Phosphopeptide enrichment with stable spatial coordination on a titanium dioxide coated glass slide

Recent advances in phosphoproteomics have established powerful tools to analyze phosphorylation events. However, their spatial localization is lost due to sample homogenization procedures prior to the analysis. Imaging mass spectrometry (IMS) has emerged as a method to visualize the spatial distribution of molecules in tissue samples, but its application is still limited to relatively abundant molecules. Due to low phosphorylation stoichiometry, direct detection and imaging of protein phosphorylation by MS has not been achieved yet. Therefore we have developed a novel phosphopeptide enrichment strategy as a potential tool for in situ affinity imaging MS (AIMS). A specific type of titanium dioxide (TiO₂)‐coated glass slides was designed and validated with casein tryptic digests for their ability to selectively retain phosphopeptides while maintaining their spatial coordination. Copyright © 2009 John Wiley & Sons, Ltd.     

Vertical agarose gel electrophoresis and electroblotting of high-molecular-weight proteins

The electrophoretic separation of high-molecular-weight proteins (> 500 kDa) using polyacrylamide is difficult because gels with a large enough pore size for adequate protein mobility are mechanically unstable. A 1% vertical sodium dodecyl sulfate (SDS)-agarose gel electrophoresis (VAGE) system has been developed that allows titin (a protein with the largest known SDS subunit size of 3000-4000 kDa) to migrate over 10 cm in a approximately 13 cm resolving gel. Such migration gives clear and reproducible separation of titin isoforms. Proteins ranging in size from myosin heavy chain ( approximately 220 kDa) up to titin can be resolved on this gel system. Electroblotting of these very large proteins was nearly 100% efficient. This VAGE system has revealed two titin size variants in rabbit psoas muscle, two N2BA bands in rabbit cardiac muscle, and species differences between titins from rat and rabbit muscle. Agarose electrophoresis should be the method of choice for separation and blotting of proteins with very large subunit sizes.     

Effect of hindered diffusion on the adsorption of proteins in agarose gel using a pore model

The hindered diffusion and binding of proteins of different sizes (lysozyme, BSA and IgG) in an agarose gel is described using adsorption kinetic and diffusional data together with an experimentally determined pore size distribution in the gel. The validity of the pore model, including variable diffusion coefficients and porosities is tested against experimental confocal microscopy data. No fitting parameters were used in the present model. The importance of knowing the gel structure is demonstrated especially for large proteins such as IgG. Experimental confocal microscopy data can be explained by the present model.     

Orientation of DNA and the agarose gel matrix in pulsed electric fields

Transient electric birefringence has been used as an analytical tool to study the orientation of DNA in agarose gels, and to study the orientation of the matrix alone. The sign of the birefringence of DNA oriented in an agarose gel is negative, as observed in free solution, indicating that the DNA molecules orient parallel to the direction of the electric field. If the median pore diameter of the gel is larger than the contour length of the DNA molecule, the DNA effectively does not see the matrix and the birefringence relaxation time is the same as observed in free solution. However, if the median pore diameter of the gel is smaller than the contour length of the DNA, the DNA molecule becomes stretched as well as oriented. For DNA molecules of moderate size (less than or equal to 4 kb), stretching in the gel causes the birefringence relaxation times to increase to the values expected for fully stretched molecules. Complete stretching is not observed for larger DNA molecules. The orientation and stretching of DNA molecules in the gel matrix indicates that end-on migration, or reptation, is a likely mechanism for DNA electrophoresis in agarose gels. When the electric field is rapidly reversed in polarity, very little change in the orientation of the DNA is observed if the DNA molecules were completely stretched and had reached their equilibrium orientation before the field was reversed in direction. Hence completely stretched, oriented DNA molecules are able to reverse their direction of migration in the electric field with little or no loss of orientation. However, if the DNA molecules were not completely stretched or if the equilibrium orientation had not been reached, substantial disorientation of the DNA molecules is observed at field reversal. The forced rate of disorientation in the reversing field is faster than the field-free rate of disorientation. Complicated patterns of reorientation can be observed after field reversal, depending on the degree of orientation in the original field direction. The effect of pulsed electric fields on the orientation of the agarose gel matrix itself was also investigated.(ABSTRACT TRUNCATED AT 400 WORDS)     

