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Immobilization of alpha1-acid glycoprotein for chromatographic studies of drug-protein binding II. correction for errors in association constant measurements.

ABSTRACT: A new method for the immobilization of alpha(1)-acid glycoprotein (AGP) in high-performance liquid chromatography (HPLC) columns was recently described for applications such as drug binding studies. Part of this earlier work used self-competition zonal elution studies to measure association equilibrium constants between immobilized AGP and R- or S-propranolol. It was later found that analysis of these data by a common equation derived for linear elution conditions gave erroneous values for experiments actually conducted under nonlinear conditions. This report discusses the nature of this error and uses frontal analysis to estimate the true binding strength between R- and S-propranolol and HPLC columns containing immobilized AGP.

SUBMITTER: Mallik R

PROVIDER: S-EPMC2386853 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature

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Immobilization of alpha1-acid glycoprotein for chromatographic studies of drug-protein binding II. correction for errors in association constant measurements.

Mallik Rangan R Xuan Hai H Guiochon Georges G Hage David S DS

Analytical biochemistry 20080202 1

A new method for the immobilization of alpha(1)-acid glycoprotein (AGP) in high-performance liquid chromatography (HPLC) columns was recently described for applications such as drug binding studies. Part of this earlier work used self-competition zonal elution studies to measure association equilibrium constants between immobilized AGP and R- or S-propranolol. It was later found that analysis of these data by a common equation derived for linear elution conditions gave erroneous values for exper ...[more]

PMID: 18294445

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Project description:BACKGROUND: High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction are crucial to many short read sequencing applications including de novo genome sequencing, genome resequencing, and digital gene expression analysis. Short read error detection is typically carried out by counting the observed frequencies of kmers in reads and validating those with frequencies exceeding a threshold. In case of genomes with high repeat content, an erroneous kmer may be frequently observed if it has few nucleotide differences with valid kmers with multiple occurrences in the genome. Error detection and correction were mostly applied to genomes with low repeat content and this remains a challenging problem for genomes with high repeat content. RESULTS: We develop a statistical model and a computational method for error detection and correction in the presence of genomic repeats. We propose a method to infer genomic frequencies of kmers from their observed frequencies by analyzing the misread relationships among observed kmers. We also propose a method to estimate the threshold useful for validating kmers whose estimated genomic frequency exceeds the threshold. We demonstrate that superior error detection is achieved using these methods. Furthermore, we break away from the common assumption of uniformly distributed errors within a read, and provide a framework to model position-dependent error occurrence frequencies common to many short read platforms. Lastly, we achieve better error correction in genomes with high repeat content. AVAILABILITY: The software is implemented in C++ and is freely available under GNU GPL3 license and Boost Software V1.0 license at "http://aluru-sun.ece.iastate.edu/doku.php?id = redeem". CONCLUSIONS: We introduce a statistical framework to model sequencing errors in next-generation reads, which led to promising results in detecting and correcting errors for genomes with high repeat content.

Dataset Information

Immobilization of alpha1-acid glycoprotein for chromatographic studies of drug-protein binding II. correction for errors in association constant measurements.

Publications

Immobilization of alpha1-acid glycoprotein for chromatographic studies of drug-protein binding II. correction for errors in association constant measurements.

Similar Datasets

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