American Institute of Mathematical Sciences

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October  2011, 4(5): 1247-1266. doi: 10.3934/dcdss.2011.4.1247

Breather-mediated energy transfer in proteins

Francesco Piazza 1, and  Yves-Henri Sanejouand 2,

1. 

Centre de Biophysique Moleculaire (CBM-CNRS), University of Orleans, Rue Charles Sadron, 45071 Orleans, France
2. 

Laboratoire Biotechnologie, Biocatalyse et Biorégulation, UMR 6204 du CNRS, Faculté des Sciences et des Techniques, 2, rue de la Houssinière, 44322 Nantes Cedex 3, France

Received  September 2009 Revised  December 2009 Published  December 2010

In this paper we investigate how energy is redistributed across protein structures, following localized kicks, within the framework of a nonlinear network model. We show that energy is directed most of the times to a few specific sites, systematically within the stiffest regions. This effect is sharpened as the energy of the kicks is increased, with fractions of transferred energy as high as 70% already for kicks above $20$ kcal/mol. Remarkably, we show that such site-selective, high-yield transfers mark the spontaneous formation of spatially localized, time-periodic vibrations at the target sites, acting as efficient energy-collecting centers. A comparison of our simulations with a previously developed theory reveals that such energy-pinning modes are discrete breathers, able to carry energy across the structure in an quasi-coherent fashion by jumping from site to site.
Keywords: Discrete Breathers, Energy transfer., Nonlinear dynamical systems, Network models, Enzymes, Proteins.
Mathematics Subject Classification: Primary: 70-XX, 37-XX, 92-XX; Secondary: 70K75, 34C15, 37N25, 92C4.
Citation: Francesco Piazza, Yves-Henri Sanejouand. Breather-mediated energy transfer in proteins. Discrete & Continuous Dynamical Systems - S, 2011, 4 (5) : 1247-1266. doi: 10.3934/dcdss.2011.4.1247
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show all references

References:
[1]

vol. 45, Kluwer Academic Publishers, Dordrecht, The Netherlands, 2001. Google Scholar

[2]

Journal of Physics A: Mathematical and General, 35 (2002), 8885-8902. doi: 10.1088/0305-4470/35/42/301.  Google Scholar

[3]

Physica D: Nonlinear Phenomena, 216 (2006), 1-30. doi: 10.1016/j.physd.2005.12.020.  Google Scholar

[4]

Fold. Des., 2 (1997), 173-181. doi: 10.1016/S1359-0278(97)00024-2.  Google Scholar

[5]

C&H/CRC Mathematical & Computational Biology Series, vol. 9, CRC press, Boca Raton, 2005. Google Scholar

[6]

Proc. Natl. Acad. Sci. USA, 80 (1983), 6571-6575. doi: 10.1073/pnas.80.21.6571.  Google Scholar

[7]

Physical Review B, 42 (1990), 4921-4927. doi: 10.1103/PhysRevB.42.4921.  Google Scholar

[8]

Nova Science Publishers, Inc., 2005. Google Scholar

[9]

Chaos, 15 (2005), 015110. doi: 10.1063/1.1854273.  Google Scholar

[10]

Advanced Series in Nonlinear Dynamics, vol. 22, World Scientific, Singapore, 2004. Google Scholar

[11]

Structure, 17 (2009), 1042-1050. doi: 10.1016/j.str.2009.06.008.  Google Scholar

[12]

Journal of Physics: Condensed Matter, 15 (2003), S1699-S1707. doi: 10.1088/0953-8984/15/18/304.  Google Scholar

[13]

Physical Review E, 71 (2005), 026606-9. doi: 10.1103/PhysRevE.71.026606.  Google Scholar

[14]

Science, 295 (2002), 1480-1481. doi: 10.1126/science.1069823.  Google Scholar

[15]

Physical Review E, 49 (1994), 5018-5024. doi: 10.1103/PhysRevE.49.5018.  Google Scholar

