Assay for molecular transport across gap junction channels in one-dimensional cell arrays

Transport across gap junction channels (GJCs) between neighboring cells is critical to synchronizing cell's electrical and metabolic activities and maintaining cell homeostasis. Here we present a non-invasive microfluidic method to measure molecular diffusion across GJCs in multiple 1D cell arrays in real time. Using the chip, selective loading of a membrane permeant fluorescence dye (carboxyfluorescein) in Normal Rat Kidney (NRK) cells shows that the dye was able to diffuse through three cells along single cell chains in ～35 minutes. Application of 100 μM 2-aminoethoxydiphenyl borate (2-APB) reversibly inhibits connexin-43 gap junctions in NRK cells; 0.8 mM 1-heptanol inhibits the diffusion partially. The method offers rapid exchange of reagents, enabling sequential screening of multiple gap junction specific drugs with only one preparation of cells. It is capable of measuring gap junction mediated diffusion between single cells.     

1H‐19F REDOR‐filtered NMR spin diffusion measurements of domain size in heterogeneous polymers

Solid state NMR spectroscopy is inherently sensitive to chemical structure and composition and thus makes an ideal method to probe the heterogeneity of multicomponent polymers. Specifically, NMR spin diffusion experiments can be used to extract reliable information about spatial domain sizes on multiple length scales, provided that magnetization selection of one domain can be achieved. In this paper, we demonstrate the preferential filtering of protons in fluorinated domains during NMR spin diffusion experiments using ¹H‐¹⁹F heteronuclear dipolar dephasing based on rotational echo double resonance (REDOR) MAS NMR techniques. Three pulse sequence variations are demonstrated based on the different nuclei detected: direct ¹H detection, plus both ¹H?¹³C cross polarization and ¹H?¹⁹F cross polarization detection schemes. This ¹H‐¹⁹F REDOR‐filtered spin diffusion method was used to measure fluorinated domain sizes for a complex polymer blend. The efficacy of the REDOR‐based spin filter does not rely on spin relaxation behavior or chemical shift differences and thus is applicable for performing NMR spin diffusion experiments in samples where traditional magnetization filters may prove unsuccessful. This REDOR‐filtered NMR spin diffusion method can also be extended to other samples where a heteronuclear spin pair exists that is unique to the domain of interest.     

LSPR Imaging: Simultaneous Single Nanoparticle Spectroscopy and Diffusional Dynamics

A wide-field localized surface plasmon resonance (LSPR) imaging method using a liquid crystal tunable filter (LCTF) is used to measure the scattering spectra of multiple Ag nanoparticles in parallel. This method provides the ability to characterize moving Ag nanoparticles by measuring the scattering spectra of the particles while simultaneously tracking their motion. Consequently, single particle diffusion coefficients can be determined. As an example, several single Ag nanoprisms are tracked, the LSPR scattering spectrum of each moving particle is obtained, and the single particle diffusion coefficient is determined from its trajectory. Coupling diffusion information with spectral information in real time is a significant advance and addresses many scientific problems, both fundamental and biological, such as cell membrane protein diffusion, functional plasmonic distributions, and nanoparticle growth mechanisms.     

MSAID: multiple sequence alignment based on a measure of information discrepancy

We propose an algorithm of global multiple sequence alignment that is based on a measure of what we call information discrepancy. The algorithm follows a progressive alignment iteration strategy that makes use of what we call a function of degree of disagreement (FDOD). MSAID begins with distance calculation of pairwise sequences, based on FDOD as a numerical scoring measure. In the next step, the resulting distance matrix is used to construct a guide tree via the neighbor-joining method. The tree is then used to produce a multiple alignment. Current alignment is next used to produce a new matrix and a new tree (with FDOD scoring measure again). This iterative process continues until convergence criteria (or a stopping rule) are satisfied. MSAID was tested and compared with other prior methods by using reference alignments from BAliBASE 2.01. For the alignments with no large N/C-terminal extensions or internal insertions MSAID received the top overall average in the tests. Moreover, the results of testing indicate that MSAID performs as well as other alignment methods with an occasional tendency to perform better than these prior techniques. We, therefore, believe that MSAID is a solid and reliable method of choice, which is often (if not always) superior to other global alignment techniques.     

