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European Biophysics Journal

, Volume 42, Issue 4, pp 291–300 | Cite as

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

  • Wojciech Pulawski
  • Slawomir Filipek
  • Anna Zwolinska
  • Aleksander Debinski
  • Krystiana Krzysko
  • Ramón Garduño-Juárez
  • Sowmya Viswanathan
  • Venkatesan Renugopalakrishnan
Original Paper

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(Qω) 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.

Keywords

Cytochrome c Molecular dynamics Inelastic neutron scattering Dynamic structure factor 

Notes

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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Copyright information

© European Biophysical Societies' Association 2012

Authors and Affiliations

  • Wojciech Pulawski
    • 1
  • Slawomir Filipek
    • 1
  • Anna Zwolinska
    • 2
    • 3
  • Aleksander Debinski
    • 1
  • Krystiana Krzysko
    • 3
    • 4
  • Ramón Garduño-Juárez
    • 5
  • Sowmya Viswanathan
    • 6
  • Venkatesan Renugopalakrishnan
    • 7
    • 8
    • 9
  1. 1.Faculty of ChemistryUniversity of WarsawWarsawPoland
  2. 2.Faculty of PharmacyMedical University of WarsawWarsawPoland
  3. 3.International Institute of Molecular and Cell BiologyWarsawPoland
  4. 4.Faculty of Physics, CoE BioExploratoriumUniversity of WarsawWarsawPoland
  5. 5.Instituto de Ciencias FísicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
  6. 6.Wellesley Hospital/Partners Healthcare SystemNewtonUSA
  7. 7.Children’s HospitalHarvard Medical SchoolBostonUSA
  8. 8.Department of Chemistry and Chemical BiologyNortheastern UniversityBostonUSA
  9. 9.Children’s HospitalHarvard Medical SchoolBostonUSA

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