cm(-1)), appear in the melibiose-induced difference spectra, and may again be assigned to COO(-) groups. The latter carboxyl groups may correspond to part or all of the acidic residues interacting with Lys or Arg in the resting state that become free upon melibiose binding.

Fourier transform infrared spectroscopic study on the Ca2+ -bound coordination structures of synthetic peptide analogues of the calcium-binding site III of troponin C

The coordination structures of Ca(2+) ion bound to synthetic peptide analogues of the calcium-binding site III of rabbit skeletal muscle troponin C (TnC) were investigated by Fourier transform infrared (FTIR) spectroscopy. The region of the COO(-) antisymmetric stretching vibration provides information about the coordination modes of a COO(-) group to a metal ion. The 34-residue peptide corresponding to the EF hand motif (helix-loop-helix) showed a band at 1552 cm(-1) in the Ca(2+)-loaded state, indicating that the side-chain COO(-) group of Glu at the 12th position serves as a ligand for Ca(2+) in the bidentate coordination mode. On the other hand, the 13-residue peptide (Ac-DRDADGYIDAEEL-NH(2)) containing the Ca(2+)-binding site III (DRDADGYIDAEE) did not show such spectral patterns in the Ca(2+)-loaded state, meaning that shorter synthetic peptide corresponding to the site III has less or no affinity for Ca(2+). It was found that the 17-residue peptide (Ac-DRDADGYIDAEELAEIF-NH(2)) is the minimum peptide necessary for the interaction of side-chain COO(-)of Glu at the 12th position with Ca(2+) in the bidentate coordination mode. We discuss the relationship between the amino acid length of synthetic peptide analogues and the formation of Ca(2+)-bound coordination structure.

Electrospun silk-BMP-2 scaffolds for bone tissue engineering

Silk fibroin fiber scaffolds containing bone morphogenetic protein 2 (BMP-2) and/or nanoparticles of hydroxyapatite (nHAP) prepared via electrospinning were used for in vitro bone formation from human bone marrow-derived mesenchymal stem cells (hMSCs). BMP-2 survived the aqueous-based electrospinnig process in bioactive form. hMSCs were cultured for up to 31 days under static conditions in osteogenic media on the scaffolds (silk/PEO/BMP-2, silk/PEO/nHAP, silk/PEO/nHAP/BMP-2) and controls (silk/PEO, silk/PEO extracted). Electrospun silk fibroin-based scaffolds supported hMSC growth and differentiation toward osteogenic outcomes. The scaffolds with the co-processed BMP-2 supported higher calcium deposition and enhanced transcript levels of bone-specific markers than in the controls, indicating that these nanofibrous electrospun silk scaffolds were an efficient delivery system for BMP-2. X-ray diffraction (XRD) analysis revealed that the apatite formed on the silk fibroin/BMP-2 scaffolds had higher crystallinity than on the silk fibroin scaffold controls. In addition, nHAP particles were incorporated into the electrospun fibrous scaffolds during processing and improved bone formation. The coexistence of BMP-2 and nHAP in the electrospun silk fibroin fibers resulted in the highest calcium deposition and upregulation of BMP-2 transcript levels when compared with the other systems. The results suggest that electrospun silk-fibroin-based scaffolds are potential candidates for bone tissue engineering. Furthermore, the mild aqueous process required to spin the fibers offers an important option for delivery of labile cytokines and other components into the system.

Secondary structure and Pd(II) coordination in S-layer proteins from Bacillus sphaericus studied by infrared and X-ray absorption spectroscopy

The S-layer of Bacillus sphaericus strain JG-A12, isolated from a uranium-mining site, exhibits a high metal-binding capacity, indicating that it may provide a protective function by preventing the cellular uptake of heavy metals and radionuclides. This property has allowed the use of this and other S-layers as self-assembling organic templates for the synthesis of nanosized heavy metal cluster arrays. However, little is known about the molecular basis of the metal-protein interactions and their impact on secondary structure. We have studied the secondary structure, protein stability, and Pd((II)) coordination in S-layers from the B. sphaericus strains JG-A12 and NCTC 9602 to elucidate the molecular basis of their biological function and of the metal nanocluster growth. Fourier transform infrared spectroscopy reveals similar secondary structures, containing approximately 35% beta-sheets and little helical structure. pH-induced infrared absorption changes of the side-chain carboxylates evidence a remarkably low pK < 3 in both strains and a structural stabilization when Pd((II)) is bound. The COO(-)-stretching absorptions reveal a predominant Pd((II)) coordination by chelation/bridging by Asp and Glu residues. This agrees with XANES and EXAFS data revealing oxygens as coordinating atoms to Pd((II)). The additional participation of nitrogen is assigned to side chains rather than to the peptide backbone. The topology of nitrogen- and carboxyl-bearing side chains appears to mediate heavy metal binding to the large number of Asp and Glu in both S-layers at particularly low pH as an adaptation to the environment from which the strain JG-A12 has been isolated. These side chains are thus prime targets for the design of engineered S-layer-based nanoclusters.

Temperature excursion infrared (TEIR) spectroscopy used to study hydrogen bonding between water and biomolecules

Water is a highly polar molecule that is capable of making four H-bonding linkages. Stability and specificity of folding of water-soluble protein macromolecules are determined by the interplay between water and functional groups of the protein. Yet, under some conditions, water can be replaced with sugar or other polar protic molecules with retention of protein structure. Infrared (IR) spectroscopy allows one to probe groups on the protein that interact with solvent, whether the solvent is water, sugar or glycerol. The basis of the measurement is that IR spectral lines of functional groups involved in H-bonding show characteristic spectral shifts with temperature excursion, reflecting the dipolar nature of the group and its ability to H-bond. For groups involved in H-bonding to water, the stretching mode absorption bands shift to lower frequency, whereas bending mode absorption bands shift to higher frequency as temperature decreases. The results indicate increasing H-bonding and decreasing entropy occurring as a function of temperature, even at cryogenic temperatures. The frequencies of the amide group modes are temperature dependent, showing that as temperature decreases, the amide group H-bonds to water strengthen. These results are relevant to protein stability as a function of temperature. The influence of solvent relaxation is demonstrated for tryptophan fluorescence over the same temperature range where the solvent was examined by infrared spectroscopy.

Thermostability and Ca2+Binding Properties of Wild Type and Heterologously Expressed PsbO Protein from Cyanobacterial Photosystem II†

Oxygenic photosynthesis takes place in the thylakoid membrane of cyanobacteria, algae, and higher plants. Initially light is absorbed by an oligomeric pigment-protein complex designated as photosystem II (PSII), which catalyzes light-induced water cleavage under release of molecular oxygen for the biosphere on our planet. The membrane-extrinsic manganese stabilizing protein (PsbO) is associated on the lumenal side of the thylakoids close to the redox-active (Mn)(4)Ca cluster at the catalytically active site of PSII. Recombinant PsbO from the thermophilic cyanobacterium Thermosynechococcus elongatus was expressed in Escherichia coli and spectroscopically characterized. The secondary structure of recombinant PsbO (recPsbO) was analyzed in the absence and presence of Ca(2+) using Fourier transform infrared spectroscopy (FTIR) and circular dichroism spectropolarimetry (CD). No significant structural changes could be observed when the PSII subunit was titrated with Ca(2+) in vitro. These findings are compared with data for spinach PsbO. Our results are discussed in the light of the recent 3D-structural analysis of the oxygen-evolving PSII and structural/thermodynamic differences between the two homologous proteins from thermophilic cyanobacteria and plants.