Literature DB >> 19368883

Synergy of NMR, computation, and X-ray crystallography for structural biology.

Blair R Szymczyna1, Rebecca E Taurog, Mark J Young, Jamie C Snyder, John E Johnson, James R Williamson.   

Abstract

NMR spectroscopy and X-ray crystallography are currently the two most widely applied methods for the determination of macromolecular structures at high resolution. More recently, significant advances have been made in algorithms for the de novo prediction of protein structure, and, in favorable cases, the predicted models agree extremely well with experimentally determined structures. Here, we demonstrate a synergistic combination of NMR spectroscopy, de novo structure prediction, and X-ray crystallography in an effective overall strategy for rapidly determining the structure of the coat protein C-terminal domain from the Sulfolobus islandicus rod-shaped virus (SIRV). This approach takes advantage of the most accessible aspects of each structural technique and may be widely applicable for structure determination.

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Year:  2009        PMID: 19368883      PMCID: PMC2705668          DOI: 10.1016/j.str.2009.03.001

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  55 in total

1.  A novel virus family, the Rudiviridae: Structure, virus-host interactions and genome variability of the sulfolobus viruses SIRV1 and SIRV2.

Authors:  D Prangishvili; H P Arnold; D Götz; U Ziese; I Holz; J K Kristjansson; W Zillig
Journal:  Genetics       Date:  1999-08       Impact factor: 4.562

2.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Mol Biol       Date:  2002-05-24       Impact factor: 5.469

3.  Toward high-resolution de novo structure prediction for small proteins.

Authors:  Philip Bradley; Kira M S Misura; David Baker
Journal:  Science       Date:  2005-09-16       Impact factor: 47.728

4.  Protein structure determination from NMR chemical shifts.

Authors:  Andrea Cavalli; Xavier Salvatella; Christopher M Dobson; Michele Vendruscolo
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-29       Impact factor: 11.205

Review 5.  Macromolecular modeling with rosetta.

Authors:  Rhiju Das; David Baker
Journal:  Annu Rev Biochem       Date:  2008       Impact factor: 23.643

6.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

7.  1H, 13C and 15N chemical shift referencing in biomolecular NMR.

Authors:  D S Wishart; C G Bigam; J Yao; F Abildgaard; H J Dyson; E Oldfield; J L Markley; B D Sykes
Journal:  J Biomol NMR       Date:  1995-09       Impact factor: 2.835

8.  Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation.

Authors:  N A Farrow; R Muhandiram; A U Singer; S M Pascal; C M Kay; G Gish; S E Shoelson; T Pawson; J D Forman-Kay; L E Kay
Journal:  Biochemistry       Date:  1994-05-17       Impact factor: 3.162

9.  CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data.

Authors:  David S Wishart; David Arndt; Mark Berjanskii; Peter Tang; Jianjun Zhou; Guohui Lin
Journal:  Nucleic Acids Res       Date:  2008-05-30       Impact factor: 16.971

10.  Phaser crystallographic software.

Authors:  Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal:  J Appl Crystallogr       Date:  2007-07-13       Impact factor: 3.304

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  18 in total

1.  Virology. A virus that infects a hyperthermophile encapsidates A-form DNA.

Authors:  Frank DiMaio; Xiong Yu; Elena Rensen; Mart Krupovic; David Prangishvili; Edward H Egelman
Journal:  Science       Date:  2015-05-22       Impact factor: 47.728

Review 2.  Large Tailed Spindle Viruses of Archaea: a New Way of Doing Viral Business.

Authors:  Rebecca Hochstein; Daniel Bollschweiler; Harald Engelhardt; C Martin Lawrence; Mark Young
Journal:  J Virol       Date:  2015-06-17       Impact factor: 5.103

Review 3.  Archaeal extrachromosomal genetic elements.

Authors:  Haina Wang; Nan Peng; Shiraz A Shah; Li Huang; Qunxin She
Journal:  Microbiol Mol Biol Rev       Date:  2015-03       Impact factor: 11.056

Review 4.  Viruses of archaea: Structural, functional, environmental and evolutionary genomics.

Authors:  Mart Krupovic; Virginija Cvirkaite-Krupovic; Jaime Iranzo; David Prangishvili; Eugene V Koonin
Journal:  Virus Res       Date:  2017-11-22       Impact factor: 3.303

5.  Computational reconstruction of multidomain proteins using atomic force microscopy data.

Authors:  Minh-Hieu Trinh; Michael Odorico; Michael E Pique; Jean-Marie Teulon; Victoria A Roberts; Lynn F Ten Eyck; Elizabeth D Getzoff; Pierre Parot; Shu-Wen W Chen; Jean-Luc Pellequer
Journal:  Structure       Date:  2012-01-11       Impact factor: 5.006

Review 6.  The enigmatic archaeal virosphere.

Authors:  David Prangishvili; Dennis H Bamford; Patrick Forterre; Jaime Iranzo; Eugene V Koonin; Mart Krupovic
Journal:  Nat Rev Microbiol       Date:  2017-11-10       Impact factor: 60.633

7.  Improved technologies now routinely provide protein NMR structures useful for molecular replacement.

Authors:  Binchen Mao; Rongjin Guan; Gaetano T Montelione
Journal:  Structure       Date:  2011-06-08       Impact factor: 5.006

8.  Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage.

Authors:  Adeline Goulet; Stéphanie Blangy; Peter Redder; David Prangishvili; Catarina Felisberto-Rodrigues; Patrick Forterre; Valérie Campanacci; Christian Cambillau
Journal:  Proc Natl Acad Sci U S A       Date:  2009-11-23       Impact factor: 11.205

9.  Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments.

Authors:  Fengbin Wang; Diana P Baquero; Leticia C Beltran; Zhangli Su; Tomasz Osinski; Weili Zheng; David Prangishvili; Mart Krupovic; Edward H Egelman
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-05       Impact factor: 11.205

Review 10.  Genomics and biology of Rudiviruses, a model for the study of virus-host interactions in Archaea.

Authors:  David Prangishvili; Eugene V Koonin; Mart Krupovic
Journal:  Biochem Soc Trans       Date:  2013-02-01       Impact factor: 5.407

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