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Volumn 10, Issue 12, 2014, Pages

Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BINDING SITES; BIOINFORMATICS; BROWNIAN MOVEMENT; COARSE-GRAINED MODELING; DIFFUSION; GENES; HYDRODYNAMICS; PROTEINS;

EID: 84919628747     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003990     Document Type: Article
Times cited : (40)

References (45)
  • 2
    • 79957549084 scopus 로고    scopus 로고
    • Dancing on DNA: kinetic aspects of search processes on DNA
    • Tafvizi A, Mirny LA, van Oijen AM, (2011) Dancing on DNA: kinetic aspects of search processes on DNA. ChempPysChem 12: 1481–1489.
    • (2011) ChempPysChem , vol.12 , pp. 1481-1489
    • Tafvizi, A.1    Mirny, L.A.2    van Oijen, A.M.3
  • 3
    • 0014945567 scopus 로고
    • Lac Repressor-Operator Interaction.3. Kinetic Studies
    • Riggs AD, Bourgeoi.S, Cohn M, (1970) Lac Repressor-Operator Interaction.3. Kinetic Studies. J Mol Biol 53: 401–417.
    • (1970) J Mol Biol , vol.53 , pp. 401-417
    • Riggs, A.D.1    Bourgeoi.S, Cohn, M.2
  • 4
    • 32944478228 scopus 로고
    • Reduction of dimensionality in biological diffusion processes
    • Adam G, Delbruck M (1968) Reduction of dimensionality in biological diffusion processes. In: Rich A, Davidson N, editors. Structural chemistry and molecular biology: W. H. Freeman and Co. San Francisco. pp. 198–215.
    • (1968) , pp. 198-215
    • Adam, G.1    Delbruck, M.2    Rich, A.3    Davidson, N.4
  • 5
    • 0019887628 scopus 로고
    • Diffusion-Driven Mechanisms of Protein Translocation on Nucleic-Acids.1. Models and Theory
    • Berg OG, Winter RB, von Hippel PH, (1981) Diffusion-Driven Mechanisms of Protein Translocation on Nucleic-Acids.1. Models and Theory. Biochemistry 20: 6929–6948.
    • (1981) Biochemistry , vol.20 , pp. 6929-6948
    • Berg, O.G.1    Winter, R.B.2    von Hippel, P.H.3
  • 6
    • 65549171477 scopus 로고    scopus 로고
    • An end to 40 years of mistakes in DNA-protein association kinetics
    • Halford SE, (2009) An end to 40 years of mistakes in DNA-protein association kinetics? Biochem Soc Trans 37: 343–348.
    • (2009) Biochem Soc Trans , vol.37 , pp. 343-348
    • Halford, S.E.1
  • 8
    • 33645807371 scopus 로고    scopus 로고
    • A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
    • Blainey PC, van Oijen AM, Banerjee A, Verdine GL, Xie XS, (2006) A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc Natl Acad Sci U S A 103: 5752–5757.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 5752-5757
    • Blainey, P.C.1    van Oijen, A.M.2    Banerjee, A.3    Verdine, G.L.4    Xie, X.S.5
  • 9
    • 35649018595 scopus 로고    scopus 로고
    • Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6
    • Gorman J, Chowdhury A, Surtees JA, Shimada J, Reichman DR, et al. (2007) Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Mol Cell 28: 359–370.
    • (2007) Mol Cell , vol.28 , pp. 359-370
    • Gorman, J.1    Chowdhury, A.2    Surtees, J.A.3    Shimada, J.4    Reichman, D.R.5
  • 11
    • 46749108829 scopus 로고    scopus 로고
    • Tumor suppressor p53 slides on DNA with low friction and high stability
    • Tafvizi A, Huang F, Leith JS, Fersht AR, Mirny LA, et al. (2008) Tumor suppressor p53 slides on DNA with low friction and high stability. Biophys J 95: L01–03.
    • (2008) Biophys J , vol.95 , pp. 1-3
    • Tafvizi, A.1    Huang, F.2    Leith, J.S.3    Fersht, A.R.4    Mirny, L.A.5
  • 12
    • 33746649820 scopus 로고    scopus 로고
    • Single molecule measurements of repressor protein 1D diffusion on DNA
    • Wang YM, Austin RH, Cox EC, (2006) Single molecule measurements of repressor protein 1D diffusion on DNA. Phys Rev Lett 97: 048302.
