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

Engineering Matrix-Free Drug Protein Nanoparticles with Promising Penetration through Biobarriers for Treating Corneal Neovascularization

Protein drugs have been widely used in treating various clinical diseases because of their high specificity, fewer side effects, and favorable therapeutic effect, but they greatly suffer from their weak permeability through tissue barriers, high sensitivity to microenvironments, degradation by proteases, and rapid clearance by the immune system. Herein, we disrupted the standard protocol where protein drugs must be delivered as the cargo via a delivery system and innovatively developed a free entrapping matrix strategy by simply mixing bevacizumab (Beva) with zinc ions to generate Beva-NPs (Beva-Zn2+), where Beva is coordinatively cross-linked by zinc ions with a loading efficiency as high as 99.2% ± 0.41%. This strategy was universal to generating various protein NPs, with different metal ions (Cu2+, Fe3+, Mg2+, Sr2+). The synthetic conditions of Beva-NPs were optimized, and the generated mechanism was investigated in detail. The entrapment, releasing profile, and the bioactivities of released Beva were thoroughly studied. By using in situ doping of the fourth-generation polyamindoamine dendrimer (G4), the Beva-G4-NPs exhibited extended ocular retention and penetration through biobarriers in the anterior segment through transcellular and paracellular pathways, effectively inhibiting corneal neovascularization (CNV) from 91.6 ± 2.03% to 13.5 ± 1.87% in a rat model of CNV. This study contributes to engineering of protein NPs by using a facile strategy for overcoming the weaknesses of protein drugs and protein NPs, such as weak tissue barrier permeability, low encapsulation efficiency, poor loading capacity, and susceptibility to inactivation.

Preparation, structure characterization, and stability analysis of peptide-calcium complex derived from porcine nasal cartilage type II collagen

BACKGROUND

Porcine nasal cartilage type II collagen-derived peptides (PNCPs) may be complexed with calcium to provide a highly bioavailable, low-cost, and effective calcium food supplement. However, the calcium-binding characteristics of PNCPs have not yet been investigated. In the present study, calcium-binding peptides were derived from porcine nasal cartilage type II collagen and the resulting PNCPs-Ca complex was characterized.

RESULTS

The study reveals that the calcium-binding capacity of PNCPs is closely related to enzymatic hydrolysis conditions. The highest calcium-binding capacity of PNCPs was observed at a hydrolysis time of 4 h, temperature of 40 °C, enzyme dosage of 1%, and solid-to-liquid ratio of 1:10. Scanning electron microscopy and energy dispersive X-ray spectroscopy revealed that the PNCPs had a pronounced capacity for calcium binding, with the PNCPs-Ca complex exhibiting a clustered structure consisting of aggregated spherical particles. Fourier-transform infrared spectroscopy, fluorescence spectroscopy, X-ray diffraction, dynamic light scattering, amino acid composition, and molecular weight distribution analyses all indicated that the PNCPs and calcium complexed via the carboxyl oxygen and amino nitrogen atoms, leading to the formation of a β-sheet structure during the chelation process. In addition, the stability of the PNCPs-Ca complex was maintained over a range of pH values consistent with those found in the human gastrointestinal tract, facilitating calcium absorption.

CONCLUSION

These research findings suggest the feasibility of converting by-products from livestock processing into calcium-binding peptides, providing a scientific basis for the development of novel calcium supplements and the potential reduction of resource waste. © 2023 Society of Chemical Industry.

Metal-protein solution interactions investigated using model systems: Thermodynamic and spectroscopic methods

