Literature DB >> 26792536

Computational crystallization.

Irem Altan1, Patrick Charbonneau2, Edward H Snell3.   

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 steps needed to realize this potential are discussed.
Copyright © 2016 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Crystallization; computational; crystallization data; crystallography; macromolecular

Mesh:

Substances:

Year:  2016        PMID: 26792536      PMCID: PMC4909510          DOI: 10.1016/j.abb.2016.01.004

Source DB:  PubMed          Journal:  Arch Biochem Biophys        ISSN: 0003-9861            Impact factor:   4.013


  61 in total

1.  Thermodynamics of Ion Pair Formations Between Charged Poly(Amino Acid)s.

Authors:  Vytautas Petrauskas; Eglė Maximowitsch; Daumantas Matulis
Journal:  J Phys Chem B       Date:  2015-09-04       Impact factor: 2.991

2.  Tapping the Protein Data Bank for crystallization information.

Authors:  Thomas S Peat; Jon A Christopher; Janet Newman
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-11-19

3.  Toward rational protein crystallization: A Web server for the design of crystallizable protein variants.

Authors:  Lukasz Goldschmidt; David R Cooper; Zygmunt S Derewenda; David Eisenberg
Journal:  Protein Sci       Date:  2007-08       Impact factor: 6.725

4.  Patterns of protein protein interactions in salt solutions and implications for protein crystallization.

Authors:  André C Dumetz; Ann M Snellinger-O'brien; Eric W Kaler; Abraham M Lenhoff
Journal:  Protein Sci       Date:  2007-09       Impact factor: 6.725

5.  Altered phase diagram due to a single point mutation in human gammaD-crystallin.

Authors:  Jennifer J McManus; Aleksey Lomakin; Olutayo Ogun; Ajay Pande; Markus Basan; Jayanti Pande; George B Benedek
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-08       Impact factor: 11.205

6.  A drunken search in crystallization space.

Authors:  Vincent J Fazio; Thomas S Peat; Janet Newman
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2014-09-30       Impact factor: 1.056

7.  SCMCRYS: predicting protein crystallization using an ensemble scoring card method with estimating propensity scores of P-collocated amino acid pairs.

Authors:  Phasit Charoenkwan; Watshara Shoombuatong; Hua-Chin Lee; Jeerayut Chaijaruwanich; Hui-Ling Huang; Shinn-Ying Ho
Journal:  PLoS One       Date:  2013-09-03       Impact factor: 3.240

8.  The application and use of chemical space mapping to interpret crystallization screening results.

Authors:  Edward H Snell; Ray M Nagel; Ann Wojtaszcyk; Hugh O'Neill; Jennifer L Wolfley; Joseph R Luft
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-11-18

9.  Establishing a training set through the visual analysis of crystallization trials. Part I: approximately 150,000 images.

Authors:  Edward H Snell; Joseph R Luft; Stephen A Potter; Angela M Lauricella; Stacey M Gulde; Michael G Malkowski; Mary Koszelak-Rosenblum; Meriem I Said; Jennifer L Smith; Christina K Veatch; Robert J Collins; Geoff Franks; Max Thayer; Christian Cumbaa; Igor Jurisica; George T Detitta
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-10-18

10.  Analysis of crystallization data in the Protein Data Bank.

Authors:  Jobie Kirkwood; David Hargreaves; Simon O'Keefe; Julie Wilson
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-09-23       Impact factor: 1.056

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  2 in total

Review 1.  What macromolecular crystallogenesis tells us - what is needed in the future.

Authors:  Richard Giegé
Journal:  IUCrJ       Date:  2017-05-24       Impact factor: 4.769

2.  Classification of crystallization outcomes using deep convolutional neural networks.

Authors:  Andrew E Bruno; Patrick Charbonneau; Janet Newman; Edward H Snell; David R So; Vincent Vanhoucke; Christopher J Watkins; Shawn Williams; Julie Wilson
Journal:  PLoS One       Date:  2018-06-20       Impact factor: 3.240

  2 in total

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