Bioinformatics Advance Access originally published online on February 10, 2004
Bioinformatics 2004 20(14):2162-2168; doi:10.1093/bioinformatics/bth066
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Bioinformatics 20(14) © Oxford University Press 2004; all rights reserved.
Discovery Note |
Protein isoelectric point as a predictor for increased crystallization screening efficiency
1 Department of Chemistry and Biochemistry and W.M. Keck Foundation Center for Molecular Structure, California State University Fullerton, Fullerton, CA 92834-6866, USA, 2 Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA and 3 Biology and Biotechnology Research Program, L-448, Lawrence Livermore National Laboratory Livermore, CA 94551, USA
Received on May 8, 2003; revised on August 11, 2003; accepted on August 18, 2003
Advance Access Publication February 10, 2004
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/
Contact: br{at}llnl.gov; kkantardjieff{at}fullerton.edu
* To whom correspondence should be addressed.
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