메뉴 건너뛰기




Volumn 134, Issue 8, 2011, Pages

Failure of one-dimensional Smoluchowski diffusion models to describe the duration of conformational rearrangements in floppy, diffusive molecular systems: A case study of polymer cyclization

Author keywords

[No Author keywords available]

Indexed keywords

CHAIN-ENDS; COMPLEX MOLECULAR SYSTEMS; DIFFUSION MODEL; EFFECTIVE DIFFUSION COEFFICIENTS; ELEMENTARY STEPS; END-TO-END DISTANCES; LENGTH SCALE; LOOP CLOSURE; MOLECULAR SYSTEMS; ONE-DIMENSIONAL MODEL; ONE-DIMENSIONAL POTENTIAL; POLYMER CHAINS; TIME-SCALES;

EID: 79952082707     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3556750     Document Type: Article
Times cited : (25)

References (52)
  • 3
    • 33751152294 scopus 로고    scopus 로고
    • 10.1021/jp951325i
    • J. Wang and P. Wolynes, J. Phys. Chem. 100 (4), 1129 (1996); 10.1021/jp951325i
    • (1996) J. Phys. Chem. , vol.100 , Issue.4 , pp. 1129
    • Wang, J.1    Wolynes, P.2
  • 5
    • 33748518934 scopus 로고    scopus 로고
    • Dominant pathways in protein folding
    • DOI 10.1103/PhysRevLett.97.108101
    • P. Faccioli, M. Sega, F. Pederiva, and H. Orland, Phys. Rev. Lett. 97 (10), 108101 (2006); 10.1103/PhysRevLett.97.108101 (Pubitemid 44362956)
    • (2006) Physical Review Letters , vol.97 , Issue.10 , pp. 108101
    • Faccioli, P.1    Sega, M.2    Pederiva, F.3    Orland, H.4
  • 7
  • 12
    • 33745896527 scopus 로고    scopus 로고
    • Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels
    • DOI 10.1103/PhysRevLett.97.020601
    • A. M. Berezhkovskii, G. Hummer, and S. M. Bezrukov, Phys. Rev. Lett. 97 (2), 020601 (2006); 10.1103/PhysRevLett.97.020601 (Pubitemid 44050353)
    • (2006) Physical Review Letters , vol.97 , Issue.2 , pp. 020601
    • Berezhkovskii, A.M.1    Hummer, G.2    Bezrukov, S.M.3
  • 14
    • 0037039980 scopus 로고    scopus 로고
    • Transition events in butane simulations: Similarities across models
    • DOI 10.1063/1.1433501
    • D. M. Zuckerman and T. B. Woolf, J. Chem. Phys. 116 (6), 2586 (2002). 10.1063/1.1433501 (Pubitemid 34167996)
    • (2002) Journal of Chemical Physics , vol.116 , Issue.6 , pp. 2586-2591
    • Zuckerman, D.M.1    Woolf, T.B.2
  • 15
    • 0842311640 scopus 로고    scopus 로고
    • 10.1063/1.1630572
    • G. Hummer, J. Chem. Phys. 120, 516 (2004). 10.1063/1.1630572
    • (2004) J. Chem. Phys. , vol.120 , pp. 516
    • Hummer, G.1
  • 19
  • 21
    • 0037215268 scopus 로고    scopus 로고
    • The topomer search model: A simple, quantitative theory of two-state protein folding kinetics
    • DOI 10.1110/ps.0220003
    • D. E. Makarov and K. W. Plaxco, Protein Sci. 12 (1), 17 (2003). 10.1110/ps.0220003 (Pubitemid 36020130)
    • (2003) Protein Science , vol.12 , Issue.1 , pp. 17-26
    • Makarov, D.E.1    Plaxco, K.W.2
  • 24
    • 0034021174 scopus 로고    scopus 로고
    • 10.1110/ps.9.3.452
    • D. J. Bicout and A. Szabo, Protein Sci 9 (3), 452 (2000). 10.1110/ps.9.3.452
    • (2000) Protein Sci , vol.9 , Issue.3 , pp. 452
    • Bicout, D.J.1    Szabo, A.2
  • 32
    • 34250356054 scopus 로고    scopus 로고
    • Extracting kinetics from single-molecule force spectroscopy: Nanopore unzipping of DNA hairpins
    • DOI 10.1529/biophysj.106.102855
    • O. K. Dudko, J. Mathe, A. Szabo, A. Meller, and G. Hummer, Biophys J. 92 (12), 4188 (2007); 10.1529/biophysj.106.102855 (Pubitemid 46910535)
    • (2007) Biophysical Journal , vol.92 , Issue.12 , pp. 4188-4195
    • Dudko, O.K.1    Mathe, J.2    Szabo, A.3    Meller, A.4    Hummer, G.5
