Protein engineering as a tool for crystallography (original) (raw)
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Protein crystallization: from purified protein to diffraction-quality crystal
Nature Methods, 2008
Determining the structure of biological macromolecules by X-ray crystallography involves a series of steps: selection of the target molecule; cloning, expression, purification and crystallization; collection of diffraction data and determination of atomic positions. However, even when pure soluble protein is available, producing high-quality crystals remains a major bottleneck in structure determination. Here we present a guide for the non-expert to screen for appropriate crystallization conditions and optimize diffraction-quality crystal growth.
Biophysical Chemistry, 2005
The crystallographic quality of protein crystals that were grown in microgravity has been compared to that of crystals that were grown in parallel on earth gravity under otherwise identical conditions. A goal of this comparison was to assess if a more accurate 3D-structure can be derived from crystallographic analysis of the former crystals. Therefore, the properties of crystals prepared with the Advanced Protein Crystallisation Facility (APCF) on earth and in orbit during the last decade were evaluated. A statistical analysis reveals that about half of the crystals produced under microgravity had a superior X-ray diffraction limit with respect of terrestrial controls. Eleven protein structures could be determined at previously unachieved resolutions using crystals obtained in the APCF. Microgravity induced features of the most relevant structures are reported. A second goal of this study was to identify the cause of the crystal quality enhancement useful for structure determination. No correlations between the effect of microgravity and other system-dependent parameters, such as isoelectric point or crystal solvent content, were found except the reduced convection during the crystallisation process. Thus, crystal growth under diffusive regime appears to be the key parameter explaining the beneficial effect of microgravity on crystal quality. The mimicry of these effects on earth in gels or in capillary tubes is discussed and the practical consequences for structural biology highlighted. D
Post-crystallization treatments for improving diffraction quality of protein crystals
Acta Crystallographica Section D Biological Crystallography, 2005
X-ray crystallography is the most powerful method for determining the three-dimensional structure of biological macromolecules. One of the major obstacles in the process is the production of high-quality crystals for structure determination. All too often, crystals are produced that are of poor quality and are unsuitable for diffraction studies. This review provides a compilation of post-crystallization methods that can convert poorly diffracting crystals into data-quality crystals. Protocols for annealing, dehydration, soaking and cross-linking are outlined and examples of some spectacular changes in crystal quality are provided. The protocols are easily incorporated into the structure-determination pipeline and a practical guide is provided that shows how and when to use the different post-crystallization treatments for improving crystal quality.
Perspectives on protein crystallisation
Progress in Biophysics & Molecular Biology, 2009
This final part on 'perspectives' is focused on new strategies that can be used to crystallise proteins and improve the crystal quality of macromolecular complexes using any of the methods reviewed in this focused issue. Some advantages and disadvantages, limitations, and plausible applications to highresolution X-ray crystallography are discussed.
Protein crystallography from the perspective of technology developments
Crystallography Reviews, 2014
Early on, crystallography was a domain of mineralogy and mathematics and dealt mostly with symmetry properties and imaginary crystal lattices. This changed when Wilhelm Conrad Röntgen discovered X-rays in 1895, and in 1912 Max von Laue and his associates discovered X-ray irradiated salt crystals would produce diffraction patterns that could reveal the internal atomic periodicity of the crystals. In the same year the father-and-son team, Henry and Lawrence Bragg successfully solved the first crystal structure of sodium chloride and the era of modern crystallography began. Protein crystallography (PX) started some 20 years later with the pioneering work of British crystallographers. In the past 50-60 years, the achievements of modern crystallography and particularly those in protein crystallography have been due to breakthroughs in theoretical and technical advancements such as phasing and direct methods; to more powerful X-ray sources such as synchrotron radiation (SR); to more sensitive and efficient X-ray detectors; to ever faster computers and to improvements in software. The exponential development of protein crystallography has been accelerated by the invention and applications of recombinant DNA technology that can yield nearly any protein of interest in large amounts and with relative ease. Novel methods, informatics platforms, and technologies for automation and high-throughput have allowed the development of large-scale, high efficiency macromolecular crystallography efforts in the field of structural genomics (SG). Very recently, the X-ray free-electron laser (XFEL) sources and its applications in protein crystallography have shown great potential for revolutionizing the whole field again in the near future.
An overview of heavy-atom derivatization of protein crystals
Acta Crystallographica Section D Structural Biology, 2016
Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative.
Optimizing Protein Complexes for Crystal Growth †
Crystal Growth & Design, 2007
Many intracellular proteins do not work on their own but rather in complex with small molecules, DNA, or other proteins. To gain a more fundamental understanding of protein interactions and their resulting functions, one requires a detailed structural model of relevant complexes. The first step in this challenge is to grow well-diffracting crystals. Three examples of protein complex crystallization will be discussed in detail below. In the first example, biophysical techniques such as fluorescence titration, isothermal titration calorimetry (ITC), and dynamic light scattering (DLS) are used to characterize the protein and assess the most suitable conditions for complex formation. The second example utilizes bioinformatic information and proteomic techniques to engineer constructs of the protein that are most favorable for crystallization. The final example uses NMR information for optimizing complex-forming conditions, which allowed the growth of better-diffracting complex crystals.
In Situ Protein Crystal Diffraction Screening
2012
The generation of high quality diffracting crystals remains an area that requires considerable person-power. Not only do crystals need to be produced and/or optimized, but such samples also have to be analyzed for their diffraction properties. While crystal shape and size are critical parameters controlling diffraction strength, diffraction screening remains the optimal manner to guide crystal growth optimization protocols. Mounting of the crystals to an appropriate sample support often requires transfer into a buffer significantly different from that the crystal is grown in, often resulting in a negative impact upon crystal morphology and diffraction properties. Modern synchrotron sources are increasingly using in situ exposure to X-rays to characterize protein crystals, with a growing number of structures being solved directly in situ, without recourse to manual handling of delicate samples. An automated approach requires crystal identification, positioning and collection of X-ray diffraction data for analysis. However, limitations are imposed by the variation in crystal size, morphology and space group. Here we review the availability and limitations of both commercial and synchrotron based infrastructures for in situ diffraction screening. We review the status of methods to establish the basic geometric features of crystals, the limitations currently inherent with in situ screening methods and we also describe our and other researchers efforts to overcome these limitations.
An approach to crystallizing proteins by synthetic symmetrization
Proceedings of the National Academy of Sciences, 2006
Previous studies of symmetry preferences in protein crystals suggest that symmetric proteins, such as homodimers, might crystallize more readily on average than asymmetric, monomeric proteins. Proteins that are naturally monomeric can be made homodimeric artificially by forming disulfide bonds between individual cysteine residues introduced by mutagenesis. Furthermore, by creating a variety of single-cysteine mutants, a series of distinct synthetic dimers can be generated for a given protein of interest, with each expected to gain advantage from its added symmetry and to exhibit a crystallization behavior distinct from the other constructs. This strategy was tested on phage T4 lysozyme, a protein whose crystallization as a monomer has been studied exhaustively. Experiments on three single-cysteine mutants, each prepared in dimeric form, yielded numerous novel crystal forms that cannot be realized by monomeric lysozyme. Six new crystal forms have been characterized. The results sugge...