Molecular modeling and spectroscopic studies on the binding of guaiacol to human immunoglobulin

The fluorogenic property of guaiacol was exploited for the first time to analyze the interaction with target protein as a probe by molecular modeling, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. Molecular docking was performed to reveal the possible binding mode or mechanism and suggested that guaiacol can strongly bind to human immu- noglobulin (HIgG). It is considered that guaiacol binds to HIgG mainly by a hydrophobic interaction and there are two hydrogen bond interactions between the drug and the residues LEU 80 and ASP 65, which is in good agreement with the results from the experimental thermodynamic parameters (the enthalpy change △H0 and the entropy change △S0 were calculated to be 65.55 kJ·mol-1 and 132.95 J·mol-1·K-1 according to the Vant’ Hoff equation). Data obtained by the fluorescence spectroscopy indicated that binding of guaiacol with HIgG leads to dramatic enhancement in the fluorescence emission intensity along with significant occurrence of efficient Frster resonance energy transfer (FRET) from the residue of HIgG to the protein bound guaiacol. From the low value of fluorescence anisotropy (r = 0.06), it is argued that the probe molecule is located in the motionally unrestricted environment of the protein. The alterations of protein’s secondary structure in the presence of guaiacol in aqueous solution were quantitatively calculated by the evidences from FT-IR and CD spectroscopes.     

Changes in the secondary structure of HMGB1 protein bonded to DNA

The stage of noncooperative interaction of the chromosomal nonhistone protein HMGB1 with DNA has been studied by spectroscopic methods and gel retardation. It was found that complexation was accompanied by compaction of the DNA molecule over a wide range of protein/DNA ratios in the complex. A circular dichroism study showed that the binding with DNA changed the secondary structure of the HMGB1 protein. Changes in the structure of the protein start under the conditions of an excess of binding sites on DNA and end at a ratio of ∼40–50 base pairs per protein molecule, the α-helicity of HMGB1 in the complex increasing by 20% compared with the free state. It is believed that the change in the secondary structure of HMGB1 during the binding with DNA underlies the mechanisms of the various functions of this protein in the cell.     

应用光谱和分子模拟法研究一种聚酰亚胺聚合物与人免疫球蛋白的相互作用

本文利用荧光猝灭法、红外光谱法及计算机模拟技术研究了一种聚酰亚胺聚合物(2,6-Bis(4-amino-2-trifluoromethyl phenoxy-4’- benzoyl)-pyridine,简称BAFP )与人免疫球蛋白（HIgG）的相互作用。同步荧光的结果定性地说明了BAFP影响水溶液中HIgG二级结构的情况。而判定BAFP影响HIgG二级结构的定量依据来自红外光谱,实验数据表明α螺旋结构的含量相比未加入药物时增加了约2.6～10.2%,,β折叠增大了约13.6～27.7%,,而β转角则减小了约23.8～30.3%。分子模拟的结果显示BAFP与HIgG的键合作用很强,并且有四个氢键在BAFP与HIgG分子的色氨酸Trp 170, 缬氨酸Val 105, 甲硫氨酸Met 139 及天冬酰胺Asn 52之间形成;同时也显示出维持药物与蛋白质的相互作用力主要是疏水作用,这与实验所得到的热力学参数判定作用力的结果相一致（依据范德霍夫公式计算得 与 的值分别为-6.70KJ.mol-1 和 71.93 J.mol-1.K-1）。     

Flow-injection analysis based on a membrane separation module and a bulk acoustic wave impedance sensor – determination of the volatile acidity of fermentation products

A novel flow-injection analysis (FIA) system has been developed for the rapid determination of the volatile acidity of some fermentation products like vinegars and juices. The proposed method is based on the diffusion of volatile acids, mainly acetic acid, across a PTFE gas-permeable membrane from an acid stream into an alkaline stream, and the acids trapped in the acceptor solution are determined online by a bulk acoustic wave impedance sensor based on changes in the conductivity of the solution. It exhibited a linear frequency response up to 10 mmol · L^–1 acetic acid with a detection limit of 50 μmol · L^–1, and the precision was better than 1% (RSD) at a through-put of 72 h^–1. The effects of operating voltage for the detector, cell constant of the electrode, composition of acceptor stream, flow rates and temperature on the FIA performance were also investigated. Received: 2 June 1997 / Revised: 7 July 1997 / Accepted: 12 July 1997     

