Protein isoelectric point as a predictor for increased crystallization screening efficiency.

Katherine A Kantardjieff; Bernhard Rupp

doi:10.1093/bioinformatics/bth066

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PubMed · 14871873

Protein isoelectric point as a predictor for increased crystallization screening efficiency.

Katherine A Kantardjieff·Bernhard Rupp

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Abstract

MOTIVATION: Increased efficiency in initial crystallization screening reduces cost and material requirements in structural genomics. Because pH is one of the few consistently reported parameters in the Protein Data Bank (PDB), the isoelectric point (pI) of a protein has been explored as a useful indirect predictor for the optimal choice of range and distribution of the pH sampling in crystallization trials. RESULTS: We have analyzed 9596 unique protein crystal forms from the August 2003 PDB and have found a significant relationship between the calculated pI of successfully crystallized proteins and the difference between pI and reported pH at which they were crystallized. These preferences provide strong prior information for the design of crystallization screening experiments with significantly increased efficiency and corresponding reduction in material requirements, leading to potential cost savings of millions of US$ for structural genomics projects involving high-throughput crystallographic structure determination. AVAILABILITY: A prototype example of a screen design and efficiency estimator program, CrysPred, is available at http://www-structure.llnl.gov/cryspred/

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Computer Simulation Crystallization Crystallography Databases, Protein Isoelectric Point Models, Chemical Models, Molecular Models, Statistical Protein Conformation Proteins Sensitivity and Specificity Sequence Analysis, Protein Comparative Study Evaluation Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.Validation Study

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Katherine A Kantardjieff, Bernhard Rupp. 2004-02-10. Protein isoelectric point as a predictor for increased crystallization screening efficiency.. https://doi.org/10.1093/bioinformatics%2Fbth066

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