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Volumn 111, Issue 23, 2014, Pages 8464-8469

Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics

Author keywords

Fluorescence; PEG; Scaled particle theory

Indexed keywords

MACROGOL 8000;

EID: 84902181715     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1316039111     Document Type: Article
Times cited : (131)

References (32)
  • 2
    • 84255189090 scopus 로고    scopus 로고
    • The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks
    • Butcher SE, Pyle AM (2011) The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Acc Chem Res 44(12):1302-1311.
    • (2011) Acc Chem Res , vol.44 , Issue.12 , pp. 1302-1311
    • Butcher, S.E.1    Pyle, A.M.2
  • 4
    • 27744523656 scopus 로고    scopus 로고
    • The cytoplasm of living cells: A functional mixture of thousands of components
    • Sear RP (2005) The cytoplasm of living cells: A functional mixture of thousands of components. J Phys Condens Matter 17(45):S3587-S3595.
    • (2005) J Phys Condens Matter , vol.17 , Issue.45
    • Sear, R.P.1
  • 5
    • 56049095755 scopus 로고    scopus 로고
    • Monovalent and divalent promoted GAAA tetraloop-receptor tertiary interactions from freely diffusing single-molecule studies
    • Fiore JL, Hodak JH, Piestert O, Downey CD, Nesbitt DJ (2008) Monovalent and divalent promoted GAAA tetraloop-receptor tertiary interactions from freely diffusing single-molecule studies. Biophys J 95(8):3892-3905.
    • (2008) Biophys J , vol.95 , Issue.8 , pp. 3892-3905
    • Fiore, J.L.1    Hodak, J.H.2    Piestert, O.3    Downey, C.D.4    Nesbitt, D.J.5
  • 6
    • 33645226091 scopus 로고    scopus 로고
    • Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker
    • Downey CD, et al. (2006) Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker. Biochemistry 45(11):3664-3673.
    • (2006) Biochemistry , vol.45 , Issue.11 , pp. 3664-3673
    • Downey, C.D.1
  • 7
    • 16244363320 scopus 로고    scopus 로고
    • Metal ions and RNA folding: A highly charged topic with a dynamic future
    • Woodson SA (2005) Metal ions and RNA folding: A highly charged topic with a dynamic future. Curr Opin Chem Biol 9(2):104-109.
    • (2005) Curr Opin Chem Biol , vol.9 , Issue.2 , pp. 104-109
    • Woodson, S.A.1
  • 8
    • 41049090929 scopus 로고    scopus 로고
    • Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
    • Zhou HX, Rivas GN, Minton AP (2008) Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 37:375-397.
    • (2008) Annu Rev Biophys , vol.37 , pp. 375-397
    • Zhou, H.X.1    Rivas, G.N.2    Minton, A.P.3
  • 9
    • 34548722169 scopus 로고    scopus 로고
    • Macromolecular crowding induces a molten globule state in the C-terminal domain of histone H1
    • DOI 10.1529/biophysj.107.104513
    • Roque A, Ponte I, Suau P (2007) Macromolecular crowding induces a molten globule state in the C-terminal domain of histone H1. Biophys J 93(6):2170-2177. (Pubitemid 47437600)
    • (2007) Biophysical Journal , vol.93 , Issue.6 , pp. 2170-2177
    • Roque, A.1    Ponte, I.2    Suau, P.3
  • 10
    • 37649016316 scopus 로고    scopus 로고
    • Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin
    • Stagg L, Zhang SQ, Cheung MS, Wittung-Stafshede P (2007) Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin. Proc Natl Acad Sci USA 104(48):18976-18981.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.48 , pp. 18976-18981
    • Stagg, L.1    Zhang, S.Q.2    Cheung, M.S.3    Wittung-Stafshede, P.4
  • 11
    • 4544278751 scopus 로고    scopus 로고
