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Low-temperature molecular dynamics simulations of horse heart cytochrome c and comparison with inelastic neutron scattering data

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Abstract

Molecular dynamics (MD) simulation combined with inelastic neutron scattering can provide information about the thermal dynamics of proteins, especially the low-frequency vibrational modes responsible for large movement of some parts of protein molecules. We performed several 30-ns MD simulations of cytochrome c (Cyt c) in a water box for temperatures ranging from 110 to 300 K and compared the results with those from experimental inelastic neutron scattering. The low-frequency vibrational modes were obtained via dynamic structure factors, S(Q, ω), obtained both from inelastic neutron scattering experiments and calculated from MD simulations for Cyt c in the same range of temperatures. The well known thermal transition in structural movements of Cyt c is clearly seen in MD simulations; it is, however, confined to unstructured fragments of loops Ω1 and Ω2; movement of structured loop Ω3 and both helical ends of the protein is resistant to thermal disturbance. Calculated and experimental S(Q, ω) plots are in qualitative agreement for low temperatures whereas above 200 K a boson peak vanishes from the calculated plots. This may be a result of loss of crystal structure by the protein–water system compared with the protein crystal.

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Acknowledgments

V.R. and S.V. acknowledge the Rothschild Foundation, NIH, NSF, USAFOSR, and the Wallace H. Coulter Foundation for support. The authors also wish to acknowledge Pittsburgh Supercomputing Center for generous allocation of Supercomputer time on TeraGrid through Project Serial Number: TG-CH090102. V.R. acknowledges neutron beam time at Argonne National Laboratory, Argonne, IL, USA.

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Authors and Affiliations

  1. Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093, Warsaw, Poland

    Wojciech Pulawski, Slawomir Filipek & Aleksander Debinski

  2. Faculty of Pharmacy, Medical University of Warsaw, ul. Banacha 1, 02-097, Warsaw, Poland

    Anna Zwolinska

  3. International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109, Warsaw, Poland

    Anna Zwolinska & Krystiana Krzysko

  4. Faculty of Physics, CoE BioExploratorium, University of Warsaw, ul. Zwirki i Wigury 93, 02-089, Warsaw, Poland

    Krystiana Krzysko

  5. Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico

    Ramón Garduño-Juárez

  6. Wellesley Hospital/Partners Healthcare System, Newton, MA, 02462, USA

    Sowmya Viswanathan

  7. Children’s Hospital, Harvard Medical School, 300 Longwood Ave., Boston, MA, 02115, USA

    Venkatesan Renugopalakrishnan

  8. Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA

    Venkatesan Renugopalakrishnan

  9. Children’s Hospital, Harvard Medical School, 20 Shattuck Street, Boston, MA, 02115, USA

    Venkatesan Renugopalakrishnan

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  1. Wojciech Pulawski
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  2. Slawomir Filipek
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  8. Venkatesan Renugopalakrishnan
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Correspondence to Venkatesan Renugopalakrishnan.

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Venkatesan Renugopalakrishnan: Dedicated to my father, Varun.

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Pulawski, W., Filipek, S., Zwolinska, A. et al. Low-temperature molecular dynamics simulations of horse heart cytochrome c and comparison with inelastic neutron scattering data. Eur Biophys J 42, 291–300 (2013). https://doi.org/10.1007/s00249-012-0874-9

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  • DOI: https://doi.org/10.1007/s00249-012-0874-9

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