Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel

doi:10.1021/jz500976m

Title: Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

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Abstract

Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were mademore »« less

Authors:: Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel

Publication Date:: Thu Jul 03 00:00:00 EDT 2014

Research Org.:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1171887

Report Number(s):: PNNL-SA-102863
KC0301020

DOE Contract Number:: AC05-76RL01830

Resource Type:: Journal Article

Journal Name:: Journal of Physical Chemistry Letters, 5(13):2235-2240

Additional Journal Information:: Journal Name: Journal of Physical Chemistry Letters, 5(13):2235-2240

Country of Publication:: United States

Language:: English

Subject:: sodium; calcium; N-methylacetamide; peptide bond, umbrella sampling

Citation Formats


                    Pluharova, Eva, Baer, Marcel D., Mundy, Christopher J., Schmidt, Burkhard, and Jungwirth, Pavel. Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics.  United States: N. p., 2014. 
        Web.  doi:10.1021/jz500976m.

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                    Pluharova, Eva, Baer, Marcel D., Mundy, Christopher J., Schmidt, Burkhard, & Jungwirth, Pavel. Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics.  United States.  https://doi.org/10.1021/jz500976m

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                    Pluharova, Eva, Baer, Marcel D., Mundy, Christopher J., Schmidt, Burkhard, and Jungwirth, Pavel. 2014.  
        "Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics".  United States.  https://doi.org/10.1021/jz500976m.

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@article{osti_1171887,

  title        = {Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics},

  author       = {Pluharova, Eva and Baer, Marcel D. and Mundy, Christopher J. and Schmidt, Burkhard and Jungwirth, Pavel},

  abstractNote = {Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is grateful for the support of the Linus Pauling Distinguished Postdoctoral Fellowship Program at PNNL.},

  doi          = {10.1021/jz500976m},

  url          = {https://www.osti.gov/biblio/1171887},
  journal      = {Journal of Physical Chemistry Letters, 5(13):2235-2240},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {Thu Jul 03 00:00:00 EDT 2014},

  month        = {Thu Jul 03 00:00:00 EDT 2014}

}

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