    • Protein folding and binding in confined spaces and in crowded solutions
    • Zhou HX (2004) Protein folding and binding in confined spaces and in crowded solutions. J Mol Recognit 17(5):368-375.
    • (2004) J Mol Recognit , vol.17 , Issue.5 , pp. 368-375
    • Zhou, H.X.1
  • 12
    • 79961136147 scopus 로고    scopus 로고
    • Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA
    • Denesyuk NA, Thirumalai D (2011) Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA. J Am Chem Soc 133(31):11858-11861.
    • (2011) J Am Chem Soc , vol.133 , Issue.31 , pp. 11858-11861
    • Denesyuk, N.A.1    Thirumalai, D.2
  • 13
    • 77953900637 scopus 로고    scopus 로고
    • Molecular crowding stabilizes folded RNA structure by the excluded volume effect
    • Kilburn D, Roh JH, Guo L, Briber RM, Woodson SA (2010) Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J Am Chem Soc 132(25):8690-8696.
    • (2010) J Am Chem Soc , vol.132 , Issue.25 , pp. 8690-8696
    • Kilburn, D.1    Roh, J.H.2    Guo, L.3    Briber, R.M.4    Woodson, S.A.5
  • 14
    • 79961215482 scopus 로고    scopus 로고
    • Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability
    • Knowles DB, LaCroix AS, Deines NF, Shkel I, Record MT, Jr. (2011) Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability. Proc Natl Acad Sci USA 108(31):12699-12704.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.31 , pp. 12699-12704
    • Knowles, D.B.1    LaCroix, A.S.2    Deines, N.F.3    Shkel, I.4    Record Jr., M.T.5
  • 15
    • 70450159038 scopus 로고    scopus 로고
    • Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes
    • Nakano S, Karimata HT, Kitagawa Y, Sugimoto N (2009) Facilitation of RNA enzyme activity in the molecular crowding media of cosolutes. J Am Chem Soc 131(46):16881-16888.
    • (2009) J Am Chem Soc , vol.131 , Issue.46 , pp. 16881-16888
    • Nakano, S.1    Karimata, H.T.2    Kitagawa, Y.3    Sugimoto, N.4
  • 16
    • 34250167241 scopus 로고    scopus 로고
    • 2+ Interactions
    • DOI 10.1016/j.jmb.2007.03.080, PII S0022283607004731
    • Lambert D, Draper DE (2007) Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions. J Mol Biol 370(5):993-1005. (Pubitemid 46899059)
    • (2007) Journal of Molecular Biology , vol.370 , Issue.5 , pp. 993-1005
    • Lambert, D.1    Draper, D.E.2
  • 17
    • 7744221005 scopus 로고    scopus 로고
    • The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability
    • DOI 10.1021/ja0463029
    • Nakano S, Karimata H, Ohmichi T, Kawakami J, Sugimoto N (2004) The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability. J Am Chem Soc 126(44):14330-14331. (Pubitemid 39463597)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.44 , pp. 14330-14331
    • Nakano, S.-I.1    Karimata, H.2    Ohmichi, T.3    Kawakami, J.4    Sugimoto, N.5
  • 18
    • 0003628866 scopus 로고
    • Statistical mechanics of rigid spheres
    • Reiss H, Frisch HL, Lebowitz JL (1959) Statistical mechanics of rigid spheres. J Chem Phys 31(2):369-380.
    • (1959) J Chem Phys , vol.31 , Issue.2 , pp. 369-380
    • Reiss, H.1    Frisch, H.L.2    Lebowitz, J.L.3
  • 19
    • 36849126695 scopus 로고
    • Scaled particle theory of fluid mixtures
    • Lebowitz JL, Helfand E, Praestga E (1965) Scaled particle theory of fluid mixtures. J Chem Phys 43(3):774.
    • (1965) J Chem Phys , vol.43 , Issue.3 , pp. 774
    • Lebowitz, J.L.1    Helfand, E.2    Praestga, E.3
  • 20
    • 33646475011 scopus 로고    scopus 로고
    • Macromolecular crowding
    • Minton AP (2006) Macromolecular crowding. Curr Biol 16(8):R269-R271.
    • (2006) Curr Biol , vol.16 , Issue.8
