Literature DB >> 19118951

Reciprocal space representations of helical objects and their projection images for helices constructed from motifs without spherical symmetry.

Seunghee Lee1, Peter C Doerschuk, John E Johnson.   

Abstract

Formulas for predicting the 3-D reciprocal space cube and 2-D reciprocal space images that are slices of the cube (corresponding to real space images that are projections of the real space cube) are derived for the case when the motif of a helical object is not spherically symmetric. These formulas generalize much-used formulas due to Cochran et al. [The structure of synthetic polypeptides. I. The transform of atoms on a helix, Acta Crystallogr. 5 (1952) 581-586], for the case of a spherically symmetric motif. The new formulas allow control of the spatial resolution of the motif ranging from low-resolution spherically symmetric motifs as in Cochran et al. through moderate-resolution nonsymmetrical motifs to atomic-resolution nonsymmetrical motifs which can also be treated by the methods of Cochran et al. as a superposition of spherically symmetric atomic motifs. The ability to control resolution may be useful in reconstruction algorithms analogous to phase extension algorithms in X-ray crystallography.

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Year:  2008        PMID: 19118951      PMCID: PMC2713744          DOI: 10.1016/j.ultramic.2008.10.014

Source DB:  PubMed          Journal:  Ultramicroscopy        ISSN: 0304-3991            Impact factor:   2.689


  14 in total

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Authors:  T S Baker; N H Olson; S D Fuller
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2.  Structure determination of tubular crystals of membrane proteins. I. Indexing of diffraction patterns.

Authors:  C Toyoshima
Journal:  Ultramicroscopy       Date:  2000-07       Impact factor: 2.689

3.  Windex: a toolset for indexing helices.

Authors:  Andrew Ward; Michael F Moody; Brian Sheehan; Ronald A Milligan; Bridget Carragher
Journal:  J Struct Biol       Date:  2003 Oct-Nov       Impact factor: 2.867

4.  A statistical approach to computer processing of cryo-electron microscope images: virion classification and 3-D reconstruction.

Authors:  Zhye Yin; Yili Zheng; Peter C Doerschuk; Padmaja Natarajan; John E Johnson
Journal:  J Struct Biol       Date:  2003 Oct-Nov       Impact factor: 2.867

5.  UCSF Chimera--a visualization system for exploratory research and analysis.

Authors:  Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Gregory S Couch; Daniel M Greenblatt; Elaine C Meng; Thomas E Ferrin
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

6.  The correlation averaging of a regularly arranged bacterial cell envelope protein.

Authors:  W O Saxton; W Baumeister
Journal:  J Microsc       Date:  1982-08       Impact factor: 1.758

7.  Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy.

Authors:  B Böttcher; S A Wynne; R A Crowther
Journal:  Nature       Date:  1997-03-06       Impact factor: 49.962

8.  Visualization of alpha-helices in tobacco mosaic virus by cryo-electron microscopy.

Authors:  T W Jeng; R A Crowther; G Stubbs; W Chiu
Journal:  J Mol Biol       Date:  1989-01-05       Impact factor: 5.469

9.  Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction.

Authors:  K Namba; R Pattanayek; G Stubbs
Journal:  J Mol Biol       Date:  1989-07-20       Impact factor: 5.469

10.  Polyhead formation in phage P22 pinpoints a region in coat protein required for conformational switching.

Authors:  Kristin N Parent; Margaret M Suhanovsky; Carolyn M Teschke
Journal:  Mol Microbiol       Date:  2007-08-03       Impact factor: 3.501

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  2 in total

1.  An introduction to maximum-likelihood methods in cryo-EM.

Authors:  Fred J Sigworth; Peter C Doerschuk; Jose-Maria Carazo; Sjors H W Scheres
Journal:  Methods Enzymol       Date:  2010       Impact factor: 1.600

2.  Multiclass maximum-likelihood symmetry determination and motif reconstruction of 3-D helical objects from projection images for electron microscopy.

Authors:  Seunghee Lee; Peter C Doerschuk; John E Johnson
Journal:  IEEE Trans Image Process       Date:  2011-02-17       Impact factor: 10.856

  2 in total

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