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HDX-analyzer: a novel package for statistical analysis of protein structure dynamics.

Liu S, Liu L, Uzuner U, Zhou X, Gu M, Shi W, Zhang Y, Dai SY, Yuan JS - BMC Bioinformatics (2011)

Bottom Line: RPY2 creates a low-level interface for R and allows the effective integration of statistical module for data processing.The results from the different statistical analysis methods are compared and shown to be similar.The statistical analysis results are overlaid with the three dimensional structure of the protein to highlight the regional structure dynamics changes in the xylanase enzyme.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA. sanminliu@gmail.com

ABSTRACT

Background: HDX mass spectrometry is a powerful platform to probe protein structure dynamics during ligand binding, protein folding, enzyme catalysis, and such. HDX mass spectrometry analysis derives the protein structure dynamics based on the mass increase of a protein of which the backbone protons exchanged with solvent deuterium. Coupled with enzyme digestion and MS/MS analysis, HDX mass spectrometry can be used to study the regional dynamics of protein based on the m/z value or percentage of deuterium incorporation for the digested peptides in the HDX experiments. Various software packages have been developed to analyze HDX mass spectrometry data. Despite the progresses, proper and explicit statistical treatment is still lacking in most of the current HDX mass spectrometry software. In order to address this issue, we have developed the HDXanalyzer for the statistical analysis of HDX mass spectrometry data using R, Python, and RPY2.

Implementation and results: HDXanalyzer package contains three major modules, the data processing module, the statistical analysis module, and the user interface. RPY2 is employed to enable the connection of these three components, where the data processing module is implemented using Python and the statistical analysis module is implemented with R. RPY2 creates a low-level interface for R and allows the effective integration of statistical module for data processing. The data processing module generates the centroid for the peptides in form of m/z value, and the differences of centroids between the peptides derived from apo and ligand-bound protein allow us to evaluate whether the regions have significant changes in structure dynamics or not. Another option of the software is to calculate the deuterium incorporation rate for the comparison. The two types of statistical analyses are Paired Student's t-test and the linear combination of the intercept for multiple regression and ANCOVA model. The user interface is implemented with wxpython to facilitate the data visualization in graphs and the statistical analysis output presentation. In order to evaluate the software, a previously published xylanase HDX mass spectrometry analysis dataset is processed and presented. The results from the different statistical analysis methods are compared and shown to be similar. The statistical analysis results are overlaid with the three dimensional structure of the protein to highlight the regional structure dynamics changes in the xylanase enzyme.

Conclusion: Statistical analysis provides crucial evaluation of whether a protein region is significantly protected or unprotected during the HDX mass spectrometry studies. Although there are several other available software programs to process HDX experimental data, HDXanalyzer is the first software program to offer multiple statistical methods to evaluate the changes in protein structure dynamics based on HDX mass spectrometry analysis. Moreover, the statistical analysis can be carried out for both m/z value and deuterium incorporation rate. In addition, the software package can be used for the data generated from a wide range of mass spectrometry instruments.

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Related in: MedlinePlus

The overlay of p value with 3D structure of xylanase. The color legend indicats the level of confidence.
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Figure 6: The overlay of p value with 3D structure of xylanase. The color legend indicats the level of confidence.

Mentions: The statistical analysis allows us to identify which region of the protein has significant structure dynamics changes upon ligand binding. As shown in Figure 6, the substrate binding of xylanase has introduced significant structure dynamics changes in many different regions of the protein. The overlay of 3D structure and significance of the changes provided another way to interpret the HDX mass spectrometry data. For example, when we overlay the p value of the different peptides with the protein structure, the regions with significant changes are highlighted and the information can help to understand the enzyme catalysis mechanisms. HDXanalyzer thus provided a powerful tool for statistical analysis of structure dynamics data, which has not been achieved for previous HDX mass spectrometry analysis software.


HDX-analyzer: a novel package for statistical analysis of protein structure dynamics.

Liu S, Liu L, Uzuner U, Zhou X, Gu M, Shi W, Zhang Y, Dai SY, Yuan JS - BMC Bioinformatics (2011)

The overlay of p value with 3D structure of xylanase. The color legend indicats the level of confidence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3044300&req=5

Figure 6: The overlay of p value with 3D structure of xylanase. The color legend indicats the level of confidence.
Mentions: The statistical analysis allows us to identify which region of the protein has significant structure dynamics changes upon ligand binding. As shown in Figure 6, the substrate binding of xylanase has introduced significant structure dynamics changes in many different regions of the protein. The overlay of 3D structure and significance of the changes provided another way to interpret the HDX mass spectrometry data. For example, when we overlay the p value of the different peptides with the protein structure, the regions with significant changes are highlighted and the information can help to understand the enzyme catalysis mechanisms. HDXanalyzer thus provided a powerful tool for statistical analysis of structure dynamics data, which has not been achieved for previous HDX mass spectrometry analysis software.

Bottom Line: RPY2 creates a low-level interface for R and allows the effective integration of statistical module for data processing.The results from the different statistical analysis methods are compared and shown to be similar.The statistical analysis results are overlaid with the three dimensional structure of the protein to highlight the regional structure dynamics changes in the xylanase enzyme.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA. sanminliu@gmail.com

ABSTRACT

Background: HDX mass spectrometry is a powerful platform to probe protein structure dynamics during ligand binding, protein folding, enzyme catalysis, and such. HDX mass spectrometry analysis derives the protein structure dynamics based on the mass increase of a protein of which the backbone protons exchanged with solvent deuterium. Coupled with enzyme digestion and MS/MS analysis, HDX mass spectrometry can be used to study the regional dynamics of protein based on the m/z value or percentage of deuterium incorporation for the digested peptides in the HDX experiments. Various software packages have been developed to analyze HDX mass spectrometry data. Despite the progresses, proper and explicit statistical treatment is still lacking in most of the current HDX mass spectrometry software. In order to address this issue, we have developed the HDXanalyzer for the statistical analysis of HDX mass spectrometry data using R, Python, and RPY2.

Implementation and results: HDXanalyzer package contains three major modules, the data processing module, the statistical analysis module, and the user interface. RPY2 is employed to enable the connection of these three components, where the data processing module is implemented using Python and the statistical analysis module is implemented with R. RPY2 creates a low-level interface for R and allows the effective integration of statistical module for data processing. The data processing module generates the centroid for the peptides in form of m/z value, and the differences of centroids between the peptides derived from apo and ligand-bound protein allow us to evaluate whether the regions have significant changes in structure dynamics or not. Another option of the software is to calculate the deuterium incorporation rate for the comparison. The two types of statistical analyses are Paired Student's t-test and the linear combination of the intercept for multiple regression and ANCOVA model. The user interface is implemented with wxpython to facilitate the data visualization in graphs and the statistical analysis output presentation. In order to evaluate the software, a previously published xylanase HDX mass spectrometry analysis dataset is processed and presented. The results from the different statistical analysis methods are compared and shown to be similar. The statistical analysis results are overlaid with the three dimensional structure of the protein to highlight the regional structure dynamics changes in the xylanase enzyme.

Conclusion: Statistical analysis provides crucial evaluation of whether a protein region is significantly protected or unprotected during the HDX mass spectrometry studies. Although there are several other available software programs to process HDX experimental data, HDXanalyzer is the first software program to offer multiple statistical methods to evaluate the changes in protein structure dynamics based on HDX mass spectrometry analysis. Moreover, the statistical analysis can be carried out for both m/z value and deuterium incorporation rate. In addition, the software package can be used for the data generated from a wide range of mass spectrometry instruments.

Show MeSH
Related in: MedlinePlus