메뉴 건너뛰기




Volumn 83, Issue 2, 2011, Pages

Configurational subdiffusion of peptides: A network study

Author keywords

[No Author keywords available]

Indexed keywords

ACCESSIBLE VOLUME; CONFIGURATION SPACE; CONTINUOUS-TIME RANDOM WALK MODELS; CONVERGENCE PROPERTIES; FRACTAL-LIKE; LINEAR PEPTIDES; MD SIMULATION; MEAN SQUARED DISPLACEMENT; MOLECULAR DYNAMICS SIMULATIONS; NETWORK MODELS; ROUSE CHAINS; SUBDIFFUSION; TIME DEPENDENCE;

EID: 79952519006     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.83.021902     Document Type: Article
Times cited : (10)

References (60)
  • 1
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • DOI 10.1038/nature06522, PII NATURE06522
    • K. Henzler-Wildman and D. Kern, Nature (London) NATUAS 0028-0836 10.1038/nature06522 450, 964 (2007). (Pubitemid 350273626)
    • (2007) Nature , vol.450 , Issue.7172 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 3
    • 10844264077 scopus 로고    scopus 로고
    • Fractional Brownian dynamics in proteins
    • DOI 10.1063/1.1806134
    • G. R. Kneller and K. Hinsen, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1806134 121, 10278 (2004). (Pubitemid 40001680)
    • (2004) Journal of Chemical Physics , vol.121 , Issue.20 , pp. 10278-10283
    • Kneller, G.R.1    Hinsen, K.2
  • 4
    • 43249110336 scopus 로고    scopus 로고
    • Subdiffusion in peptides originates from the fractal-like structure of configuration space
    • DOI 10.1103/PhysRevLett.100.188103
    • T. Neusius, I. Daidone, and I. M. Sokolov, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.188103 100, 188103 (2008). (Pubitemid 351656434)
    • (2008) Physical Review Letters , vol.100 , Issue.18 , pp. 188103
    • Neusius, T.1    Daidone, I.2    Sokolov, I.M.3    Smith, J.C.4
  • 5
    • 22344432186 scopus 로고    scopus 로고
    • Quasielastic neutron scattering and relaxation processes in proteins: Analytical and simulation-based models
    • DOI 10.1039/b502040a
    • G. R. Kneller, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10.1039/b502040a 7, 2641 (2005). (Pubitemid 41001322)
    • (2005) Physical Chemistry Chemical Physics , vol.7 , Issue.13 , pp. 2641-2655
    • Kneller, G.R.1
  • 7
    • 27144465458 scopus 로고    scopus 로고
    • Observation of a power-law memory Kernel for fluctuations within a single protein molecule
    • DOI 10.1103/PhysRevLett.94.198302, 198302
    • W. Min, G. Luo, B. J. Cherayil, S. C. Kou, and X. S. Xie, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.198302 94, 198302 (2005). (Pubitemid 41493017)
    • (2005) Physical Review Letters , vol.94 , Issue.19 , pp. 1-4
    • Min, W.1    Luo, G.2    Cherayil, B.J.3    Kou, S.C.4    Xie, X.S.5
  • 8
    • 19744382497 scopus 로고    scopus 로고
    • PRLTAO 0031-9007 10.1103/PhysRevLett.93.180603
    • S. C. Kou and X. S. Xie, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.180603 93, 180603 (2004).
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 180603
    • Kou, S.C.1    Xie, X.S.2
  • 9
    • 0037461522 scopus 로고    scopus 로고
    • JCPSA6 0021-9606 10.1063/1.1521154
    • H. Yang and X. Sunney Xie, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1521154 117, 10965 (2002).
    • (2002) J. Chem. Phys. , vol.117 , pp. 10965
    • Yang, H.1    Sunney Xie, X.2
  • 10
    • 79952519866 scopus 로고    scopus 로고