Structure of lipid A from the marine gram-negative bacterium <Emphasis Type="Italic">Pseudoalteromonas nigrifaciens</Emphasis> IAM 13010<Superscript>T</Superscript>

The structure of lipid A from the marine γ-proteobacterium Pseudoalteromonas nigrifaciens IAM 13010^T that was prepared by hydrolysis of the corresponding lipopolysaccharide by acetic acid (1%) was determined by chemical analysis, ¹³C NMR spectroscopy, and MALDI/TOF and LSIMS mass spectrometry. It was shown that lipid A is a β-1,6-bonded disaccharide of glucosamine that is substituted by two phosphoric acids (in the C1 and C4′ positions), two (R)-3-hydroxyalkanoic (normal and branched) acids with ester bonding (at the C3 and C3′-positions), and (R)-3-hydroxydodecanoic and (R)-3-dodecanoyloxydodecanoic acids (both with amide bonding at C2′ and C2, respectively). It was hypothesized that this type of structure is typical of lipid A from bacteria of the genus Pseudoalteromonas in general. __________ Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 425–429, September–October, 2007.     

LC–MS Determination and Pharmacokinetic Study of a Novel Sulfonylurea: Potential Hypoglycemic Agent in Rat Plasma

To support preclinical pharmacokinetic investigation of 1-[4-[2-(4-bromobenzene-sulfonaminoethyl)phenylsufonyl]-3-(trans-4-methylcyclohexyl)urea (G004), a rapid, sensitive and specific high-performance liquid chromatography–electrospray ionization mass spectrometry (LC–ESI-MS) method was developed and validated. Glibenclamide was employed as internal standard. After liquid–liquid extraction the analyte was analyzed on a Kromasil C₁₈ column (150 × 2.0 mm i.d.) with a mobile phase consisted of acetonitrile–water (0.05% acetic acid), 30:70 (v/v). The flow rate was 0.2 mL min⁻¹. Detection was performed on a quadrupole mass spectrometer using an electrospray ionization interface and the selected-ion monitoring (SIM) mode. The retention time was about 3.5 and 4.2 min for Glibenclamide and G004, respectively. The assay was linear over the concentration range of 2.0–500.0 ng mL⁻¹. Extraction Recovery of G004 in rat plasma was more than 87%. The intra- and inter-assay precision was lower than 11.5% (CV). This validated method was successfully applied to the pharmacokinetics of G004 in rats.     

Synthesis and Gelation Behavior of Cholesteryl Glycinate Anthraquinone‐2‐Carboxylamide and Cholesteryl Glycinate 9,10‐Dimethyloxyl Anthracene‐2‐Carboxylamide

Cholesteryl glycinate anthraquinone‐2‐carboxylamide (CGAC), an electron acceptor, and cholesteryl glycinate 9,10‐dimethyloxyl anthracene‐2‐carboxylamide (CGDAC), an electron donor, were synthesized and characterized via ¹H NMR, IR and elemental analysis. Gelation studies demonstrated that acetic acid and some mixed solvents containing more than 30% acetic acid could be efficiently gelled by CGAC. Unlike CGAC, CGDAC could not gel any of the solvents tested. SEM and AFM studies showed that the gelator in the gel system of CGAC‐acetic acid self‐assembled into a fiber‐like tubular structure, and the tubules were further self‐tangled into networks. Introduction of CGDAC into the CGAC‐acetic acid system had little effect upon the gel properties of the CGAC‐acetic acid system. This observation was explained by considering interruption of the possible donor‐acceptor interaction between CGAC and CGDAC due to protonation of the latter. Comparing the structure and gelation properties of CGAC with those of similar structures reported in the literature further indicates that a small change in the structure of the linker between the A (aromatic) part and S (steroidal) part of the ALS type gelators affects the gelation behaviors of the ALS type gelators significantly.     