The first-row D-block metal ions are essential for the physiology of living organisms, functioning as cofactors in metalloproteins or structural components for enzymes: almost half of all proteins require metals to perform the biological function. Understanding metal-protein interactions is crucial to unravel the mysteries behind molecular biology, understanding the effects of metal imbalance and toxicity or the diseases due to disorders in metal homeostasis. Metal-protein interactions are dynamic: they are noncovalent and affected by the environment to which the system is exposed. To reach a complete comprehension of the system, different conditions must be considered for the experimental investigation, in order to get information on the species distribution, the ligand coordination modes, complex stoichiometry and geometry. Thinking about the whole environment where a protein acts, investigations are often challenging, and simplifications are required to study in detail the mechanisms of metal interaction. This chapter is intended to help researchers addressing the problem of the complexity of metal-protein interactions, with particular emphasis on the use of peptides as model systems for the metal coordination site. The thermodynamic and spectroscopic methods most widely employed to investigate the interaction between metal ions and peptides in solution are here covered. These include solid-phase peptide synthesis, potentiometric titrations, calorimetry, electrospray ionization mass spectrometry, UV-Vis spectrophotometry, circular dichroism (CD), nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). Additional experimental methods, which can be employed to study metal complexes with peptides, are also briefly mentioned. A case-study is finally reported providing a practical example of the investigation of metal-protein interaction by means of thermodynamic and spectroscopic methods applied to peptide model systems.

Spectroscopic Characterization of the Divalent Metal Docking Motif to Isolated Cyanobenzoate: Direct Observation of Tridentate Binding to ortho-Cyanobenzoate and Implications for the CN Response

Cryogenic ion vibrational spectra of D₂-tagged cyanobenzoate (CBA) derivatives are obtained and analyzed to characterize the intrinsic spectroscopic responses of the -CO₂^- headgroup to its location on the ring in both the isolated anions and the cationic complexes with divalent metal ions, M²⁺ (M = Mg, Ca, Sr). The benzonitrile functionality establishes the different ring isomers (para, meta, ortho) according to the location of the carboxylate and provides an additional reporter on the molecular response to the proximal charge center. The aromatic carboxylates display shifts slightly smaller than those observed for a related aliphatic system upon metal ion complexation. Although the CBA anions display very similar band patterns for all three ring positions, upon complexation with metal ions, the ortho isomer yields dramatically different spectral responses in both the -CO₂^- moiety and the CN group. This behavior is traced to the emergence of a tridentate binding motif unique to the ortho isomer in which the metal ions bind to both the oxygen atoms of the carboxylate group and the N atom of the cyano group. In that configuration, the -CO₂^- moiety is oriented perpendicular to the phenyl ring, and the CN stretching fundamental is both strong and red-shifted relative to its behavior in the isolated neutral. The behaviors of the metal-bound ortho complexes occur in contrast to the usual blue shifts associated with "Lewis" type binding of metal ions end-on to -CN. The origins of these spectroscopic features are analyzed with the aid of electronic structure calculations, which also explore differences expected for complexation of monovalent cations to the ortho carboxylate. The resulting insights have implications for understanding the balance between electrostatic and steric interactions at metal binding sites in chemical and biological systems.

Chitosan-collagen-hydroxyapatite membranes for tissue engineering

Tissue engineering is growing in developing new technologies focused on providing effective solutions to degenerative pathologies that affect different types of connective tissues. The search for biocompatible, bioactive, biodegradable, and multifunctional materials has grown significantly in recent years. Chitosan, calcium phosphates collagen, and their combination as composite materials fulfill the required properties and could result in biostimulation for tissue regeneration. In the present work, the chitosan/collagen/hydroxyapatite membranes were prepared with different concentrations of collagen and hydroxyapatite. Cell adhesion was evaluated by MTS assay for two in vitro models. Additionally, cytotoxicity of the different membranes employing hemolysis of erythrocytes isolated from human blood was carried out. The structure of the membranes was analyzed by X-rays diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and thermal stability properties by thermogravimetric methods (TGA). The highest cell adhesion after 48 h was obtained for chitosan membranes with the highest hydroxyapatite and collagen content. All composite membranes showed good cell adhesion and low cytotoxicity, suggesting that these materials have a significant potential to be used as biomaterials for tissue engineering. Graphical abstract.