    • See supplemental material at [http://link.aps.org/supplemental/10.1103/ PhysRevE.83.021902] for mathematical details of the present paper.
  • 11
    • 33845656521 scopus 로고    scopus 로고
    • Dynamics of Unfolded Polypeptide Chains in Crowded Environment Studied by Fluorescence Correlation Spectroscopy
    • DOI 10.1016/j.jmb.2006.10.021, PII S0022283606013593
    • H. Neuweiller, M. Löllmann, S. Doose, and M. Sauer, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2006.10.021 365, 856 (2007). (Pubitemid 44960355)
    • (2007) Journal of Molecular Biology , vol.365 , Issue.3 , pp. 856-869
    • Neuweiler, H.1    Lollmann, M.2    Doose, S.3    Sauer, M.4
  • 12
    • 33644524695 scopus 로고    scopus 로고
    • PLEEE8 1539-3755 10.1103/PhysRevE.73.022102
    • J. Tang and R. A. Marcus, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.73.022102 73, 022102 (2006).
    • (2006) Phys. Rev. e , vol.73 , pp. 022102
    • Tang, J.1    Marcus, R.A.2
  • 13
    • 0026320866 scopus 로고
    • SCIEAS 0036-8075 10.1126/science.1749933
    • H. Frauenfelder, S. G. Sligar, and P. G. Wolynes, Science SCIEAS 0036-8075 10.1126/science.1749933 254, 1598 (1991).
    • (1991) Science , vol.254 , pp. 1598
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 14
    • 0023452103 scopus 로고
    • ADPHAH 0001-8732 10.1080/00018738700101072
    • S. Havlin and D. Ben-Avraham, Adv. Phys. ADPHAH 0001-8732 10.1080/00018738700101072 36, 695 (1987).
    • (1987) Adv. Phys. , vol.36 , pp. 695
    • Havlin, S.1    Ben-Avraham, D.2
  • 18
    • 84946449441 scopus 로고
    • MOPHAM 0026-8976 10.1080/00268978400100801
    • D. Brown and J. H. R. Clarke, Mol. Phys. MOPHAM 0026-8976 10.1080/00268978400100801 51, 1243 (1984).
    • (1984) Mol. Phys. , vol.51 , pp. 1243
    • Brown, D.1    Clarke, J.H.R.2
  • 19
    • 0000388705 scopus 로고    scopus 로고
    • JCCHDD 0192-8651 10.1002/(SICI)1096-987X(199709)18:12<1463::AID- JCC4>3.0.CO;2-H
    • B. Hess, H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije, J. Comput. Chem. JCCHDD 0192-8651 10.1002/(SICI)1096-987X(199709)18:12<1463:: AID-JCC4>3.0.CO;2-H 18, 1463 (1997).
    • (1997) J. Comput. Chem. , vol.18 , pp. 1463
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.C.3    Fraaije, J.G.E.M.4
  • 21
    • 33846823909 scopus 로고
    • JCPSA6 0021-9606 10.1063/1.464397
    • T. Darden, D. York, and L. Pedersen, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.464397 98, 10089 (1993).
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 23
    • 0033654297 scopus 로고    scopus 로고
    • ARPLAP 0066-426X 10.1146/annurev.physchem.51.1.129
    • D. Bashford and D. A. Case, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.51.1.129 51, 129 (2000).
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 129
    • Bashford, D.1    Case, D.A.2
  • 25
    • 0037046727 scopus 로고    scopus 로고
    • Parametrization of a generalized Born/solvent-accessible surface area model and applications to the simulation of protein dynamics
    • DOI 10.1021/jp020058v
    • J. Zhu, Y. Shi, and H. Liu, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp020058v 106, 4844 (2002). (Pubitemid 35281997)
    • (2002) Journal of Physical Chemistry B , vol.106 , Issue.18 , pp. 4844-4853
    • Zhu, J.1    Shi, Y.2    Liu, H.3
  • 26
    • 0032484151 scopus 로고    scopus 로고
    • Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
    • DOI 10.1006/jmbi.1998.2172
