Structural features of the L-argininamide-binding DNA aptamer studied with ESI-FTMS

The 24-mer DNA aptamer of Harada and Frankel ( Harada, K.; Frankel, A. D. EMBO J. 1995, 14, 5798-5811) that binds L-argininamide (L-Arm) was studied by electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). This DNA folds into a stem and loop such that the loop is able to engulf L-Arm. As controls, two derivatives of the same base composition, one with the same stem but a scrambled loop and the other with no ability to form a secondary structure, were studied. The two DNAs that could fold into stem-loop structures showed a more negatively charged distribution of ions than the linear control. This tendency was preserved in the presence of ligand; complexes expected to have more secondary structure had ions with more negative charges. Distinct species corresponding to no, one, and two bound L-Arm molecules were observed for each DNA. The fractional peak intensities were fit to a straightforward binding model and binding constants were obtained. Thus, ESI-FTMS can provide both qualitative and quantitative data regarding the structure of DNA and its interactions with noncovalent ligands.

A nonmonotonic dependence of standard rate constant on reorganization energy for heterogeneous electron transfer processes on electrode surface

In the present work a nonmonotonic dependence of standard rate constant (k(0)) on reorganization energy (lambda) was discovered qualitatively from electron transfer (Marcus-Hush-Levich) theory for heterogeneous electron transfer processes on electrode surface. It was found that the nonmonotonic dependence of k(0) on lambda is another result, besides the disappearance of the famous Marcus inverted region, coming from the continuum of electronic states in electrode: with the increase of lambda, the states for both Process I and Process II ET processes all vary from nonadiabatic to adiabatic state continuously, and the lambda dependence of k(0) for Process I is monotonic thoroughly, while for Process II on electrode surface the lambda dependence of k(0) could show a nonmonotonicity.

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.

Kinetics of ytterbium(III) extraction with Cyanex 272 using a constant interfacial cell with laminar flow

Studies have been made on the kinetics of ytterbium(III) with bis-(2,4,4-trimethylpentyl) phosphinic acid (Cyanex 272, HA) in n-heptane using a constant interfacial cell with laminar flow. The stiochiometry and the equilibrium constant of the extracted complex formation reaction between Yb3+ and Cyanex 272 are determined. The extraction rate is dependent of the stirring rate. This fact together with the Ea value suggests that the mass transfer process is a mixed chemical reaction-diffusion controlled at lower temperature, whereas it is entirely diffusion controlled at higher temperature. The rate equations for the ytterbium extraction with Cyanex 272 have been obtained. The rate-determining step is also made by predictions derived from interfacial reaction models, and through the approximate solutions of the flux equation, diffusion parameters and thickness of the diffusion film have been calculated.

Mass transfer kinetics of yttrium(III) using a constant interfacial cell with laminar flow. Part II. Extraction with Cyanex 272

The yttrium(III) extraction kinetics and mechanism with bis-(2,4,4-trimethyl-pentyl) phosphinic acid (Cyanex 272, HA) dissolved in heptane have been investigated by constant interfacial cell with laminar flow. The data has been analyzed in terms of pseudo-first order constants. Studies on the effects of stirring rate, temperature, acidity in aqueous phase, and extractant concentration on the extraction rate show that the extraction regime is dependent on the extraction conditions. The plot of interfacial area on the rate has shown a linear relationship. This fact together with the strong surface activity of Cyanex 272 at heptane-water interfaces has made the interface the most probable location for the chemical reactions. The forward, reverse rate equations and extraction rate constant for the yttrium extraction with Cyanex 272 have been obtained under the experimental conditions. The rate-determining step has been also predicted from interfacial reaction models. The predictions have been found to be in good agreement with the rate equations obtained from experimental data, confirming the basic assumption that the chemical reaction is located at the liquid-liquid interface.

Mass transfer kinetics of yttriium(III) using a constant interfacial cell with laminar flow. Part I. Extraction with Cyanex 302

The interfacial tension is measured for Cyanex 302 in heptane and adsorption parameters are calculated according to Gibbs equation and Szyskowski isotherm. The results indicate that Cyanex 302 has a high interfacial activity, allowing easy extraction reaction to take place at the liquid-liquid interface. The extraction kinetics of yttrium(III) with Cyanex 302 in heptane are investigated by a constant interfacial cell with laminar flow. The effects of stirring rate, temperature and specific interfacial area on the extraction rate are discussed. The results suggest that the extraction kinetics is a mixed regime with film diffusion and an aqueous one-step chemical reaction proposed to be the rate-controlling step. Assuming the mass transfer process can be formally treated as a pseudo-first-order reversible reaction with respect to the metal cation, the rate equation for the extraction reaction of yttrium(III) with Cyanex 302 at pH <5 is obtained as follows:R-f = 10(-7.85)[Y(OH)(2)(+)]((a))[H(2)A(2)]((o))(1.00)[H+]((a))(-1.00)Diffusion parameters and rate constants are calculated through approximate solutions of the flux equation.