Desalination of duck egg white by biocoagulation to obtain peptide-ferrous chelate as iron delivery system: Preparation, characterization, and Fe2+ release evaluation in vitro

The annual output of salted duck egg white (SDEW) is estimated to be over 1.5 million tons in China, most of which is discarded due to high salt content. This has led to serious waste and environmental impact. Therefore, we developed an eco-friendly biocoagulation separation technology by combining chitosan and sodium alginate in order to produce a novel iron-binding peptide (DPs-Fe2+) from SDEW. The structure of DPs-Fe2+ was characterized by ultraviolet-visible spectroscopy, fluorescence spectroscopy, and Fourier transform infrared spectroscopy, followed by measuring DPs-Fe2+ response in a simulated digestion/Caco-2 cell model. Results showed that chitosan and sodium alginate complex could remove 91.21% of salt from SDEW, and the protein recovery rate reached 95.50%. Characterization results indicated that DPs bonded with Fe2+ to form a soluble chelate. Moreover, Caco-2 cell monolayer model indicated that the transport rate of Fe2+ was as high as 10.02% at 0.1 mg/ml concentration of digested chelates. The results demonstrate the potential application of DPs as a novel carrier for enhancing iron absorption. This research contributes to the development of an effective industrial desalination method and highlights an opportunity for recycling an otherwise discarded processing byproduct. PRACTICAL APPLICATION: Salted duck egg whites (SDEW) are the primary byproduct of salted egg yolk production, most of which is discarded due to high salt content. Hence, efficient utilization of the high-value proteins in SDEW is an urgent problem that must be resolved. Herein, we developed an effective industrial desalination method by combining chitosan and sodium alginate, which achieved excellent SDEW desalination and protein recovery. Furthermore, we produced a novel iron-binding peptide (DPs-Fe2+), which enhanced the transportation and absorption of Fe2+ in Caco-2 cell model, suggesting its potential as an iron supplement.

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.

Antarctic Krill Derived Nonapeptide as an Effective Iron-Binding Ligand for Facilitating Iron Absorption via the Small Intestine

A novel nonapeptide DTDSEEEIR identified from Antarctic krill (Euphausia superba) iron-binding peptides was used in this study to analyze its iron-binding sites and structural changes after iron coordination. The enzymatic resistance and transport of DTDSEEEIR-iron during gastrointestinal digestion and absorption as well as the relationship between the DTDSEEEIR stability and the enhancement of iron absorption were further explored. Results revealed that iron ions spontaneously bound to the carboxyl, hydroxyl, and amino groups of the DTDSEEEIR peptide, which induced the folding of DTDSEEEIR to form a more orderly structure. The DTDSEEEIR peptide remained stable to a certain extent (79.60 ± 0.19%) after gastrointestinal digestion and the coordination of iron improved the digestive stability of the DTDSEEEIR peptide (93.89 ± 1.37%). Moreover, the stability of DTDSEEEIR across intestinal epithelium had a positive effect on iron absorption, which implied that DTDSEEEIR might carry iron ions through intestinal epithelial cells.

Elucidation of a Copper Binding Site in Proinsulin C-peptide and Its Implications for Metal-Modulated Activity

The connecting peptide (C-peptide) is a hormone with promising health benefits in ameliorating diabetes-related complications, yet mechanisms remain elusive. Emerging studies point to a possible dependence of peptide activity on bioavailable metals, particularly Cu(II) and Zn(II). However, little is known about the chemical nature of the interactions, hindering advances in its therapeutic applications. This work uncovers the Cu(II)-binding site in C-peptide that may be key to understanding its metal-dependent function. A combination of spectroscopic studies reveal that Cu(II) and Zn(II) bind to C-peptide at specific residues in the N-terminal region of the peptide and that Cu(II) is able to displace Zn(II) for C-peptide binding. The data point to a Cu(II)-binding site consisting of 1N3O square-planar coordination that is entropically driven. Furthermore, the entire random coil peptide sequence is needed for specific metal binding as mutations and truncations reshuffle the coordinating residues. These results expand our understanding of how metals influence hormone activity and facilitate the discovery and validation of both new and established paradigms in peptide biology.

