Literature DB >> 18827972

Solution NMR structure determination of proteins revisited.

Martin Billeter1, Gerhard Wagner, Kurt Wüthrich.   

Abstract

This 'Perspective' bears on the present state of protein structure determination by NMR in solution. The focus is on a comparison of the infrastructure available for NMR structure determination when compared to protein crystal structure determination by X-ray diffraction. The main conclusion emerges that the unique potential of NMR to generate high resolution data also on dynamics, interactions and conformational equilibria has contributed to a lack of standard procedures for structure determination which would be readily amenable to improved efficiency by automation. To spark renewed discussion on the topic of NMR structure determination of proteins, procedural steps with high potential for improvement are identified.

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Year:  2008        PMID: 18827972      PMCID: PMC2748914          DOI: 10.1007/s10858-008-9277-8

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  15 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium.

Authors:  Thomas B Acton; Kristin C Gunsalus; Rong Xiao; Li Chung Ma; James Aramini; Michael C Baran; Yi-Wen Chiang; Teresa Climent; Bonnie Cooper; Natalia G Denissova; Shawn M Douglas; John K Everett; Chi Kent Ho; Daphne Macapagal; Paranji K Rajan; Ritu Shastry; Liang-Yu Shih; G V T Swapna; Michael Wilson; Margaret Wu; Mark Gerstein; Masayori Inouye; John F Hunt; Gaetano T Montelione
Journal:  Methods Enzymol       Date:  2005       Impact factor: 1.600

3.  Evaluating protein structures determined by structural genomics consortia.

Authors:  Aneerban Bhattacharya; Roberto Tejero; Gaetano T Montelione
Journal:  Proteins       Date:  2007-03-01

4.  Growth of novel protein structural data.

Authors:  Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2007-02-20       Impact factor: 11.205

5.  The challenge of protein structure determination--lessons from structural genomics.

Authors:  Lukasz Slabinski; Lukasz Jaroszewski; Ana P C Rodrigues; Leszek Rychlewski; Ian A Wilson; Scott A Lesley; Adam Godzik
Journal:  Protein Sci       Date:  2007-11       Impact factor: 6.725

6.  A graphical approach to tracking and reporting target status in structural genomics.

Authors:  Xiaokang Pan; Gary E Wesenberg; John L Markley; Brian G Fox; George N Phillips; Craig A Bingman
Journal:  J Struct Funct Genomics       Date:  2008-01-31

7.  Quality of protein crystal structures.

Authors:  Eric N Brown; S Ramaswamy
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-08-17

8.  XtalPred: a web server for prediction of protein crystallizability.

Authors:  Lukasz Slabinski; Lukasz Jaroszewski; Leszek Rychlewski; Ian A Wilson; Scott A Lesley; Adam Godzik
Journal:  Bioinformatics       Date:  2007-10-05       Impact factor: 6.937

9.  Structural genomics projects in Japan.

Authors:  S Yokoyama; H Hirota; T Kigawa; T Yabuki; M Shirouzu; T Terada; Y Ito; Y Matsuo; Y Kuroda; Y Nishimura; Y Kyogoku; K Miki; R Masui; S Kuramitsu
Journal:  Nat Struct Biol       Date:  2000-11

10.  NMR data collection and analysis protocol for high-throughput protein structure determination.

Authors:  Gaohua Liu; Yang Shen; Hanudatta S Atreya; David Parish; Ying Shao; Dinesh K Sukumaran; Rong Xiao; Adelinda Yee; Alexander Lemak; Aneerban Bhattacharya; Thomas A Acton; Cheryl H Arrowsmith; Gaetano T Montelione; Thomas Szyperski
Journal:  Proc Natl Acad Sci U S A       Date:  2005-07-18       Impact factor: 11.205

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  27 in total

1.  Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle.

Authors:  Alexandra Choutko; Alice Glättli; César Fernández; Christian Hilty; Kurt Wüthrich; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2010-10-05       Impact factor: 1.733

2.  SAGA: rapid automatic mainchain NMR assignment for large proteins.

Authors:  Gordon M Crippen; Aikaterini Rousaki; Matthew Revington; Yongbo Zhang; Erik R P Zuiderweg
Journal:  J Biomol NMR       Date:  2010-03-16       Impact factor: 2.835

3.  Automated protein structure calculation from NMR data.

Authors:  Mike P Williamson; C Jeremy Craven
Journal:  J Biomol NMR       Date:  2009-01-10       Impact factor: 2.835

4.  Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation.

Authors:  Jorge A Vila; Yelena A Arnautova; Osvaldo A Martin; Harold A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2009-09-08       Impact factor: 11.205

5.  The eNMR platform for structural biology.

Authors:  Alexandre M J J Bonvin; Antonio Rosato; Tsjerk A Wassenaar
Journal:  J Struct Funct Genomics       Date:  2010-03-13

6.  CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO.

Authors:  Paul Guerry; Viet Dung Duong; Torsten Herrmann
Journal:  J Biomol NMR       Date:  2015-04-28       Impact factor: 2.835

7.  Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA.

Authors:  Lena Buchner; Peter Güntert
Journal:  J Biomol NMR       Date:  2015-03-22       Impact factor: 2.835

8.  Enhanced biosynthetically directed fractional carbon-13 enrichment of proteins for backbone NMR assignments.

Authors:  Broc R Wenrich; Reilly E Sonstrom; Riju A Gupta; David Rovnyak
Journal:  Protein Expr Purif       Date:  2015-08-06       Impact factor: 1.650

Review 9.  Retinal dynamics during light activation of rhodopsin revealed by solid-state NMR spectroscopy.

Authors:  Michael F Brown; Gilmar F J Salgado; Andrey V Struts
Journal:  Biochim Biophys Acta       Date:  2009-08-28

10.  Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.

Authors:  Jorge A Vila; Harold A Scheraga
Journal:  Acc Chem Res       Date:  2009-10-20       Impact factor: 22.384

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