[16]

Physics Reports, 295 (1998), 181-264. doi: 10.1016/S0370-1573(97)00068-9.  Google Scholar

[17]

Physics Reports, 467 (2008), 1-116. doi: 10.1016/j.physrep.2008.05.002.  Google Scholar

[18]

Proteins, 23 (1995), 177-186. doi: 10.1002/prot.340230207.  Google Scholar

[19]

Nature, 450 (2007), 913-916. doi: 10.1038/nature06407.  Google Scholar

[20]

Proteins, 33 (1998), 417-429. doi: 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8.  Google Scholar

[21]

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[22]

Phys. Rev. Lett., 87 (2001), 165501. doi: 10.1103/PhysRevLett.87.165501.  Google Scholar

[23]

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[24]

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[25]

Int. J. Quant. Chem., 10 (1983), 181-199. Google Scholar

[26]

Proc. Natl. Acad. Sci. USA, 79 (1982), 1346-1350. doi: 10.1073/pnas.79.4.1346.  Google Scholar

[27]

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[28]

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[29]

Springer, Berlin, 1995. Google Scholar

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[31]

Phys. Biol, 5 (2008), 026001. doi: 10.1088/1478-3975/5/2/026001.  Google Scholar

[32]

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[33]

Europhysics Letters, 47 (1999), 421-427. doi: 10.1209/epl/i1999-00405-1.  Google Scholar

[34]

The Journal of Physical Chemistry B, 110 (2006), 6987-6990. doi: 10.1021/jp0556862.  Google Scholar

[35]

Structure, 15 (2007), 565-575. doi: 10.1016/j.str.2007.03.013.  Google Scholar

[36]

EPL, 78 (2007), 26001. doi: 10.1209/0295-5075/78/26001.  Google Scholar

[37]

Proteins, 67 (2007), 350-359. doi: 10.1002/prot.21353.  Google Scholar

[38]

J. Chem. Phys., 113 (2000), 7702-7711. doi: 10.1063/1.1313554.  Google Scholar

[39]

Physical Review B, 46 (1992), 6161-6168. doi: 10.1103/PhysRevB.46.6161.  Google Scholar

[40]

Journal of Biological Physics, 35 (2009), 57-72. doi: 10.1007/s10867-009-9135-2.  Google Scholar

[41]

Physics Reports, 217 (1992), 1-67. doi: 10.1016/0370-1573(92)90093-F.  Google Scholar

[42]

University of Chicago Press, Chicago, 1965. Google Scholar

[43]

Protein Engineering Design and Selection, 14 (2001), 1-6. doi: 10.1093/protein/14.1.1.  Google Scholar

[44]

Physical Review Letters, 77 (1996), 1905-1908. doi: 10.1103/PhysRevLett.77.1905.  Google Scholar

[45]

Journal of Molecular Biology, 378 (2008), 1-11. doi: 10.1016/j.jmb.2008.02.034.  Google Scholar

[46]

Molecular Biosystems, 5 (2009), 207-216. doi: 10.1039/b819720b.  Google Scholar

[47]

HFSP Journal, 2 (2008), 61-64. doi: 10.2976/1.2894846.  Google Scholar

[48]

Journal of Physics: Condensed Matter, 14 (2002), R1035-R1062. doi: 10.1088/0953-8984/14/39/202.  Google Scholar

[49]

Physical Review Letters, 88 (2001), 018102. doi: 10.1103/PhysRevLett.88.018102.  Google Scholar

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Physical Review Letters, 84 (2000), 5435-5438. doi: 10.1103/PhysRevLett.84.5435.  Google Scholar

[51]

Structure, 13 (2005), 893-904. doi: 10.1016/j.str.2005.03.015.  Google Scholar

[52]

Journal of Physical Chemistry B, 107 (2003), 1698-1707. doi: 10.1021/jp026462b.  Google Scholar

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