Small-molecule microarrays: development of novel linkers and an efficient detection method for bound proteins

Novel isocyanate and diazoketone linkers possessing polyoxypropylenediamine as a spacer for small-molecule microrray are developed. White light interferometry is introduced to detect bound proteins on the glass slides without using chemically modified proteins.     

Simple and efficient method for heterologous expression of clostridial proteins

Many clostridial proteins are poorly produced in Escherichia coli. It has been suggested that this phenomena is due to the fact that several types of codons common in clostridial coding sequences are rarely used in E. coli and the quantities of the corresponding tRNAs in E. coli are not sufficient to ensure efficient translation of the corresponding clostridial sequences. To address this issue, we amplified three E. coli genes, ileX, argU, and leuW, in E. coli; these genes encode tRNAs that are rarely used in E. coli (the tRNAs for the ATA, AGA, and CTA codons, respectively). Our data demonstrate that amplification of ileX dramatically increased the level of production of most of the clostridial proteins tested, while amplification of argU had a moderate effect and amplification of leuW had no effect. Thus, amplification of certain tRNA genes for rare codons in E. coli improves the expression of clostridial genes in E. coli, while amplification of other tRNAs for rare codons might not be needed for improved expression. We also show that amplification of a particular tRNA gene might have different effects on the level of protein production depending on the prevalence and relative positions of the corresponding codons in the coding sequence. Finally, we describe a novel approach for improving expression of recombinant clostridial proteins that are usually expressed at a very low level in E. coli.     

A method for efficient isotopic labeling of recombinant proteins

A rapid and efficient approach for preparing isotopically labeled recombinant proteins is presented. The method is demonstrated for ¹³C labeling of the C-terminal domain of angiopoietin-2, ¹⁵N labeling of ubiquitin and for ²H/¹³C/¹⁵N labeling of the Escherichia coli outer-membrane lipoprotein Lpp-56. The production method generates cell mass using unlabeled rich media followed by exchange into a small volume of labeled media at high cell density. Following a short period for growth recovery and unlabeled metabolite clearance, the cells are induced. The expression yields obtained provide a fourfold to eightfold reduction in isotope costs using simple shake flask growths.     

Fast screening method for detection of acyl-HSL-degrading soil isolates

A reliable method was developed for screening of bacteria isolates capable of degrading acyl-HSLs, the signal molecules in quorum-sensing-mediated processes of many Proteobacteria. The microtiter assay was based on the use of a GFP-marked Escherichia coli strain, which fluoresces upon the presence of acyl-HSLs. Measurement of GFP fluorescence with a Molecular Imager FX scanner (fluorometer) detected isolates capable of degrading acyl-HSLs. The potential of this method was demonstrated by isolation of different bacteria from a potato rhizosphere able to inactivate synthetic and natural acyl HSLs produced by Pectobacterium carotovorum subsp. carotovorum (Pcc) (Erwinia carotovora subsp. carotovora (Ecc)).     

Fast method for two-dimensional electrophoresis of proteins from biological samples

The method for two-dimensional gel electrophoresis of J. Klose and M. Feller [(1981) Electrophoresis 2, 12-24] has been simplified by reducing the thickness of the gels from 3.5 to 1.1 mm for isoelectric focusing gels and from 3.5 to 0.84 mm for sodium dodecyl sulfate slab gels. Thin gels need less reagents and smaller sample volumes. Cooling of the thin gels during electrophoresis is more effective, which allows the use of higher electric power. Therefore, less time is required for an electrophoretic run (approx 4 h). The resolution increases due to the smaller size of the spots. The time required for staining the gels is reduced from at least 3 days to about 1 h. The method has been tested with a protein sample from the filamentous fungus Fusarium solani.     

Fast detection of common geometric substructure in proteins.

