Computational crystallization

Archives of Biochemistry and Biophysics
Irem AltanEdward H Snell

Abstract

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 ste...Continue Reading

References

Jul 5, 1992·Journal of Molecular Biology·J B MitchellS L Price
Oct 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·J A ThomsonG B Benedek
Aug 1, 1996·Quarterly Reviews of Biophysics·N E ChayenM Wulff
May 20, 1998·Structure·A MatteL T Delbaere
Oct 16, 2003·Proceedings of the National Academy of Sciences of the United States of America·Sheh-Yi SheuE W Schlag
Feb 12, 2004·Bioinformatics·Katherine A Kantardjieff, Bernhard Rupp
May 8, 2004·Bioinformatics·Li ChenJohn Westbrook
Jul 1, 1997·Acta Crystallographica. Section D, Biological Crystallography·F BonnetéS Veesler
Aug 25, 2004·Methods : a Companion to Methods in Enzymology·Neer Asherie
Aug 25, 2004·Methods : a Companion to Methods in Enzymology·Zygmunt S Derewenda
Nov 23, 2005·Acta Crystallographica. Section D, Biological Crystallography·Thomas S PeatJanet Newman
Nov 30, 2005·Proteins·Pawel SmialowskiDmitrij Frishman
Dec 22, 2005·Acta Crystallographica. Section D, Biological Crystallography·Zygmunt S Derewenda, Peter G Vekilov
Jul 1, 2006·FEBS Letters·Ian M Overton, Geoffrey J Barton
Oct 24, 2006·Acta Crystallographica. Section D, Biological Crystallography·Mathieu CharlesFrançoise Bonneté
Nov 1, 2006·Proceedings of the National Academy of Sciences of the United States of America·Megan J AndersonStephen R Quake
Feb 24, 2007·Biochemical and Biophysical Research Communications·Ke ChenMandana Rahbari
Mar 24, 2007·Bioinformatics·Baris E SuzekCathy H Wu
Jul 28, 2007·Protein Science : a Publication of the Protein Society·Lukasz GoldschmidtDavid Eisenberg
Sep 4, 2007·Protein Science : a Publication of the Protein Society·André C DumetzAbraham M Lenhoff
Oct 9, 2007·Bioinformatics·Lukasz SlabinskiAdam Godzik
Oct 10, 2007·Proceedings of the National Academy of Sciences of the United States of America·Jennifer J McManusGeorge B Benedek
Nov 18, 2008·Nucleic Acids Research·Helen M BermanJoshua La Baer
Nov 20, 2008·Acta Crystallographica. Section D, Biological Crystallography·Edward H SnellJoseph R Luft
Nov 21, 2008·Acta Crystallographica. Section D, Biological Crystallography·Edward H SnellGeorge T Detitta
Nov 21, 2008·Acta Crystallographica. Section D, Biological Crystallography·Edward H SnellGeorge T DeTitta
Dec 27, 2008·Trends in Biotechnology·Emmanuel Saridakis, Naomi E Chayen
Jan 21, 2009·Acta Crystallographica. Section D, Biological Crystallography·Michael Tung, D Travis Gallagher
Apr 25, 2009·Acta Crystallographica. Section D, Biological Crystallography·Marcin Cieślik, Zygmunt S Derewenda
Aug 4, 2009·BMC Structural Biology·Lukasz KurganSamad Jahandideh
Sep 17, 2009·Biochemical and Biophysical Research Communications·Marcin J Mizianty, Lukasz Kurgan
Jan 5, 2010·Protein and Peptide Letters·Krishna Kumar KandaswamyRajeev Gangal
Feb 24, 2010·Journal of Structural and Functional Genomics·György Babnigg, Andrzej Joachimiak
Mar 20, 2010·The Journal of Physical Chemistry. B·Sameer TalrejaPaul J A Kenis
May 7, 2010·Acta Crystallographica. Section D, Biological Crystallography·Zygmunt S Derewenda
Jun 21, 2011·Bioinformatics·Marcin J Mizianty, Lukasz Kurgan
Mar 24, 2012·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Janet NewmanFrank von Delft
Jun 26, 2012·Journal of Theoretical Biology·Samad Jahandideh, Abbas Mahdavi
Mar 7, 2014·Acta Crystallographica. Section D, Biological Crystallography·Samad JahandidehAdam Godzik

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Citations

May 10, 2016·Archives of Biochemistry and Biophysics·Ana Cámara-Artigas, José Antonio Gavira
Feb 6, 2018·The Journal of Physical Chemistry. B·Irem AltanPatrick Charbonneau

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