Structural diversity of lanthanide-amino acid complexes under near physiological pH conditions and their recognition of single-stranded DNA

We reported here four structures of lanthanide-amino acid complexes obtained under near physiological pH conditions and their individual formula can be described as [Tb-2(DL-Cys)(4)(H2O)(8)]Cl-2 (1), [Eu-4(mu(3)-OH)(4)(L-Asp)(2)(L-HAsp)(3)(H2O)(7)] Cl center dot 11.5H(2)O (2), [Eu-8-(L-HVal) (16)(H2O)(32)]Cl-24 center dot 12.5H(2)O (3), and [Tb-2(DL-HVal)(4)(H2O)(8)]Cl-6 center dot 2H(2)O (4). These complexes showed diverse structures and have shown potential application in DNA detection. We studied the interactions of the complexes with five single-stranded DNA and found different fluorescence enhancement, binding affinity and binding stoichiometry when the complexes are bound to DNA.

NMR and pattern recognition studies on the acute biochemical effects of Lu(NO3)(3)

Pattern recognition methods were applied to the analysis of 600 MHz H-1 NMR spectra of urine from rats dosed with compounds that induced organ-specific damage in the liver and kidney. Male Wistar rats were separated into groups (n=4) and each was treated with one of following compounds: HgCl2, CCl4, Lu(NO3)(3) and Changle (a kind of rare earth complex mixed with La, Ce, Pr and Nd). Urine samples from the rats dosed with HgCl2, CCl4 and Lu(NO3)(3) were collected over a 24 h time course and the samples from the rats administrated with Changle were gained after 3 months. These samples were measured by 600 MHz NMR spectroscopy. Each spectrum was data-processed to provide 223 intensity-related descriptors of spectra. Urine spectral data corresponding to the time intervals, 0-8 h (HgCl2 and CCl4), 4-8 (Lu(NO3)(3)) h and 90 d (Changle) were analyzed using principal component analysis (PCA). Successful classification of the toxicity and biochemical effects of Lu(NO3)(3) was achieved.

Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Application of electrochemical impedance spectroscopy for monitoring allergen-antibody reactions using gold nanoparticle-based biomolecular immobilization method

Gold nanoparticles were used to enhance the immobilization amount and retain the immunoactivity of recombinant dust mite allergen Der f2 immobilized on a glassy carbon electrode (GCE). The interaction between allergen and antibody was studied by electrochemical impedance spectroscopy (EIS). Self-assembled Au colloid layer (Phi = 16 nm) deposited on (3-mercaptopropyl)trimethoxysilane (MPTS)-modified GCE offered a basis to control the immobilization of allergen Der f2. The impedance measurements were based on the charge transfer kinetics of the [Fe(CN)(6)](3-/4-) redox pair, compared with bare GCE, the immobilization of allergen Der f2 and the allergen-antibody interaction that occurred on the electrode surface altered the interfacial electron transfer resistance and thereby slowed down the charge transfer kinetics by reducing the active area of the electrode or by preventing the redox species in electrolyte solution from approaching the electrode. The interactions of allergen with various concentrations of monoclonal antibody were also monitored through the change of impedance response. The results showed that the electron transfer resistance increased with increasing concentrations of monoclonal antibody.

Discrimination of herbal medicines by molecular spectroscopy and chemical pattern recognition

The molecular spectroscopy (including near infrared diffuse reflection spectroscopy, Raman spectroscopy and infrared spectroscopy) with OPUS/Ident software was applied to clustering ginsengs according to species and processing methods. The results demonstrate that molecular spectroscopic analysis could provide a rapid, nondestructive and reliable method for identification of Chinese traditional medicine. It's found that the result of Raman spectroscopic analysis was the best one among these three methods. Comparing with traditional methods, which are laborious and time consuming, the molecular spectroscopic analysis is more effective.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Electrochemical recognition of alkali metal ions at the micro-water 1,2-dichloroethane interface using a calix[4]arene derivative

In this paper, a calix[4]arene derivative, 5,11,17,23-butyl-25,26,27,28-tetra-(ethanoxycarbonyl)-methoxy-calix[4]arene (L), is investigated as a host to recognize alkali metal ions (Li+, Na+, K+, Rb+ and Cs+) at the interface between two immiscible electrolyte solutions (ITIES). Well-defined cyclic voltammograms are obtained at the micro- and nano-water \ 1,2-dichloroethane (W \ DCE) interfaces supported at micro- and nano-pipets.