    • (2006) Phys Rev Lett , vol.97
    • Wang, Y.M.1    Austin, R.H.2    Cox, E.C.3
  • 13
    • 34249932435 scopus 로고    scopus 로고
    • Probing transcription factor dynamics at the single-molecule level in a living cell
    • Elf J, Li GW, Xie XS, (2007) Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316: 1191–1194.
    • (2007) Science , vol.316 , pp. 1191-1194
    • Elf, J.1    Li, G.W.2    Xie, X.S.3
  • 14
    • 84862624197 scopus 로고    scopus 로고
    • The lac repressor displays facilitated diffusion in living cells
    • Hammar P, Leroy P, Mahmutovic A, Marklund EG, Berg OG, et al. (2012) The lac repressor displays facilitated diffusion in living cells. Science 336: 1595–1598.
    • (2012) Science , vol.336 , pp. 1595-1598
    • Hammar, P.1    Leroy, P.2    Mahmutovic, A.3    Marklund, E.G.4    Berg, O.G.5
  • 15
    • 10044223573 scopus 로고    scopus 로고
    • Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential
    • Slutsky M, Mirny LA, (2004) Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential. Biophys J 87: 4021–4035.
    • (2004) Biophys J , vol.87 , pp. 4021-4035
    • Slutsky, M.1    Mirny, L.A.2
  • 16
    • 0018472170 scopus 로고
    • The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations
    • Schurr JM, (1979) The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations. Biophys Chem 9: 413–414.
    • (1979) Biophys Chem , vol.9 , pp. 413-414
    • Schurr, J.M.1
  • 17
    • 44949217503 scopus 로고    scopus 로고
    • Diffusion constant of a nonspecifically bound protein undergoing curvilinear motion along DNA
    • Bagchi B, Blainey PC, Xie XS, (2008) Diffusion constant of a nonspecifically bound protein undergoing curvilinear motion along DNA. J Phys Chem B 112: 6282–6284.
    • (2008) J Phys Chem B , vol.112 , pp. 6282-6284
    • Bagchi, B.1    Blainey, P.C.2    Xie, X.S.3
  • 18
    • 58149345492 scopus 로고    scopus 로고
    • Protein Sliding along DNA: Dynamics and Structural Characterization
    • Givaty O, Levy Y, (2009) Protein Sliding along DNA: Dynamics and Structural Characterization. J Mol Biol 385: 1087–1097.
    • (2009) J Mol Biol , vol.385 , pp. 1087-1097
    • Givaty, O.1    Levy, Y.2
  • 19
    • 81055141525 scopus 로고    scopus 로고
    • Frustration in protein-DNA binding influences conformational switching and target search kinetics
    • Marcovitz A, Levy Y, (2011) Frustration in protein-DNA binding influences conformational switching and target search kinetics. Proc Natl Acad Sci U S A 108: 17957–17962.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 17957-17962
    • Marcovitz, A.1    Levy, Y.2
  • 20
    • 84865714640 scopus 로고    scopus 로고
    • p53 searches on DNA by rotation-uncoupled sliding at C-terminal tails and restricted hopping of core domains
    • Terakawa T, Kenzaki H, Takada S, (2012) p53 searches on DNA by rotation-uncoupled sliding at C-terminal tails and restricted hopping of core domains. J Am Chem Soc 134: 14555–14562.
    • (2012) J Am Chem Soc , vol.134 , pp. 14555-14562
    • Terakawa, T.1    Kenzaki, H.2    Takada, S.3
  • 21
    • 3242730909 scopus 로고
    • The theory of polymer dynamics
    • Doi M, Edwards SF (1988) The theory of polymer dynamics. Oxford: Oxford University Press.
    • (1988)
    • Doi, M.1    Edwards, S.F.2
  • 22
    • 36549098189 scopus 로고
    • A 2nd-Order Algorithm for the Simulation of the Brownian Dynamics of Macromolecular Models
    • Iniesta A, Delatorre JG, (1990) A 2nd-Order Algorithm for the Simulation of the Brownian Dynamics of Macromolecular Models. J Chem Phys 92: 2015–2018.
    • (1990) J Chem Phys , vol.92 , pp. 2015-2018
    • Iniesta, A.1    Delatorre, J.G.2
  • 23
    • 84933517499 scopus 로고
    • Variational treatment of hydrodynamic interaction in polymers
    • Rotne J, Prager S, (1969) Variational treatment of hydrodynamic interaction in polymers. J Chem Phys 50: 4831–4837.
