FTIR investigation of the conformational properties of the cyanide bound horse metmyoglobin

The IR spectra of horse metmyoglobin ligated with the various isotopic forms of the cyanide ion at pH 7.4 display an asymmetric isotope-sensitive profile in the C–N stretching region. Replacement of the water solvent by D₂O or reducing the pH to 5.5 downshift the center frequency of the profiles by ≈1 cm⁻¹ indicating that the Fe–C–N is hydrogen bonded. The measured profiles did not conform to any of the known peak shapes indicating that they are the sum of a number of overlapping peaks. Several techniques have been used to determine the exact number of overlapping peaks such as peak fitting, peak shape analysis and spectral deconvolution. The results indicate that the profiles are the sum of five C–N stretching bands. The five bands were attributed to the existence of the C–N vibrators in the cavities of different Mb-CN conformational states. The variations in the C–N stretching frequency were interpreted in term of the variation in polar interactions between the bound cyanide ion and the surrounding protein in these states.     

Molecular and conformational properties of comb-like polymers with ionically bound side chains studied in organic solvent

Conformational and dynamo-optical properties of a homologous series of poly(cetyltrimethylammonium 2-acrylamido-2-methylpropane sulfonates) with molecular masses ranging from 80 to 700?kDa were studied in chloroform solutions by viscometry, dynamic light scattering, sedimentation, and flow birefringence. The Mark–Kuhn–Houwink Equations for this polymer in chloroform were obtained; the values of hydrodynamic diameter and the Kuhn segment length as well as the value of intrinsic anisotropy of polarizability of the monomer unit were defined.     

Combined on-line transmission FTIR measurements and BTEM analysis for the kinetic study of a consecutive reaction in aqueous-organic phase medium

Combined on-line transmission FTIR spectroscopy and band-target entropy minimization (BTEM) analysis were employed in order to monitor and analyze the kinetics of the alkaline hydrolysis reaction of diethyl phthalate (DEP) in aqueous-ethanol solvent mixture. This reaction is irreversible and involves two consecutive steps with the formation of the observable mono-ion intermediate species. The pure component mid-FTIR spectra of the reactive species involved in this reaction, namely DEP, mono-ion intermediate and di-ion product were successfully reconstructed using BTEM. Their corresponding concentrations were also calculated and subsequently employed to derive the kinetic rate parameters. The effect of temperature and the solvent mixture compositions on these two consecutive reaction steps were also discussed. The temperature variation study showed that both reaction rate coefficients increased with temperature. Both rate coefficients were also affected by the solvent mixture compositions and reached minimum values at certain water-ethanol solvent composition (circa 60% (v/v)). This study shows the utility of combined on-line transmission FTIR spectroscopy and chemometric techniques for the present, rather complex, consecutive organic reaction. Moreover, the present type of approach could facilitate better understanding of a wide variety of organic reactions that are performed in aqueous and mixed aqueous-organic solvents.     

Kinetic study of a complex triangular reaction system in alkaline aqueous-ethanol medium using on-line transmission FTIR spectroscopy and BTEM analysis

The kinetics of the base-catalyzed reaction of methyl 4-hydroxybenzoate in aqueous-ethanol solvent medium was studied and analyzed via combined on-line transmission FTIR spectroscopy and Band-Target Entropy Minimization (BTEM) technique. This reaction is considered complex since it involves simultaneous hydrolysis and ethanolysis reactions of methyl 4-hydrozybenzoate (MP) to form ethyl 4-hydroxybenzoate (EP) as an intermediate and sodium 4-hydroxybenzoate as a final product. The pure component spectra of the reactive species involved in the reaction were reconstructed using BTEM technique. Their corresponding real concentrations were calculated and subsequently used for analyzing the kinetics of this triangular reaction system. The effects of temperature and solvent mixture compositions were studied. In general, the results show that the rates of both hydrolysis and ethanolysis reactions increase with temperature. Addition of ethanol to the solvent mixture also reduces the rates of the hydrolysis reactions. The effect of solvent mixture on the rate of ethanolysis reaction is more complex and influenced by at least two competing factors, namely the concentration of ethoxide ion in the solution and the stabilization effect on the reactant. The enthalpy and entropy activation parameters, ΔH^‡ and ΔS^‡, of both the hydrolysis and ethanolysis reactions were determined using the Eyring equation and the activation parameters confirm the associative nature in the elementary steps in these reactions. Finally, it is shown that the dominant synthetic pathway in this triangular system changes from direct hydrolysis of methyl 4-hydrozybenzoate to the indirect pathway via ethanolysis and then hydrolysis depending on the solvent mixture composition.     