    • Minton, A.P.1
  • 21
    • 84866515544 scopus 로고    scopus 로고
    • The role of counterion valence and size in GAAA tetraloop-receptor docking/undocking kinetics
    • Fiore JL, Holmstrom ED, Fiegland LR, Hodak JH, Nesbitt DJ (2012) The role of counterion valence and size in GAAA tetraloop-receptor docking/undocking kinetics. J Mol Biol 423(2):198-216.
    • (2012) J Mol Biol , vol.423 , Issue.2 , pp. 198-216
    • Fiore, J.L.1    Holmstrom, E.D.2    Fiegland, L.R.3    Hodak, J.H.4    Nesbitt, D.J.5
  • 23
    • 84860768295 scopus 로고    scopus 로고
    • Thermodynamic origins of monovalent facilitated RNA folding
    • Holmstrom ED, Fiore JL, Nesbitt DJ (2012) Thermodynamic origins of monovalent facilitated RNA folding. Biochemistry 51(18):3732-3743.
    • (2012) Biochemistry , vol.51 , Issue.18 , pp. 3732-3743
    • Holmstrom, E.D.1    Fiore, J.L.2    Nesbitt, D.J.3
  • 25
    • 34547507851 scopus 로고    scopus 로고
    • Effects of crowding and confinement on the structures of the transition state ensemble in proteins
    • DOI 10.1021/jp068201y
    • Cheung MS, Thirumalai D (2007) Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J Phys Chem B 111(28):8250-8257. (Pubitemid 47184401)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.28 , pp. 8250-8257
    • Cheung, M.S.1    Thirumalai, D.2
  • 26
    • 0000254227 scopus 로고
    • A neutron-scattering study of poly(ethylene glycol) in electrolyte-solutions
    • Thiyagarajan P, Chaiko DJ, Hjelm RP (1995) A neutron-scattering study of poly(ethylene glycol) in electrolyte-solutions. Macromolecules 28(23):7730-7736.
    • (1995) Macromolecules , vol.28 , Issue.23 , pp. 7730-7736
    • Thiyagarajan, P.1    Chaiko, D.J.2    Hjelm, R.P.3
  • 28
    • 64849085465 scopus 로고    scopus 로고
    • Enthalpy-driven RNA folding: Single-molecule thermodynamics of tetraloop-receptor tertiary interaction
    • Fiore JL, Kraemer B, Koberling F, Edmann R, Nesbitt DJ (2009) Enthalpy-driven RNA folding: Single-molecule thermodynamics of tetraloop-receptor tertiary interaction. Biochemistry 48(11):2550-2558.
    • (2009) Biochemistry , vol.48 , Issue.11 , pp. 2550-2558
    • Fiore, J.L.1    Kraemer, B.2    Koberling, F.3    Edmann, R.4    Nesbitt, D.J.5
  • 29
    • 77957916566 scopus 로고    scopus 로고
    • Solvent viscosity and friction in protein folding dynamics
    • Hagen SJ (2010) Solvent viscosity and friction in protein folding dynamics. Curr Protein Pept Sci 11(5):385-395.
    • (2010) Curr Protein Pept Sci , vol.11 , Issue.5 , pp. 385-395
    • Hagen, S.J.1
  • 30
    • 0035949430 scopus 로고    scopus 로고
    • Stabilization of proteins in confined spaces
    • Zhou HX, Dill KA (2001) Stabilization of proteins in confined spaces. Biochemistry 40(38):11289-11293.
    • (2001) Biochemistry , vol.40 , Issue.38 , pp. 11289-11293
    • Zhou, H.X.1    Dill, K.A.2
  • 31
    • 0020184671 scopus 로고
    • How crowded is the cytoplasm?
    • Fulton AB (1982) How crowded is the cytoplasm? Cell 30(2):345-347.
    • (1982) Cell , vol.30 , Issue.2 , pp. 345-347
    • Fulton, A.B.1
  • 32
    • 0043009734 scopus 로고    scopus 로고
    • Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity
    • and erratum (2003) 10(10):872
    • Khvorova A, Lescoute A, Westhof E, Jayasena SD (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol 10(9):708-712, and erratum (2003) 10(10):872.
    • (2003) Nat Struct Biol , vol.10 , Issue.9 , pp. 708-712
    • Khvorova, A.1    Lescoute, A.2    Westhof, E.3    Jayasena, S.D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.