Infrared analysis of ligand- and oxidation-induced conformational changes in hemoglobins and myoglobins

Infrared Spectroscopy: A New Frontier in Hematological Disease Diagnosis

Hematological diseases, due to their complex nature and diverse manifestations, pose significant diagnostic challenges in healthcare. The pressing need for early and accurate diagnosis has driven the exploration of novel diagnostic techniques. Infrared (IR) spectroscopy, renowned for its noninvasive, rapid, and cost-effective characteristics, has emerged as a promising adjunct in hematological diagnostics. This review delves into the transformative role of IR spectroscopy and highlights its applications in detecting and diagnosing various blood-related ailments. We discuss groundbreaking research findings and real-world applications while providing a balanced view of the potential and limitations of the technique. By integrating advanced technology with clinical needs, we offer insights into how IR spectroscopy may herald a new era of hematological disease diagnosis.

Central and Peripheral Fatigue Evaluation during Physical Exercise in Athletic Horses by Means of Raman Spectroscopy

The evaluation of the performance levels in athletic horses is of major importance to prevent sports injuries. Raman spectroscopy is an innovative technique that allows for a rapid evaluation of biomolecules in biological fluids. It also permits qualitative and quantitative sample analyses, which lead to the simultaneous determination of the components of the examined biological fluids. On the basis of this, the Raman spectroscopy technique was applied on serum samples collected from five Italian Saddle horses subjected to a standardized obstacle course preceded by a warm-up to evaluate the applicability of this technique for the assessment of central and peripheral fatigue in athletic horses. Blood samples were collected via jugular venipuncture in a vacutainer tube with a clot activator before exercise, immediately after exercise, and 30 min and 1 h after the end of the obstacle course. Observing the obtained Raman spectra, the major changes due to the experimental conditions appeared in the (1300-1360) cm^-1 and (1385-1520) cm^-1 bands. In the (1300-1360) cm^-1 band, lipids and tryptophan were identified; in the (1385-1520) cm^-1 band, leucine, glycine, isoleucine, lactic acid, tripeptide, adenosine, and beta carotene were identified. A significant effect of exercise was recorded on all the sub-bands. In particular, a change immediately after exercise versus before exercise was found. Moreover, the mean lactic concentration was positively correlated with the Raman area of the sub-band assigned to lactic acid. In this context, the application of Raman spectroscopy on blood serum samples represents a useful technique for secondary-structure protein identification to investigate the metabolic changes that occur in athletic horses during physical exercise.

Nanoengineering of eco-friendly silver nanoparticles using five different plant extracts and development of cost-effective phenol nanosensor

The production of environmentally friendly silver nanoparticles (AgNPs) has aroused the interest of the scientific community due to their wide applications mainly in the field of environmental pollution detection and water quality monitoring. Here, for the first time, five plant leaf extracts were used for the synthesis of AgNPs such as Basil, Geranium, Eucalyptus, Melia, and Ruta by a simple and eco-friendly method. Stable AgNPs were obtained by adding a silver nitrate (AgNO₃) solution with the leaves extract as reducers, stabilizers and cappers. Only, within ten minutes of reaction, the yellow mixture changed to brown due to the reduction of Ag⁺ ions to Ag atoms. The optical, structural, and morphology characteristics of synthesized AgNPs were determined using a full technique like UV-visible spectroscopy, FTIR spectrum, XRD, EDX spectroscopy, and the SEM. Thus, Melia azedarach was found to exhibit smaller nanoparticles (AgNPs-M), which would be interesting for electrochemical application. So, a highly sensitive electrochemical sensor based on AgNPs-M modified GCE for phenol determination in water samples was developed, indicating that the AgNPs-M displayed good electrocatalytic activity. The developed sensor showed good sensing performances: a high sensitivity, a low LOD of 0.42 µM and good stability with a lifetime of about one month, as well as a good selectivity towards BPA and CC (with a deviation less than 10%) especially for nanoplastics analysis in the water contained in plastics bottles. The obtained results are repeatable and reproducible with RSDs of 5.49% and 3.18% respectively. Besides, our developed sensor was successfully applied for the determination of phenol in tap and mineral water samples. The proposed new approach is highly recommended to develop a simple, cost effective, ecofriendly, and highly sensitive sensor for the electrochemical detection of phenol which can further broaden the applications of green silver NPs.