A Thermodynamic Study on the Binding of Calcium Ion with Myelin Basic Protein

The interaction of myelin basic protein (MBP) from the bovine central nervous system with divalent calcium ion was studied by isothermal titration calorimetry at 27 °C in aqueous solution. The extended solvation model was used to reproduce the enthalpies of Ca²⁺-MBP interaction over the whole range of Ca²⁺ concentrations. The solvation parameters recovered from the solvation model were attributed to the structural change of MBP due to the metal ion interaction. It was found that there is a set of two identical and non-interacting binding sites for Ca²⁺ ions. The association equilibrium constant is 0.021 μmol⋅dm⁻³. The molar enthalpy of binding is ΔH=−15.10 kJ⋅mol⁻¹.     

A rapid automated method for wine analysis based upon sequential injection (SI)-FTIR spectrometry

A new process control methodology for the simultaneous determination of sugars, alcohols and organic acids in wine based on multivariate evaluation of mid-IR transmission spectra of wine samples is presented. In addition to ethanol several lower level wine components (glucose, fructose, glycerol, citric-, tartaric-, malic-, lactic- and acetic acid) were determined. To establish a multivariate calibration model a set of 72 calibration solutions was prepared and measured, using a novel, fully automated sequential injection (SI) system with Fourier transform infrared (FTIR) detection. The resulting spectra were evaluated using a partial least square (PLS) model. The developed PLS model was then applied to the analysis of real wine samples containing 79–91 g L^–1 ethanol, 5.9–8.1 g L^–1 glycerol, 0.4–6.9 g L^–1 glucose, 1.5–7.5 g L^–1 fructose, 0.3–1.6 g L^–1 citric acid, 1.0–1.7 g L^–1 tartaric acid, 0.02–3.2 g L^–1 malic acid, 0.4–2.8 g L^–1 lactic acid and 0.15–0.60 g L^–1 acetic acid, yielding results which were in good agreement with those obtained by an external reference method (HPLC-IR). The short analysis time (less than 3 min) together with high reproducibility makes the newly developed method applicable to process control and screening purposes (average of the standard deviations calculated from four repetitive measurements of six different real samples: ethanol: 0.55 g L^–1, glycerol: 0.037 g L^–1, glucose: 0.056 g L^–1, fructose: 0.036 g L^–1, citric acid: 0.020 g L^–1, tartaric acid: 0.010 g L^–1, malic acid: 0.052 g L^–1, lactic acid: 0.012 g L^–1 and acetic acid: 0.026 g L^–1). Received: 21 January 1998 / Revised: 5 March 1998 / Accepted: 6 March 1998     

FIRE: predicting the spatial proximity of protein residues from 3D NOESY–HSQC

 We address the problem of the prediction of residue spatial proximity in a protein, through the automatic processing of a 3D ¹⁵N NOESY–HSQC. The spatial distance between residues is estimated from a spectral match value calculated using a comparison of the resonances involving the amide hydrogens. The method is shown to provide a good estimation of a large number of residue spatial proximities, in the case of two experimental 3D spectra, recorded on proteins of α and β secondary structures. It is tested on simulated data sets against the protein size, secondary structure and the quality of the signal. More than 70% of the sequential assignment is correctly predicted, and the prediction is better for the α than for the β secondary structure. The medium- and long-range correlations seem equally well predicted for all the secondary structures. The efficiency of the method is compared to a previously proposed spectral correlation approach. Received: 5 July 2000 / Accepted: 8 September 2000 / Published online: 19 January 2001     

The influence of the binding of low molecular weight surfactants on the thermal stability and secondary structure of IgG

The effect of low molecular weight surfactants on the thermal stability of immunoglobulin G is studied by differential scanning calorimetry. The corresponding change in the secondary structure is investigated using circular dichroism spectroscopy and the rate of aggregate formation, both in the presence and absence of surfactant, is monitored by dynamic light scattering. At low surfactant concentrations (SDS/Tween 20 mixture) the thermal stability of the protein was not affected. With increasing surfactant concentration the protein structure is perturbed, most probably due to hydrophobic interaction with the surfactant, leading to a lower thermal stability. At even higher concentrations the surfactant molecules encapsulate the protein molecules, so that the unfolded state is strongly suppressed due to restricted conformational freedom in a confined volume. Interaction with the surfactant mixture at intermediate concentration influences the secondary structure of IgG strongly, i.e. α-helix and random coil conformations are promoted and the amounts of β-sheets and β-turns are reduced.     

