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Volumn 415, Issue , 2014, Pages 440-448

Fractals and self-organized criticality in proteins

Author keywords

Evolution; Hydrophilic; Hydrophobic; Scaling; Sequence; Surface area

Indexed keywords

BIOCHEMISTRY; CRITICALITY (NUCLEAR FISSION); PROTEINS;

EID: 84907483629     PISSN: 03784371     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.physa.2014.08.034     Document Type: Article
Times cited : (46)

References (41)
  • 1
    • 35949034896 scopus 로고
    • The renormalization group: Critical phenomena and the Kondo problem
    • K.G. Wilson The renormalization group: critical phenomena and the Kondo problem Rev. Modern Phys. 47 1975 773 840
    • (1975) Rev. Modern Phys. , vol.47 , pp. 773-840
    • Wilson, K.G.1
  • 2
    • 5844290410 scopus 로고
    • Self-organized criticality - An explanation of 1/f noise
    • P. Bak, C. Tang, and K. Wiesenfeld Self-organized criticality - an explanation of 1/f noise Phys. Rev. Lett. 59 1987 381
    • (1987) Phys. Rev. Lett. , vol.59 , pp. 381
    • Bak, P.1    Tang, C.2    Wiesenfeld, K.3
  • 3
    • 79961030753 scopus 로고    scopus 로고
    • Universal fractal scaling of self-organized networks
    • P.J. Laurenti, K.E. Joyce, and Q.K. Telesford Universal fractal scaling of self-organized networks Physica A 390 2011 3608 3613
    • (2011) Physica A , vol.390 , pp. 3608-3613
    • Laurenti, P.J.1    Joyce, K.E.2    Telesford, Q.K.3
  • 4
    • 0020118274 scopus 로고
    • Neural networks and physical systems with emergent collective computational abilities
    • J.J. Hopfield Neural networks and physical systems with emergent collective computational abilities Proc. Natl. Acad. Sci. USA 79 1982 2554 2558
    • (1982) Proc. Natl. Acad. Sci. USA , vol.79 , pp. 2554-2558
    • Hopfield, J.J.1
  • 5
    • 36749042711 scopus 로고    scopus 로고
    • Dynamical synapses causing self-organized criticality in neural networks
    • A. Levina, J.M. Herrmann, and T. Geisel Dynamical synapses causing self-organized criticality in neural networks Nat. Phys. 3 2007 857 860
    • (2007) Nat. Phys. , vol.3 , pp. 857-860
    • Levina, A.1    Herrmann, J.M.2    Geisel, T.3
  • 6
    • 33846546999 scopus 로고    scopus 로고
    • Amino acid hydrophobicity and accessible surface area
    • M.A. Moret, and G.F. Zebende Amino acid hydrophobicity and accessible surface area Phys. Rev. E 75 2007 011920
    • (2007) Phys. Rev. e , vol.75 , pp. 011920
    • Moret, M.A.1    Zebende, G.F.2
  • 7
    • 84860533303 scopus 로고    scopus 로고
    • Diffusion of knowledge and globalization in the Web of twentieth century science
    • G.G. Naumis, and J.C. Phillips Diffusion of knowledge and globalization in the Web of twentieth century science Phys. A 391 2012 3995 4003
    • (2012) Phys. A , vol.391 , pp. 3995-4003
    • Naumis, G.G.1    Phillips, J.C.2
  • 8
    • 84879488849 scopus 로고    scopus 로고
    • Dynamics of glass relaxation at room temperature
    • R.C. Welch, J.R. Smith, and M. Potuzak Dynamics of glass relaxation at room temperature Phys. Rev. Lett. 110 2013 265901
    • (2013) Phys. Rev. Lett. , vol.110 , pp. 265901
    • Welch, R.C.1    Smith, J.R.2    Potuzak, M.3
  • 9
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • J. Kyte, and R.F. Doolittle A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157 1982 105 132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 10
    • 71449100768 scopus 로고    scopus 로고
    • Scaling and self-organized criticality in proteins: Lysozyme c
    • J.C. Phillips Scaling and self-organized criticality in proteins: lysozyme c Phys. Rev. E 80 2009 051916
    • (2009) Phys. Rev. e , vol.80 , pp. 051916
    • Phillips, J.C.1
  • 11
    • 34147167680 scopus 로고    scopus 로고
    • On the relationship between sequence and structure similarities in proteomics
    • E. Krissinel On the relationship between sequence and structure similarities in proteomics Bioinformatics 23 2007 717 723
    • (2007) Bioinformatics , vol.23 , pp. 717-723
    • Krissinel, E.1
  • 12
    • 78649728415 scopus 로고    scopus 로고
    • Local cooperativity in an amyloidogenic state of human lysozyme observed at atomic resolution
    • A. Dhulesia, N. Cremades, and J.R. Kumita Local cooperativity in an amyloidogenic state of human lysozyme observed at atomic resolution J. Am. Chem. Soc. 132 2010 15580 15588
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 15580-15588
    • Dhulesia, A.1    Cremades, N.2    Kumita, J.R.3