Systematic FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin under Various Denaturation Conditions

Human serum albumin (HSA) is the most abundant protein in blood plasma. HSA is involved in the transport of hormones, fatty acids, and some other compounds, maintenance of blood pH, osmotic pressure, and many other functions. Although this protein is well studied, data about its conformational changes upon different denaturation factors are fragmentary and sometimes contradictory. This is especially true for FTIR spectroscopy data interpretation. Here, the effect of various denaturing agents on the structural state of HSA by using FTIR spectroscopy in the aqueous solutions was systematically studied. Our data suggest that the second derivative deconvolution method provides the most consistent interpretation of the obtained IR spectra. The secondary structure changes of HSA were studied depending on the concentration of the denaturing agent during acid, alkaline, and thermal denaturation. In general, the denaturation of HSA in different conditions is accompanied by a decrease in α-helical conformation and an increase in random coil conformation and the intermolecular β-strands. Meantime, some variation in the conformational changes depending on the type of the denaturation agent were also observed. The increase of β-structural conformation suggests that HSA may form amyloid-like aggregates upon the denaturation.

Bacterial indoleacetic acid-induced synthesis of colloidal Ag2O nanocrystals and their biological activities

The biosynthesis and biological activity of colloidal Ag₂O nanocrystals have not been well studied, although they have potential applications in many fields. For the first time, we developed a reducing agent free, cost-effective technique for Ag₂O biosynthesis using Xanthomonas sp. P5. The optimal conditions for Ag₂O synthesis were 50 °C, pH 8, and 2.5 mM AgNO₃. Using these conditions the yield of Ag₂O obtained at 10 h was about five times higher than that obtained at 12 h under unoptimized conditions. Ag₂O was characterized by FESEM-EDS, TEM, dynamic light scattering, XRD, and UV-Visible spectroscopy. Indoleacetic acid produced by the strain P2 was involved in the synthesis of Ag₂O. Ag₂O exhibited a broad antimicrobial spectrum against several human pathogens. Furthermore, Ag₂O exhibited 1,1-diphenyl-2-picrylhydrazyl (IC₅₀ = 25.1 µg/ml) and 2,2'-azinobis-3-ethylbenzothiazoline-6-sulfonate (IC₅₀ = 16.8 µg/ml) radical scavenging activities, and inhibited collagenase (IC₅₀ = 27.9 mg/ml). Cytotoxicity of Ag₂O was tested in fibroblast cells and found to be non-toxic, demonstrating biocompatibility.

Near infrared light induces post-translational modifications of human red blood cell proteins

There is a growing body of evidence that near infrared (NIR) light exerts beneficial effects on cells. Its usefulness in the treatment of cancer, acute brain injuries, strokes and neurodegenerative disorders has been proposed. The mechanism of the NIR action is probably of photochemical nature, however it is not fully understood. Here, using a relatively simple biological model, human red blood cells (RBCs), and a polychromatic non-polarized light source, we investigate the impact of NIR radiation on the oxygen carrier, hemoglobin (Hb), and anion exchanger (AE1, Band 3). The exposure of intact RBCs to NIR light causes quaternary transitions in Hb, dehydration of proteins and decreases the amount of physiologically inactive methemoglobin, as detected by Raman spectroscopy. These effects are accompanied by a lowering of the intracellular pH (pHi) and changes in the cell membrane topography, as documented by atomic force microscopy (AFM). All those changes are in line with our previous studies where alterations of the membrane fluidity and membrane potential were attributed to NIR action on RBCs. The rate of the above listed changes depends strictly on the dose of NIR light that the cells receive, nonetheless it should not be considered as a thermal effect.

Extracting Infrared Spectra of Protein Secondary Structures Using a Library of Protein Spectra and the Ramachandran Plot

Infrared (IR) spectra from 1200 to 1800 cm(-1) of the pure α-helix and β-sheet secondary structures have been extracted using a covariant least-squares procedure which relates a library of 40 infrared (IR) solution protein spectra from the work of Dong, Carpenter, and Caughey and amino acid fractions of the proteins based on assignments by STRIDE (secondary structure identification) of Eisenhaber and Argos. The excitonic splitting of the β-sheet structures is determined for this library of solution proteins. The method is extended to find a set of spectral basis functions that analyze IR spectra of protein samples for α-helix and β-sheet content. A rigorous error analysis including covariance, the correlations between the input library spectra, was used to justify the results and avoid less meaningful results. The utility of the results on α-helix and β-sheet regions is demonstrated by detecting protein changes due to cancer in imaging Fourier transform IR (FTIR) spectra of liver tissue slices. This work ends with a method to extract IR spectra of less prominent torsional angle distributions.

