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Molecular dynamics simulation of plastocyanin potential energy fluctuations: 1/f noise

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  • Bizzarri, Anna Rita
  • Cannistraro, Salvatore

Abstract

Molecular dynamics simulations of plastocyanin, an electron transfer copper containing protein involved in the photosynthetic process, have been performed in both the hydrated and dry state. An analysis of the potential energy fluctuations during a 500 ps dynamical evolution of the macromolecule reveals the presence of a 1/fα noise in the related spectral density. Such a phenomenon is shown to persist in a wide temperature range (from 100 to 300 K) for both the systems. The occurrence of 1/fα noise, which can be traced back to the existence, in protein systems, of thermally activated processes, seems to be a peculiarity of the dynamical behaviour of proteins. An analysis of the temperature dependence of the α exponent allowed us to extract information about the distribution of the conformational energy barriers and its dependence on the hydration level.

Suggested Citation

  • Bizzarri, Anna Rita & Cannistraro, Salvatore, 1999. "Molecular dynamics simulation of plastocyanin potential energy fluctuations: 1/f noise," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 267(3), pages 257-270.
    • Handle: RePEc:eee:phsmap:v:267:y:1999:i:3:p:257-270
    DOI: 10.1016/S0378-4371(98)00651-7
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    Cited by:

    1. Jose A Garcia-Lazaro & Bashir Ahmed & Jan W H Schnupp, 2011. "Emergence of Tuning to Natural Stimulus Statistics along the Central Auditory Pathway," PLOS ONE, Public Library of Science, vol. 6(8), pages 1-7, August.

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    Keywords

    1/f noise; Protein dynamics;

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