    • M. Schaefer, C. Bartels, and M. Karplus, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1998.2172 284, 835 (1998). (Pubitemid 28550026)
    • (1998) Journal of Molecular Biology , vol.284 , Issue.3 , pp. 835-848
    • Schaefer, M.1    Bartels, C.2    Karplus, M.3
  • 29
    • 0000577041 scopus 로고
    • PRLTAO 0031-9007 10.1103/PhysRevLett.68.2696
    • A. E. García, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.68.2696 68, 2696 (1992).
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 2696
    • García, A.E.1
  • 32
    • 0032907372 scopus 로고    scopus 로고
    • BIOJAU 0006-3495 10.1016/S0006-3495(99)77185-7
    • K. S. Kostov and K. F. Freed, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(99)77185-7 76, 149 (1999).
    • (1999) Biophys. J. , vol.76 , pp. 149
    • Kostov, K.S.1    Freed, K.F.2
  • 33
    • 28344443264 scopus 로고    scopus 로고
    • Multiple time scale dynamics of distance fluctuations in a semiflexible polymer: A one-dimensional generalized Langevin equation treatment
    • DOI 10.1063/1.2109809, 204903
    • P. Debnath, W. Min, X. S. Xie, and B. J. Cherayil, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2109809 123, 204903 (2005). (Pubitemid 41721315)
    • (2005) Journal of Chemical Physics , vol.123 , Issue.20 , pp. 1-8
    • Debnath, P.1    Min, W.2    Xie, X.S.3    Cherayil, B.J.4
  • 34
    • 0344252790 scopus 로고
    • JCPSA6 0021-9606 10.1063/1.1699180
    • P. E. Rouse, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1699180 21, 1272 (1953).
    • (1953) J. Chem. Phys. , vol.21 , pp. 1272
    • Rouse, P.E.1
  • 36
    • 27144546670 scopus 로고    scopus 로고
    • Fractons in proteins: Can they lead to anomalously decaying time autocorrelations?
    • DOI 10.1103/PhysRevLett.95.098106, 098106
    • R. Granek and J. Klafter, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.95.098106 95, 098106 (2005). (Pubitemid 41505889)
    • (2005) Physical Review Letters , vol.95 , Issue.9 , pp. 1-4
    • Granek, R.1    Klafter, J.2
  • 37
    • 44149087864 scopus 로고    scopus 로고
    • Proteins: Coexistence of stability and flexibility
    • DOI 10.1103/PhysRevLett.100.208101
    • S. Reuveni, R. Granek, and J. Klafter, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.208101 100, 208101 (2008). (Pubitemid 351718017)
    • (2008) Physical Review Letters , vol.100 , Issue.20 , pp. 208101
    • Reuveni, S.1    Granek, R.2    Klafter, J.3
  • 38
    • 0024025743 scopus 로고
    • BIPMAA 0006-3525 10.1002/bip.360270609
    • R. M. Venable and R. W. Pastor, Biopolymers BIPMAA 0006-3525 10.1002/bip.360270609 27, 1001 (1988).
    • (1988) Biopolymers , vol.27 , pp. 1001
    • Venable, R.M.1    Pastor, R.W.2
  • 39
    • 0141993702 scopus 로고    scopus 로고
    • Protein conformational dynamics probed by single-molecule electron transfer
    • DOI 10.1126/science.1086911
    • H. Yang, G. Luo, P. Karnchanaphanurach, T.-M. Louie, I. Rech, S. Cova, L. Xun, and X. Sunney Xie, Science SCIEAS 0036-8075 10.1126/science.1086911 302, 262 (2003). (Pubitemid 37248752)
    • (2003) Science , vol.302 , Issue.5643 , pp. 262-266
    • Yang, H.1    Luo, G.2    Karnchanaphanurach, P.3    Louie, T.-M.4    Rech, I.5    Cova, S.6    Xun, L.7    Xie, X.S.8
  • 41
    • 73449138268 scopus 로고    scopus 로고
    • JCPSA6 0021-9606 10.1063/1.3274678
    • S. Fugmann and I. M. Sokolov, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3274678 131, 235104 (2009).