Preparation of sheep bone collagen peptide–calcium chelate using enzymolysis-fermentation methodology and its structural characterization and stability analysis

In this study, enzymatic hydrolysis and Lactobacillus fermentation were used in combination to prepare collagen peptide with high free calcium content, followed by the addition of anhydrous ethanol to obtain peptide–calcium chelate. The optimal conditions for the fermentation of enzymatic hydrolysate (glucose 3%, inoculum size 6%, 24.5 h, 37 °C and pH 6.5) were determined by response surface methodology (RSM), under which a free calcium content of 2212.58 mg/100 g was obtained. The calcium–chelating capacity was 42.57 ± 0.09%. The results of ultraviolet absorption spectrum, Fourier transform infrared (FT-IR) spectra, differential scanning calorimeter (DSC), X-ray diffraction and amino acid analysis indicated that calcium could be chelated through carboxyl oxygen and amino nitrogen atoms of collagen peptides, forming peptide–calcium chelate. The chelate is stable at 30–80 °C of temperatures and during in simulated gastrointestinal digestion, which could promote calcium absorption in human. The test intended to provide a basis for developing a novel calcium supplement and promoting utilization of sheep bone.

In this study, enzymatic hydrolysis and Lactobacillus fermentation were used in combination to prepare collagen peptide with high free calcium content, followed by the addition of anhydrous ethanol to obtain peptide–calcium chelate.

Facile Synthesis of Triangular and Hexagonal Anionic Gold Nanoparticles and Evaluation of Their Cytotoxicity

Comprehension of the shape-dependent properties of gold nanoparticles (AuNPs) could benefit the advancements in cellular uptake efficiency. Spherical AuNPs have generally been used for drug delivery, and recent research has indicated that the cellular uptake of triangular AuNPs was higher than that of spherical ones. Previous reports have also revealed that chemically synthesized AuNPs were cytotoxic. Therefore, we have developed a facile, cost-effective, and environmentally friendly method for synthesizing triangular and hexagonal anionic AuNPs. The zeta potential of the synthesized AuNPs was negative, which indicated that their surface could be easily functionalized with positively charged molecules to upload drugs or biomolecules. Transmission electron microscopy (TEM) images illustrated that the largest particle size of the synthesized quasi-hexagonal AuNPs was 61 nm. The TEM images also illustrated that two types of equilateral-triangular AuNPs were synthesized: One featured sharp and the other rounded corners. The sides of the smallest and largest triangular AuNPs were 23 and 178 nm, respectively. Energy-dispersive X-ray spectra of the green-synthesized AuNPs indicated that they consisted entirely of elemental Au. The cytotoxicity of the green-synthesized AuNPs was evaluated using 3T3-L1 adipocytes. Using cell viability data, we determined that the green-synthesized AuNPs did not exhibit any cytotoxic effects on 3T3-L1 adipocytes.

Calcium Delivery System Assembled by a Nanostructured Peptide Derived from the Sea Cucumber Ovum

In this study, the binding mechanism, morphological, and conformational analysis of the complex of a sea cucumber ovum derived octapeptide (EDLAALEK) with Ca²⁺ as well as its calcium delivery behavior via the gastrointestinal (GI) tract were investigated. The Ca²⁺ specifically bound to two carboxyl oxygen atoms of C-terminal Glu and Asp on the EDLAALEK peptide at a stoichiometric ratio of 1:1. Calcium coordination induced the self-assembly of the EDLAALEK peptide, resulting in the formation of a nanocomposite with a crystal structure. Furthermore, the formed nanocomposite went through dissociation and self-assembly during in vitro GI digestion, accompanied by the release and rechelation of Ca²⁺, which was related to changes in their secondary structure. Nevertheless, the GI digests of the EDLAALEK-calcium complex could significantly enhance Ca²⁺ absorption across Caco-2 cell monolayers. The findings suggest that the sea cucumber ovum derived peptide has the potential as an efficient nanocarrier to transport calcium through the GI system.

Nanophosphor-Based Contrast Agents for Spectral X-ray Imaging

Lanthanide-based nanophosphors (NPhs) are herein developed as contrast agents for spectral X-ray imaging, highlighting the chemical, macromolecular and structural differences derived from ligand exchange on computed tomography (CT) and solvent dispersibility. Taking advantage of the ability of spectral X-ray imaging with photon-counting detectors to perform image acquisition, analysis, and processing at different energy windows (bins), enhanced signal of our K-edge materials was derived, improving sensitivity of CT imaging, and differentiation between water, tumor-mimic phantoms, and contrast materials. Our results indicate that the most effective of our oleic acid-stabilized K-edge nanoparticles can achieve 2-4x higher contrast than the examined iodinated molecules, making them suitable for deep tissue imaging of tissues or tumors. On the other hand, ligand exchange yielding poly(acrylic acid)-stabilized K-edge nanoparticles allows for high dispersibility and homogeneity in water, but with a lower contrast due to the high density of the polymer grafted, unless further engineering is probed. This is the first well-defined study that manages to correlate NPh grafting density with CT numbers and water dispersibility, laying the groundwork for the development of the next generation CT-guided diagnostic and/or theranostic 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.

