Literature DB >> 19765976

High-throughput crystallography for structural genomics.

Andrzej Joachimiak1.   

Abstract

Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now more than 55000 protein structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal, and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact.

Entities:  

Mesh:

Year:  2009        PMID: 19765976      PMCID: PMC2764548          DOI: 10.1016/j.sbi.2009.08.002

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  65 in total

1.  Protein crystallization for genomics: towards high-throughput optimization techniques.

Authors:  Naomi E Chayen; Emmanuel Saridakis
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-05-29

2.  Multiparametric scaling of diffraction intensities.

Authors:  Zbyszek Otwinowski; Dominika Borek; Wladyslaw Majewski; Wladek Minor
Journal:  Acta Crystallogr A       Date:  2003-04-25       Impact factor: 2.290

3.  A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site.

Authors:  Lucy Stols; Minyi Gu; Lynda Dieckman; Rosemarie Raffen; Frank R Collart; Mark I Donnelly
Journal:  Protein Expr Purif       Date:  2002-06       Impact factor: 1.650

4.  Use of limited proteolysis to identify protein domains suitable for structural analysis.

Authors:  Chris M Koth; Stephen M Orlicky; Stephan M Larson; Aled M Edwards
Journal:  Methods Enzymol       Date:  2003       Impact factor: 1.600

5.  Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS.

Authors:  Dennis Pantazatos; Jack S Kim; Heath E Klock; Raymond C Stevens; Ian A Wilson; Scott A Lesley; Virgil L Woods
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-08       Impact factor: 11.205

Review 6.  Protein expression systems for structural genomics and proteomics.

Authors:  Shigeyuki Yokoyama
Journal:  Curr Opin Chem Biol       Date:  2003-02       Impact factor: 8.822

7.  Automation of protein purification for structural genomics.

Authors:  Youngchang Kim; Irina Dementieva; Min Zhou; Ruiying Wu; Lour Lezondra; Pearl Quartey; Grazyna Joachimiak; Olga Korolev; Hui Li; Andrzej Joachimiak
Journal:  J Struct Funct Genomics       Date:  2004

Review 8.  Discovering functional novelty in metagenomes: examples from light-mediated processes.

Authors:  Amoolya H Singh; Tobias Doerks; Ivica Letunic; Jeroen Raes; Peer Bork
Journal:  J Bacteriol       Date:  2008-10-10       Impact factor: 3.490

9.  Cold-shock induced high-yield protein production in Escherichia coli.

Authors:  Guoliang Qing; Li-Chung Ma; Ahmad Khorchid; G V T Swapna; Tapas K Mal; Masanori Mitta Takayama; Bing Xia; Sangita Phadtare; Haiping Ke; Thomas Acton; Gaetano T Montelione; Mitsuhiko Ikura; Masayori Inouye
Journal:  Nat Biotechnol       Date:  2004-06-13       Impact factor: 54.908

10.  Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure.

Authors:  W A Hendrickson; J R Horton; D M LeMaster
Journal:  EMBO J       Date:  1990-05       Impact factor: 11.598

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  53 in total

Review 1.  Ice breaking in GPCR structural biology.

Authors:  Qiang Zhao; Bei-li Wu
Journal:  Acta Pharmacol Sin       Date:  2012-01-30       Impact factor: 6.150

2.  Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome.

Authors:  James E Bray
Journal:  J Struct Funct Genomics       Date:  2012-02-22

Review 3.  Diagnosing the decline in pharmaceutical R&D efficiency.

Authors:  Jack W Scannell; Alex Blanckley; Helen Boldon; Brian Warrington
Journal:  Nat Rev Drug Discov       Date:  2012-03-01       Impact factor: 84.694

4.  An automated pipeline to screen membrane protein 2D crystallization.

Authors:  Changki Kim; Martin Vink; Minghui Hu; James Love; David L Stokes; Iban Ubarretxena-Belandia
Journal:  J Struct Funct Genomics       Date:  2010-03-27

5.  Spatially addressed combinatorial protein libraries for recombinant antibody discovery and optimization.

Authors:  Hongyuan Mao; James J Graziano; Tyson M A Chase; Cornelia A Bentley; Omar A Bazirgan; Neil P Reddy; Byeong Doo Song; Vaughn V Smider
Journal:  Nat Biotechnol       Date:  2010-10-24       Impact factor: 54.908

6.  Biocrystallography: past, present, future.

Authors:  Richard Giegé; Claude Sauter
Journal:  HFSP J       Date:  2010-04-22

Review 7.  Metagenomics and the protein universe.

Authors:  Adam Godzik
Journal:  Curr Opin Struct Biol       Date:  2011-04-14       Impact factor: 6.809

Review 8.  X-ray crystallography over the past decade for novel drug discovery - where are we heading next?

Authors:  Heping Zheng; Katarzyna B Handing; Matthew D Zimmerman; Ivan G Shabalin; Steven C Almo; Wladek Minor
Journal:  Expert Opin Drug Discov       Date:  2015-07-15       Impact factor: 6.098

9.  A rational protocol for the successful crystallization of L-amino-acid oxidase from Bothrops atrox.

Authors:  Raquel Melo Alves; Patricia Rosa Feliciano; Suely Vilela Sampaio; Maria Cristina Nonato
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-03-25

Review 10.  High-throughput structural biology of metabolic enzymes and its impact on human diseases.

Authors:  Wyatt W Yue; Udo Oppermann
Journal:  J Inherit Metab Dis       Date:  2011-02-22       Impact factor: 4.982

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