Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure

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Abstract

Proteins have been shown to exhibit strange/anomalous dynamics displaying non-Debye density of vibrational states, anomalous spread of vibrational energy, large conformational changes, non-exponential decay of correlations, and nonexponential unfolding times. The anomalous behavior may, in principle, stem from various factors affecting the energy landscape under which a protein vibrates. Investigating the origins of such unconventional dynamics, we focus on the structure-dynamics interplay and introduce a stochastic approach to the vibrational dynamics of proteins. We use diffusion, a method sensitive to the structural features of the protein fold and them alone, in order to probe protein structure. Conducting a large-scale study of diffusion on over 500 Protein Data Bank structures we find it to be anomalous, an indication of a fractal-like structure. Taking advantage of known and newly derived relations between vibrational dynamics and diffusion, we demonstrate the equivalence of our findings to the existence of structurally originated anomalies in the vibrational dynamics of proteins. We conclude that these anomalies are a direct result of the fractal-like structure of proteins. The duality between diffusion and vibrational dynamics allows us to make, on a single-molecule level, experimentally testable predictions. The time dependent vibrational mean square displacement of an amino acid is predicted to be subdiffusive. The thermal variance in the instantaneous distance between amino acids is shown to grow as a power law of the equilibrium distance. Mean first passage time analysis is offered as a practical tool that may aid in the identification of amino acid pairs involved in large conformational changes.

Original languageEnglish
Pages (from-to)13696-13700
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume107
Issue number31
DOIs
StatePublished - 3 Aug 2010

Keywords

  • Anomalous diffusion
  • Gaussian network model
  • Intramolecular distance distributions
  • Mean first passage time
  • Protein dynamics

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