We consider the problem of identifying common three-dimensional substructures between proteins. Our method is based on comparing the shape of the alpha-carbon backbone structures of the proteins in order to find three-dimensional (3D) rigid motions that bring portions of the geometric structures into correspondence. We propose a geometric representation of protein backbone chains that is compact yet allows for similarity measures that are robust against noise and outliers. This representation encodes the structure of the backbone as a sequence of unit vectors, defined by each adjacent pair of alpha-carbons. We then define a measure of the similarity of two protein structures based on the root mean squared (RMS) distance between corresponding orientation vectors of the two proteins. Our measure has several advantages over measures that are commonly used for comparing protein shapes, such as the minimum RMS distance between the 3D positions of corresponding atoms in two proteins. A key advantage is that this new measure behaves well for identifying common substructures, in contrast with position-based measures where the nonmatching portions of the structure dominate the measure. At the same time, it avoids the quadratic space and computational difficulties associated with methods based on distance matrices and contact maps. We show applications of our approach to detecting common contiguous substructures in pairs of proteins, as well as the more difficult problem of identifying common protein domains (i.e., larger substructures that are not necessarily contiguous along the protein chain).     

A sensitive and specific method for quantitative estimation of carbamylation in proteins

A simple, rapid, reproducible, and specific micromethod for the estimation of carbamylation of proteins is described. The method is based on permanganate oxidation of radioactive carbamyl derivatives of protein to form urea and on the specific decomposition of urea by urease.     

A universal method for detection of amyloidogenic misfolded proteins

Diseases associated with the misfolding of endogenous proteins, such as Alzheimer's disease and type II diabetes, are becoming increasingly prevalent. The pathophysiology of these diseases is not totally understood, but mounting evidence suggests that the misfolded protein aggregates themselves may be toxic to cells and serve as key mediators of cell death. As such, an assay that can detect aggregates in a sensitive and selective fashion could provide the basis for early detection of disease, before cellular damage occurs. Here we report the evolution of a reagent that can selectively capture diverse misfolded proteins by interacting with a common supramolecular feature of protein aggregates. By coupling this enrichment tool with protein specific immunoassays, diverse misfolded proteins and sub-femtomole amounts of oligomeric aggregates can be detected in complex biological matrices. We anticipate that this near-universal approach for quantitative misfolded protein detection will become a useful research tool for better understanding amyloidogenic protein pathology as well as serve as the basis for early detection of misfolded protein diseases.     

MUSTA--a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins.

Here we present an algorithm designed to carry out multiple structure alignment and to detect recurring substructural motifs. So far we have implemented it for comparison of protein structures. However, this general method is applicable to comparisons of RNA structures and to detection of a pharmacophore in a series of drug molecules. Further, its sequence order independence permits its application to detection of motifs on protein surfaces, interfaces, and binding/active sites. While there are many methods designed to carry out pairwise structure comparisons, there are only a handful geared toward the multiple structure alignment task. Most of these tackle multiple structure comparison as a collection of pairwise structure comparison tasks. The multiple structural alignment algorithm presented here automatically finds the largest common substructure (core) of atoms that appears in all the molecules in the ensemble. The detection of the core and the structural alignment are done simultaneously. The algorithm begins by finding small substructures that are common to all the proteins in the ensemble. One of the molecules is considered the reference; the others are the source molecules. The small substructures are stored in special arrays termed combinatorial buckets, which define sets of multistructural alignments from the source molecules that coincide with the same small set of reference atoms (C(alpha)-atoms here). These substructures are initial small fragments that have congruent copies in each of the proteins. The substructures are extended, through the processing of the combinatorial buckets, by clustering the superpositions (transformations). The method is very efficient.     

A method for the estimation of proteins in colored or turbid solutions

The many photometric methods of protein estimation give unsatisfactory results with highly colored solutions. Some plant pigment-protein complexes are not precipitable with trichloracetic acid; therefore the dye binding methods are not applicable. A rapid procedure has been devised where the protein is complexed with excess copper, the noncomplexed copper removed by an ion-exchange resin, and the copper complexed to polypeptide then estimated by atomic absorption spectrophotometry. The copper complex is proportional to the amount of protein and different proteins give the same result in the range of 0.05 to 1 mg.     