FTIR studies of conformational energies of poly(acrylic acid) in cast films

Fourier transform infrared (FTIR) spectroscopic measurements have been undertaken to estimate the conformational energies of poly(acrylic acid) (PAA) cast films in the temperature range of 40–130°C. The temperature dependence of the IR spectra in the C=O stretching region has been analyzed to yield the side-chain and backbone conformational energies. The estimated energies are close to those previously obtained by polarized Raman spectroscopic measurements for PAA solutions. Combining the FTIR value of conformational energy with the simplified rotational isomeric state (RIS) model proposed in the Raman analysis provides a persistence length in accordance with earlier SAXS experiments. The data also agree with the Gibbs-DiMarzio predictions, further substantiating the validity of the analysis. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys, 35: 507–515, 1997     

Effects of solute-matrix interaction on monitoring the conformational changes of immobilized proteins by surface plasmon resonance sensor

A real-time and labeling-free surface plasmon resonance (SPR) sensor was used to monitor the conformational changes of immobilized globule proteins (RNase A and lysozyme) in chemical unfolding and refolding. The effects of chemical denaturants on the protein structures were investigated. The methodology in protein conformational study on the solid surface is refined through the theoretic calculations and the conformational information of native/denatured proteins in solution. Additionally, our observation illustrates that the ambient buffer solution is merit to influence the refractive index of immobilized protein films and directly be observed from the SPR resonance angle shifts.     

Effects of urea induced protein conformational changes on ion exchange chromatographic behavior

Urea is widely employed to facilitate protein separations in ion exchange chromatography at various scales. In this work, five model proteins were used to examine the chromatographic effects of protein conformational changes induced by urea in ion exchange chromatography. Linear gradient experiments were carried out at various urea concentrations and the protein secondary and tertiary structures were evaluated by far UV CD and fluorescence measurements, respectively. The results indicated that chromatographic retention times were well correlated with structural changes and that they were more sensitive to tertiary structural change. Steric Mass Action (SMA) isotherm parameters were also examined and the results indicated that urea induced protein conformational changes could affect both the characteristic charge and equilibrium constants in these systems. Dynamic light scattering analysis of changes in protein size due to urea-induced unfolding indicated that the size of the protein was not correlated with SMA parameter changes. These results indicate that while urea-induced structural changes can have a marked effect on protein chromatographic behavior in IEX, this behavior can be quite complicated and protein specific. These differences in protein behavior may provide insight into how these partially unfolded proteins are interacting with the resin material.     

Non-natural amino acids as modulating agents of the conformational space of model glycopeptides

The synthesis and conformational analysis in aqueous solution of different alpha-methyl-alpha-amino acid diamides, derived from serine, threonine, beta-hydroxycyclobutane-alpha-amino acids, and their corresponding model beta-O-glucopeptides, are reported. The study reveals that the presence of an alpha-methyl group forces the model peptides to adopt helix-like conformations. These folded conformations are especially significant for cyclobutane derivatives. Interestingly, this feature was also observed in the corresponding model glucopeptides, thus indicating that the alpha-methyl group and not the beta-O-glucosylation process largely determines the conformational preference of the backbone in these structures. On the other hand, atypical conformations of the glycosidic linkage were experimentally determined. Therefore, when a methyl group was located at the Cbeta atom with an R configuration, the glycosidic linkage was rather rigid. Nevertheless, when the S configuration was displayed, a significant degree of flexibility was observed for the glycosidic linkage, thus showing both alternate and eclipsed conformations of the psi(s) dihedral angle. In addition, some derivatives exhibited an unusual value for the phi(s) angle, which was far from a value of -60 degrees expected for a conventional beta-O-glycosidic linkage. In this sense, the different conformations exhibited by these molecules could be a useful tool in obtaining systems with conformational preferences "à la carte".     