    • (2009) J. Chem. Phys. , vol.131 , pp. 235104
    • Fugmann, S.1    Sokolov, I.M.2
  • 44
  • 48
    • 34547337735 scopus 로고    scopus 로고
    • Occupation time statistics in the quenched trap model
    • DOI 10.1103/PhysRevLett.98.250601
    • S. Burov and E. Barkai, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.98.250601 98, 250601 (2007). (Pubitemid 47139918)
    • (2007) Physical Review Letters , vol.98 , Issue.25 , pp. 250601
    • Burov, S.1    Barkai, E.2
  • 49
    • 0032374086 scopus 로고    scopus 로고
    • Energy landscape of a native protein: Jumping-among-minima model
    • DOI 10.1002/(SICI)1097-0134(19981201)33:4<496::AID-PROT4>3.0.CO;2-1
    • A. Kitao, S. Hayward, and N. Go, Proteins: Struct., Funct., Genet. PSFGEY 0887-3585 10.1002/(SICI)1097-0134(19981201)33:4<496::AID-PROT4>3.0.CO;2-1 33, 496 (1998). (Pubitemid 28565734)
    • (1998) Proteins: Structure, Function and Genetics , vol.33 , Issue.4 , pp. 496-517
    • Kitao, A.1    Hayward, S.2    Go, N.3
  • 50
    • 0040307478 scopus 로고
    • PRPLCM 0370-1573 10.1016/0370-1573(90)90099-N
    • J.-P. Bouchaud and A. Georges, Phys. Rep. PRPLCM 0370-1573 10.1016/0370-1573(90)90099-N 195, 127 (1990).
    • (1990) Phys. Rep. , vol.195 , pp. 127
    • Bouchaud, J.-P.1    Georges, A.2
  • 51
    • 0141508296 scopus 로고
    • PLRBAQ 1098-0121 10.1103/PhysRevB.12.2455
    • H. Scher and E. W. Montroll, Phys. Rev. B PLRBAQ 1098-0121 10.1103/PhysRevB.12.2455 12, 2455 (1975).
    • (1975) Phys. Rev. B , vol.12 , pp. 2455
    • Scher, H.1    Montroll, E.W.2
  • 52
    • 0002641421 scopus 로고    scopus 로고
    • PRPLCM 0370-1573 10.1016/S0370-1573(00)00070-3
    • R. Metzler and J. Klafter, Phys. Rep. PRPLCM 0370-1573 10.1016/S0370-1573(00)00070-3 339, 1 (2000).
    • (2000) Phys. Rep. , vol.339 , pp. 1
    • Metzler, R.1    Klafter, J.2
  • 53
    • 68949103890 scopus 로고    scopus 로고
    • PLEEE8 1539-3755 10.1103/PhysRevE.80.011109
    • T. Neusius, I. M. Sokolov, and J. C. Smith, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.80.011109 80, 011109 (2009).
    • (2009) Phys. Rev. e , vol.80 , pp. 011109
    • Neusius, T.1    Sokolov, I.M.2    Smith, J.C.3
  • 54
    • 0042797442 scopus 로고    scopus 로고
    • Cambridge University Press, Cambridge
    • D. J. Wales, Energy Landscapes (Cambridge University Press, Cambridge, 2003).
    • (2003) Energy Landscapes
    • Wales, D.J.1
  • 58
    • 34247339716 scopus 로고    scopus 로고
    • Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states
    • DOI 10.1063/1.2714539
    • F. Noé, I. Horenko, C. Schütte, and J. C. Smith, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2714539 126, 155102 (2007). (Pubitemid 46644961)
    • (2007) Journal of Chemical Physics , vol.126 , Issue.15 , pp. 155102
    • Noe, F.1    Horenko, I.2    Schutte, C.3    Smith, J.C.4
  • 59
    • 34247338100 scopus 로고    scopus 로고
    • Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
    • DOI 10.1063/1.2714538
    • J. D. Chodera, N. Singhal, V. S. Pande, K. A. Dill, and W. C. Swope, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2714538 126, 155101 (2007). (Pubitemid 46644960)
    • (2007) Journal of Chemical Physics , vol.126 , Issue.15 , pp. 155101
    • Chodera, J.D.1    Singhal, N.2    Pande, V.S.3    Dill, K.A.4    Swope, W.C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.