Obtaining information about protein secondary structures in aqueous solution using Fourier transform IR spectroscopy

Fourier transform IR (FTIR) spectroscopy is a nondestructive technique for structural characterization of proteins and polypeptides. The IR spectral data of polymers are usually interpreted in terms of the vibrations of a structural repeat. The repeat units in proteins give rise to nine characteristic IR absorption bands (amides A, B and I-VII). Amide I bands (1,700-1,600 cm(-1)) are the most prominent and sensitive vibrational bands of the protein backbone, and they relate to protein secondary structural components. In this protocol, we have detailed the principles that underlie the determination of protein secondary structure by FTIR spectroscopy, as well as the basic steps involved in protein sample preparation, instrument operation, FTIR spectra collection and spectra analysis in order to estimate protein secondary-structural components in aqueous (both H2O and deuterium oxide (D2O)) solution using algorithms, such as second-derivative, deconvolution and curve fitting. Small amounts of high-purity (>95%) proteins at high concentrations (>3 mg ml(-1)) are needed in this protocol; typically, the procedure can be completed in 1-2 d.

Use of infrared spectroscopy to monitor protein structure and stability

One of the most versatile methods for monitoring the structure of proteins, either in solution or in the solid state, is Fourier transform infrared spectroscopy. Also known as mid-range infrared, which covers the frequency range from 4000 to 400 cm(-1), this wavelength region includes bands that arise from three conformationally sensitive vibrations within the peptide backbone (amide I, II and III). Of these vibrations, amide I is the most widely used and can provide information on secondary structure composition and structural stability. One of the advantages of infrared spectroscopy is that it can be used with proteins that are either in solution or in the solid state. The use of infrared to monitor protein structure and stability is summarized herein. In addition, specialized infrared methods are presented, such as techniques for the study of membrane proteins and oriented samples. In addition, there is a growing body of literature on the use of infrared to follow reaction kinetics and ligand binding in proteins, as well as a number of infrared studies on protein dynamics. Finally, the potential for using near-infrared spectroscopy to study protein structure is introduced.

Time-resolved flow-flash FT-IR difference spectroscopy: the kinetics of CO photodissociation from myoglobin revisited

Fourier-transform infrared (FT-IR) difference spectroscopy has been proven to be a significant tool in biospectroscopy. In particular, the step-scan technique monitors structural and electronic changes at time resolutions down to a few nanoseconds retaining the multiplex advantage of FT-IR. For the elucidation of the functional mechanisms of proteins, this technique is currently limited to repetitive systems undergoing a rapid photocycle. To overcome this obstacle, we developed a flow-flash experiment in a miniaturised flow channel which was integrated into a step-scan FT-IR spectroscopic setup. As a proof of principle, we studied the rebinding reaction of CO to myoglobin after photodissociation. The use of microfluidics reduced the sample consumption drastically such that a typical step-scan experiment takes only a few 10 ml of a millimolar sample solution, making this method particularly interesting for the investigation of biological samples that are only available in small quantities. Moreover, the flow cell provides the unique opportunity to assess the reaction mechanism of proteins that cycle slowly or react irreversibly. We infer that this novel approach will help in the elucidation of molecular reactions as complex as those of vectorial ion transfer in membrane proteins. The potential application to the oxygen splitting reaction of cytochrome c oxidase is discussed.

