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Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

Author

Listed:
  • Anders S Christensen
  • Troels E Linnet
  • Mikael Borg
  • Wouter Boomsma
  • Kresten Lindorff-Larsen
  • Thomas Hamelryck
  • Jan H Jensen

Abstract

We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.

Suggested Citation

  • Anders S Christensen & Troels E Linnet & Mikael Borg & Wouter Boomsma & Kresten Lindorff-Larsen & Thomas Hamelryck & Jan H Jensen, 2013. "Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-10, December.
    • Handle: RePEc:plo:pone00:0084123
    DOI: 10.1371/journal.pone.0084123
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    References listed on IDEAS

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    1. Thomas Hamelryck & Mikael Borg & Martin Paluszewski & Jonas Paulsen & Jes Frellsen & Christian Andreetta & Wouter Boomsma & Sandro Bottaro & Jesper Ferkinghoff-Borg, 2010. "Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized," PLOS ONE, Public Library of Science, vol. 5(11), pages 1-11, November.
    2. Kresten Lindorff-Larsen & Robert B. Best & Mark A. DePristo & Christopher M. Dobson & Michele Vendruscolo, 2005. "Simultaneous determination of protein structure and dynamics," Nature, Nature, vol. 433(7022), pages 128-132, January.
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