Crystallization of Protein–DNA Complexes

Abstract

Determination of atomic resolution structures of protein–deoxyribonucleic acid (DNA) complexes using X‐ray crystallography requires preparation of high‐quality crystalline specimens. The preparation of such samples remains an empirical endeavour, more art than science. Nonetheless, decades of experience have yielded a large body of practical strategies and techniques towards this end. Such efforts with protein–DNA complexes enjoy special advantages, but also involve control of a larger set of variables. High purity, chemical and conformational, preparations of both macromolecules are important. Crystallogenesis of protein–DNA complexes is favoured by careful choice of the sequence and the terminal bases and/or base pairs of the DNA target. Modern crystallisation screens, which encapsulate the accumulated wisdom of prior investigations, serve as an excellent starting point for experimentation.

Key Concepts:

  • An atomic level analysis of a macromolecule by X‐ray crystallography requires preparation of high‐quality crystals of the entity of interest.

  • Preparation of crystalline specimens requires highly concentrated solutions of the molecules of interest. Success is favoured when high chemical and conformational purity has been achieved.

  • Extensive experience in preparation of protein crystals can be applied to growth of protein–DNA crystals. Additionally, the length, composition, and identity of the termini of the DNA molecule play significant roles in crystallisation.

  • Initial crystallisation trials are set up using a concentrated stock of protein–DNA complex of interest with premade formulations that sparsely sample crystallisation space. Precipitation and crystal formation under these conditions are used to direct efforts for further crystallisation experiments. The experiments are repeated until crystals suitable for X‐ray diffraction are obtained.

Keywords: Crystallisation; protein–DNA complex; X‐ray crystallography; light scattering; mass spectrometry; limited proteolysis; multiwavelength anomalous diffraction (MAD); single‐wavelength anomalous diffraction (SAD)

Figure 1.

Macromolecular crystallisation. Initial crystallisation trials are set up using a concentrated stock of protein–DNA complex of interest with premade formulations that sparsely sample crystallisation space. A large number of crystal screens are now commercially available, including those designed for crystallisation of protein–nucleic acid complexes. The drops are inspected and the ‘hits’ and/or interesting trends are identified. New formulations are then prepared based on the conditions that result in the hits and used for reproduction and optimisation of the crystals. The experiments are repeated until crystals suitable for X‐ray diffraction are obtained.

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Pakotiprapha, Danaya, and Jeruzalmi, David(Nov 2014) Crystallization of Protein–DNA Complexes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0002720.pub3]