Crystallographic and theoretical studies of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid (1/1) with intermolecular O–H···N hydrogen bonds and S···O heteroatom interactions

Abstract  The molecular and crystal structure of a 1:1 co-crystal of 4,4′-dimethyl-7,7′-bi([1,2,5]thiadiazolo[3,4-b]pyridylidene)–chloranilic acid, (1), has been determined by X-ray diffraction at the monoclinic space group P2₁/c with cell parameters of a = 8.422(6), b = 7.343(4), c = 16.112(7) ?, β = 104.988(8)°, V = 962.5(10) ?³ and Z = 2. In the crystal structure, two components connect via the intermolecular O–H···N hydrogen bonds [2.804(4) ?] and S···O heteroatom interaction [2.945(3) ?] with R ₂ ²(7) couplings to form a unique and infinite one-dimensional supramolecular tape structure. The calculations of (1) at the HF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels can almost reproduce X-ray geometry. In addition, the distances of the intermolecular O–H···N and S···O interactions by MP2/6-31G(d) and B3LYP/6-31G(d) levels agree well with those in the crystal. The calculated binding energies corrected BSSE and ZPE are −4.487 (HF), −7.473 (MP2), and −5.640 (B3LYP) kcal/mol. The results suggest that the complex (1) is very stable and the dispersion interaction is significantly important for the attractive intermolecular interaction in (1). The NBO analysis has revealed that the n(N) → σ*(O–H) interaction gives the strongest stabilization to the system and the major interaction for the intermolecular S···O contact is n(O) → σ*(S–N). Index Abstract  In the crystal structure of the title compound, the molecules are linked by intermolecular O–H···N hydrogen bonds and short S···O heteroatom interactions with R ₂ ²(7) couplings to construct a unique and infinite one-dimensional supramolecular tape structure.      

Preparation and utilization of a molecularly imprinted polymer for solid phase extraction of tramadol

In this paper, a highly selective molecularly imprinted polymer (MIP) for tramadol hydrochloride, a drug used to treat moderate to severe pain, was prepared and its use as solid-phase extraction (SPE) sorbent was demonstrated. The molecularly imprinted solid-phase extraction procedure followed by high performance liquid chromatography with ultraviolet detector (MISPE-HPLC) was developed for selective extraction and determination of tramadol in human plasma and urine. The optimal conditions for molecularly imprinted solid-phase extraction (MISPE) consisted of conditioning with 1 mL methanol and 1 mL of deionized water at neutral pH, loading of tramadol sample (50 μg L⁻¹) at pH 7.5, washing using 1 mL acetone and elution with 3 × 1 mL of 10% (v/v) acetic acid in methanol. The MIP selectivity was evaluated by checking several substances with similar molecular structures to that of tramadol. Results from the HPLC analyses showed that the calibration curve of tramadol (using MIP from human plasma and urine) is linear in the ranges of 6–100 and 3–120 μg L⁻¹ with good precisions (1.9% and 2.9% for 5.0 μg L⁻¹), respectively. The recoveries for plasma and urine samples were higher than 81%.      

Use of high-voltage electroaccumulation for lowering the detection limit for silver in stripping voltammetry

The use of high-voltage electroaccumulation in the determination of silver by stripping voltammetry at a mechanically renewed graphite electrode with an area of 2.5 × 10⁻³ cm² in 0.2% boric acid acidified with acetic acid at a voltage of 400 V and at an accumulation time of 5 min lowered the detection limit for silver to 1 × 10⁻¹² M.     

Sol–gel synthesis and characterization of titania monolith with bimodal porosity

Monolithic titania materials with macro-mesoporosity bimodal texture have been prepared through a template-free sol–gel approach, based on the reaction of hydrolysis and polycondensation of titanium isopropoxide promoted by the slow released water from esterification between acetic acid and methanol under a strong acidic condition. With the coarsening of the titania oligomers, phase separation and sol–gel transition processes take place so as to form a homogeneous gel system that will change into a monolith after aging, drying and heat treatment. The synthesized titania monolith possesses a specific surface area of 77 m² g⁻¹ (calcined at 350 °C), an anatase with partly rutile crystallite structure and great mechanical strength. The synthesis method applied here is simple and easy to implement as no extra chemical modifier such as poly(ethylene oxide) (PEO) and formamide is needed to control the process. The properties of biomodal porous structure, satisfactory surface area and high mechanical strength will enable the monolith to be served as a chromatography column to separate phosphorus organo-compounds.     

