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Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide

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Summary

The influence of water binding on the conformational dynamics of the cyclic decapeptide antamanide dissolved in the model lipophilic environment chloroform is investigated by NMR relaxation measurements. The water-peptide complex has a lifetime of 35 μs at 250 K, which is longer than typical lifetimes of water-peptide complexes reported in aqueous solution. In addition, there is a rapid intracomplex mobility that probably involves librational motions of the bound water or water molecules hopping between different binding sites. Water binding restricts the flexibility of antamanide. The experimental findings are compared with GROMOS molecular dynamics simulations of antamanide with up to eight bound water molecules. Within the simulation time of 600 ps, no water molecule leaves the complex. Additionally, the simulations show a reduced flexibility for the complex in comparison with uncomplexed antamanide. Thus, there is a qualitative agreement between the experimental NMR results and the computer simulations.

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Author notes

  1. Jeffrey W. Peng

    Present address: Vertex Pharmaceuticals Inc., 130 Waverly Street, 02139-4242, Cambridge, MA, U.S.A.

  2. Celia A. Schiffer

    Present address: Department of Protein Engineering, Genentech, Inc., 460 Point San Bruno Boulevard, 94080, South San Francisco, CA, U.S.A.

  3. Ping Xu

    Present address: Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, H4P 2R2, Montreal, PQ, Canada

Authors and Affiliations

  1. Laboratorium für Physikalische Chemie, ETH-Zentrum, Universitätsstrasse 22, CH-8092, Zürich, Switzerland

    Jeffrey W. Peng, Celia A. Schiffer, Ping Xu, Wilfred F. van Gunsteren & Richard R. Ernst

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  1. Jeffrey W. Peng
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  2. Celia A. Schiffer
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  4. Wilfred F. van Gunsteren
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Peng, J.W., Schiffer, C.A., Xu, P. et al. Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide. J Biomol NMR 8, 453–476 (1996). https://doi.org/10.1007/BF00228147

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  • DOI: https://doi.org/10.1007/BF00228147

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