  • 13
    • 0034599488 scopus 로고    scopus 로고
    • Discrete element simulations of dense packings and heaps made of spherical and non-spherical particles
    • H.G. Matuttis, S. Luding, and H.J. Herrmann Discrete element simulations of dense packings and heaps made of spherical and non-spherical particles Powder Technol. 109 2000 278 292
    • (2000) Powder Technol. , vol.109 , pp. 278-292
    • Matuttis, H.G.1    Luding, S.2    Herrmann, H.J.3
  • 14
    • 36049058980 scopus 로고
    • Spectral distribution of scattered light in a simple fluid
    • R.D. Mountain Spectral distribution of scattered light in a simple fluid Rev. Modern Phys. 38 1966 205 214
    • (1966) Rev. Modern Phys. , vol.38 , pp. 205-214
    • Mountain, R.D.1
  • 15
    • 84875466478 scopus 로고    scopus 로고
    • Fractal nature of protein surface roughness: A note on quantification of change of surface roughness in active sites, before and after binding
    • A. Banerji, and C. Navare Fractal nature of protein surface roughness: a note on quantification of change of surface roughness in active sites, before and after binding J. Mol. Recognit. 26 2013 201 214
    • (2013) J. Mol. Recognit. , vol.26 , pp. 201-214
    • Banerji, A.1    Navare, C.2
  • 16
    • 0031576361 scopus 로고    scopus 로고
    • Intermediate sequences increase the detection of homology between sequences
    • J. Park, S.A. Teichmann, and T. Hubbard Intermediate sequences increase the detection of homology between sequences J. Mol. Biol. 273 1997 349 354
    • (1997) J. Mol. Biol. , vol.273 , pp. 349-354
    • Park, J.1    Teichmann, S.A.2    Hubbard, T.3
  • 17
    • 34247359602 scopus 로고    scopus 로고
    • Conditional targeted cell ablation in zebrafish: A new tool for regeneration studies
    • S. Curado, R.M. Anderson, and B. Jungblut Conditional targeted cell ablation in zebrafish: a new tool for regeneration studies Dev. Dyn. 236 2007 1025 1035
    • (2007) Dev. Dyn. , vol.236 , pp. 1025-1035
    • Curado, S.1    Anderson, R.M.2    Jungblut, B.3
  • 18
    • 0042467550 scopus 로고    scopus 로고
    • Rationalization of the effects of mutations on peptide and protein aggregation rates
    • F. Chiti, M. Stefani, and N. Taddei Rationalization of the effects of mutations on peptide and protein aggregation rates Nature 424 2003 805 808
    • (2003) Nature , vol.424 , pp. 805-808
    • Chiti, F.1    Stefani, M.2    Taddei, N.3
  • 19
    • 84864473624 scopus 로고    scopus 로고
    • Dependence of alpha-helical and beta-strand amino acid propensities on the overall protein fold type
    • K. Fujiwara, H. Toda, and M. Ikeguchi Dependence of alpha-helical and beta-strand amino acid propensities on the overall protein fold type BMC Struct. Biol. 12 2012 18
    • (2012) BMC Struct. Biol. , vol.12 , pp. 18
    • Fujiwara, K.1    Toda, H.2    Ikeguchi, M.3
  • 20
    • 77957144851 scopus 로고    scopus 로고
    • Position-specific propensities of amino acids in the beta-strand
    • N. Bhattacharjee, and P. Biswas Position-specific propensities of amino acids in the beta-strand BMC Struct. Biol. 10 2010 29
    • (2010) BMC Struct. Biol. , vol.10 , pp. 29
    • Bhattacharjee, N.1    Biswas, P.2
  • 21
    • 5044235541 scopus 로고    scopus 로고
    • Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
    • A.M. Fernandez-Escamilla, F. Rousseau, and J. Schymkowitz Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins Nature Biotechnol. 22 2004 1302 1306
    • (2004) Nature Biotechnol. , vol.22 , pp. 1302-1306
    • Fernandez-Escamilla, A.M.1    Rousseau, F.2    Schymkowitz, J.3
  • 22
    • 0036166319 scopus 로고    scopus 로고
    • Kinetic partitioning of protein folding and aggregation
    • F. Chiti, N. Taddei, and F. Baroni Kinetic partitioning of protein folding and aggregation Nature Struct. Biol. 9 2002 137 143
    • (2002) Nature Struct. Biol. , vol.9 , pp. 137-143
    • Chiti, F.1    Taddei, N.2    Baroni, F.3
  • 23
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • K.A. Dill, and H.S. Chan From Levinthal to pathways to funnels Nature Struct. Biol. 4 1997 10 19
    • (1997) Nature Struct. Biol. , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 26
    • 0015977588 scopus 로고
    • The interpretation of protein structures: Total volume, group volume distributions and packing density
    • F.M. Richards The interpretation of protein structures: total volume, group volume distributions and packing density J. Mol. Biol. 82 1974 1 14
