Dataset Information

Tunable activated esters for lysine labeling in proteome

ABSTRACT: The development of various heteroaromatic activated esters designed for selective lysine labeling within the proteome for profiling purposes. Through systematic optimization of the reactivity and selectivity of these esters, we identified a series of effective probe molecules suitable for both in vitro and cellular applications. These findings are of considerable importance for enhancing our comprehension of protein functionalities and mechanisms, facilitated by the precise identification and analysis of protein labeling and profiling.

ORGANISM(S): Homo Sapiens

SUBMITTER: Rui Wang

PROVIDER: PXD051323 | iProX | Tue Apr 09 00:00:00 BST 2024

REPOSITORIES: iProX

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Publications

Tunable Activated Esters Enable Lysine-Selective Protein Labeling and Profiling.

Wan Chuan C Yang Dongyan D An Yuhao Y Kong Lingwei L Zhou Ziyuan Z Tang Li L Zhang Zhe Z Dai Yaohong Y Wang Rui R

Analytical chemistry 20241107 46

Lysine residues on protein surfaces are abundant and often found in enzyme active sites, making them critical targets for studying undruggable proteins. However, the varied microenvironment surrounding lysine residues results in a wide range of p<i>K</i><sub>a</sub> values, complicating site-specific covalent binding. In this study, we address the challenges posed by the diverse reactivity of amino side chains by modulating the amide reaction activity of heteroaromatic activated esters. By fine- ...[more]

PMID: 39509607

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Project description:Background: With the growing availability of entire genome sequences, an increasing number of scientists can exploit oligonucleotide microarrays for genome-scale expression studies. While probe-design is a major research area, relatively little work has been reported on the optimization of microarray protocols. Results: As shown in this study, suboptimal conditions can have considerable impact on biologically relevant observations. For example, deviation from the optimal temperature by one degree Celsius lead to a loss of 44% of differentially expressed genes identified. While genes from thousands of Gene Ontology categories were affected, transcription factors and other low-copy-number regulators were disproportionately lost. Calibrated protocols are thus required in order to take full advantage of the large dynamic range of microarrays. For an objective optimization of protocols we introduce an approach that maximizes the amount of information obtained per experiment. A comparison of two typical samples is sufficient for this calibration. We ensure, however, that optimization results are independent of the samples and the specific measures used for calibration. Both simulations and spike-in experiments confirm an unbiased determination of generally optimal experimental conditions. Conclusions: Well calibrated hybridization conditions are thus easily achieved and necessary for the efficient detection of differential expression. They are essential for the sensitive profiling of low-copy-number molecules. This is particularly critical for studies of transcription factor expression, or the inference and study of regulatory networks. Supporting material, including source code and data, is available at http://bioinf.boku.ac.at/pub/optMA2010/. Optimization of hybridization temperature via an assessment of differential expression between two samples (male vs female Drosophila melanogaster) in 6 technical replicates (3 regular + 3 dye-swaps) for hybridizations at different temperatures (in two batches of 50, 52, 54, and 56; and 47, 49, 50, and 51 degree Celsius, with the repeated hybridization at 50 degree Celsius serving to demonstrate batch-to-batch stability).

Dataset Information

Tunable activated esters for lysine labeling in proteome

Publications

Tunable Activated Esters Enable Lysine-Selective Protein Labeling and Profiling.

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