메뉴 건너뛰기




Volumn 110, Issue 12, 2013, Pages 4500-4505

From mechanical folding trajectories to intrinsic energy landscapes of biopolymers

Author keywords

[No Author keywords available]

Indexed keywords

BIOPOLYMER; DNA; LEUCINE ZIPPER PROTEIN; NUCLEIC ACID; PROTEIN; RNA;

EID: 84875249565     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1214051110     Document Type: Article
Times cited : (81)

References (33)
  • 1
    • 16344371778 scopus 로고    scopus 로고
    • RNA and protein folding: Common themes and variations
    • Thirumalai D, Hyeon C (2005) RNA and protein folding: Common themes and variations. Biochemistry 44(13):4957-4970.
    • (2005) Biochemistry , vol.44 , Issue.13 , pp. 4957-4970
    • Thirumalai, D.1    Hyeon, C.2
  • 5
    • 0029010695 scopus 로고
    • Kinetics of protein folding: Nucleation mechanism, time scales, and pathways
    • Guo Z, Thirumalai D (1995) Kinetics of protein folding: Nucleation mechanism, time scales, and pathways. Biopolymers 36(1):83-102.
    • (1995) Biopolymers , vol.36 , Issue.1 , pp. 83-102
    • Guo, Z.1    Thirumalai, D.2
  • 6
    • 27144510594 scopus 로고    scopus 로고
    • Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways
    • Klimov DK, Thirumalai D (2005) Symmetric connectivity of secondary structure elements enhances the diversity of folding pathways. J Mol Biol 353(5):1171-1186.
    • (2005) J Mol Biol , vol.353 , Issue.5 , pp. 1171-1186
    • Klimov, D.K.1    Thirumalai, D.2
  • 7
    • 80055087629 scopus 로고    scopus 로고
    • The complex folding network of single calmodulin molecules
    • Stigler J, Ziegler F, Gieseke A, Gebhardt JCM, Rief M (2011) The complex folding network of single calmodulin molecules. Science 334(6055):512-516.
    • (2011) Science , vol.334 , Issue.6055 , pp. 512-516
    • Stigler, J.1    Ziegler, F.2    Gieseke, A.3    Gebhardt, J.C.M.4    Rief, M.5
  • 8
    • 33750970551 scopus 로고    scopus 로고
    • Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid
    • Woodside MT, et al. (2006) Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science 314(5801):1001-1004.
    • (2006) Science , vol.314 , Issue.5801 , pp. 1001-1004
    • Woodside, M.T.1
  • 9
    • 33646587736 scopus 로고    scopus 로고
    • Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins
    • Woodside MT, et al. (2006) Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc Natl Acad Sci USA 103(16):6190-6195.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.16 , pp. 6190-6195
    • Woodside, M.T.1
  • 10
    • 80053216036 scopus 로고    scopus 로고
    • Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism
    • Neupane K, Yu H, Foster DAN, Wang F, Woodside MT (2011) Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism. Nucleic Acids Res 39(17):7677-7687.
    • (2011) Nucleic Acids Res , vol.39 , Issue.17 , pp. 7677-7687
    • Neupane, K.1    Yu, H.2    Foster, D.A.N.3    Wang, F.4    Woodside, M.T.5
  • 11
    • 76649093956 scopus 로고    scopus 로고
    • Full distance-resolved folding energy landscape of one single protein molecule
    • Gebhardt JCM, Bornschlögl T, Rief M (2010) Full distance-resolved folding energy landscape of one single protein molecule. Proc Natl Acad Sci USA 107(5):2013-2018.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.5 , pp. 2013-2018
    • Gebhardt, J.C.M.1    Bornschlögl, T.2    Rief, M.3
  • 12
    • 84857926431 scopus 로고    scopus 로고
    • The molten globule state is unusually deformable under mechanical force
    • Elms PJ, Chodera JD, Bustamante C, Marqusee S (2012) The molten globule state is unusually deformable under mechanical force. Proc Natl Acad Sci USA 109(10): 3796-3801.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.10 , pp. 3796-3801
    • Elms, P.J.1    Chodera, J.D.2    Bustamante, C.3    Marqusee, S.4
  • 13
    • 33646203784 scopus 로고    scopus 로고
    • Forced-unfolding and force-quench refolding of RNA hairpins
    • Hyeon C, Thirumalai D (2006) Forced-unfolding and force-quench refolding of RNA hairpins. Biophys J 90(10):3410-3427.
    • (2006) Biophys J , vol.90 , Issue.10 , pp. 3410-3427
    • Hyeon, C.1    Thirumalai, D.2
  • 14
    • 34247609813 scopus 로고    scopus 로고
    • Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments
    • Manosas M, et al. (2007) Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Biophys J 92(9):3010-3021.
    • (2007) Biophys J , vol.92 , Issue.9 , pp. 3010-3021
    • Manosas, M.1
  • 15
    • 84867021896 scopus 로고    scopus 로고
    • Auto- and cross-power spectral analysis of dual trap optical tweezer experiments using Bayesian inference
    • von Hansen Y, Mehlich A, Pelz B, Rief M, Netz RR (2012) Auto- and cross-power spectral analysis of dual trap optical tweezer experiments using Bayesian inference. Rev Sci Instrum 83(9):095116.