Two-focus fluorescence correlation spectroscopy: a new tool for accurate and absolute diffusion measurements.

We present a new method to measure absolute diffusion coefficients at nanomolar concentrations with high precision. Based on a modified fluorescence correlation spectroscopy (FCS)-setup, this method is improved by introducing an external ruler for measuring the diffusion time by generating two laterally shifted and overlapping laser foci at a fixed and known distance. Data fitting is facilitated by a new two-parameter model to describe the molecule detection function (MDF). We present a recorded MDF and show the excellent agreement with the fitting model. We measure the diffusion coefficient of the red fluorescent dye Atto655 under various conditions and compare these values with a value achieved by gradient pulsed field NMR (GPF NMR). From these measurements we conclude, that the new measurement scheme is robust against optical and photophysical artefacts which are inherent to standard FCS. With two-focus-FCS, the diffusion coefficient of 4.26 x 10(-6) cm2s(-1) for Atto655 in water at 25 degrees C compares well with the GPF NMR value of 4.28 x 10(-6) cm2s(-1).     

NaCl对烷基苯磺酸盐Gemini表面活性剂水溶液性质的影响

采用旋滴法测定了烷基苯磺酸盐Gemini表面活性剂Ia水溶液与正庚烷的界面张力,用超微电极循环伏安法测定了水溶液中Ia的胶束扩散系数.结果发现,NaCl的加入能够使界面张力降低2倍左右,使Ia的胶束扩散系数变大;Ia浓度增大,胶束扩散系数变小,而NaCl浓度增大,胶束扩散系数变大.这些变化说明NaCI的加入使得Ia胶束大小发生了变化.这是由于NaCl的加入降低了Ia离子头基之间的静电斥力,使得Ia分子排列更加紧密,更有效降低了油水的界面张力,使胶束形状变小;同时胶束表面电荷得到中和,胶束的静电斥力相应减小,胶束流动性相应增加,从而表现出较大的胶柬扩散系数.     

Measuring the mutual diffusion coefficient for dodecyl acrylate in low molecular weight poly(dodecyl acrylate) with laser line deflection (Wiener's Method) and the fluorescence of pyrene

Diffusion of small molecules into glassy polymers is quite complicated and almost always non-Fickian. Little work has been done with the diffusion of low molecular weight polymers that are liquids at room temperature (such as poly(dodecyl acrylate)) into their miscible monomers. We have studied three molecular weights under 20 000 to determine if poly(dodecyl acrylate) diffusion into dodecyl acrylate could be treated with Fick's law and if so to determine the values of the diffusion coefficients. We compare two methods for measuring the diffusion of dodecyl acrylate into poly(dodecyl acrylate): We used laser line deflection (Wiener's method) and improved upon the method from published reports. We also used the dependence of pyrene's fluorescence on the viscosity to measure the concentration distribution, and thus to extract the diffusion coefficient. After an initial relaxation period, diffusion in all cases followed Fick's law with a single concentration-independent diffusion coefficient. Comparison of the diffusion coefficients obtained by both methods yielded the same order of magnitude for the diffusion coefficients (10(-7) cm2/s) and showed the same trend in the dependence on the average molecular weight of the polymer (a decrease in the diffusion coefficient with an increase in the molecular weight).     

