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Title: Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the casemore » of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.« less
Authors:
 [1] ;  [2] ; ;  [3] ; ;  [1] ;  [4] ;  [3] ;  [5] ;  [6]
  1. University of Göttingen, (Germany)
  2. (IBMB-CSIC), (Spain)
  3. Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain)
  4. Durham University, (United Kingdom)
  5. (ICREA), (Spain)
  6. (Germany)
Publication Date:
OSTI Identifier:
22347768
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 70; Journal Issue: Pt 6; Other Information: PMCID: PMC4051508; PMID: 24914984; PUBLISHER-ID: rr5060; OAI: oai:pubmedcentral.nih.gov:4051508; Copyright (c) Pröpper, Meindl 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; AUGMENTATION; CRYSTALLOGRAPHY; CRYSTALS; DENSITY; DNA; INTERACTIONS; MATHEMATICAL SOLUTIONS; MODIFICATIONS; PACKAGING; POTENTIALS; PROTEINS; SOLUTIONS