Old Fold in a New X-Ray Diffraction Dataset? Low-Resolution Molecular Replacement Using Representative Structural Templates Can Provide Phase Information

Rajavel, M and Warrier, Thulasi and Gopal, B (2006) Old Fold in a New X-Ray Diffraction Dataset? Low-Resolution Molecular Replacement Using Representative Structural Templates Can Provide Phase Information. In: Proteins: Structure, Function, and Bioinformatics, 64 (4). pp. 923-930.

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Abstract

The advent of structural genomics has led to a dramatic increase in the number of structures deposited in the Protein Data Bank. The number of new folds, however, still remains a very small fraction of the total number of deposited structures. Recent data on the progress of the structural genomics initiative reveals that more than 85% of target proteins that progress to the stage of data collection and structure determination have a known fold. Enzymes, which tend to exploit reaction space while adopting a common stable scaffold, contribute significantly to this observation. Herein, we evaluate a method to examine the old fold in a new dataset scenario likely to be encountered in the structural genomics pipeline. We demonstrate that a fold detection strategy based on secondary structure signatures followed by molecular replacement using a minimalist model can be effectively used to solve the phase problem in X-ray crystallography without further recourse to heavy atom derivatives or multiple anomalous dispersion techniques. Three common folds—the triosephosphate isomerase (TIM), adenine nucleotide alpha hydrolase-like (HUP), and RNA recognition motif (RRM)—were examined using this approach. The results presented herein also provide an estimate of the extent of phase information that can be derived from a single domain in a large multidomain structure

Item Type:	Journal Article
Publication:	Proteins: Structure, Function, and Bioinformatics
Publisher:	John Wiley & Sons, Inc.
Additional Information:	Copyright of this article belongs to John Wiley & Sons, Inc.
Keywords:	structural genomics; common folds; molecular replacement; low-resolution phasing
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	25 Aug 2008
Last Modified:	19 Sep 2010 04:31
URI:	http://eprints.iisc.ac.in/id/eprint/8584

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