Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.

In vitro study on the binding of neutral red to bovine serum albumin by molecular spectroscopy

In this paper, the binding of neutral red (NR) to bovine serum albumin (BSA) under physiological conditions has been studied by spectroscopy method including fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. The Stern-Volmer fluorescence quenching constant (K-SV), binding constant (K-b) and the number of binding sites (It) were measured by fluorescence quenching method. Fluorescence experiments were also performed at different ionic strengths. It was found K-SV was ionic strength dependent, which indicated the electrostatic interactions were part of the binding forces. The distance r between donor (BSA) and acceptor (NR) was obtained according to Foster's non-radiative energy transfer theory. CD spectroscopy and FT-IR spectroscopy were used to investigate the structural information of BSA molecules on the binding of NR, and the results showed no change of BSA conformation in our experimental conditions.

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.

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

We study the nature of biomolecular binding. We found that in general there exists several thermodynamic phases: a native binding phase, a non-native phase, and a glass or local trapping phase. The quantitative optimal criterion for the binding specificity is found to be the maximization of the ratio of the binding transition temperature versus the trapping transition temperature, or equivalently the ratio of the energy gap of binding between the native state and the average non-native states versus the dispersion or variance of the non-native states. This leads to a funneled binding energy landscape.

Determination of mercury with a flow injection quartz tube atomic absorption spectrometry

A method was developed for the determination of micro mercury in the soil, plants and the traditional Chinese medicine using flow injection quartz tube-atomic absorption spectrometry. The effect of the factors such as acidity,. the carrier solution, the flow rate of reductive solution and argon gas, etc. on the determination was studied. When vanadic oxide, nitric acid and sulfuric acid were used to decompose the sample reliable result could be obtained. The characteristic mass of the method is 59 pg, the detection limit is 0.028 mug/L, RSD is < 3.9% and the recovery is in the range of 94% &SIM; 102%.

Simultaneous spectrophotometric determination of zinc, cadmium and mercury with hybrid linear analysis

A new method for simultaneous spectrophotometric determination of Zn, Cd and Hg using 2-(5-Br-2-pyridylazo)-5-diethylaminophenol as the color developing reagent was proposed. The absorption spectra of these three complexes have similar features with severe overlap in visible spectral range. For resolving these spectra, hybrid linear analysis was used, and the pure spectrum of each component was obtained from the calibration mixtures by least squares method. The effects of reaction condition, selection of wavelengths, determination of pure spectrum and additivity of absorbances etc. on the determination were discussed. The proposed method offers the advantages of simple, rapid, and accuracy. It has been successfully applied to the simultaneous determination of Zn, Cd and Hg in synthetic sample. A comparison was also made with the partial least squares method.

Determination of mercury in biological samples using organic compounds as matrix modifiers by inductively coupled plasma mass spectrometry

A method was developed for the determination of total mercury in biological samples. The effects of aqueous ammonia, ethylenediamine and triethanolamine on Hg signal intensity by inductively coupled plasma mass spectrometry has been evaluated and the possible mechanisms discussed. It has been proved that the signal intensity of Hg significantly increases with adding, in the presence of small amounts of aqueous ammonia, ethylenediamine or triethanolamine. The normalized intensity (the signal intensity ratio with amine and without amine) of Hg increases as the concentration of aqueous ammonia, ethylenediamine or triethanolamine increases, but the degree of enhancement of aqueous ammonia was smaller than that of ethylenediamine and triethanolamine. The normalized intensity of Hg with aqueous ammonia, ethylenediamine and triethanolamine decreases as the nebulizer flow rate increases, but decreasing degree of aqueous ammonia was smaller than that of ethylenediamine and triethanolamine. The higher the RF powers the higher the normalized intensity of Hg at the same nebulizer flow rate. The addition of aqueous ammonia, ethylenediamine and triethanolamine into analytical solutions significantly improved the transport efficiency of Hg. The detection limit of Hg is improved about ten times by the addition of ethylenediamine or triethanolamine under the optimum experimental parameters. The method has been used to determine mercury in biological standard reference materials (SRM). The analytical results are very close to the certified values and the determined values for similar samples.

Overview on the environmental analysis of mercury in China

This paper summarizes some of the research and evaluation studies about mercury analysis in the environment during the past years in China. The main contents is as follows: 1) Determination of total mercury and speciation of mercury in air; 2) Storage and handling of water samples; 3) pre-treatment of solid samples; 4) Determination of total mercury and speciation of mercury in water and solid samples; 5) Certified reference materials.

Probing lanthanide ions binding on tRNA(Phe) by H-1 NMR

The structure of phenylalanine transfer ribonucleic acid (tRNA(Phe)) in solution was explored by H-1 NMR spectroscopy to evaluate the effect of lanthanide ion on the structural and conformational change. It was found that La3+ ions possess specific effects on the imino proton region of the H-1 NMR spectra for yeast tRNA(Phe). The dependence of the imino proton spectra of yeast tRNA(Phe) as a function of La3+ concentration was examined, and the results suggest that the tertiary base pair G(15). C-48, which is located in the terminal in the augmented dihydrouridine helix (D-helix), was markedly affected by La3+ (shifted to downfield by as much as 0.35). Base pair U-8. A(14) in yeast tRNA(Phe), which are stacked on G(15). C-48, was also affected by added La3+ when 1 similar to 2 Mg2+ were also present. Another imino proton that may be affected by La3+ in yeast tRNA(Phe) is that of the tertiary base pair G(19). C-56. The assignment of this resonance in yeast tRNA(Phe) is tentative since it is located in the region of highly overlapping resonances beween 12.6 and 12.2. This base pair helps to anchor the D-loop to the T Psi C loop. The binding of La3+ caused conformational change of tRNA, which is responsible for shifts to upfield or downfield in H-1 NMR spectra.

BINDING OF CYTOCHROME-C WITH 4-PYRIDYL DERIVATIVES MODIFIED ON THE GOLD ELECTRODE

In this work, the adsorption or binding of cytochrome c with 4-pyridyl derivatives modified on the gold electrode was studied. It was found that the concentrations of electrolyte had much influence on the adsorption of cytochrome c. At lower concentration

LUMINESCENCE AND ENERGY MIGRATION IN THE OXYAPATITE CA2GD8(SIO4)6O2 DOPED WITH SEVERAL RARE-EARTH AND MERCURY-LIKE IONS

Energy transfer phenomena have been observed by activating the oxyapatite host-lattice Ca2Gd8(SiO4)6O2 with Eu3+, Tb3+, Dy3+, Sm3+. This is based on the energy migration in the Gd3+ sublattice and trapping by the activators. The trapping efficiency for G

POLYANILINE-DISPERSED MERCURY-ELECTRODE FOR THE DETECTION OF MONOCHLORAMINE AND DICHLORAMINE

A novel type of electrochemical detector based on a polyaniline-dispersed mercury-coated glassy carbon chemically modified electrode was investigated for the detection of monochloramine and dichloramine. A polyaniline dispersed-mercury modified electrode, which was prepared by coating polyaniline on a thin mercury film electrode using fast-sweep voltammetry, was developed. The selectivity could be altered using various counter ions incorporated into the polymer. The results indicated that the use of a conducting polymer-based electrochemical sensor for the selective determination of chloramine is a feasible approach.