Nd-Fe-B alloy-densified agarose gel for expanded bed adsorption of proteins

Novel dense composite adsorbents for expanded bed adsorption of protein have been fabricated by coating 4% agarose gel onto Nd-Fe-B alloy powder by a water-in-oil emulsification method. Two composite matrices, namely Nd-Fe-B alloy-densified agarose (NFBA) gels with different size distributions and densities, NFBA-S (50-165 microm, 1.88 g/ml) and NFBA-L (140-300 microm, 2.04 g/ml), were produced. Lysozyme was used as a model protein to test the adsorption capacity and kinetics for the NFBA gels modified by Cibacron blue 3GA (CB-NFBA gels). Liquid-phase dispersion behavior in the expanded beds was examined by measurements of residence time distributions, and compared with that of Streamline SP (Amersham-Pharmacia Biotech, Sweden). The dependence of axial mixing in the expanded beds on flow velocity, bed expansion degree. settled bed height, and viscosity of liquid phase was investigated. Breakthrough curves of lysozyme in the expanded beds of the CB-NFBA gels were also examined. The dynamic binding capacity at 5% breakthrough was 23.3 mg/ml matrix for the CB-NFBA-S gels, and 16.7 mg/ml matrix for the CB-NFBA-L, at a flow velocity of 220 cm/h. The results indicate that the NFBA gels are promising for expanded bed adsorption of proteins.     

Faster isolation of recombinant factor VIII SQ, with a superporous agarose matrix.

A superporous agarose matrix was compared with a corresponding homogenous matrix in the isolation of recombinant factor VIII SQ (r-VIII SQ) by immunoaffinity chromatography. As a reference, the commercially available Sepharose FastFlow, used for a similar purification in the industry, was also evaluated. Breakthrough curves are described for flows between 50 and 400 cm/h with pre-purified r-VIII SQ and with cell culture broth. The superporous gel gave the best performance and a 1000-fold purification was obtained in a one-step procedure. The superporous matrix made it possible to increase the throughput about four-fold, presumably due to its better mass transfer properties. The importance of the ligand distribution profile is discussed based upon immunofluorescence microscopy data.     

Testing of nonlinear electrofrictiophoresis in agarose gel

It was theoretically predicted earlier that if a periodic force without constant component is applied to a particle, then the particle can produce a directed drift in some direction. The effect is named nonlinear electrofrictiophoresis, because it is crucial for its appearance that the friction force depends on the particle's velocity in a nonlinear manner. We test a possibility to observe this effect when a mixture of fragments of DNA (the DNA ladder) moves in the agarose gel. For this purpose, we study the nonlinear characteristics of a DNA ladder movement in the gel. The gels with the ladder were run under various electric field strengths. It was found that the friction coefficient for each DNA fragment in the ladder depends on the migration velocity, suggesting that energy dissipation during migration is a nonlinear function of velocity. This nonlinearity makes the system under consideration suitable for observing nonlinear electrofrictiophoresis. A possible velocity of directed drift under periodic electric drive without constant component was estimated numerically for experimentally observed dependencies. The velocity appeared to be comparable with that of migration under a constant field of moderate strength. A possible mechanism of energy dissipation during movement of DNA through the gel is discussed.     

Development of a novel two-dimensional gel electrophoresis protocol with agarose native gel electrophoresis

A new protocol for conducting two-dimensional (2D) electrophoresis was developed by combining the recently developed agarose native gel electrophoresis with either vertical sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat SDS agarose gel electrophoresis. Our innovative technique utilizes His/MES buffer (pH 6.1) during the first-dimensional (1D) agarose native gel electrophoresis, which allows for the simultaneous and clear visualization of basic and acidic proteins in their native states or complex structures. Our agarose gel electrophoresis is a true native electrophoresis, unlike blue native–PAGE, which relies on the intrinsic charged states of the proteins and their complexes without the need for dye binding. In the 2D, the gel strip from the 1D agarose gel electrophoresis is soaked in SDS and placed on top of the vertical SDS–PAGE gels or the edge of the flat SDS–MetaPhor high-resolution agarose gels. This allows for customized operation using a single electrophoresis device at a low cost. This technique has been successfully applied to analyze various proteins, including five model proteins (BSA, factor Xa, ovotransferrin, IgG, and lysozyme), monoclonal antibodies with slightly different isoelectric points, polyclonal antibodies, and antigen–antibody complexes, as well as complex proteins such as IgM pentamer and β-galactosidase tetramer. Our protocol can be completed within a day, taking approximately 5–6 h, and can be expanded further into Western blot analysis, mass spectrometry analysis, and other analytical methods.     

Electrokinetic motion of a micro oil droplet under a glass slide

Electrokinetic motion of a micro oil droplet beneath a glass slide was experimentally investigated in this paper. The micro oil droplets were released under the glass slide in an aqueous solution and the motion along the glass slide was measured by a microscope. The experimental results indicate that while the electrokinetic mobility increases with the applied electric field, it decreases with the oil droplet size and the ionic concentration of the aqueous solution, respectively. By changing the zeta potential of the glass‐liquid interface using polybrene coating from negative to positive, the direction of the electrokinetic mobility is reversed and the absolute value of the electrokinetic mobility increases significantly. Finally, pH effects were also investigated, and it was found that the electrokinetic mobility of the droplets reaches a maximum at pH = 6～8.     

