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S Tsoka

Publications and source records attributed to S Tsoka.

10 recordsLinked to original sources
PubMed2001

Functional versatility and molecular diversity of the metabolic map of Escherichia coli.

We have analyzed the known metabolic enzymes of Escherichia coli in relation to their biochemical reaction properties and their involvement in biochemical pathways. All enzymes involved in small-molecule metabolism and their corresponding protein sequences have been extracted from the EcoCyc database. These 548 metabolic enzymes are clustered into 405 protein families according to sequence similarity. In this study, we examine the functional versatility within enzyme families in terms of their reaction capabilities and pathway participation. In addition, we examine the molecular diversity of reactions and pathways according to their presence across enzyme families. These complex, many-to-many relationships between protein sequence and biochemical function reveal a significant degree of correlation between enzyme families and reactions. Pathways, however, appear to require more than one enzyme type to perform their complex biochemical transformations. Finally, the distribution of enzyme family members across different pathways provides support for the "recruitment" hypothesis of biochemical pathway evolution.

Amino Acid Sequence↗
PubMed2000

Genome sequences and great expectations.

To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that function can be predicted for almost two-thirds of the 73,500 genes that were analyzed. Despite progress in computational biology, there will always be a great need for large-scale experimental determination of protein function.

Animals↗
PubMed2000

Recent developments and future directions in computational genomics.

Computational genomics is a subfield of computational biology that deals with the analysis of entire genome sequences. Transcending the boundaries of classical sequence analysis, computational genomics exploits the inherent properties of entire genomes by modelling them as systems. We review recent developments in the field, discuss in some detail a number of novel approaches that take into account the genomic context and argue that progress will be made by novel knowledge representation and simulation technologies.

Animals↗
PubMed2000

CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts.

MOTIVATION: Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions. RESULTS: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. The detection of low-complexity regions is highly specific for single residue types. It is shown that this approach is sufficient for masking database query sequences without generating false positives. The algorithm is benchmarked against widely available algorithms using the 210 genes of Plasmodium falciparum chromosome 2, a dataset known to contain a large number of low-complexity regions. AVAILABILITY: CAST (version 1.0) executable binaries are available to academic users free of charge under license. Web site entry point, server and additional material: http://www.ebi.ac.uk/research/cgg/services/cast/

Algorithms↗
PubMed1999

Virus-like particle analysis in yeast homogenate using a laser light-scattering assay.

Virus-like particles (VLPs) expressed intracellularly by the yeast S. cerevisiae have helped set the framework of a wide range of biologicals, particularly as carriers for viral antigens. This article investigates the use of dynamic light scattering (DLS) for the rapid evaluation of the concentration and purity of VLPs to aid the complex purification strategy. Development of the assay was performed in a high background process stream (yeast homogenate) and involved a change in the signal proportional to the VLP concentration by addition of antibodies that bind on the VLP surface and detection of that size change by DLS. Overall, the assay was found to provide a significant improvement of rapid monitoring alternatives for VLPs, exhibiting good sensitivity and speed of measurement. Data are given for the use of the DLS-based assay for optimization of VLP release during a yeast cell disruption treatment.

Antibodies, Monoclonal↗
PubMed1998

Rapid monitoring of virus-like particles using an optical biosensor: a feasibility study.

Virus-like particles (VLPs) are multimeric proteins expressed by Saccharomyces cerevisiae. The particles are approximately 80 nm in diameter and they are used as a framework for a range of biological products; for example as carriers of viral antigens. Rapid monitoring of purified VLPs was investigated using an optical biosensor. The aim was to develop an assay which may be employed for real-time bioprocess monitoring of VLPs. Problems of mass transfer of analyte were overcome through selection of a planar biosensor surface, in preference to the traditional polymer-coated surface. To prolong the surface activity for interaction analysis, a sandwich assay was developed which involved the use of a secondary capture species. It was shown that VLP concentration in pure solution could be determined within 10 min.

Biosensing Techniques↗
PubMed1994

Selection of chromatographic protein purification operations based on physicochemical properties.

The charge characteristics of four proteins (conalbumin, ovalbumin, apotransferrin, and soybean trypsin inhibitor) were determined over a range of pH using an electrophoretic technique (titration curve). HPLC anion-exchange chromatography for each of the proteins was performed to investigate whether electrophoretic and chromatographic results could be correlated. It was found that charge density, estimated from the electrophoretic titration curves (as net charge divided by the protein molecular weight) in most cases correlates extremely well the retention of the protein in terms of time needed for the protein to be eluted from the column. This correlation was far better than that of net charge or that of surface charge (net charge/surface area). The performance of anion-exchange chromatography, hydrophobic interaction chromatography, and gel filtration using preparative columns on an FPLC were compared. The ability of each method to separate the components of the mixture of the four proteins was assessed by calculating the resolution of the chromatographic results obtained for each pair of proteins. Using the concept of the deviation factor (DF) between individual properties of pairs of proteins (charge density, molecular weight, hydrophobicity), the separation efficiency factor (eta s) could be calculated. Resolution results showed that anion exchange was the best technique for separating the proteins followed by hydrophobic interaction chromatography and gel filtration. Calculations for efficiency, eta s, confirmed the superiority of anion-exchange chromatography as a separation method over gel filtration. For hydrophobic interaction chromatography, it was not possible to find a suitable parameter to express DF and, consequently, eta s. An appropriate way to express the hydrophobicity of a protein, as a physicochemical property, that can be used in the expression of DF should be investigated.

Animals↗
PubMedDate not supplied

Selective flocculation and precipitation for the improvement of virus-like particle recovery from yeast homogenate.

The purification of an intracellular product from a complex mixture of contaminants after cell disruption is a common problem in processes downstream of fermentation systems. This is particularly challenging for the recovery of particulate (80 nm in diameter) multimeric protein products, named virus-like particles (VLPs), from cell debris and other intracellular components. Selective flocculation for debris removal followed by selective precipitation of the target protein can be used as a preclarification step to aid purification. In this paper, selective borax flocculation of cell debris in yeast homogenate, followed by selective poly(ethylene glycol) precipitation of VLPs are defined with a view to demonstrating their potential in aiding the initial clarification stages of the purification sequence. The translation from laboratory scale to pilot scale operation is addressed, demonstrating the challenge of scale-up of solid-liquid separation stages for biological particle processing.

Borates↗