NMR法研究小分子在SiO2/PSA核壳复合颗粒中的扩散行为

以正己烷为探针分子,采用基于常梯度自旋回波序列的核磁共振技术(CFG-NMR)研究了小分子在SiO2颗粒和通过相转化法制备的SiO2/Poly(styrene-co-acrylic acid) (SiO2/PSA)复合颗粒中的扩散行为。根据双位点模型和分子交换的理论,采用两组份指数拟合实验得到的1H CFG-NMR信号衰减曲线,表明正己烷在SiO2颗粒和SiO2/PSA颗粒中具有两个相差一个数量级的扩散系数。在相同的扩散时间下,正己烷在SiO2/PSA颗粒中的两个扩散系数小于其在SiO2颗粒中的两个扩散系数,说明复合颗粒壳层的聚合物膜对正己烷的扩散具有阻碍作用。与此同时,通过改变常梯度自旋回波序列中的扩散时间,发现正己烷在复合粒子中的扩散系数强烈依赖于扩散时间的大小。     

Simultaneous measurement of diffusion along multiple directions

This paper introduces the first NMR approach for simultaneously measuring the full diffusion tensor. Using magnetic field gradients of different directions to generate multiple modulations of nuclear spin magnetization, multiple echoes of different modulations are acquired in a single scan to simultaneously measure diffusion along different directions. The experimental demonstrations were conducted in both isotropic and anisotropic systems. Since the diffusion anisotropy holds structural and dynamical information, this approach may be useful for monitoring liquid crystals and electrolytes in metastable states and for studying fluidity in situ in porous networks and in vivo in biological systems.     

PGSE‐WATERGATE,a new tool for NMR diffusion‐based studies of ligand–macromolecule binding

A new pulsed gradient spin‐echo NMR diffusion sequence, PGSE‐WATERGATE, which is based on the extremely efficient WATERGATE solvent suppression sequence, is presented. The sequence is simple to set up and particularly suited to measuring the diffusion coefficients of small ligands in aqueous solution such as is commonly required in pharmaceutical and combinatorial applications. It also affords the possibility of measuring the diffusion of exchangeable resonances, which is often impossible in conjunction with other suppression schemes. Further, a trivial modification of the sequence affords the possibility of multiple solvent suppression, thereby increasing its suitability to LC–NMR applications. The utility of the sequence is demonstrated on the salicylate–bovine serum albumin system. The dissociation constant, K_d, and the number of binding sites were found to be 0.030 M and 33, respectively. Importantly, the extremely high degree of suppression provided by the new sequence allowed the salicylate diffusion coefficients to be measured over a very wide concentration range sufficient to show that the salicylate–bovine serum albumin system is not well described by a simple two‐site model. Previous studies in the literature have been based on data from a smaller concentration range, for which this model gives an apparently good fit. Copyright © 2002 John Wiley & Sons, Ltd.     

Effective simulations of gas diffusion through kinetically accessible tunnels in multisubunit proteins: O2 pathways and escape routes in T-state deoxyhemoglobin

The diffusion of small gases to special binding sites within polypeptide matrices pivotally defines the biochemical specificity and reactivity of proteins. We investigate here explicit O(2) diffusion in adult human hemoglobin (HbA) as a case study employing the recently developed temperature-controlled locally enhanced sampling (TLES) method and vary the parameters to greatly increase the simulation efficiency. The method is carefully validated against standard molecular dynamics (MD) simulations and available experimental structural and kinetic data on ligand diffusion in T-state deoxyHbA. The methodology provides a viable alternative approach to traditional MD simulations and/or potential of mean force calculations for: (i) characterizing kinetically accessible diffusion tunnels and escape routes for light ligands in porous proteins; (ii) very large systems when realistic simulations require the inclusion of multiple subunits of a protein; and (iii) proteins that access short-lived conformations relative to the simulation time. In the case of T-state deoxyHbA, we find distinct ligand diffusion tunnels consistent with the experimentally observed disparate Xe cavities in the α- and β-subunits. We identify two distal barriers including the distal histidine (E7) that control access to the heme. The multiple escape routes uncovered by our simulations call for a review of the current popular hypothesis on ligand escape from hemoglobin. Larger deviations from the crystal structure during simulated diffusion in isolated α- and β-subunits highlight the dampening effects of subunit interactions and the importance of including all subunits of multisubunit proteins to map realistic kinetically accessible diffusion tunnels and escape routes.     