    • (1969) J Chem Phys , vol.50 , pp. 4831-4837
    • Rotne, J.1    Prager, S.2
  • 24
    • 36849101815 scopus 로고
    • Transport properties of polymer chains in dilute solution - hydrodynamic interaction
    • Yamakawa H, (1970) Transport properties of polymer chains in dilute solution - hydrodynamic interaction. J Chem Phys 53: 436–443.
    • (1970) J Chem Phys , vol.53 , pp. 436-443
    • Yamakawa, H.1
  • 25
    • 0032827044 scopus 로고    scopus 로고
    • Calculation of hydrodynamic properties of macromolecular bead models with overlapping spheres
    • Carrasco B, Garcia de la Torre J, Zipper P, (1999) Calculation of hydrodynamic properties of macromolecular bead models with overlapping spheres. Eur Biophys J 28: 510–515.
    • (1999) Eur Biophys J , vol.28 , pp. 510-515
    • Carrasco, B.1    Garcia de la Torre, J.2    Zipper, P.3
  • 26
    • 84868515547 scopus 로고    scopus 로고
    • Molecular biology of the cell, 4th edition
    • Lamond AI, (2002) Molecular biology of the cell, 4th edition. Nature 417: 383–383.
    • (2002) Nature , vol.417 , pp. 383
    • Lamond, A.I.1
  • 28
    • 84919630353 scopus 로고    scopus 로고
    • Schlick T (2002) Molecular modeling and simulation: an interdisciplinary guide. New York: Springer.
    • (2002)
    • Schlick, T.1
  • 29
    • 68349122535 scopus 로고    scopus 로고
    • Nanoscale Forces and Their Uses in Self-Assembly
    • Bishop KJM, Wilmer CE, Soh S, Grzybowski BA, (2009) Nanoscale Forces and Their Uses in Self-Assembly. Small 5: 1600–1630.
    • (2009) Small , vol.5 , pp. 1600-1630
    • Bishop, K.J.M.1    Wilmer, C.E.2    Soh, S.3    Grzybowski, B.A.4
  • 30
    • 36749113356 scopus 로고
    • Monte-Carlo Study of a Phase-Separating Liquid-Mixture by Umbrella Sampling
    • Torrie GM, Valleau JP, (1977) Monte-Carlo Study of a Phase-Separating Liquid-Mixture by Umbrella Sampling. J Chem Phys 66: 1402–1408.
    • (1977) J Chem Phys , vol.66 , pp. 1402-1408
    • Torrie, G.M.1    Valleau, J.P.2
  • 31
    • 84986497803 scopus 로고
    • Multidimensional Free-Energy Calculations Using the Weighted Histogram Analysis Method
    • Kumar S, Rosenberg JM, Bouzida D, Swendsen RH, Kollman PA, (1995) Multidimensional Free-Energy Calculations Using the Weighted Histogram Analysis Method. J Comput Chem 16: 1339–1350.
    • (1995) J Comput Chem , vol.16 , pp. 1339-1350
    • Kumar, S.1    Rosenberg, J.M.2    Bouzida, D.3    Swendsen, R.H.4    Kollman, P.A.5
  • 32
    • 0033039369 scopus 로고    scopus 로고
    • Hydrodynamic properties of rigid particles: comparison of different modeling and computational procedures
    • Carrasco B, Garcia de la Torre J, (1999) Hydrodynamic properties of rigid particles: comparison of different modeling and computational procedures. Biophys J 76: 3044–3057.
    • (1999) Biophys J , vol.76 , pp. 3044-3057
    • Carrasco, B.1    Garcia de la Torre, J.2
  • 33
    • 0001229341 scopus 로고    scopus 로고
    • Calculation of hydrodynamic properties of globular proteins from their atomic-level structure
    • Garcia De La Torre J, Huertas ML, Carrasco B, (2000) Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys J 78: 719–730.
    • (2000) Biophys J , vol.78 , pp. 719-730
    • Garcia De La Torre, J.1    Huertas, M.L.2    Carrasco, B.3
  • 34
    • 0000535950 scopus 로고
    • Monte-Carlo Calculation of Hydrodynamic Properties of Freely Jointed, Freely Rotating, and Real Polymethylene Chains
    • Garcia De La Torre J, Jimenez A, Freire JJ, (1982) Monte-Carlo Calculation of Hydrodynamic Properties of Freely Jointed, Freely Rotating, and Real Polymethylene Chains. Macromolecules 15: 148–154.