An improved intracellular staining protocol for efficient detection of nuclear proteins in YFP-expressing cells

Intracellular staining is a widely used flow cytometry (FCM)-based technique to detect the expression of cytoslio nucleic antigens. However, intracellular staining of cells expressing cytosolic fluorescent protein (FP) markers was proven to be problematic as significant loss of the FP-signal was routinely observed. Using splenocytes harvested from mice constitutively expressing the enhanced yellow fluorescent proteins (YFP) as a model, we modified the widely used intracellular staining protocol and successfully achieved simultaneous detection of both the nuclear proteins and YFP in T-regulatory cells. The improved protocol can be used to perform antibody-based intracellular characterization of FP-labeled target cells, while maintaining their fluorescent reporter signals for easy tracing and identification.     

Advanced negative detection method comparable to silver stain for SDS-PAGE separated proteins detection

In order to achieve an easy, rapid and sensitive protocol to detect proteins in polyacrylamide gel, an advanced negative detection method comparable to silver stain is described. When a gel was incubated with Phloxine B and followed by the development in acidic solution, the zones where forming protein-dye complex were selectively transparent, unlike opaque gel background. Within 50 min after electrophoresis, down to 0.1–0.4 ng of gel-separated proteins (similar with silver stain) could be observed, without labor-intensive and time-consuming procedure. Comparing with the most common negative stain method, Imidazole-zinc stain, Phloxine B stain has been shown higher sensitivity and distinct contrast between the transparent protein bands/spots and opaque background than those; furthermore, it is no longer necessary to concern about retention time of observation. This technique may provide a sensitive and practical choice for proteomics researches.     

An efficient method for the detection and elimination of systematic error in high-throughput screening

MOTIVATION: High-throughput screening (HTS) is an early-stage process in drug discovery which allows thousands of chemical compounds to be tested in a single study. We report a method for correcting HTS data prior to the hit selection process (i.e. selection of active compounds). The proposed correction minimizes the impact of systematic errors which may affect the hit selection in HTS. The introduced method, called a well correction, proceeds by correcting the distribution of measurements within wells of a given HTS assay. We use simulated and experimental data to illustrate the advantages of the new method compared to other widely-used methods of data correction and hit selection in HTS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

An immunoassay method for quantitative detection of proteins using single antibodies

A new immunoassay method called specific analyte labeling and recapture assay (SALRA) to quantitatively measure protein abundance was developed, and the assay conditions were optimized. The key features of this method include labeling the antigen bound to the capture antibody, eluting the labeled antigen, and recapturing it by the same capture antibody on the detection plate. The reporter molecules on the labeled antigen provide a convenient and reliable means for signal detection. We demonstrated that the dose-response curve of SALRA was comparable to that of sandwich enzyme-linked immunosorbent assay (ELISA) and better than that of the antigen direct labeling method. In addition, multiple proteins can be measured simultaneously by SALRA. Using the SALRA method, the detection limit for most of the cytokines tested was approximately 0.01 ng/ml. Further SALRA tests on interleukin 6 (IL-6) showed the linear dose-response was 3.3 to 0.01 ng/ml, the accuracy of the test was 71 to 91%, the intraassay variation was 3.6 to 7.4%, and the interassay variation was 3.8 to 10.0%. The applications of SALRA include quantitatively measuring proteins for which there are no ELISA tools available and providing a new platform for protein microarrays.     

Development of a new and simple method for the detection of histidine-tagged proteins

To develop a general method for the detection of histidine-tagged proteins, the interactions of the histidine epitope tag of MutH and MutL proteins with the epitope specific monoclonal anti-His6 antibody were monitored by a label-free direct method using impedance spectroscopy. The immunosensor was fabricated by covalent coupling of the antibody on a conducting polymer coated electrode surface. The impedance of the antibody modified electrode was decreased after binding to the histidine-tagged proteins. The specificity of the sensor was demonstrated by showing that no impedance change was occurred when the sensor was exposed to both of non-tagged MutH and MutL proteins. The specific interaction was further characterized using quartz crystal microbalance studies. Based on impedance measurements, the linear ranges were obtained from 50.0 to 125.0 and 50.0 to 250.0 micorg/ml, for His-tag MutH and His-tag MutL proteins, respectively. The detection limits were determined to be 37.8 and 59.1 microg/ml, for His-tag MutH and His-tag MutL proteins, respectively.