Preparative two-dimensional gel electrophoresis with agarose gels in the first dimension for high molecular mass proteins

A two-dimensional gel electrophoresis (2-DE) method that uses an agarose isoelectric focusing (IEF) gel in the first dimension (agarose 2-DE) was compared with an immobilized pH gradient 2-DE method (IPG-Dalt). The former method was shown to produce significant improvements in the 2-D electrophoretic separation of high molecular mass proteins larger than 150 kDa, up to 500 kDa, and to have a higher loading capacity, as much as 1.5 mg proteins in total for micropreparative runs. The extraction medium found best in this study for agarose 2-DE of mammal tissues was 6 M urea, 1 M thiourea, 0.5% 2-mercaptoethanol, protease inhibitor cocktail (Complete Mini EDTA-free), 1% Triton X-100 and 3% 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS). Trichloroacetic acid (TCA) treatment of the agarose gel after IEF is to be carefully weighed beforehand, because some high molecular mass proteins were less likely to enter the second-dimensional polyacrylamide gel after TCA fixation, and proteins such as mouse skeletal muscle actin gave pseudospots in the agarose 2-DE patterns without TCA fixation. As a good compromise we suggest fixation of proteins in the agarose gel with TCA for one hour or less. The first-dimensional agarose IEF gel containing Pharmalyte as a carrier ampholyte was 180 mm in length and 2.5-4.8 mm in diameter. The gel diameter was shown to determine the loading capacity of the agarose 2-DE, and 1.5 mg liver proteins in total were successfully separated by the use of a 4.8 mm diameter agarose gel.     

Natural poly-histidine affinity tag for purification of recombinant proteins on cobalt(II)-carboxymethylaspartate crosslinked agarose

A natural 19-amino-acid poly-histidine affinity tag was cloned at the N-terminus of three recombinant proteins. The vectors containing the DNA of the fusion proteins were used for transformation of Escherichia coli DH5alpha cells. Each protein was expressed, extracted and purified in one chromatographic step. The purification procedure for each protein can be accomplished in less than 1 h. A new type of immobilized metal ion affinity chromatography adsorbent--Co2+-carboxymethylaspartate agarose Superflow--was utilized at linear flow-rates as high as 5 cm/min. The final preparation of each protein is with purity greater than 95% as ascertained by sodium dodecyl sulfate-electrophoresis. Recovery for each purified protein was higher than 77% of the initial loaded amount as judged by biological activity. The operational capacity of Co2+-carboxymethylaspartate agarose for each protein was determined.     

Patterning nanoparticles in a three-dimensional matrix using an electric-field-assisted gel transferring technique

In this paper, we describe an electric-field-assisted gel transferring technique for patterning on two- and three-dimensional media. The transfer process starts with the preparation of a block of agarose gel doped with charged nanoparticles or molecules on top of a screen mask with desired patterns. This gel/mask construct is then brought into contact with the appropriate receiving medium, such as a polymer membrane or a piece of flat hydrogel. An electric field is applied to transfer the doped charged nanoparticles or molecules into the receiving medium with a pattern defined by the screen mask. This printing method is rapid and convenient, the results are reproducible, and the process can be done without using expensive micro/nanofabrication facilities. The capability to pattern structures such as arrays of nanoparticles into three-dimensional hydrogels may find applications for positioning cell signaling molecules to control cell growth and migration.     

On-bead screening of a library to detect host-guest complexation by an aniline reporter

We developed a new labeling reagent and a color assay system in water to detect binding between target molecules and library members on beads, which is free of label-induced artifacts that can cause misleading results.     

Enhanced detection of gold nanoparticles in agarose gel electrophoresis

Gel electrophoresis is a powerful tool in gold nanoparticle (AuNP) research. While the technique is sensitive to the size, charge, and shape of particles, its optimal performance requires a relatively large amount of AuNP in the loading wells for visible detection of bands. We here describe a novel and more sensitive method for detecting AuNPs in agarose gels that involves staining the gel with the common organic fluorophore fluorescein, to produce AuNP band intensities that are linear with nanoparticle concentration and almost an order of magnitude larger than those obtained without staining the gel.     

Water structure in nanopores of agarose gel by Raman spectroscopy

The evolution of water structure during the gelation process is examined in aqueous solution of agarose using Raman spectroscopy of the O-H stretching band. The measurements have been performed at room temperature for different concentrations of agarose, which yields different dimensions of nanopores in the network of the created gel. Our results show that water confined in the gel pores exhibits evident changes in the local order of molecules in comparison with bulk water and water in the sol state. During the sol-gel transition the number of molecules that participate in the regular tetrahedral H-bond structure increases, and the effect is stronger for higher concentration of the biopolymer.