Biomimetic synthesis and characterisation of protein capped silver nanoparticles

A controlled and up-scalable route for the biosynthesis of silver nanopartilces (NPs) mediated by fungal proteins of Coriolus versicolor has been undertaken for the first time. The fungus when challenged with silver nitrate solution accumulated silver NPs on its surface in 72h which could be reduced to 1h by tailoring the reaction conditions. Under alkaline conditions, the reaction was much faster and could easily proceed at room temperature even without stirring. The resulting Ag NPs displayed controllable structural and optical properties depending on the experimental parameters such as pH and reaction temperatures. The average size, morphology, and structure of particles were determined by AFM, TEM, XRD and UV/Visible absorption spectrophotometry. Fourier transform infrared study disclosed that the amino groups were bound to the particles, which was accountable for the stability of NPs. It further confirmed the presence of protein as the stabilizing and capping agent surrounding the silver NPs. Experiments were conducted both with, media in which fungus was initially harvested and that of pristine fungal mycelium alone. Under normal conditions, in the case of media extracellular synthesis took place whereby other than the fungal proteins, glucose was also responsible for the reduction. In the case of fungal mycelium, the intracellular formation of Ag NPs, could be tailored to give both intracellular and extracellular Ag NPs under alkaline conditions whereby the surface S-H groups of the fungus played a major role.

Spectroscopic study on the communication between a heme a3 propionate, Asp399 and the binuclear center of cytochrome c oxidase from Paracoccus denitrificans

The proton pumping mechanism of cytochrome c oxidase on a molecular level is highly disputed. Recently theoretical calculations and real time electron transfer measurements indicated the involvement of residues in the vicinity of the ring A propionate of heme a3, including Asp399 and the CuB ligands His 325, 326. In this study we probed the interaction of Asp399 with the binuclear center and characterize the protonation state of its side chain. Redox induced FTIR difference spectra of mutations at the site in direct comparison to wild type, indicate that below pH 5 Asp 399 displays signals typical for the deprotonation of the acidic residue with reduction of the enzyme. Interestingly at a pH higher than 5, no contributions from Asp 399 are evident. In order to probe the interaction of the site with the binuclear center we followed the rebinding of CO by infrared spectroscopy for mutations on residue Asp399 to Glu, Asn and Leu. Previously different CO conformers have been identified for bacterial cytochrome c oxidases, and its pH dependent behaviour discussed to be relevant for catalysis. Interestingly we observe the lack of this pH dependency and a strong influence on the observable conformers for all mutants studied here, clearly suggesting a communication of the site with the heme-copper center and the nearby histidine residues.

Equilibrium titrations of acid-induced unfolding–refolding and salt-induced molten globule of cytochrome c by FT-IR spectroscopy

Despite extensive investigations on the acid-unfolded and acid/salt-induced molten globule(-like) states of cytochrome c using variety of techniques, structural features of the acid-unfolded state in terms of residual secondary structures and the structural transition between the acid-unfolded and acid/salt-refolded states have not been fully characterized beyond the circular dichroism (CD) spectroscopy. It is unusual that secondary structure(s) of the unfolded state leading to the molten globule state, an important protein folding intermediate, as determined by CD was not fully corroborated by independent experimental method(s). In this study, we carried out an equilibrium titration of acid-induced unfolding and subsequent acid- and salt-induced refolding of cytochrome c using Fourier transform infrared spectroscopy. The spectral profiles of the equilibrium titration reveal new structural details about the acid-unfolded state and the structural transition associated with the acid/salt-refolded molten globule(-like) states of cytochrome c.

Characterization of hemoglobin immobilized on γ-zirconium phosphate

The fact that different gamma-zirconium phosphate (gamma-ZrP) preintercalation method induced varied degree and type of conformational change of the adsorption protein was confirmed by characterization techniques including circular dichroism (CD), fourier transform infrared spectroscopy (FTIR) and X-ray powder diffraction (XRD) analysis. The results indicated that the association of hemoglobin with gamma-ZrP preintercalated using butylamine was correlated with conformational change in the secondary structure of the protein. gamma-ZrP which was preintercalated with tetra (n-butylammonium) hydroxide caused the conformational change of Hemoglobin in both the secondary structure and the tertiary structure. X-ray powder diffraction analysis was used to analyze the crystalline structure of the nanocomposites prepared by relamination. The adsorption isotherms of Hemoglobin on different matrices were set up and fitted with Langmuir and Freundlich equations.

