Literature DB >> 18441029

Determination of protein structures--a series of fortunate events.

Maksymilian Chruszcz1, Alexander Wlodawer, Wladek Minor.   

Abstract

Determination of a macromolecular structure using x-ray diffraction is a multistep process that involves a plethora of techniques involving molecular biology, bioinformatics, and physical sciences. Counterintuitively, the success of any or all individual steps does not guarantee the success of the overall process. This review examines the difficulties presented by each step on the path from a gene to the final publication, together with certain lucky (or unlucky) circumstances that can affect the velocity along that path.

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Year:  2008        PMID： 18441029      PMCID： PMC2426657          DOI： 10.1529/biophysj.108.131789

Source DB:  PubMed          Journal:  Biophys J        ISSN： 0006-3495            Impact factor:   4.033


  64 in total

1.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.

Authors:  N Ban; P Nissen; J Hansen; P B Moore; T A Steitz
Journal:  Science       Date:  2000-08-11       Impact factor: 47.728

2.  Metal chelate affinity chromatography, a new approach to protein fractionation.

Authors:  J Porath; J Carlsson; I Olsson; G Belfrage
Journal:  Nature       Date:  1975-12-18       Impact factor: 49.962

3.  The structural genomics experimental pipeline: insights from global target lists.

Authors:  Nicholas O'Toole; Marek Grabowski; Zbyszek Otwinowski; Wladek Minor; Miroslaw Cygler
Journal:  Proteins       Date:  2004-08-01

4.  Towards rationalization of crystallization screening for small- to medium-sized academic laboratories: the PACT/JCSG+ strategy.

Authors:  Janet Newman; David Egan; Thomas S Walter; Ran Meged; Ian Berry; Marouane Ben Jelloul; Joel L Sussman; David I Stuart; Anastassis Perrakis
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-09-28

5.  SHELXL: high-resolution refinement.

Authors:  G M Sheldrick; T R Schneider
Journal:  Methods Enzymol       Date:  1997       Impact factor: 1.600

6.  Parameters for crystal growth of ribosomal subunits.

Authors:  A Yonath; J Müssig; H G Wittmann
Journal:  J Cell Biochem       Date:  1982       Impact factor: 4.429

7.  A survey of protein-protein complex crystallizations.

Authors:  Sergei Radaev; Sean Li; Peter D Sun
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-05-12

8.  Intrinsic protein disorder in complete genomes.

Authors:  A K Dunker; Z Obradovic; P Romero; E C Garner; C J Brown
Journal:  Genome Inform Ser Workshop Genome Inform       Date:  2000

9.  New protein fold revealed by a 2.3-A resolution crystal structure of nerve growth factor.

Authors:  N Q McDonald; R Lapatto; J Murray-Rust; J Gunning; A Wlodawer; T L Blundell
Journal:  Nature       Date:  1991-12-05       Impact factor: 49.962

10.  Catalysis in the crystal: synchrotron radiation studies with glycogen phosphorylase b.

Authors:  J Hajdu; K R Acharya; D I Stuart; P J McLaughlin; D Barford; N G Oikonomakos; H Klein; L N Johnson
Journal:  EMBO J       Date:  1987-02       Impact factor: 11.598
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  30 in total

1.  Structure of a calcium-dependent 11R-lipoxygenase suggests a mechanism for Ca2+ regulation.

Authors:  Priit Eek; Reet Järving; Ivar Järving; Nathaniel C Gilbert; Marcia E Newcomer; Nigulas Samel
Journal:  J Biol Chem       Date:  2012-05-09       Impact factor: 5.157

2.  Predicting the X-ray lifetime of protein crystals.

Authors:  Oliver B Zeldin; Sandor Brockhauser; John Bremridge; James M Holton; Elspeth F Garman
Journal:  Proc Natl Acad Sci U S A       Date:  2013-12-02       Impact factor: 11.205

3.  Post-translational modifications differentially affect IgG1 conformation and receptor binding.

Authors:  Damian Houde; Yucai Peng; Steven A Berkowitz; John R Engen
Journal:  Mol Cell Proteomics       Date:  2010-01-26       Impact factor: 5.911

4.  Protein flexibility: coordinate uncertainties and interpretation of structural differences.

Authors:  Alexander A Rashin; Abraham H L Rashin; Robert L Jernigan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-10-22

Review 5.  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

6.  Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness.

Authors:  Avinash Jaiganesh; Pedro De-la-Torre; Aniket A Patel; Domenic J Termine; Florencia Velez-Cortes; Conghui Chen; Marcos Sotomayor
Journal:  Structure       Date:  2018-07-19       Impact factor: 5.006

7.  Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations.

Authors:  Pengfei Li; Alexander V Soudackov; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2018-02-19       Impact factor: 15.419

8.  Impact of Mutations on the Binding Pocket of Soybean Lipoxygenase: Implications for Proton-Coupled Electron Transfer.

Authors:  Pengfei Li; Alexander V Soudackov; Sharon Hammes-Schiffer
Journal:  J Phys Chem Lett       Date:  2018-10-29       Impact factor: 6.475

9.  NMR Structure and Dynamics of the Resuscitation Promoting Factor RpfC Catalytic Domain.

Authors:  Vincenzo Maione; Alessia Ruggiero; Luigi Russo; Alfonso De Simone; Paolo Vincenzo Pedone; Gaetano Malgieri; Rita Berisio; Carla Isernia
Journal:  PLoS One       Date:  2015-11-17       Impact factor: 3.240

10.  To automate or not to automate: this is the question.

Authors:  M Cymborowski; M Klimecka; M Chruszcz; M D Zimmerman; I A Shumilin; D Borek; K Lazarski; A Joachimiak; Z Otwinowski; W Anderson; W Minor
Journal:  J Struct Funct Genomics       Date:  2010-06-06
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