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. 2015 May 1;31(9):1444-51.
doi: 10.1093/bioinformatics/btv011. Epub 2015 Jan 7.

Using isoelectric point to determine the pH for initial protein crystallization trials

Jobie Kirkwood  1 , David Hargreaves  1 , Simon O'Keefe  1 , Julie Wilson  2
Affiliations

Using isoelectric point to determine the pH for initial protein crystallization trials

Jobie Kirkwood et al. Bioinformatics. .

Abstract

Motivation: The identification of suitable conditions for crystallization is a rate-limiting step in protein structure determination. The pH of an experiment is an important parameter and has the potential to be used in data-mining studies to help reduce the number of crystallization trials required. However, the pH is usually recorded as that of the buffer solution, which can be highly inaccurate.

Results: Here, we show that a better estimate of the true pH can be predicted by considering not only the buffer pH but also any other chemicals in the crystallization solution. We use these more accurate pH values to investigate the disputed relationship between the pI of a protein and the pH at which it crystallizes.

Availability and implementation: Data used to generate models are available as Supplementary Material.

Contact: julie.wilson@york.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Net charge of the sequence CRV with varying pH
Fig. 2.
Fig. 2.
Organization of data used for linear regression modelling
Fig. 3.
Fig. 3.
Accuracy of pH values. The pH obtained by spectrophotometry is shown plotted against the pH predicted by an artificial neural network in (A) and the pH of the buffer in (B)
Fig. 4.
Fig. 4.
Histogram showing errors in predicted and buffer pH values in relation to the spectrophotometric pH
Fig. 5.
Fig. 5.
Histograms showing the absolute difference between the pI and the closest pH at which crystals were obtained for proteins in the SGC dataset. (a) shows group 1 (structure determined), (b) shows group 2 (diffraction to at least 3.6 Å), (c) shows group 3 (at least one protein crystal) and (d) shows group 4 (crystal to be followed up)
See this image and copyright information in PMC

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