Literature DB >> 20347992

Prediction of protein crystallization outcome using a hybrid method.

Frank H Zucker1, Christine Stewart, Jaclyn dela Rosa, Jessica Kim, Li Zhang, Liren Xiao, Jenni Ross, Alberto J Napuli, Natascha Mueller, Lisa J Castaneda, Stephen R Nakazawa Hewitt, Tracy L Arakaki, Eric T Larson, Easwara Subramanian, Christophe L M J Verlinde, Erkang Fan, Frederick S Buckner, Wesley C Van Voorhis, Ethan A Merritt, Wim G J Hol.   

Abstract

The great power of protein crystallography to reveal biological structure is often limited by the tremendous effort required to produce suitable crystals. A hybrid crystal growth predictive model is presented that combines both experimental and sequence-derived data from target proteins, including novel variables derived from physico-chemical characterization such as R(30), the ratio between a protein's DSF intensity at 30°C and at T(m). This hybrid model is shown to be more powerful than sequence-based prediction alone - and more likely to be useful for prioritizing and directing the efforts of structural genomics and individual structural biology laboratories.
Copyright © 2010 Elsevier Inc. All rights reserved.

Entities:  

Mesh:

Substances:

Year:  2010        PMID: 20347992      PMCID: PMC2957526          DOI: 10.1016/j.jsb.2010.03.016

Source DB:  PubMed          Journal:  J Struct Biol        ISSN: 1047-8477            Impact factor:   2.867


  35 in total

1.  SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.

Authors:  P Bertone; Y Kluger; N Lan; D Zheng; D Christendat; A Yee; A M Edwards; C H Arrowsmith; G T Montelione; M Gerstein
Journal:  Nucleic Acids Res       Date:  2001-07-01       Impact factor: 16.971

2.  Optimisation of aryl substitution leading to potent methionyl tRNA synthetase inhibitors with excellent gram-positive antibacterial activity.

Authors:  Richard L Jarvest; John M Berge; Murray J Brown; Pamela Brown; John S Elder; Andrew K Forrest; C S V Houge-Frydrych; Peter J O'Hanlon; David J McNair; Stephen Rittenhouse; Robert J Sheppard
Journal:  Bioorg Med Chem Lett       Date:  2003-02-24       Impact factor: 2.823

3.  Thermofluor-based high-throughput stability optimization of proteins for structural studies.

Authors:  Ulrika B Ericsson; B Martin Hallberg; George T Detitta; Niek Dekker; Pär Nordlund
Journal:  Anal Biochem       Date:  2006-08-10       Impact factor: 3.365

4.  ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction.

Authors:  Ian M Overton; Gianandrea Padovani; Mark A Girolami; Geoffrey J Barton
Journal:  Bioinformatics       Date:  2008-02-19       Impact factor: 6.937

5.  The use of systematic N- and C-terminal deletions to promote production and structural studies of recombinant proteins.

Authors:  Susanne Gräslund; Johanna Sagemark; Helena Berglund; Lars-Göran Dahlgren; Alex Flores; Martin Hammarström; Ida Johansson; Tetyana Kotenyova; Martina Nilsson; Pär Nordlund; Johan Weigelt
Journal:  Protein Expr Purif       Date:  2007-11-22       Impact factor: 1.650

6.  Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts.

Authors:  Heath E Klock; Eric J Koesema; Mark W Knuth; Scott A Lesley
Journal:  Proteins       Date:  2008-05-01

7.  Heterologous expression of proteins from Plasmodium falciparum: results from 1000 genes.

Authors:  Christopher Mehlin; Erica Boni; Frederick S Buckner; Linnea Engel; Tiffany Feist; Michael H Gelb; Lutfiyah Haji; David Kim; Colleen Liu; Natascha Mueller; Peter J Myler; J T Reddy; Joshua N Sampson; E Subramanian; Wesley C Van Voorhis; Elizabeth Worthey; Frank Zucker; Wim G J Hol
Journal:  Mol Biochem Parasitol       Date:  2006-04-18       Impact factor: 1.759

8.  A simple method for displaying the hydropathic character of a protein.

Authors:  J Kyte; R F Doolittle
Journal:  J Mol Biol       Date:  1982-05-05       Impact factor: 5.469

9.  High-throughput thermal scanning: a general, rapid dye-binding thermal shift screen for protein engineering.

Authors:  Jason J Lavinder; Sanjay B Hari; Brandon J Sullivan; Thomas J Magliery
Journal:  J Am Chem Soc       Date:  2009-03-25       Impact factor: 15.419

10.  Protein disorder prediction: implications for structural proteomics.

Authors:  Rune Linding; Lars Juhl Jensen; Francesca Diella; Peer Bork; Toby J Gibson; Robert B Russell
Journal:  Structure       Date:  2003-11       Impact factor: 5.006

View more
  3 in total

1.  PROSPERO: online prediction of crystallographic success from experimental results and sequence.

Authors:  Frank H Zucker; Hae Young Kim; Ethan A Merritt
Journal:  J Appl Crystallogr       Date:  2012-05-16       Impact factor: 3.304

2.  Computational approaches to selecting and optimising targets for structural biology.

Authors:  Ian M Overton; Geoffrey J Barton
Journal:  Methods       Date:  2011-08-27       Impact factor: 3.608

3.  Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

Authors:  Diana Fusco; Timothy J Barnum; Andrew E Bruno; Joseph R Luft; Edward H Snell; Sayan Mukherjee; Patrick Charbonneau
Journal:  PLoS One       Date:  2014-07-02       Impact factor: 3.240

  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.