Downhill kinetics of biomolecular interface binding: Globally connected scenario

We study the kinetics of the biomolecular binding process at the interface using energy landscape theory. The global kinetic connectivity case is considered for a downhill funneled energy landscape. By solving the kinetic master equation, the kinetic time for binding is obtained and shown to have a U-shape curve-dependence on the temperature. The kinetic minimum of the binding time monotonically decreases when the ratio of the underlying energy gap between native state and average non-native states versus the roughness or the fluctuations of the landscape increases. At intermediate temperatures,fluctuations measured by the higher moments of the binding time lead to non-Poissonian, non-exponential kinetics. At both high and very low temperatures, the kinetics is nearly Poissonian and exponential.

Drug-human serum albumin binding studied by capillary electrophoresis with electrochemiluminescence detection

A new technique for investigating drug-protein binding was developed employing capillary electrophoresis (CE) coupled with tris(2,2'-bipyridyl) ruthenium(II) [Ru(bPY)(3)(2+)] electrochemiluminescence (ECL) (CE-ECL) detection after equilibrium dialysis. Three basic drugs, namely pridinol, procyclidine and its analogue trihexyphenidyl, were successfully separated by capillary zone electrophoresis with end-column Ru(bPY)(3)(2+) ECL detection. The relative drug binding to human serum albumin (HSA) for each single drug as well'as for the three drugs binding simultaneously was calculated. It was found that the three antiparkinsonian drugs compete for the same binding site on HSA. This work demonstrated that Ru(bPY)(3)(2+) CE-ECL can be a suitable technique for studying drug-protein binding.

Influence of shear on crystallization behavior of the beta phase in isotactic polypropylene with beta-nucleating agent

Wide-angle X-ray diffraction (WAXD) was used to investigate the effects of shear on the crystallization behavior of polypropylene (PP) with beta-nucleating agent. The melt was subjected to shear at the shear rate from 0.5 to 60 s(-1) for 5 s with a CSS450 shear stage. For the PP with low content of the additive, the formation mechanism of the beta crystals is almost the same as that of pure isotactic polypropylene (iPP), viz., shear induces. Otherwise, for the samples with high content of the additive, the formation mechanism of the beta form are nucleating agent induces. The results clearly show that shear restrains the formation of high beta phase for the melt with additive.

Gadolinium heteropoly complex K-17[Gd(P2W17O61)(2)] as a potential MRI contrast agent

Gadolinium heteropoly complex K-17[Gd(P2W17O61)(2)] has been evaluated by in vitro and in vivo experiments as a potential contrast agent for magnetic resonance imaging (MRI). The thermal analysis and conductivity study indicate that this complex has good thermal stability and wide pH stability range. The T-1 relaxivity is 7.59 mM(-1) s(-1) in aqueous solution and 7.97 mM(-1) s(-1) in 0.725 mmol l(-1) bovine serum albumin (BSA) solution at 25degreesC and 9.39 T, respectively. MR imaging of three male Sprague-Dawley rats showed remarkable enhancement in rat liver after intravenous injection, which persisted longer than with Gd-DTPA. The signal intensity increased by 57.1 +/- 16.9% during the whole imaging period at 0.082 mmol kg(-1) dose. Our preliminary in vitro and in vivo studies indicate that K-17[Gd(P2W17O61)(2)] is a potential liver-specific MRI contrast agent.

Enthalpy/entropy compensation: Influence of DNA flanking sequence on the binding of 7-amino actinomycin D to its primary binding site in short DNA duplexes

The effect of the context of the flanking sequence on ligand binding to DNA oligonucleotides that contain consensus binding sites was investigated for the binding of the intercalator 7-amino actinomycin D. Seven self-complementary DNA oligomers each containing a centrally located primary binding site, 5'-A-G-C-T-3', flanked on either side by the sequences (AT)(n) or (AA)(n) (with n = 2, 3, 4) and AA(AT)(2), were studied. For different flanking sequences, (AA)(n)-series or (AT)(n)-series, differential fluorescence enhancements of the ligand due to binding were observed. Thermodynamic studies indicated that the flanking sequences not only affected DNA stability and secondary structure but also modulated ligand binding to the primary binding site. The magnitude of the ligand binding affinity to the primary site was inversely related to the sequence dependent stability. The enthalpy of ligand binding was directly measured by isothermal titration calorimetry, and this made it possible to parse the binding free energy into its energetic and entropic terms.

