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Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

Potrzebowski, Wojciech LU and André, Ingemar LU (2015) In Nature Methods 12(7). p.679-679
Abstract
For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology... (More)
For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Nature Methods
volume
12
issue
7
pages
679 - 679
publisher
Nature Publishing Group
external identifiers
  • pmid:25961412
  • wos:000357405700028
  • scopus:84934443962
ISSN
1548-7105
DOI
10.1038/nmeth.3399
language
English
LU publication?
yes
id
becb39ab-5590-4dfa-b8bf-32842c177523 (old id 5453545)
date added to LUP
2015-06-23 17:34:58
date last changed
2017-10-01 03:09:48
@article{becb39ab-5590-4dfa-b8bf-32842c177523,
  abstract     = {For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints.},
  author       = {Potrzebowski, Wojciech and André, Ingemar},
  issn         = {1548-7105},
  language     = {eng},
  number       = {7},
  pages        = {679--679},
  publisher    = {Nature Publishing Group},
  series       = {Nature Methods},
  title        = {Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.},
  url          = {http://dx.doi.org/10.1038/nmeth.3399},
  volume       = {12},
  year         = {2015},
}