Application of periodic density functional theory calculations for exploring copper(II) coordination effects on the mesophase behavior of p-n-alkoxybenzoic acids

Copper(II) benzoates ([Formula: see text]OBA-Cu) with various terminal alkoxy carbon numbers, [Formula: see text]–12, were prepared from [Formula: see text]-[Formula: see text]-alkoxy benzoic acids (nOBAs). Fourier transform infrared (IR) experiments suggested that dimerization through copper(II) chelating bidentate coordination created [Formula: see text]OBA-Cu with a linear rod-like structure, similar to the hydrogen-bonded structure of its parent [Formula: see text]OBA. However, the coordination structure of [Formula: see text]OBA-Cu changed during heating. Periodic density functional theory calculations provided valuable insight into the possible arrangement of the parent and copper(II)-coordinated [Formula: see text]OBAs. The formation of binuclear complexes between two adjacent [Formula: see text]OBA-Cu dimers forced [Formula: see text]OBA-Cu to arrange itself in a layer and exhibit smectic A mesophase. Accordingly, four types of IR stretching absorption of benzoyl carbonyl were observed in binuclear [Formula: see text]OBA-Cu complexes, replacing the original symmetric and asymmetric vibrations of benzoyl carboxylate in chelating bidentate coordination. The lateral association by [Formula: see text]–[Formula: see text] interactions between adjacent parent [Formula: see text]OBA dimers preferred a progressive smectic C arrangement. The origin of the odd–even effect was understood from the consideration of the molecular structure.

The formation mechanism of a sea cucumber ovum derived heptapeptide–calcium nanocomposite and its digestion/absorption behavior

Calcium coordination induced the self-assembly of the sea cucumber ovum derived heptapeptide (NDEELNK), resulting in the formation of the nanocomposite with potential function to transport calcium through the gastrointestinal system.

Coordination to Divalent Cations by Calcium-Binding Proteins

Fourier-transform infrared spectroscopy (FTIR) is a powerful tool for examining the metal coordination of the side chain COO^- groups of Glu and Asp on Ca²⁺-binding proteins in solution. The behavior of COO^- symmetric stretch can be investigated by using protein samples in H₂O solution. However, it is difficult to obtain information about the behavior of the COO^- antisymmetric stretch in H₂O solution, because the COO^- antisymmetric stretching band overlaps with the amide II band. Therefore, to obtain reliable infrared spectra in the region of COO^- antisymmetric stretch, exchangeable protons in the protein should be completely deuterated by incubating the apoprotein dissolved in D₂O under mild heating conditions.

Functional Calcium Binding Peptides from Pacific Cod (Gadus macrocephalus) Bone: Calcium Bioavailability Enhancing Activity and Anti-Osteoporosis Effects in the Ovariectomy-Induced Osteoporosis Rat Model

Calcium binding peptides from Pacific cod (Gadus macrocephalus) bone have attracted attention due to their potential effects on bone health. In this study, calcium binding peptides (CBP) were prepared from Pacific cod bone by trypsin and neutral protease. Ultraviolet spectra, circular dichroism (CD), and Fourier transform infrared spectroscopy (FTIR) revealed that carboxyl and amino groups in CBP could bind to Ca²⁺, and form the peptide-calcium complex (CBP-Ca). Single-pass intestinal perfusion (SPIP) experiments indicated that the intestinal calcium absorption was significantly enhanced (p < 0.01) in CBP-Ca treated Wistar rats. The anti-osteoporosis activity of CBP-Ca was investigated in the ovariectomized (OVX) Wistar rat model. The administration of CBP-Ca significantly (p < 0.01) improved the calcium bioavailability, trabecular bone structure, bone biomechanical properties, bone mineral density, and bone mineralization degree. CBP-Ca notably (p < 0.01) increased serum calcium, however, it remarkably (p < 0.01) reduced the levels of osteocalcin (OCN), bone alkaline phosphatase (BALP), tartrate-resistant acid phosphatase isoform 5b (TRAP5b), and C-telopeptide of type I collagen (CTX-1) in serum. Results suggested that the cod bone derived CBP could bind with calcium, improve the intestinal calcium absorption, calcium bioavailability, and serum calcium, then reduce the bone turnover rate, and thus ameliorate osteoporosis.

