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ARCIMBOLDO on coiled coils.

Iracema Caballero1, Massimo Sammito1, Claudia Millán1

  • 1Structural Biology Unit, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain.

Acta Crystallographica. Section D, Structural Biology
|March 14, 2018
PubMed
Summary
This summary is machine-generated.

ARCIMBOLDO software has been optimized for solving coiled-coil protein structures, overcoming resolution limits by refining fragment placement and orientation. This specialized mode enhances coiled-coil structure determination, even with lower-resolution data.

Keywords:
ARCIMBOLDOPhaserSHELXEcoiled coilsphasing

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Area of Science:

  • Structural biology
  • X-ray crystallography
  • Computational methods in structural analysis

Background:

  • The phase problem in X-ray crystallography is a major hurdle in determining protein structures.
  • Coiled-coil protein structures present unique challenges due to anisotropic diffraction and translational symmetry.
  • Existing methods like ARCIMBOLDO require adaptation for complex structures like coiled-coils.

Purpose of the Study:

  • To develop and validate a specialized mode within ARCIMBOLDO for solving coiled-coil protein structures.
  • To address limitations in current structure solution methods for coiled-coil proteins, particularly at lower resolutions.
  • To improve the accuracy and efficiency of coiled-coil structure determination using crystallographic data.

Main Methods:

  • Integration of Phaser for fragment localization with SHELXE for density modification and autotracing.
  • Utilized polyalanine helical fragments as search models for helical structures.
  • Tested ARCIMBOLDO_LITE on 150 coiled-coil structures across various resolutions (0.9-3.0 Å).

Main Results:

  • Identified and addressed specific issues in solving coiled-coil structures with ARCIMBOLDO.
  • Phaser v.2.7+ features are crucial for correcting anisotropy and enabling translation solutions.
  • Developed strategies to differentiate true solutions from pseudo-solutions, especially at resolutions worse than 2.3 Å, including helix reversal and re-evaluation.

Conclusions:

  • A specialized ARCIMBOLDO mode ('coiled_coil') has been developed, enhancing coiled-coil structure solution.
  • This mode extends the effective resolution limit for coiled-coil structure determination.
  • The optimized method improves the identification of correct coiled-coil structures and can be accessed via command line or CCP4i interface.