    • (1974) J. Mol. Biol. , vol.82 , pp. 1-14
    • Richards, F.M.1
  • 27
    • 0024354001 scopus 로고
    • Solvent effects on protein motion and protein effects on solvent motion - Dynamics of the active-site region of lysozyme
    • C.L. Brooks, and M. Karplus Solvent effects on protein motion and protein effects on solvent motion - dynamics of the active-site region of lysozyme J. Mol. Biol. 208 1989 159 181
    • (1989) J. Mol. Biol. , vol.208 , pp. 159-181
    • Brooks, C.L.1    Karplus, M.2
  • 28
    • 0030711616 scopus 로고    scopus 로고
    • Molecular switch in signal transduction: Reaction paths of the conformational changes in Ras p21
    • J.P. Ma, and M. Karplus Molecular switch in signal transduction: reaction paths of the conformational changes in Ras p21 Proc. Natl. Acad. Sci. USA 94 1997 11905 11910
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 11905-11910
    • Ma, J.P.1    Karplus, M.2
  • 29
    • 0037125971 scopus 로고    scopus 로고
    • The structural basis for the transition from Ras-GTP to Ras-GDP
    • B.E. Hall, D. Bar-Sagi, and N. Nassar The structural basis for the transition from Ras-GTP to Ras-GDP Proc. Natl. Acad. Sci. USA 99 2002 12138 12142
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 12138-12142
    • Hall, B.E.1    Bar-Sagi, D.2    Nassar, N.3
  • 30
    • 79961113464 scopus 로고    scopus 로고
    • Fractality of eroded coastlines of correlated landscapes
    • P.A. Morais, E.A. Oliveira, and N.A.M. Araujo Fractality of eroded coastlines of correlated landscapes Phys. Rev. E 84 2011 016102
    • (2011) Phys. Rev. e , vol.84 , pp. 016102
    • Morais, P.A.1    Oliveira, E.A.2    Araujo, N.A.M.3
  • 31
    • 64549088424 scopus 로고    scopus 로고
    • Spontaneous emergence of modularity in a model of evolving individuals and in real networks
    • J. He, J. Sun, and M.W. Deem Spontaneous emergence of modularity in a model of evolving individuals and in real networks Phys. Rev. E 79 2009 031907
    • (2009) Phys. Rev. e , vol.79 , pp. 031907
    • He, J.1    Sun, J.2    Deem, M.W.3
  • 32
    • 84887297074 scopus 로고    scopus 로고
    • Parameter space compression underlies emergent theories and predictive models
    • B.B. Machta, R. Chachra, and M.K. Transtrum Parameter space compression underlies emergent theories and predictive models Science 342 2013 604 607
    • (2013) Science , vol.342 , pp. 604-607
    • Machta, B.B.1    Chachra, R.2    Transtrum, M.K.3
  • 34
    • 44149087864 scopus 로고    scopus 로고
    • Proteins: Coexistence of stability and flexibility
    • S. Reuveni, R. Granek, and J. Klafter Proteins: coexistence of stability and flexibility Phys. Rev. Lett. 100 2008 208101
    • (2008) Phys. Rev. Lett. , vol.100 , pp. 208101
    • Reuveni, S.1    Granek, R.2    Klafter, J.3
  • 35
    • 84868685944 scopus 로고    scopus 로고
    • Self-organized criticality and color vision: A guide to water-protein landscape evolution
    • J.C. Phillips Self-organized criticality and color vision: a guide to water-protein landscape evolution Phys. A 392 2012 468 473
    • (2012) Phys. A , vol.392 , pp. 468-473
    • Phillips, J.C.1
  • 36
    • 84922127771 scopus 로고    scopus 로고
    • Punctuated evolution of influenza virus neuraminidase (A/H1N1) under opposing migration and vaccination pressures
    • J.C. Phillips Punctuated evolution of influenza virus neuraminidase (A/H1N1) under opposing migration and vaccination pressures BioMed Res. Int. 2014 907381
    • (2014) BioMed Res. Int. , pp. 907381
    • Phillips, J.C.1
  • 39
    • 84880046455 scopus 로고    scopus 로고
    • Backbone fractal dimension and fractal hybrid orbital of protein structure
    • X. Peng, W. Qi, and M. Wang Backbone fractal dimension and fractal hybrid orbital of protein structure Commun. Nonlinear Sci. Numer. Simul. 18 2013 3373 3381
    • (2013) Commun. Nonlinear Sci. Numer. Simul. , vol.18 , pp. 3373-3381
    • Peng, X.1    Qi, W.2    Wang, M.3
  • 41
    • 0001058199 scopus 로고
    • Low-frequency modes in proteins - Use of the effective-medium approximation to interpret the fractal dimension observed in electron-spin relaxation measurements
    • R. Elber, and M. Karplus Low-frequency modes in proteins - use of the effective-medium approximation to interpret the fractal dimension observed in electron-spin relaxation measurements Phys. Rev. Lett. 56 1986 394 397
    • (1986) Phys. Rev. Lett. , vol.56 , pp. 394-397
    • Elber, R.1    Karplus, M.2


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