    • (1982) Macromolecules , vol.15 , pp. 148-154
    • Garcia De La Torre, J.1    Jimenez, A.2    Freire, J.J.3
  • 35
    • 65249094240 scopus 로고    scopus 로고
    • Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins
    • Frembgen-Kesner T, Elcock AH, (2009) Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins. J Chem Theory Comput 5: 242–256.
    • (2009) J Chem Theory Comput , vol.5 , pp. 242-256
    • Frembgen-Kesner, T.1    Elcock, A.H.2
  • 36
    • 78349288528 scopus 로고    scopus 로고
    • Absolute Protein-Protein Association Rate Constants from Flexible, Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association
    • Frembgen-Kesner T, Elcock AH, (2010) Absolute Protein-Protein Association Rate Constants from Flexible, Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association. Biophys J 99: L75–L77.
    • (2010) Biophys J , vol.99 , pp. L75-L77
    • Frembgen-Kesner, T.1    Elcock, A.H.2
  • 37
    • 84919630352 scopus 로고    scopus 로고
    • Revzin A (1990) The Biology of Nonspecific DNA Protein Interactions: Taylor & Francis.
  • 39
    • 0024121530 scopus 로고
    • Diffusion in a Rough Potential
    • Zwanzig R, (1988) Diffusion in a Rough Potential. Proc Natl Acad Sci U S A 85: 2029–2030.
    • (1988) Proc Natl Acad Sci U S A , vol.85 , pp. 2029-2030
    • Zwanzig, R.1
  • 40
    • 84866597924 scopus 로고    scopus 로고
    • Are Hydrodynamic Interactions Important in the Kinetics of Hydrophobic Collapse
    • Li JY, Morrone JA, Berne BJ, (2012) Are Hydrodynamic Interactions Important in the Kinetics of Hydrophobic Collapse? Journal of Physical Chemistry B 116: 11537–11544.
    • (2012) Journal of Physical Chemistry B , vol.116 , pp. 11537-11544
    • Li, J.Y.1    Morrone, J.A.2    Berne, B.J.3
  • 41
    • 84882423343 scopus 로고    scopus 로고
    • How hydrophobic drying forces impact the kinetics of molecular recognition
    • Mondal J, Morrone JA, Berne BJ, (2013) How hydrophobic drying forces impact the kinetics of molecular recognition. Proc Natl Acad Sci U S A 110: 13277–13282.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 13277-13282
    • Mondal, J.1    Morrone, J.A.2    Berne, B.J.3
  • 42
    • 84862945185 scopus 로고    scopus 로고
    • Interplay between hydrodynamics and the free energy surface in the assembly of nanoscale hydrophobes
    • Morrone JA, Li J, Berne BJ, (2012) Interplay between hydrodynamics and the free energy surface in the assembly of nanoscale hydrophobes. J Phys Chem B 116: 378–389.
    • (2012) J Phys Chem B , vol.116 , pp. 378-389
    • Morrone, J.A.1    Li, J.2    Berne, B.J.3
  • 43
    • 0027367276 scopus 로고
    • Brownian Dynamics Simulations of Probe and Self-Diffusion in Concentrated Protein and DNA Solutions
    • Dwyer JD, Bloomfield VA, (1993) Brownian Dynamics Simulations of Probe and Self-Diffusion in Concentrated Protein and DNA Solutions. Biophys J 65: 1810–1816.
    • (1993) Biophys J , vol.65 , pp. 1810-1816
    • Dwyer, J.D.1    Bloomfield, V.A.2
  • 44
    • 84865177208 scopus 로고    scopus 로고
    • Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations
    • Ando T, Chow E, Saad Y, Skolnick J, (2012) Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations. J Chem Phys 137.
    • (2012) J Chem Phys , vol.137
    • Ando, T.1    Chow, E.2    Saad, Y.3    Skolnick, J.4
  • 45
    • 84919687619 scopus 로고    scopus 로고
    • Phenix
    • X. L, Chow E. Large-scale Hydrodynamic Brownian Simulations on Multicore and Manycore Architectures; 2014; Phenix, AZ.
    • (2014)


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