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BLASTing away preconceptions in crystallization trials.

ABSTRACT: Crystallization is in many cases a critical step for solving the three-dimensional structure of a protein molecule. Determining which set of chemicals to use in the initial screen is typically agnostic of the protein under investigation; however, crystallization efficiency could potentially be improved if this were not the case. Previous work has assumed that sequence similarity may provide useful information about appropriate crystallization cocktails; however, the authors are not aware of any quantitative verification of this assumption. This research investigates whether, given current information, one can detect any correlation between sequence similarity and crystallization cocktails. BLAST was used to quantitate the similarity between protein sequences in the Protein Data Bank, and this was compared with three estimations of the chemical similarities of the respective crystallization cocktails. No correlation was detected between proteins of similar (but not identical) sequence and their crystallization cocktails, suggesting that methods of determining screens based on this assumption are unlikely to result in screens that are better than those currently in use.

SUBMITTER: Abrahams GJ

PROVIDER: S-EPMC6404862 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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BLASTing away preconceptions in crystallization trials.

Abrahams Gabriel Jan GJ Newman Janet J

Acta crystallographica. Section F, Structural biology communications 20190221 Pt 3

Crystallization is in many cases a critical step for solving the three-dimensional structure of a protein molecule. Determining which set of chemicals to use in the initial screen is typically agnostic of the protein under investigation; however, crystallization efficiency could potentially be improved if this were not the case. Previous work has assumed that sequence similarity may provide useful information about appropriate crystallization cocktails; however, the authors are not aware of any ...[more]

PMID: 30839293

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BLASTing away preconceptions in crystallization trials.

Publications

BLASTing away preconceptions in crystallization trials.

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