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.

Characterization of postmortem biochemical changes in rabbit plasma using ATR-FTIR combined with chemometrics: A preliminary study

Postmortem interval (PMI) determination is one of the most challenging tasks in forensic medicine due to a lack of accurate and reliable methods. It is especially difficult for late PMI determination. Although many attempts with various types of body fluids based on chemical methods have been made to solve this problem, few investigations are focused on blood samples. In this study, we employed an attenuated total reflection (ATR)-Fourier transform infrared (FTIR) technique coupled with principle component analysis (PCA) to monitor biochemical changes in rabbit plasma with increasing PMI. Partial least square (PLS) model was used based on the spectral data for PMI prediction in an independent sample set. Our results revealed that postmortem chemical changes in compositions of the plasma were time-dependent, and various components including proteins, lipids and nucleic acids contributed to the discrimination of the samples at different time points. A satisfactory prediction within 48h postmortem was performed by the combined PLS model with a good fitting between actual and predicted PMI of 0.984 and with an error of ±1.92h. In consideration of the simplicity and portability of ATR-FTIR, our preliminary study provides an experimental and theoretical basis for application of this technique in forensic practice.

Individual and combined toxic effect of nickel and chromium on biochemical constituents in E. coli using FTIR spectroscopy and Principle component analysis

Ni and Cr are ubiquitous pollutants in the aquatic environments. These heavy metals elicit toxicities to aquatic organisms including microbes. In this study, interaction of the two heavy metals on the toxicity in Escherichia coli (E. coli) was studied using FTIR spectroscopy. The binding of Ni(II) to E. coli was stronger than that for Cr(VI). Cr exhibited antagonistic effects in the presence of Ni in E. coli. FTIR analysis showed a decrease in lipid content in the presence of Ni and not for Cr. Further, a decrease in band area was observed in the region of 3000-2800cm(-1) and at ~1455cm(-1) due to a decrease in fatty acids and lipid molecules. The band area ratio of lipid was used to monitor the changes in fatty acids due to metal toxicity. Principle component method helps to discriminates the results between control and metal toxicities in E. coli from the FTIR data. The study shows the importance of metal interaction and its toxicity on E. coli.

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.

Coordination polymers based on a glycine-derivative ligand

The combination of a glycine-derivative supramolecular salt with lanthanide(iii) chloride hydrates under hydrothermal conditions (120 °C, 48 h) produced a family of isotypical materials formulated as [Ln(bodt)(Hbodt)].

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.

Relevance of the sterilization-induced effects on the properties of different hydroxyapatite nanoparticles and assessment of the osteoblastic cell response

Hydroxyapatite (Hap) is a calcium phosphate with a chemical formula that closely resembles that of the mineral constituents found in hard tissues, thereby explaining its natural biocompatibility and wide biomedical use. Nanostructured Hap materials appear to present a good performance in bone tissue applications because of their ability to mimic the dimensions of bone components. However, bone cell response to individual nanoparticles and/or nanoparticle aggregates lost from these materials is largely unknown and shows great variability. This work addresses the preparation and characterization of two different Hap nanoparticles and their interaction with osteoblastic cells. Hap particles were produced by a wet chemical synthesis (WCS) at 37°C and by hydrothermal synthesis (HS) at 180°C. As the ultimate in vivo applications require a sterilization step, the synthesized particles were characterized 'as prepared' and after sterilization (autoclaving, 120°C, 20 min). WCS and HS particles differ in their morphological (size and shape) and physicochemical properties. The sterilization modified markedly the shape, size and aggregation state of WCS nanoparticles. Both particles were readily internalized by osteoblastic cells by endocytosis, and showed a low intracellular dissolution rate. Concentrations of WCS and HS particles less than 500 μg ml(-1) did not affect cell proliferation, F-actin cytoskeleton organization and apoptosis rate and increased the gene expression of alkaline phosphatase and BMP-2. The two particles presented some differences in the elicited cell response. In conclusion, WCS and HS particles might exhibit an interesting profile for bone tissue applications. Results suggest the relevance of a proper particle characterization, and the interest of an individual nanoparticle targeted research.

