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Title: Deformable elastic network refinement for low-resolution macromolecular crystallography

Abstract

An overview of applications of the deformable elastic network (DEN) refinement method is presented together with recommendations for its optimal usage. Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

Authors:
 [1];  [2];  [3];  [4];  [2]
  1. Forschungszentrum Jülich, 52425 Jülich (Germany)
  2. (Germany)
  3. Stanford University School of Medicine, Stanford, CA 94305 (United States)
  4. Stanford University School of Medicine, J. H. Clark Center, 318 Campus Drive, Stanford, CA 94305 (United States)
Publication Date:
OSTI Identifier:
22347746
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 70; Journal Issue: Pt 9; Other Information: PMCID: PMC4157441; PMID: 25195739; PUBLISHER-ID: rr5077; OAI: oai:pubmedcentral.nih.gov:4157441; Copyright (c) Schröder et al. 2014; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; CRYSTAL STRUCTURE; CRYSTALS; FLEXIBILITY; POTENTIALS; RECOMMENDATIONS; RESOLUTION

Citation Formats

Schröder, Gunnar F., E-mail: gu.schroeder@fz-juelich.de, Heinrich-Heine University Düsseldorf, 20225 Düsseldorf, Levitt, Michael, Brunger, Axel T., E-mail: gu.schroeder@fz-juelich.de, and Forschungszentrum Jülich, 52425 Jülich. Deformable elastic network refinement for low-resolution macromolecular crystallography. Denmark: N. p., 2014. Web. doi:10.1107/S1399004714016496.
Schröder, Gunnar F., E-mail: gu.schroeder@fz-juelich.de, Heinrich-Heine University Düsseldorf, 20225 Düsseldorf, Levitt, Michael, Brunger, Axel T., E-mail: gu.schroeder@fz-juelich.de, & Forschungszentrum Jülich, 52425 Jülich. Deformable elastic network refinement for low-resolution macromolecular crystallography. Denmark. doi:10.1107/S1399004714016496.
Schröder, Gunnar F., E-mail: gu.schroeder@fz-juelich.de, Heinrich-Heine University Düsseldorf, 20225 Düsseldorf, Levitt, Michael, Brunger, Axel T., E-mail: gu.schroeder@fz-juelich.de, and Forschungszentrum Jülich, 52425 Jülich. Mon . "Deformable elastic network refinement for low-resolution macromolecular crystallography". Denmark. doi:10.1107/S1399004714016496.
@article{osti_22347746,
title = {Deformable elastic network refinement for low-resolution macromolecular crystallography},
author = {Schröder, Gunnar F., E-mail: gu.schroeder@fz-juelich.de and Heinrich-Heine University Düsseldorf, 20225 Düsseldorf and Levitt, Michael and Brunger, Axel T., E-mail: gu.schroeder@fz-juelich.de and Forschungszentrum Jülich, 52425 Jülich},
abstractNote = {An overview of applications of the deformable elastic network (DEN) refinement method is presented together with recommendations for its optimal usage. Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.},
doi = {10.1107/S1399004714016496},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
number = Pt 9,
volume = 70,
place = {Denmark},
year = {Mon Sep 01 00:00:00 EDT 2014},
month = {Mon Sep 01 00:00:00 EDT 2014}
}
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