Layer-by-layer assembly of multilayer films composed of avidin and biotin-labeled antibody for immunosensing

Protein multilayers composed of avidin and biotin-labeled antibody (bio-Ab) were prepared on gold surface by layer-by-layer assembly technology using the high specific binding constant (K-a: approximate to 10(15) M-1) between avidin and biotin. The assembly process of the multilayer films was monitored by using real-time BIA technique based on surface plasmon resonance (SPR). The multilayer films were also characterized by electrochemical impedance spectroscopy (EIS) and reflection absorption Fourier transform infrared spectroscopy (FTIR). The results indicate that the growth of the multilayer is uniform. From response of SPR for each layer, the stoichiometry S for the interaction between avidin and bio-Ab is calculated to be 0.37 in the multilayer whereas 0.82 in the first layer. The protein mass concentration for each layer was also obtained. The schematic figure for the multilayer assembly was proposed according to the layer mass, concentration and S value. The utility of the mutilayer films for immunosensing has been investigated via their subsequent interaction with hIgG. The binding ability of the multilayer increased for one to three layers of antibody, and then reach saturation after the fourth layer. These layer-by-layer constructed antibody multilayers enhance the binding ability than covalently immobilized monolayer antibody. This technology can be also used for construction of other thin films for immunosensing and biosensor.

Kinetic characteristics of the interaction between morphine and its antibody by SPR competitive immunoassay

It is impossible for surface plasmon resonance to measure directly the binding kinetics between a low-molecular-weight analyte interacting and its immobilized binding partner. Solution competition method was applied to the kinetic study of the interaction between morphine and its antibody. The affinity constant between the antibody of morphine and morphine-BSA immobilized on the sensor chip was also obtained. The result showed that the affinity of polyclonal antibody is stronger than that of monoclonal antibody. And it also indicated that the protein combined with the analyte affected the binding of antibody to antigen.

Studies on the interaction of porphyrin with antibody with fluorescent spectrum and UV-Vis differential spectra

After meso-tetra (alpha, alpha, alpha, alpha-O-phenylacetyl benzene)porphyrin combined with McAb 1F2, there was a significant hyperchromic effect, indicating that the combination of porphyrin and antibody is rigid and compact, aromatic amino acids exist at the combining sites of antigen in antibody. These aromatic amino acids are Trys and Trps, but the numbers of Trp are more than that found for Trys. The stochiometric ratio of porphyrin to 1F2 is 1:1, the disassociation constant was determined as(2.084+/-0.216) x 10(-10) mol/L by a method of fluorescence quenching, showing that both have a high affinity.

Computer simulation of human iodothyronine deiodinase single-chain antibody

Iodothyronine plays a major role in growth, basic metabolism and organ formation. It has an extremely limited source in the body. In this thesis, we designed iodothyronine(T4) as hapten. Then a single chain antibody displayed on phange was obtained from a human phage displaying a single chain antibody library. The specific genes of E3 was subcloned in P-5E vector. According to its amino acid sequences, we simulate its three dimention structure by computer. It has never been reported in PDB.

Studied on the interactions of antibody-porphyrin by circular dichroism and ultraviolet-visible spectrophotometry

Circular dichoism and UV-vis measurements were used to study the interaction between porphyrin and monoclonal antibodies ( McAbs). McAbs-porphyrin complex formation is usually accompanied by significant bathochromic shift and hyperchromicity changes of the absorption maxima in the porphyrin soret band region. Induced CD spectra in the same region (350 similar to 450 nm) were detected upon complex formation. They follow Lamb-Beer's law and exhibit isosbestic behavior. Both the UV-Vis and induced CD spectra of the antibody: porphyrin complex remain unchanged over a broad pH range ( pH 6 similar to 11), indicating remarkable stability of the complex and reflecting the dominant role of hydrophobic interaction between the hapten benzophenone and the antibody combining site.

Studies on enzymological properties of antibody elicited by meso-tetra(alpha, alpha, alpha, alpha-O-phenylacetyl benzene)porphyrin

meso-Tetra (alpha, alpha, alpha, alpha-O-phenylacetyl benzene) porphyrin was used as a complete antigen to elicit monoclonal antibody 1F2 through the immunization and cell fusion techniques. McAb 1F2 obtained was demonstrated very pure by HPLC and MALDI/TOFMS. The retention time of McAb 1F2 was 2. 63 min. The subtype of McAb 1F2 was IgG2a. The relative molecular weight was 156 678. 8. When the McAb 1F2-porphyrin was formed, the maximal absorption of the porphyrin soret region had a redshift from 408 to 416 nm and hyperchromical effect, showing that the antigen-antibody combination was rigid and intense, and the abzyme constancy was high. But compared with HRP, the activity of the abzyme was only 4. 687 5 U/mg and 1. 899 % of that of HRP. Its K-m was 20. 29 mmol/L, k(cat) 396. 82 min(-1), k(cat)/K-m. 1. 955 7 X 10(4) L . mol(-1) . min(-1).

Preparation of europium induced conformation-specific anti-calmodulin monoclonal antibody

Monoclonal antibody technique was employed to detect the conformational difference of CaM induced by metal ions. A trivalent europium ion induced conformation-specific anti-calmodulin monoclonal antibody was successfully prepared with europium-saturated calmodulin as antigen.