Isolation of hemoglobin with metal–organic frameworks Y(BTC)(H_2O)_6

The hierarchical metal-organic frameworks(MOFs),such as Y(BTC)(H_2O)_6,are prepared with yttrium nitrate and benzene-1,3,5-tricarboxylic acid at room temperature.The product is characterized by Fourier transform infrared(FT-IR),X-ray diffraction(XRD),scanning electron microscopy(SEM)and thermogravimetric analysis(TGA).The Y(BTC)(H_2O)_6 particles are sufficiently rigid for performing solid phase extraction and they exhibit favorable selectivity toward the adsorption of hemoglobin.The adsorption behavior of hemoglobin onto the Y(BTC)(H_2O)_6 fits the Langmuir adsorption model with a theoretical adsorption capacity of 555.6 mg g 1.An adsorption efficiency of 87.7%for 100μg mL 1hemoglobin in 1 mL sample solution(at pH 6.0)is achieved with 0.40 mg Y(BTC)(H20)6.77.3%of the retained hemoglobin is readily recovered using a 0.5%(m/v)SDS solution as the stripping reagent.Circular dichroism spectra indicated that the conformation of hemoglobin is maintained during the adsorption-desorption process.The MOFs material is applied for the isolation of hemoglobin from human blood and the purity of the obtained hemoglobin is further verified by sodium dodecyl sulfate polyacrylamide gel electrophoresis(SDS-PAGE).     

Infrared spectroscopic investigation of the conformational properties of furan-2-carboxylates

As an extension of previous studies on furan-2-aldehyde, we have investigated methyl furan-2-carboxylate, ethyl furan-2-carboxylate and methyl furan-2-thiolcarboxylate in order to obtain detailed information on their conformational properties. The skeletal vibrations of the i.r. spectra in different solvents (carbon tetrachloride, acetonitrile, chloroform) and in one liquid phase show the existence of two conformers, the syn and anti forms. The conformational equilibria do not appear to be temperature-dependent, or to be altered by change of phase from liquid to solid. The relative enthalpy differences between the two conformers is indicated by the effect of solvent polarity on their ratios.     

Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein

The periplasmic lysine-, arginine-, ornithine-binding protein (LAOBP) traps its ligands by a large hinge bending movement between two globular domains. The overall geometry of the binding site remains largely unchanged between the open (unliganded) and closed (liganded) forms, with only a small number of residues exhibiting limited movement of their side chains. However, in the case of the ornithine-bound structure, the backbone peptide bond between Asp11 and Thr12 undergoes a large rotation. Molecular dynamics simulations have been used to investigate the origin and mechanism of this backbone movement. Simulations allowing flexibility of a limited region and of the whole binding site, with and without bound ligands, suggest that this conformational change is induced by the binding of ornithine, leading to the stabilisation of an energetically favourable alternative conformation.     

Systematic stepsize variation: Efficient method for searching conformational space of polypeptides

A new and efficient method for overcoming the multiple minima problem of polypeptides, the systematic stepsize variation (SSV) method, is presented. The SSV is based on the assumption that energy barriers can be passed over by sufficiently large rotations about rotatable bonds: randomly chosen dihedral angles are updated starting with a small stepsize (i.e., magnitude of rotation). A new structure is accepted only if it possesses a lower energy than the precedent one. Local minima are passed over by increasing the stepsize systematically. When no new structures are found any longer, the simulation is continued with the starting structure, but other trajectories will be followed due to the random order in updating the torsional angles. First, the method is tested with Met-enkephalin, a peptide with a known global minimum structure; in all runs the latter is found at least once. The global minimum conformations obtained in the simulations show deviations of ±0.0004 kcal/mol from the reference structure and, consequently, are perfectly superposable. For comparison, Metropolis Monte Carlo simulated annealing (MMC-SA) is performed. To estimate the efficiency of the algorithm depending on the complexity of the optimization problem, homopolymers of Ala and Gly of different lengths are simulated, with both the SSV and the MMC-SA method. The comparative simulations clearly reveal the higher efficiency of SSV compared with MMC-SA. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1470–1481, 1998     

Dielectric spectroscopy as a probe for the investigation of conformational properties of proteins