Vibrational analysis of mononitrosyl complexes in hemerythrin and flavodiiron proteins: relevance to detoxifying NO reductase

Flavodiiron proteins (FDPs) play important roles in the microbial nitrosative stress response in low-oxygen environments by reductively scavenging nitric oxide (NO). Recently, we showed that FMN-free diferrous FDP from Thermotoga maritima exposed to 1 equiv NO forms a stable diiron-mononitrosyl complex (deflavo-FDP(NO)) that can react further with NO to form N(2)O [Hayashi, T.; Caranto, J. D.; Wampler, D. A; Kurtz, D. M., Jr.; Moënne-Loccoz, P. Biochemistry 2010, 49, 7040-7049]. Here we report resonance Raman and low-temperature photolysis FTIR data that better define the structure of this diiron-mononitrosyl complex. We first validate this approach using the stable diiron-mononitrosyl complex of hemerythrin, Hr(NO), for which we observe a ν(NO) at 1658 cm(-1), the lowest ν(NO) ever reported for a nonheme {FeNO}(7) species. Both deflavo-FDP(NO) and the mononitrosyl adduct of the flavinated FPD (FDP(NO)) show ν(NO) at 1681 cm(-1), which is also unusually low. These results indicate that, in Hr(NO) and FDP(NO), the coordinated NO is exceptionally electron rich, more closely approaching the Fe(III)(NO(-)) resonance structure. In the case of Hr(NO), this polarization may be promoted by steric enforcement of an unusually small FeNO angle, while in FDP(NO), the Fe(III)(NO(-)) structure may be due to a semibridging electrostatic interaction with the second Fe(II) ion. In Hr(NO), accessibility and steric constraints prevent further reaction of the diiron-mononitrosyl complex with NO, whereas in FDP(NO) the increased nucleophilicity of the nitrosyl group may promote attack by a second NO to produce N(2)O. This latter scenario is supported by theoretical modeling [Blomberg, L. M.; Blomberg, M. R.; Siegbahn, P. E. J. Biol. Inorg. Chem. 2007, 12, 79-89]. Published vibrational data on bioengineered models of denitrifying heme-nonheme NO reductases [Hayashi, T.; Miner, K. D.; Yeung, N.; Lin, Y.-W.; Lu, Y.; Moënne-Loccoz, P. Biochemistry 2011, 50, 5939-5947 ] support a similar mode of activation of a heme {FeNO}(7) species by the nearby nonheme Fe(II).

Ca(2+)-binding reduces conformational flexibility of RC-LH1 core complex from thermophile Thermochromatium tepidum

The light-harvesting complex, LH1, of thermophile purple bacteria Thermochromatium tepidum consists of an array of α- and β-polypeptides which assemble the photoactive bacteriochlorophyll and closely interact with the membrane-lipids. In this study, we investigated the effect of calcium and manganese ions on the protein structure and thermostability of the reaction centre (RC)-LH1/lipid complex. The binding of Ca(2+), but not Mn(2+) is shown to shift the LH1 Q ( y ) absorption maximum from ~889 to 915 nm and to significantly raise the thermostability of the RC-LH1 complex. The ATR-FTIR spectra indicate that interaction of Ca(2+) as monitored by the carboxylates' vibration of aspartate residues, but not Mn(2+) induces changes in the α-helix packing arrangement. The reduced rate of (1)H/(2)H exchange of proteins' amide protons shows that the accessibility to (2)H(2)O is significantly lowered in Ca(2+)-substituted RC-LH1/lipid complexes. In particular, exchange with the associated lipid molecules, is significantly retarded. These results suggest that the thermostability of the RC-LH1 complex is raised by the distinct interaction with calcium cations which reduces the RC-LH1/lipid dynamics, particularly, at the membrane-water interface.