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Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

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Abstract

Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) simulations constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational sampling in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies.

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Abbreviations

AMBER:

Assisted model building with energy refinement

DFT:

Density functional theory

MCPB:

Metal center parameter builder

MD:

Molecular dynamics

MRD-NMR:

Metal restrained dynamics nuclear magnetic resonance

NMR:

Nuclear magnetic resonance

NOE:

Nuclear Overhauser enhancements

QM/MM:

Quantum mechanical/molecular mechanical

QM/MM MD:

Quantum mechanical/molecular mechanical molecular dynamics

RDC:

Residual dipolar couplings

RD-NMR:

Restrained dynamics nuclear magnetic resonance

RMSD:

Root mean square deviation

XAS:

X-ray absorption spectroscopy

PDB:

Protein data bank

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Acknowledgments

We gratefully acknowledge the United States National Institutes of Health for support of this study (GM044974 to K.M.M. and GM042569 to D.P.G.) and high performance computing at the University of Florida (UFHPC) for providing and maintaining the computational resources used to perform this study. We also thank Sarah Gordon for helpful discussions.

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  1. Chul Won Lee

    Present address: Department of Chemistry, Chonnam National University, Kwangju, 500-757, Korea

Authors and Affiliations

  1. Department of Chemistry and the Quantum Theory Project, University of Florida, 2238 New Physics Building, P.O. Box 118435, Gainesville, FL, 32611-8435, USA

    Dhruva K. Chakravorty, Bing Wang & Kenneth M. Merz Jr.

  2. Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA

    Chul Won Lee, Alfredo J. Guerra & David P. Giedroc

Authors
  1. Dhruva K. Chakravorty
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  2. Bing Wang
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Correspondence to David P. Giedroc or Kenneth M. Merz Jr..

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Chakravorty, D.K., Wang, B., Lee, C.W. et al. Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods. J Biomol NMR 56, 125–137 (2013). https://doi.org/10.1007/s10858-013-9729-7

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