A double quantum (129)Xe NMR experiment for probing xenon in multiply-occupied cavities of solid-state inclusion compounds

A method is presented for detecting multiple xenon atoms in cavities of solid-state inclusion compounds using (129)Xe double quantum NMR spectroscopy. Double quantum filtered (129)Xe NMR spectra, performed on the xenon clathrate of Dianin's compound were obtained under high-resolution Magic-Angle Spinning (MAS) conditions, by recoupling the weak (129)Xe-(129)Xe dipole-dipole couplings that exist between xenon atoms in close spatial proximity. Because the (129)Xe-(129)Xe dipole-dipole couplings are generally weak due to dynamics of the atoms and to large internuclear separations, and since the (129)Xe Chemical Shift Anisotropy (CSA) tends to be relatively large, a very robust dipolar recoupling sequence was necessary, with the symmetry-based SR26 dipolar recoupling sequence proving appropriate. We have also attempted to measure the (129)Xe-(129)Xe dipole-dipole coupling constant between xenon atoms in the cavities of the xenon-Dianin's compound clathrate and have found that the dynamics of the xenon atoms (as investigated with molecular dynamics simulations) as well as (129)Xe multiple spin effects complicate the analysis. The double quantum NMR method is useful for peak assignment in (129)Xe NMR spectra because peaks arising from different types of absorption/inclusion sites or from different levels of occupancy of single sites can be distinguished. The method can also help resolve ambiguities in diffraction experiments concerning the order/disorder in a material.     

Integrating protein secondary structure prediction and multiple sequence alignment

Modern protein secondary structure prediction methods are based on exploiting evolutionary information contained in multiple sequence alignments. Critical steps in the secondary structure prediction process are (i) the selection of a set of sequences that are homologous to a given query sequence, (ii) the choice of the multiple sequence alignment method, and (iii) the choice of the secondary structure prediction method. Because of the close relationship between these three steps and their critical influence on the prediction results, secondary structure prediction has received increased attention from the bioinformatics community over the last few years. In this treatise, we discuss recent developments in computational methods for protein secondary structure prediction and multiple sequence alignment, focus on the integration of these methods, and provide some recommendations for state-of-the-art secondary structure prediction in practice.     

Estimation of Self‐Diffusion Coefficients of Small Penetrants in Semicrystalline Polymers Using Single‐Sided NMR

A simple and fast way to measure proton self‐diffusion coefficients of small penetrant molecules in semicrystalline polymers is introduced. The approach takes advantage of the strong static gradient of a mobile single‐sided NMR sensor and it is demonstrated on PE samples with varying degrees of crystallinity fully saturated in either toluene or n‐hexane. The self‐diffusion coefficients were measured using the gradient stimulated echo sequence appended with a CPMG. It is also shown for the first time, with demonstration on PE plates several millimeter thick with different aging histories, that one‐dimensional profiles of self‐diffusion coefficients as a function of depth can be easily obtained.     

PFG-NMR as a Tool for Determining Self-Diffusivities of Various Probe Molecules through H-ZSM-5 Zeolites

The understanding of major zeolite applications is partially based on diffusion of molecules inside or outside microporous networks. However, it is still a challenge to measure such phenomena. The diffusion ordered nuclear magnetic resonance spectroscopy (DOSY) technique has been reported to measure a probe molecule‘s diffusion inside porous solids. Pulsed-field gradient (PFG)-NMR has been used herein to measure the self-diffusivity of different probe molecules, such as neopentane, benzene, toluene and 1-dodecene with increasing dynamic diameter, respectively, on a series of H-ZSM-5 zeolites. The latter materials exhibit different crystal sizes, Si/Al ratios and the presence (or absence) of crystalline defects. In addition, shaped zeolite bodies representing industrial catalysts were compared with the afore-mentioned samples.     

A new method for analyzing H5N1 avian influenza virus

In this paper a novel method for phylogenetic analysis of H5N1 avian influenza virus has been proposed. At first we provide a mapping of virus protein sequence. Based on this mapping, we propose a new distance measure and make use of the corresponding similarity matrix to construct phylogenic tree without requiring multiple alignment. As an application, we construct phylogenic tree for 123 species of H5N1 avian influenza virus. The phylogeny obtained is generally consistent with evolutionary trees constructed in previous studies.     

