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BLASTing away preconceptions in crystallization trials.

Gabriel Jan Abrahams1, Janet Newman1

  • 1Manufacturing (Biomedical), CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia.

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|March 7, 2019
PubMed
Summary
This summary is machine-generated.

Protein crystallization is key for structural biology. This study found no link between protein sequence similarity and effective crystallization cocktails, suggesting current screening methods are as good as any sequence-based approach.

Keywords:
BLASTPDBProtein Data BankREMARK 280crystallizationsequences

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Computational Biology

Background:

  • Protein crystallization is essential for determining three-dimensional protein structures.
  • Current crystallization screening methods are generally protein-agnostic.
  • Previous assumptions suggest protein sequence similarity might guide crystallization cocktail selection.

Purpose of the Study:

  • To investigate the correlation between protein sequence similarity and crystallization cocktails.
  • To quantitatively verify if sequence similarity can predict suitable crystallization conditions.
  • To assess if sequence-based screening improves upon existing methods.

Main Methods:

  • Utilized BLAST to quantify sequence similarity among proteins in the Protein Data Bank.
  • Compared protein sequence similarity with chemical similarity estimations of their crystallization cocktails.
  • Analyzed data to detect any statistically significant correlation.

Main Results:

  • No significant correlation was detected between proteins with similar (but not identical) sequences and their crystallization cocktails.
  • The findings do not support the hypothesis that sequence similarity predicts crystallization success.
  • Current methods for selecting crystallization screens are not demonstrably improved by sequence similarity data.

Conclusions:

  • Sequence similarity does not appear to be a reliable predictor of optimal crystallization cocktails.
  • Developing protein-specific crystallization screens based on sequence similarity is unlikely to outperform current agnostic approaches.
  • Further research may be needed to identify novel predictors for protein crystallization.