In this brief paper, we review recent and significant results obtained in our laboratory by dielectric spectroscopy (DS). This is a multi purpose and very sensitive approach to investigate structural features of biological systems. DS at radiofrequencies is particularly powerful in the study of structural and conformational properties of proteins. We report on results obtained on three well-known proteins: lysozyme, cytochrome-c and metmyoglobin, which represent very useful models for folding/unfolding studies. The influence of pH and temperature as well as presence of trehalose as a co-solvent, was determined by estimation of the effective hydrodynamic radius and electric dipole moment of the protein in solution. In particular, trehalose was shown to affect the alkaline transition of cytochrome. Conformational effects on the three above-mentioned proteins were observed in a temperature range near the physiological ones. Dynamical properties of lysozyme in mixtures water-glycerol are also discussed. Parallel measurements of photon correlation spectroscopy (PCS) and DS indicated that both translational and rotational diffusive behavior are coherent with the Debye-Stokes-Einstein hydrodynamic model.     

Conformational selection of the AGA*IA(M) heparin pentasaccharide when bound to the fibroblast growth factor receptor

The interaction of the synthetic pentasaccharide AGA*IA(M) (GlcNS,6S-GlcA-GlcNS,3S,6S-IdoA2S-GlcNS,6S-Me) with the extracellular Ig2 domain of the fibroblast growth factor receptor (FGFR2) has been studied by NMR and computational methods. Analysis of the heparin pentasaccharide in the free state and in the complex indicates the existence of a conformational selection process. Although an equilibrium exists between the (1)C(4) and (2)S(0) conformers (ratio 60:40) of the 2-O-sulfo-α-L-iduronate ring (IdoA2S) in the free state, FGFR2 selects only the unique twisted-boat (2)S(0) conformation of this IdoA2S residue. In addition, the protein residues involved in the binding with AGA*IA(M) have also been characterized. The NMR results obtained, from both the ligand and protein perspective, were employed to model the bound conformation of the pentasaccharide by a combined docking and molecular dynamic simulation approach.     

Fabrication of hexagonal boron nitride based 2D nanopore sensor for the assessment of electro-chemical responsiveness of human serum transferrin protein

In this work, we present a step-by-step workflow for the fabrication of 2D hexagonal boron nitride (h-BN) nanopores which are then used to sense holo-human serum transferrin (hSTf) protein at pH ∼8 under applied voltages ranging from +100 mV to +800 mV. 2D nanopores are often used for DNA, however, there is a great void in the literature for single-molecule protein sensing and this, to the best of our knowledge, is the first time where h-BN—a material with large band-gap, low dielectric constant, reduced parasitic capacitance and minimal charge transfer induced noise—is used for protein profiling. The corresponding ΔG (change in pore conductance due to analyte translocation) profiles showed a bimodal Gaussian distribution where the lower and higher ΔG distributions were attributed to (pseudo-) folded and unfolded conformations respectively. With increasing voltage, the voltage induced unfolding increased (evident by decrease in ΔG) and plateaued after ∼400 mV of applied voltage. From the ΔG versus voltage profile corresponding to the pseudo-folded state, we calculated the molecular radius of hSTf, and was found to be ∼3.1 nm which is in close concordance with the literature reported value of ∼3.25 nm.     

1H NMR spectroscopic studies of the conformational isomers of pyrrolidinofullerenes

Mixed bis-adduct derivatives of C60 containing a pyrrolidine and a malonate methano group were synthesized. Three regioisomers, the e', the trans-2, and the trans-3, were isolated and characterized. In-depth NMR studies of these methano-pyrrolidinofullerenes showed that the nitrogen inversion on the pyrrolidine moiety is not a fast event in the 1H NMR time scale as previously regarded. Solvent effects, variable temperature experiments, and protonation of the pyrrolidine nitrogen are addressed.     

Determination of peroxide value of edible oils by FTIR spectroscopy with the use of the spectral reconstitution technique