Monitoring Diffusion of Reptating Polymer Chains by a Direct Energy Transfer Method: A Monte Carlo Simulation

A kinetic Monte Carlo method was used to simulate the diffusion of reptating polymer chains across an interface. A time‐resolved fluorescence technique in conjunction with a direct energy transfer method was used to measure the extent of diffusion of dye‐labeled reptating polymer chains. The diffusion of donor‐ and acceptor‐labeled polymer chains between adjacent compartments was randomly generated. The fluorescence decay profiles of donor molecules were simulated at several diffusion steps to produce mixing of the polymer chains. Mixing ratios of donor‐ and acceptor‐labeled polymer chains in compartments were measured at various stages (snapshots) of diffusion. It was observed that for a given molecular weight, the average interpenetration contour length was found to be proportional to the mixing ratio. Monte Carlo analysis showed that the curvilinear diffusion coefficient is inversely proportional to the weight of polymer chains during diffusion.     

Experimental studies using a single pellet high temperature diffusion cell reactor

It is very important to know the effective diffusivities of reactant gases through the porous solid matrices for a diffusion limited reaction. The single pellet high temperature diffusion cell reactor is used to measure the effective diffusivities of argon and nitrogen during the sequence of calcination, sintering, salt addition and sulfation of Greer limestone. This system can be used to study and gas—solid reaction systems where the solid phase undergoes changes between 25 and 1200°C.     

Quantifying the relationships among drug classes

The similarity of drug targets is typically measured using sequence or structural information. Here, we consider chemo-centric approaches that measure target similarity on the basis of their ligands, asking how chemoinformatics similarities differ from those derived bioinformatically, how stable the ligand networks are to changes in chemoinformatics metrics, and which network is the most reliable for prediction of pharmacology. We calculated the similarities between hundreds of drug targets and their ligands and mapped the relationship between them in a formal network. Bioinformatics networks were based on the BLAST similarity between sequences, while chemoinformatics networks were based on the ligand-set similarities calculated with either the Similarity Ensemble Approach (SEA) or a method derived from Bayesian statistics. By multiple criteria, bioinformatics and chemoinformatics networks differed substantially, and only occasionally did a high sequence similarity correspond to a high ligand-set similarity. In contrast, the chemoinformatics networks were stable to the method used to calculate the ligand-set similarities and to the chemical representation of the ligands. Also, the chemoinformatics networks were more natural and more organized, by network theory, than their bioinformatics counterparts: ligand-based networks were found to be small-world and broad-scale.     

Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion measurements

It is important to characterize drug-albumin binding during drug discovery and lead optimization as strong binding may reduce bioavailability and/or increase the drug's in vivo half-life. Despite knowing about the location of human serum albumin (HSA) drug binding sites and the residues important for binding, less is understood about the binding dynamics between exogenous drugs and endogenous fatty acids. In contrast to highly specific antibody-antigen interactions, the conformational flexibility of albumin allows the protein to adopt multiple conformations of approximately equal energy in order to accommodate a variety of ligands. Nuclear magnetic resonance (NMR) diffusion measurements are a simple way to quantitatively describe ligand-protein interactions without prior knowledge of the number of binding sites or the binding stoichiometry. This method can also provide information about ligand orientation at the binding site due to buildup of exchange-transferred NOE (trNOE) on the diffusion time scale of the experiment. The results of NMR diffusion and NOE experiments reveal multiple binding interactions of HSA with dansylglycine, a drug site II probe, and caprylate, a medium-chain fatty acid that also has primary affinity for HSA's drug site II. Interligand NOE (ilNOE) detected in the diffusion analysis of a protein solution containing both ligands provides insight into the conformations adopted by these ligands while bound in common HSA binding pockets. The results demonstrate the ability of NMR diffusion experiments to identify ternary complex formation and show the potential of this method for characterizing other biologically important ternary structures, such as enzyme-cofactor-inhibitor complexes.