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

Proceedings of the National Academy of Sciences of the United States of America
Shlomi ReuveniJ Klafter

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, nonexponential 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 d...Continue Reading

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Citations

May 24, 2012·Proceedings of the National Academy of Sciences of the United States of America·Mary Grace I GalinatoNicolai Lehnert
May 9, 2013·Proceedings of the National Academy of Sciences of the United States of America·Georg A Gottwald, Ian Melbourne
Mar 13, 2014·Proceedings of the National Academy of Sciences of the United States of America·Shlomi ReuveniJoseph Klafter
May 27, 2011·Cellular and Molecular Life Sciences : CMLS·Anirban Banerji, Indira Ghosh
Apr 12, 2016·The Journal of Physical Chemistry. B·David M Leitner
Mar 10, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Shlomi ReuveniRony Granek
Mar 10, 2012·Physical Review Letters·Shlomi ReuveniRony Granek
Oct 4, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·David A KenwrightVictoria J Allan
Jan 15, 2016·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Tal RotbartMichael Urbakh
Jan 20, 2018·Soft Matter·Jonas Grimm, Maxim Dolgushev
Jan 15, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Shlomi ReuveniJoseph Klafter
Oct 3, 2015·Physical Review Letters·Nikolaj KulvelisOliver Mülken
Apr 15, 2016·Physical Review. E·Hongxiao LiuZhongzhi Zhang
Jan 20, 2018·Physical Review. E·Maxim DolgushevJoachim P Wittmer
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Sep 22, 2018·The Journal of Physical Chemistry. B·Pablo Turjanski, Diego U Ferreiro
Sep 13, 2019·The Journal of Physical Chemistry. B·David M LeitnerKorey M Reid

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