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Title: Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

Abstract

A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

Authors:
 [1];  [1];  [2]; ;  [1];  [1];  [2]
  1. International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland)
  2. (Poland)
Publication Date:
OSTI Identifier:
22347697
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 71; Journal Issue: Pt 3; Other Information: PMCID: PMC4356372; PMID: 25760616; PUBLISHER-ID: wa5082; OAI: oai:pubmedcentral.nih.gov:4356372; Copyright (c) Chojnowski et al. 2015; 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; COMPUTER CODES; CRYSTAL STRUCTURE; CRYSTALS; DENSITY; DNA; ELECTRON DENSITY; ELECTRONS; MOLECULES; PEAKS; PHOSPHATES; RESOLUTION

Citation Formats

Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl, Waleń, Tomasz, University of Warsaw, Banacha 2, 02-097 Warsaw, Piątkowski, Paweł, Potrzebowski, Wojciech, Bujnicki, Janusz M., and Adam Mickiewicz University, Umultowska 89, 61-614 Poznan. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps. Denmark: N. p., 2015. Web. doi:10.1107/S1399004715000383.
Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl, Waleń, Tomasz, University of Warsaw, Banacha 2, 02-097 Warsaw, Piątkowski, Paweł, Potrzebowski, Wojciech, Bujnicki, Janusz M., & Adam Mickiewicz University, Umultowska 89, 61-614 Poznan. Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps. Denmark. doi:10.1107/S1399004715000383.
Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl, Waleń, Tomasz, University of Warsaw, Banacha 2, 02-097 Warsaw, Piątkowski, Paweł, Potrzebowski, Wojciech, Bujnicki, Janusz M., and Adam Mickiewicz University, Umultowska 89, 61-614 Poznan. Sun . "Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps". Denmark. doi:10.1107/S1399004715000383.
@article{osti_22347697,
title = {Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps},
author = {Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl and Waleń, Tomasz and University of Warsaw, Banacha 2, 02-097 Warsaw and Piątkowski, Paweł and Potrzebowski, Wojciech and Bujnicki, Janusz M. and Adam Mickiewicz University, Umultowska 89, 61-614 Poznan},
abstractNote = {A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.},
doi = {10.1107/S1399004715000383},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
number = Pt 3,
volume = 71,
place = {Denmark},
year = {Sun Mar 01 00:00:00 EST 2015},
month = {Sun Mar 01 00:00:00 EST 2015}
}
  • The interpretation of a 20 Å resolution electron-density map using segmentation and pattern-recognition-based identification of domain shapes is described. A novel approach to obtaining structural information from macromolecular X-ray data extending to resolutions as low as 20 Å is presented. Following a simple map-segmentation procedure, the approximate shapes of the domains forming the structure are identified. A pattern-recognition comparative analysis of these shapes and those derived from the structures of domains from the PDB results in candidate structural models that can be used for a fit into the density map. It is shown that the placed candidate models can bemore » employed for subsequent phase extension to higher resolution.« less
  • No abstract prepared.
  • RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeatedly in RNA hairpin and internal loops, and are observed to be composed of a limited number of common 'structural elements'. In addition to secondary and tertiary structure motifs, there are functional motifs specific for certain biological roles and binding motifs that serve to complexmore » metals or other ligands. Research is continuing into the identification and classification of RNA structural motifs and is being initiated to predict motifs from sequence, to trace their phylogenetic relationships and to use them as building blocks in RNA engineering.« less
  • Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less