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.

Synthesis and evaluation of novel polysaccharide-Gd-DTPA compounds as contrast agent for MRI

Macromolecular conjugates of two kinds of natural polysaccharides, that from Panax quinquefolium linn (PQPS) and Ganoderma applanatum pat (GAPS), with gadolinium-diethylenetriaminepenta-acetic acid (Gd-DTPA) have been synthesized and characterized by means of FTIR, elementary analysis and ICP-AES. Their stability was investigated by competition study with Ca2+, EDTA (ethylenediaminetetraacetic acid) and DTPA. Polysaccharide-bound complexes exhibit T-1 relaxivities of 1.5-1.7 times that of Gd-DTPA in D2O at 25degreesC and 9.4T. MR imaging of Sprague-Dawley (SD) rats showed remarkable enhancement in rat liver and kidney after i.v. injection of these two complexes: liver parenchyma 60.9+/-5.6%, 57.8+/-7.4% at 65-85 min; kidney 144.9+/-14.5%, 199.9+/-25.4% at 10-30 min for PQPS-GdDTPA, GAPS-Gd-DTPA at gadolinium dose of 0.083 and 0.082 mmol/kg, respectively. Our preliminary in vivo and in vitro study indicates that the two kinds of polysaccharide-bound complexes are potential tissue-specific contrast agents for MRI.

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.

Arabinogalactan as a carrier for contrast agent in magnetic resonance imaging

Arabinogalactan-Gd-DTPA was synthesized by the reaction of diethylenetriaminepenta-acetic acid (DTPA) bisanhydride with polysaccharide in dry DMSO and characterized by FTIR, elemental analysis and ICP-AES. Its stability was investigated by competition with Ca2+, EDTA, DTPA. The t(1)-relaxivity is 8.06 mmol(-1) . L . s(-1) in D2O, 8.48 mmol(-1) . L . s(-1) in 0.725 mmol . L-1 BSA, respectively. t(1)-weighted MR imaging of rat kidney and liver showed a remarkable enhancement post injection of Arabinogalactan-Gd-DTPA. The results indicate that the arabinogalactan-Gd-DTPA is a potential contrast agent for MRI.