Separation of yttrium from heavy lanthanide by CA-100 using the complexing agent

The selective extraction of yttrium front heavy lanthanide by liquid-liquid extraction using CA-100 in the presence of the complexing agent, such as EDTA, DTPA, and HEDTA was investigated. The extraction of heavy lanthanide in the present of the complexing agent was Suppressed when compared to that of Y because of the masking effect, but the selective extraction of Y was enhanced. All complexing agents formed 1: 1 complex with rare earth elements (RE), and only free rare earth ions could take part in the extraction. The condition for separation was obtained by exploring the effects of the complexing agent concentration, the extractant concentration, pH and the equilibration time on the extraction of the heavy rare earth elements.

Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible 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. 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. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

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.

In situ synthesis and characterization of multiwalled carbon nanotube/Au nanoparticle composite materials

An effective and facile in Situ reduction approach for the fabrication of carbon nanotube-supported Au nanoparticle (CNT/Au NP) composite nanomaterials is demonstrated in this article. Linear polyethyleneimine (PEI) is ingeniously used as both a functionalizing agent for the multiwalled carbon nanotubes (MWNTs) and a reducing agent for the formation of An NPs. This method involves a simple mixing process followed by a mild heating process. This approach does not need the exhaustive surface oxidation process of CNTs. The coverage of Au NPs on CNTs is tunable by varying the experimental parameters, such as the initial molar ratio of PEI to HAuCl4, the relative concentration of PEI and HAUCl(4) to MWNTs, and the temperature and duration of the heat treatment. More importantly, even the heterogeneous CNT/Au composite nanowires are obtainable through this method. TEM, XPS, and XRD are all used to characterize the CNT/Au composite materials. In addition, the optical and electrocatalytic properties are investigated.

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.

Selective separation of yttrium by CA-100 in the presence of a complexing agent

The selective separation of Y from yttrium solution containing small heavy rare earth (HRE) impurities (Ho, Er, Tm, Yb, Lu) by liquid-liquid extraction using CA-100 in the presence of a water-soluble complexing agent of ethylenediaminetetraacetic acid (EDTA) was experimentally studied at 298K. Experiments were carried Out in two feeds, Feed-I: [RE](f) = 4.94 x 10(-3) M, Y = 98.5%, HRE (Ho, Er, Tm, Yb, Lu) = 1.5%; Feed-II: [RE](f) = 4.94 x 10(-3) M, Y = 99.9%, HRE (Ho, Er, Tm, Yb, Lu) = 0.1%, as a function of equilibrium pH (pH(eq)), the concentration ratio of [EDTA]:[HRE impurities]. It was shown that the extraction of HRE in the presence of EDTA was suppressed when compared to that of Y because of the masking effect, while the selective extraction of Y was enhanced and the separation factors increased to maximum at appropriate condition for Feed-I: Y/Ho = 1.53, Y/Er = 3.09, Y/Tm = 5.61, Y/Yb = 12.04, Y/Lu = 27.51 at pH 4.37 and [EDTA]:[HRE impurities] = 4: 1, for Feed-II: Y/Ho = 1.32, Y/Er = 1.91, Y/Tm = 2.00, Y/Yb = 3.05, Y/Lu = 3.33 at pH 4.42 and [EDTA]: [HRE impurities] = 8:1. The separation and purification of Y by this method was discussed.

Effect of borohydride as reducing agent on the structures and electrochemical properties of Pt/C catalyst

In this paper, we found that boron deposited on the surface of support when sodium borohydride used as reducing agent during the preparation of Pt/C catalyst. The deposition of boron markedly reduces particle size of Pt, raises electrochemical active surface (EAS) area of catalyst and electrochemical activity for hydrogen evolution or oxygen reduction reaction (ORR) compared with which prepared using other reducing agents (hydrogen and formaldehyde).

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.

Triphenylmethanethiol: a novel rigid capping agent for gold nanoclusters

In this article, we employed triphenylmethanethiol (TPMT) as a novel rigid agent for capping gold nanoparticles and the TPMT monolayer-protected gold nanoparticles were characterized by various analytical techniques. High-resolution transmission electron microscopy showed a narrow dispersed gold core with an average core diameter of ca. 3.6 nm. The UV/vis spectrum revealed the surface plasmon absorbance at 528 nm. The p-pi conjugated structure of the TPMT ligand was confirmed by nuclear magnetic resonance. Differential scanning calorimetry and Fourier transform infrared spectroscopy revealed the rigid nature of the TPMT chains.