  • 33
    • 0037566231 scopus 로고    scopus 로고
    • 10.1021/jp027481o
    • I. V. Gopich and A. Szabo, J. Phys. Chem. B 107 (21), 5058 (2003); 10.1021/jp027481o
    • (2003) J. Phys. Chem. B , vol.107 , Issue.21 , pp. 5058
    • Gopich, I.V.1    Szabo, A.2
  • 35
    • 0021508431 scopus 로고
    • 10.1016/S0006-3495(84)84040-0
    • E. Haas and I. Z. Steinberg, Biophysical J. 46, 429 (1984); 10.1016/S0006-3495(84)84040-0
    • (1984) Biophysical J. , vol.46 , pp. 429
    • Haas, E.1    Steinberg, I.Z.2
  • 36
    • 34548101355 scopus 로고    scopus 로고
    • Topography of the free-energy landscape probed via mechanical unfolding of proteins
    • DOI 10.1063/1.1931659, 234915
    • S. Kirmizialtin, L. Huang, and D. E. Makarov, J. Chem. Phys. 122 (23), 234915 (2005); 10.1063/1.1931659 (Pubitemid 40925796)
    • (2005) Journal of Chemical Physics , vol.122 , Issue.23 , pp. 1-12
    • Kirmizialtin, S.1    Huang, L.2    Makarov, D.E.3
  • 38
    • 61749084334 scopus 로고    scopus 로고
    • 10.1021/ar800128x
    • D. E. Makarov, Acc. Chem. Res. 42 (2), 281 (2009); 10.1021/ar800128x
    • (2009) Acc. Chem. Res. , vol.42 , Issue.2 , pp. 281
    • Makarov, D.E.1
  • 44
    • 84955266913 scopus 로고    scopus 로고
    • 10.1103/PhysRevLett.104.048101
    • Y. Suzuki and O. K. Dudko, Phys. Rev. Lett. 104 (4), 048101 (2010). 10.1103/PhysRevLett.104.048101
    • (2010) Phys. Rev. Lett. , vol.104 , Issue.4 , pp. 048101
    • Suzuki, Y.1    Dudko, O.K.2
  • 47
    • 0037471054 scopus 로고    scopus 로고
    • 10.1103/PhysRevLett.90.080601
    • I. M. Sokolov, Phys. Rev. Lett. 90 (8), 080601 (2003). 10.1103/PhysRevLett.90.080601
    • (2003) Phys. Rev. Lett. , vol.90 , Issue.8 , pp. 080601
    • Sokolov, I.M.1
  • 48
    • 34547925924 scopus 로고    scopus 로고
    • 10.1063/1.2178805
    • C. Hyeon and D. Thirumalai, J. Chem. Phys. 124 (10), 104905 (2006); 10.1063/1.2178805
    • (2006) J. Chem. Phys. , vol.124 , Issue.10 , pp. 104905
    • Hyeon, C.1    Thirumalai, D.2
  • 49
    • 0037038514 scopus 로고    scopus 로고
    • Effects of chain stiffness on the dynamics of loop formation in polypeptides. Appendix: Testing a 1-dimensional diffusion model for peptide dynamics
    • DOI 10.1021/jp020829v
    • L. J. Lapidus, P. J. Steinbach, W. A. Eaton, A. Szabo, and J. Hofrichter, J. Phys. Chem. B 106, 11628 (2002). 10.1021/jp020829v (Pubitemid 35361136)
    • (2002) Journal of Physical Chemistry B , vol.106 , Issue.44 , pp. 11628-11640
    • Lapidus, L.J.1    Steinbach, P.J.2    Eaton, W.A.3    Szabo, A.4    Hofrichter, J.5
  • 50
    • 41049106200 scopus 로고    scopus 로고
    • The rate constant of polymer reversal inside a pore
    • DOI 10.1063/1.2890006
    • L. Huang and D. E. Makarov, J. Chem. Phys. 128 (11), 114903 (2008). 10.1063/1.2890006 (Pubitemid 351423244)
    • (2008) Journal of Chemical Physics , vol.128 , Issue.11 , pp. 114903
    • Huang, L.1    Makarov, D.E.2
  • 51
    • 0004074550 scopus 로고
    • (Clarendon Press, Oxford University Press, Oxford, New York)
    • M. Doi and S. F. Edwards, The theory of polymer dynamics (Clarendon Press, Oxford University Press, Oxford, New York, 1986).
    • (1986) The Theory of Polymer Dynamics
    • Doi, M.1    Edwards, S.F.2
  • 52
    • 0000842103 scopus 로고
    • 10.1016/0301-0104(75)80083-8
    • M. Doi, Chem. Phys. 9, 455 (1975). 10.1016/0301-0104(75)80083-8
    • (1975) Chem. Phys. , vol.9 , pp. 455
    • Doi, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.