Spectral reconstitution (SR), a technique that has been developed to facilitate mid-FTIR transmission analysis of inherently viscous samples, was applied to simplify and automate a previously reported FTIR method for the determination of peroxide value (PV) of edible oils. The basis of the PV determination is the rapid reaction of triphenylphosphine (TPP) with the hydroperoxides present in an oil to produce triphenylphosphine oxide (TPPO), which exhibits a readily measurable absorption band at 542 cm⁻¹. In the SR procedure, the viscosity of oil samples is reduced by mixing them with a diluent, which allows them to be readily loaded into a flow-through transmission cell. The spectra of the neat oil samples are then reconstituted from those of the diluted samples by using the absorption of a spectral marker present in the diluent to determine the dilution ratio. For the SR-based PV method, the TPP reagent was added to the diluent, which consisted of odorless mineral spirits (OMS) containing methylcyclopentadienyl manganese tricarbonyl (MMT) as the spectral marker. Sample preparation for PV analysis involved mixing ∼10 ml of oil with ∼25 ml of the TPP-containing diluent; accurate weighing or delivery of precise volumes was not required because the dilution ratio was determined spectroscopically from the intensity of the ν(CO) absorption of MMT at 1942 cm⁻¹ in the spectrum of the diluted sample relative to that in the spectrum of the diluent. Calibration standards, prepared by gravimetric addition of TPPO to a peroxide-free oil, were handled in the same manner, and a linear calibration equation relating the concentration of TPPO (expressed as the equivalent PV) to the absorbance of TPPO at 542 cm⁻¹ relative to a baseline at 530 cm⁻¹ in the reconstituted spectra was obtained, with a regression S.D. of ±0.15 meq/kg oil. PV determinations on two sets of validation samples, spanning PV ranges of 0-20 and 0-2 meq/kg oil, were carried out in parallel by the AOCS titrimetric and SR-based FTIR procedures, and comparison of the results of duplicate analyses by the two methods indicated that the latter was more reproducible and slightly more sensitive. The SR-based PV method, when implemented on an autosampler-equipped FTIR system, allowed for the automated analysis of ∼90 samples per hour.     

Intrinsic information content of NMR dipolar couplings: a conformational investigation of 1,3-butadiene in a nematic phase.

The conformational equilibrium of 1,3-butadiene in a condensed fluid phase is investigated by liquid-crystal NMR spectroscopy. The full set of D(HH) and D(CH) dipolar couplings is determined from the analysis of the (1)H spectra of the three 1,3-butadiene most-abundant isotopomers (i.e. the all (12)C and the two single-labeled (13)C isotopomers) for a total of 21 independent dipolar couplings. A very good starting set of spectral parameters for the analysis of the (1)H spectrum is determined in a semiautomated way by the analysis of the (N-1) (specifically, N=6, the number of 1/2 spin nuclei in the spin system) quantum refocused (5QR), and not (5Q), spectra. As an alternative approach, a Monte Carlo (MC) numerical simulation, capable of predicting the solute ordering, is tested to simulate the 5QR spectrum. The set of D(ij) couplings is very good, proving that the MC method can represent a novel, valid alternative to the existing spectral simplification procedures. The experimentally determined dipolar-coupling data set is fully compatible with the 1,3-butadiene conformational distribution reported in the literature for isolated molecules, indicating the presence of about 99 % of s-trans conformer. With regards to the remaining 1 %, in spite of the direct and very strong dependence of the observables on the molecular structure, it was not possible to discriminate between the planar s-cis and s-gauche forms, both of which produce a very good fit of the dipolar couplings. Vibrational corrections, up to the anharmonic term, were applied; the calculated geometrical parameters are in good- although not exact-agreement with those reported in the literature from experimental and theoretical investigations. This result can be considered as supporting the methodology used for obtaining the structure and conformational distribution of a flexible molecule in a liquid phase.     

NMR investigation on the conformational properties of N-[2-pyridyl-N-oxide]-amino derivatives

The proton NMR spectra of N-[2-pyridyl-N-oxide]-derivatives of primary and secondary ethylamines, containing a substituent R on the C atom bearing the amino function, have been completely analysed in terms of the fundamental NMR parameters. The preferred conformations of the compounds investigated were established by the indications from NOE experiments as well as: (1) the long range coupling across the five bond between the aminic hydrogen and the proton in 4-position of the pyridine-N-oxide ring (⁵J_m^H,NH ～ 0·5 c/s), (2) the value of the vicinal coupling constant in the fragment CHNH (³J_NHCH ～ 7–9 c/s), (3) the large deshielding (Δτ ～ 1–1·5 ppm) observed for the resonance position of the proton on the asymmetric C atom in secondary amine derivatives with respect to the corresponding primary ones, and (4) the diamagnetic shielding produced on protons in position 3 and 4 of the pyridine-N-oxide ring by different aromatic groups introduced in the R substituent.The NMR data confirmed the preferred rotamers previously suggested on the basis of ORD and CD measurements.