Analysis of crystallization data in the Protein Data Bank

Kirkwood, Jobie; Hargreaves, David; O’Keefe, Simon; Wilson, Julie

doi:10.1107/s2053230x15014892

Cited by 21 publications

(24 citation statements)

References 57 publications

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“…Acidic proteins has pI lower than 7, more likely to crystallize around one pH unit above their pI, while basic proteins more likely to crystallize lower than their pI about 1.5-3 pH units [2]. Generally, protein aggregation or precipitation when the solubility decrease at pH close to the isoelectric point (pI).…”

Section: Isoelectric Point (Pi) Ph and Temperaturementioning

confidence: 99%

Important Factors Influencing Protein Crystallization

Abdalla¹

2016

Glob J Biotechnol Biomater Sci

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The solution of crystallization problem was introduced around twenty years ago, with the introduction of crystallization screening methods. Here reported some of the factors which affect protein crystallization, solubility, Concentration of precipitant, concentration of macromolecule, ionic strength, pH, temperature, and organism source of macromolecules, reducing or oxidizing environment, additives, ligands, presence of substrates, inhibitors, coenzymes, metal ions and rate of equilibration. The aim of this paper to give very helpful advice for crystallization.

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Section: Isoelectric Point (Pi) Ph and Temperaturementioning

confidence: 99%

Important Factors Influencing Protein Crystallization

Abdalla¹

2016

Glob J Biotechnol Biomater Sci

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“…, PO 4 2À ) combined with the most successful crystallization reagents (Tung & Gallagher, 2009) and a revised set of crystallization reagents (McPherson & Gavira, 2014;Bergfors, 2008;McPherson, 2001McPherson, , 1976Ames et al, 1998;Jancarik & Kim, 1991), we created a sparse-matrix screen of 96 crystallization solutions (supplementary file S1). The occurrences of the most common salts, precipitants and pH ranges in the Biological Macromolecular Crystallization Database (BMCD; Tung & Gallagher, 2009) and Berkeley Screen solutions are described in Table 1. In 1968, an alcohol oxidase was the first protein crystallized using a polyethylene glycol (PEG) (Janssen & Ruelius, 1968;Kirkwood et al, 2015). PEGs became extensively used for crystallization after the McPherson study using PEGs of various molecular weights was published in 1976 (McPherson, 1976).…”

Section: àmentioning

confidence: 99%

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

et al. 2017

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Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.

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“…Despite these caveats, the information present is clearly useful. For example, Kirkwood et al [31] used “cleaned” PDB data to confirm that acidic proteins (pI < 7) tend to crystallize at 1.0 pH unit above their pI and that basic proteins (pI > 7) tend to crystallize 1.5–3.0 pH units below their pI, in agreement with previous studies [32]. However, the PDB captures no information on other chemical conditions that may have yielded crystals, the range of chemical space sampled, or the other experimental outcomes that result.…”

Section: Experimental Crystallization Datamentioning

confidence: 99%

Computational crystallization

Altan

Snell

2016

Archives of Biochemistry and Biophysics

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Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed.

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Analysis of crystallization data in the Protein Data Bank

Abstract: In a large-scale study using data from the Protein Data Bank, some of the many reported findings regarding the crystallization of proteins were investigated.

Cited by 21 publications

References 57 publications

Important Factors Influencing Protein Crystallization

Important Factors Influencing Protein Crystallization

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

Computational crystallization

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