Inhibition of Human Hemoglobin Autoxidaiton by Sodium n-Dodecyl Sulphate

The effect of sodium n-dodecyl sulphate (SDS) on hemoglobin autoxidation was studied in the presence of a 100 mM phosphate buffer (pH 7.0) by different methods. These included spectrophotometry, fluorescence technique, cyclic voltametry, differential scanning calorimetry, and densitometry. Spectroscopic studies showed that SDS concentrations up to 1 mM increased deoxy-, decreases oxy-, and had no significant effect on the met- conformation of hemoglobin. Therefore, a SDS concentration up to 1 mM increased the deoxy form of hemoglobin as the folded, compact state and decreases the oxy conformation. The turbidity measurements and differential scanning calorimetry techniques indicated a more stable conformation for hemoglobin in the presence of SDS up to 1 mM. Electrochemical studies also confirmed a more difficult oxidation under these conditions. The induction of the deoxy form in the presence of SDS was confirmed by densitometry techniques. The compact structure of deoxyhemoglobin blocks the formation of met-conformation in low SDS concentrations.

Analysis of the interaction between monoclonal antibodies and human hemoglobin (native and cross-linked) using a surface plasmon resonance (SPR) biosensor

To develop a stable immuno-assay system for quantification of human hemoglobin (Hb), the interaction between various antibodies and Hb was studied using a surface plasmon resonance (SPR) biosensor in the BIAcore equipment (Amersham Pharmacia Biotech) with an immobilized anti-Hb antibody sensor chip. When polyclonal antibodies were used, the immuno-reactivity of purified and commercially available Hb decreased drastically with incubation times up to 14 h. This instability of immuno-reactivity of Hb is attributable to the conformational changes in Hb induced by oxidation. On the other hand, of the sixteen monoclonal antibodies tested, four antibodies (MSU-102, -103, -106 and -115) were found to maintain their immuno-reactivities at least up to 24 h. During long-term storage, however, the immuno-reactivity of Hb with these monoclonal antibodies decreased significantly. The chemical betabeta-cross-linking of Hb was effectively able to stabilize the structure of Hb and immuno-reactivity with monoclonal antibodies such as MSU-103 for periods at least up to 70 days. Therefore, the combination of specific monoclonal antibodies such as MSU-103 and a betabeta-cross-linked Hb standard could be used for the quantification of Hb.

Secondary structure dependent on metal ions of copper,zinc superoxide dismutase investigated by Fourier transform IR spectroscopy

Copper, zinc superoxide dismutase (Cu2Zn2-SOD) from bovine erythrocyte and its metal ion free derivatives, E2Zn2-SOD, Cu2E2-SOD, and E2E2-SOD (E: empty) were prepared and their secondary structures were investigated by Fourier transform ir spectroscopy. In 20 mM deuterated phosphate buffer (pD 7.5) solution at room temperature, the native Cu2Zn2-SOD contains about 34% beta-strand, 17% beta-turn, and 49% unordered structures, which is similar to the content determined by x-ray crystal structural analysis. The metal ion free derivatives decrease the component of beta-strand and increase the unordered structure component in trend. Especially in the cases of zinc-free derivatives, Cu2E2-SOD and E2E2-SOD, about 24% beta-strand, 20% beta-turn, and 57% unordered structures are obtained. The result indicates that the zinc ion plays an important role in determining the secondary structure of copper,zinc superoxide dismutase.

FTIR studies of recombinant human granulocyte-macrophage colony-stimulating factor in aqueous solutions: secondary structure, disulfide reduction and thermal behavior

Fourier transform infrared spectroscopy (FTIR) has been used to investigate the secondary structure, disulfide reduction and thermal behavior of recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) in aqueous solutions. The contributions of amino-acid side-chain groups to the amide I bands of rhGM-CSF in H2O and in D2O solutions were carefully scrutinized, as 40% of the total 127 amino-acid residues of rhGM-CSF is side-chain absorptive (asparagine, glutamine, etc.). The FTIR results indicated that rhGM-CSF is composed of 46% alpha-helix, 7% beta-sheet, 23% turn and 24% loop/irregular structures which are in good agreement with the X-ray diffractional data. Reduction of rhGM-CSF with dithiothreitol caused apparent unfolding of the native conformation followed by the time-dependent increase of beta-aggregation bands which arose at 1622 and 1693 cm(-1) in H2O, 1613 and 1684 cm(-1) in D2O solutions. The result also showed that tertiary structure can change independently of the secondary structure. Thermal denaturation of rhGM-CSF took place at 55 to 70 degrees C and the denatured protein adopted an irregular structure as revealed by the FTIR spectra. The thermal denaturation did not show the formation of intermolecular beta-aggregates which is typical of most thermal denatured proteins. Moreover, it is partly reversible, indicating a special thermal stability of rhGM-CSF.