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Structures of TraI in solution

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Abstract

Bacterial conjugation, a DNA transfer mechanism involving transport of one plasmid strand from donor to recipient, is driven by plasmid-encoded proteins. The F TraI protein nicks one F plasmid strand, separates cut and uncut strands, and pilots the cut strand through a secretion pore into the recipient. TraI is a modular protein with identifiable nickase, ssDNA-binding, helicase and protein–protein interaction domains. While domain structures corresponding to roughly 1/3 of TraI have been determined, there has been no comprehensive structural study of the entire TraI molecule, nor an examination of structural changes to TraI upon binding DNA. Here, we combine solution studies using small-angle scattering and circular dichroism spectroscopy with molecular Monte Carlo and molecular dynamics simulations to assess solution behavior of individual and groups of domains. Despite having several long (>100 residues) apparently disordered or highly dynamic regions, TraI folds into a compact molecule. Based on the biophysical characterization, we have generated models of intact TraI. These data and the resulting models have provided clues to the regulation of TraI function.

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Notes

  1. Certain commercial equipment, instruments, materials, suppliers, or software are identified in this paper to foster understanding. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the materials or equipment identified are necessarily the best available for the purpose.

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Acknowledgments

This material is based upon work supported by the National Institute of General Medical Sciences under grant number R01 GM61017, American Recovery and Reinvestment Act under grant number R01 GM61017, and the Dimitri V. d’Arbeloff fellowship. This work benefitted from CCP-SAS software developed through a joint Engineering and Physical Sciences Research Council (EP/K039121/1) and National Science Foundation (CHE-1265821) grant.

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Authors and Affiliations

  1. NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD, 20899, USA

    Nicholas J. Clark, Susan Krueger & Joseph E. Curtis

  2. Department of Molecular and Cellular Biochemistry, Biomedical and Biological Sciences Research Building, University of Kentucky, 741 S Limestone Avenue, Lexington, KY, 40536, USA

    Madushi Raththagala

  3. James Madison University, Physics and Chemistry Building, Rm 1174, Harrisonburg, VA, 22807, USA

    Nathan T. Wright

  4. Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA

    Elizabeth A. Buenger & Joel F. Schildbach

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  1. Nicholas J. Clark
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  2. Madushi Raththagala
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  5. Joel F. Schildbach
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Correspondence to Joseph E. Curtis.

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Clark, N.J., Raththagala, M., Wright, N.T. et al. Structures of TraI in solution. J Mol Model 20, 2308 (2014). https://doi.org/10.1007/s00894-014-2308-3

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