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Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings

Journal of Biomolecular NMR volume 60, pages 241–264 (2014)Cite this article

Abstract

Within the past two decades, there has been an increase in the acquisition of residual dipolar couplings (RDC) for investigations of biomolecular structures. Their use however is still not as widely adopted as the traditional methods of structure determination by NMR, despite their potential for extending the limits in studies that examine both the structure and dynamics of biomolecules. This is in part due to the difficulties associated with the analysis of this information-rich data type. The software analysis tool REDCRAFT was previously introduced to address some of these challenges. Here we describe and evaluate a number of additional features that have been incorporated in order to extend its computational and analytical capabilities. REDCRAFT’s more traditional enhancements integrate a modified steric collision term, as well as structural refinement in the rotamer space. Other, non-traditional improvements include: the filtering of viable structures based on relative order tensor estimates, decimation of the conformational space based on structural similarity, and forward/reverse folding of proteins. Utilizing REDCRAFT’s newest features we demonstrate de-novo folding of proteins 1D3Z and 1P7E to within less than 1.6 Å of the corresponding X-ray structures, using as many as four RDCs per residue and as little as two RDCs per residue, in two alignment media. We also show the successful folding of a structure to less than 1.6 Å of the X-ray structure using {Ci−1–Ni, Ni–Hi, and Ci−1–Hi} RDCs in one alignment medium, and only {Ni–Hi} in the second alignment medium (a set of data which can be collected on deuterated samples). The program is available for download from our website at http://ifestos.cse.sc.edu.

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Acknowledgments

This work was supported by NIH Grant Numbers 1R01GM081793 and P20 RR-016461 to Dr. Homayoun Valafar.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, 29208, USA

    Mikhail Simin, Stephanie Irausquin, Casey A. Cole & Homayoun Valafar

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  1. Mikhail Simin
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  2. Stephanie Irausquin
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  3. Casey A. Cole
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  4. Homayoun Valafar
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Correspondence to Homayoun Valafar.

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Simin, M., Irausquin, S., Cole, C.A. et al. Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings. J Biomol NMR 60, 241–264 (2014). https://doi.org/10.1007/s10858-014-9871-x

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  • DOI: https://doi.org/10.1007/s10858-014-9871-x

Keywords

  • REDCRAFT
  • Structure
  • Dynamics
  • RDC
  • Dipolar
  • Computational