Kinetics of Y(III) stripping for the system Y/HCl/Cyanex 272-P507/heptane with constant interfacial area cell with laminar flow

Kinetics and mechanism of stripping of yttrium(III) previously extracted by mixtures of bis(2,4,4-trimethylpentyl)phosphinic acid (Cyanex 272, HA), and 2-ethylhexyl phosphonic acid mono-2-ethylhexl ester (P507, HB) dissolved in heptane have been investigated by constant interfacial-area cell by laminar flow. The corresponding equilibrium stripping equation and equilibrium constant were obtained. The studies of effects of the stirring rate and temperature on the stripping rate show that the stripping regime is dependent on the stripping conditions. The plot of interfacial area on the rate has shown a linear relationship. This fact together with the strong surface activity of mixtures of Cyanex 272 and P507 at heptane-water interfaces makes the interface the most probable locale for the chemical reactions. The stripping rate constant is obtained, and the value is compared with that of the system with Cyanex 272 and P507 alone. It is concluded that the stripping ability with the mixtures is easier than that of P507 due to lower the activation energy of the mixtures. The stripping rate equation has also been obtained, and the rate-determining steps are the two-step interfacial chemical reactions as predicted from interfacial reaction models.

Kinetics of cerium(IV) extraction with DEHEHP from HNO3-HF medium using a constant interfacial cell with laminar flow

Studies of the extraction kinetics of cerium(IV) into n-heptane solutions of di(2-ethylhexyl)-2-ethylhexyl phosphonate DEHEHP from HNO3-HF solutions have been carried out using a constant interfacial cell with laminar flow. The experimental hydrodynamic conditions were chosen so that the contribution of diffusion to the measured rate of reaction was minimized. The data were analyzed in terms of pseudo-first order constants. The effects of the stirring rate, specific interfacial area, and temperature on the extraction rate showed that the most probable reaction zone is in the aqueous homogeneous phase. The results were compared with those of the system without HF. It was concluded that the presence of HF decreases the extraction rate of cerium. The addition of HF increases the activation energy for the forward reaction from 21.2 to 55.3 kJ/mol and for the reverse process from 57.9 to 79.0 kJ/mol. According to the experimental data correlated as a function of the concentration of the relevant species involved in the extraction reaction, the corresponding rate equation was deduced as follows:-d[Ce]/dt = k[Ce] center dot B-0.62 center dot HF-0.58 center dot [NO3-](0.57)

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.

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.

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.

The structural transition of DNA-Tris(1,10-phenanthroline) cobalt(III) complexes in ethanol-water solution

The interaction of DNA with Tris(1,10-phenanthroline) cobalt(III) was studied by means of atomic force microscopy. Changes in the morphologies of DNA complex in the presence of ethanol may well indicate the crucial role of electrostatic force in causing DNA condensation. With the increase of the concentration of ethanol, electrostatic interaction is enhanced corresponding to a lower dielectric constant. Counterions condense along the sugar phosphate backbone of DNA when e is lowered and the phosphate charge density can thus be neutralized to the level of DNA condensation. Electroanalytical measurement of DNA condensed with Co(phen)(3)(3+) in ethanol solution indicated that intercalating reaction remains existing. According to both the microscopic and spectroscopic results, it can be found that no secondary structure transition occurs upon DNA condensing. B-A conformation transition takes place at more than 60% ethanol solution.

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.

Kinetics and mechanism of Y(III) extraction with CA-100 using a constant interfacial cell with laminar flow

The Yttrium(III) extraction kinetics and mechanism with secnonylphonoxy acetic acid (CA-100) were investigated by a constant interfacial cell with laminar flow. The studies of interfacial tension and solubility of extractant and effects of the stirring rate, temperature, specific interfacial area and species concentration on the extraction rate showed that the extraction regime was dependent on the extraction conditions and the most probable reaction zone was at the liquid-liquid interface. The rate equation of extracting yttrium by CA-100 in heptane was Rf = k[Y3+]((a))[H(2)A(2)]((o))(0.88)[H+]((a))(-1.08).