    • (2012) Rev Sci Instrum , vol.83 , Issue.9 , pp. 095116
    • Von Hansen, Y.1    Mehlich, A.2    Pelz, B.3    Rief, M.4    Netz, R.R.5
  • 16
    • 84859465192 scopus 로고    scopus 로고
    • Direct observation of multiple misfolding pathways in a single prion protein molecule
    • Yu H, et al. (2012) Direct observation of multiple misfolding pathways in a single prion protein molecule. Proc Natl Acad Sci USA 109(14):5283-5288.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.14 , pp. 5283-5288
    • Yu, H.1
  • 17
    • 78650753691 scopus 로고    scopus 로고
    • Free energy profiles from single-molecule pulling experiments
    • Hummer G, Szabo A (2010) Free energy profiles from single-molecule pulling experiments. Proc Natl Acad Sci USA 107(50):21441-21446.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.50 , pp. 21441-21446
    • Hummer, G.1    Szabo, A.2
  • 19
    • 47749150330 scopus 로고    scopus 로고
    • Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes
    • Hyeon C, Morrison G, Thirumalai D (2008) Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. Proc Natl Acad Sci USA 105(28):9604-9609.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.28 , pp. 9604-9609
    • Hyeon, C.1    Morrison, G.2    Thirumalai, D.3
  • 22
    • 33646987405 scopus 로고
    • Optimized Monte Carlo data analysis
    • Ferrenberg AM, Swendsen RH (1989) Optimized Monte Carlo data analysis. Phys Rev Lett 63(12):1195-1198.
    • (1989) Phys Rev Lett , vol.63 , Issue.12 , pp. 1195-1198
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 23
    • 52949088587 scopus 로고    scopus 로고
    • Statistically optimal analysis of samples from multiple equilibrium states
    • Shirts MR, Chodera JD (2008) Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys 129(12):124105.
    • (2008) J Chem Phys , vol.129 , Issue.12 , pp. 124105
    • Shirts, M.R.1    Chodera, J.D.2
  • 24
    • 79960305090 scopus 로고    scopus 로고
    • Measuring the folding landscape of a harmonically constrained biopolymer
    • de Messieres M, Brawn-Cinani B, La Porta A (2011) Measuring the folding landscape of a harmonically constrained biopolymer. Biophys J 100(11):2736-2744.
    • (2011) Biophys J , vol.100 , Issue.11 , pp. 2736-2744
    • De Messieres, M.1    Brawn-Cinani, B.2    La Porta, A.3
  • 26
    • 33645091911 scopus 로고    scopus 로고
    • Single molecule unzipping of coiled coils: Sequence resolved stability profiles
    • Bornschlögl T, Rief M (2006) Single molecule unzipping of coiled coils: Sequence resolved stability profiles. Phys Rev Lett 96(11):118102.
    • (2006) Phys Rev Lett , vol.96 , Issue.11 , pp. 118102
    • Bornschlögl, T.1    Rief, M.2
  • 27
    • 0026331267 scopus 로고
    • X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil
    • O'Shea EK, Klemm JD, Kim PS, Alber T (1991) X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254(5031):539-544.
    • (1991) Science , vol.254 , Issue.5031 , pp. 539-544
    • O'Shea, E.K.1    Klemm, J.D.2    Kim, P.S.3    Alber, T.4
  • 28
    • 40449108888 scopus 로고    scopus 로고
    • Single-molecule dynamics of mechanical coiled-coil unzipping
    • Bornschlögl T, Rief M (2008) Single-molecule dynamics of mechanical coiled-coil unzipping. Langmuir 24(4):1338-1342.
    • (2008) Langmuir , vol.24 , Issue.4 , pp. 1338-1342
    • Bornschlögl, T.1    Rief, M.2
  • 29
    • 33846193288 scopus 로고    scopus 로고
    • Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
    • Hyeon C, Dima RI, Thirumalai D (2006) Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins. Structure 14(11):1633-1645.
    • (2006) Structure , vol.14 , Issue.11 , pp. 1633-1645
    • Hyeon, C.1    Dima, R.I.2    Thirumalai, D.3
  • 30
    • 0033005899 scopus 로고    scopus 로고
    • Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
    • Betancourt MR, Thirumalai D (1999) Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 8(2):361-369.
    • (1999) Protein Sci , vol.8 , Issue.2 , pp. 361-369
    • Betancourt, M.R.1    Thirumalai, D.2
  • 31
    • 38049119865 scopus 로고    scopus 로고
    • Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations
    • Mickler M, et al. (2007) Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations. Proc Natl Acad Sci USA 104(51): 20268-20273.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.51 , pp. 20268-20273
    • Mickler, M.1
  • 32
    • 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
  • 33
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • Ermak DL, McCammon JA (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69(4):1352-1360.
    • (1978) J Chem Phys , vol.69 , Issue.4 , pp. 1352-1360
    • Ermak, D.L.1    McCammon, J.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.