Effect of electron-withdrawing power of the substituted group on?OH radical reaction with substituted aryl sulphides: A pulse radiolysis study

In neutral aqueous solution of (phenylthio)acetic acid, hydroxyl radical is observed to react with a bimolecular rate constant of 7.2 × 10^-1 dm³ mol⁻s⁻ and the transient absorption bands are assigned to^•OH radical addition to benzene and sulphur with a rough estimated values of 50 and 40% respectively. The reaction of the^•OH radical with diphenyl sulphide (k = 4.3 × 10⁸ dm³ mol⁻¹ s⁻¹) is observed to take place with formation of solute radical cation, OH-adduct at sulphur and benzene with estimated values of about 12, 28 and 60% respectively. The transient absorption bands observed on reaction of^•OH radical, in neutral aqueous solution of 4-(methylthio)phenyl acetic acid, are assigned to solute radical cation (λ_max = 550 and 730 nm), OH-adduct at sulphur (λ_max = 360 nm) and addition at benzene ring (λ_max = 320 nm). The fraction of^•OH radical reacting to form solute radical cation is observed to depend on the electron-withdrawing power of substituted group. In acidic solutions, depending on the concentration of acid and electron-withdrawing power, solute radical cation is the only transient species formed on reaction of^•OH radical with the sulphides studied.     

A thermodynamic study on the interaction of nickel ion with myelin basic protein by isothermal titration calorimetry

The interaction of myelin basic protein (MBP) from the bovine central nervous system with divalent nickel ion was studied by isothermal titration calorimetry at 37 and 47 °C in Tris buffer solution at pH = 7. The new solvation model was used to reproduce the heats of MBP + Ni²⁺ interaction over the whole Ni²⁺ concentrations. It was found that MBP has three identical and independent binding sites for Ni²⁺ ions. The intrinsic dissociation equilibrium constant and the molar enthalpy of binding are 89.953 μM, −14.403 kJ mol⁻¹ and 106.978 μM, −14.026 kJ mol⁻¹ at 37 and 47 °C, respectively. The binding parameters recovered from the new solvation model were correlated to the structural changes of MBP due to its interaction with nickel ion interaction. It was found that in the low and high concentrations of the nickel ions, the MBP structure was destabilized.     

Development of a HPLC Method for Analysis of Linear Alkylbenzene Sulphonates and Detection by UV and FTIR Spectroscopy Using Thermospray Interface

 A reversed-phase high performance liquid chromatography (RP-HPLC) method, with acetic acid and sodium perchlorate phase modifiers, was developed to separate a mixture of linear alkylbenzene sulphonates (LAS), containing 10 to 13 carbon atoms. The effects of methanol-water compositions and concentrations of used modifiers were investigated and compared. The separation achieved with 50 mg L⁻¹ acetic acid was found satisfactory whereas a concentration of 10 g L⁻¹ sodium perchlorate was preferred. Chromatograms obtained with UV and Fourier transform infrared (FTIR) detection showed almost similar features and HPLC-FTIR interface spectra of LAS components exhibited excellent agreement of absorption features to those of standard FTIR spectrum and no thermal degradation was found to occur. Received May 20, 1998 Revision March 25, 1999.     

A naked-eye,selective and sensitive chemosensor for fluoride ion

Effect of the addition of six different anions on the absorption and fluorescence spectra of acridine yellow G (AYG) was examined. Only the F⁻ anion could induce a visible color change observable with naked eye and a strong fluorescence quenching with K _SV of 8.3 × 10⁴ mol⁻¹ L in CH₃CN solutions. Calculated results of the interaction between the F⁻ anion and acridine yellow G using the B3LYP/6-31G(d) program showed that the intermolecular charge transfer through the formation of an H-bond between AYG and F⁻ is an essential sensor mechanism.     

Influence of the water molecules (n?=?1–6) on the interaction between Li+, Na+, K+ cations and indole molecule as tryptophan amino acid residue

Influence of the addition of water molecules (n = 1–6) on the interaction energy between Li⁺, Na⁺, K⁺ cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation–π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation–π interaction indicates that there is a correlation between the electron density (ρ(r)) in the cage critical points generated upon complexation and the distance between metal cation and centroid of phenyl ring in indole molecule.