메뉴 건너뛰기




Volumn 337, Issue 4, 2004, Pages 789-797

Does native state topology determine the RNA folding mechanism?

Author keywords

Biasing potential; Bulk kinetics; Distributed computing; LJ, Lennard Jones; Mechanism; RMSD, root mean squared deviations; RNA folding

Indexed keywords

RNA; TRANSFER RNA;

EID: 1642265837     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.02.024     Document Type: Article
Times cited : (41)

References (37)
  • 1
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • Baker D. A surprising simplicity to protein folding. Nature. 405:2000;39-42.
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 2
    • 0033521194 scopus 로고    scopus 로고
    • First principles prediction of protein folding rates
    • Debe D.A., Goddard W.A. First principles prediction of protein folding rates. J. Mol. Biol. 294:1999;619-625.
    • (1999) J. Mol. Biol. , vol.294 , pp. 619-625
    • Debe, D.A.1    Goddard, W.A.2
  • 3
    • 0034687123 scopus 로고    scopus 로고
    • Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics
    • Plaxco K.W., Simons K.T., Ruczinski I., David B. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry. 39:2000;11177-11183.
    • (2000) Biochemistry , vol.39 , pp. 11177-11183
    • Plaxco, K.W.1    Simons, K.T.2    Ruczinski, I.3    David, B.4
  • 4
    • 0037133574 scopus 로고    scopus 로고
    • How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
    • Makarov D.E., Keller C.A., Plaxco K.W., Metiu H. How the folding rate constant of simple, single-domain proteins depends on the number of native contacts. Proc. Natl Acad. Sci. USA. 99:2002;3535-3539.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 3535-3539
    • Makarov, D.E.1    Keller, C.A.2    Plaxco, K.W.3    Metiu, H.4
  • 5
    • 0037423710 scopus 로고    scopus 로고
    • Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates
    • Jewett A.I., Pande V.S., Plaxco K.W. Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. J. Mol. Biol. 326:2003;247-253.
    • (2003) J. Mol. Biol. , vol.326 , pp. 247-253
    • Jewett, A.I.1    Pande, V.S.2    Plaxco, K.W.3
  • 6
    • 0034691149 scopus 로고    scopus 로고
    • Native topology determines force-induced unfolding pathways in globular proteins
    • Klimov D.K., Thirumalai D. Native topology determines force-induced unfolding pathways in globular proteins. Proc. Natl Acad. Sci. USA. 97:2000;7254-7259.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 7254-7259
    • Klimov, D.K.1    Thirumalai, D.2
  • 7
    • 0035946940 scopus 로고    scopus 로고
    • Role of native topology investigated by multiple unfolding simulations of four SH3 domains
    • Gsponer J., Caflisch A. Role of native topology investigated by multiple unfolding simulations of four SH3 domains. J. Mol. Biol. 309:2001;285-298.
    • (2001) J. Mol. Biol. , vol.309 , pp. 285-298
    • Gsponer, J.1    Caflisch, A.2
  • 8
    • 0035793713 scopus 로고    scopus 로고
    • Native topology or specific interactions: What is more important for protein folding?
    • Ferrara P., Caflisch A. Native topology or specific interactions: what is more important for protein folding? J. Mol. Biol. 306:2001;837-850.
    • (2001) J. Mol. Biol. , vol.306 , pp. 837-850
    • Ferrara, P.1    Caflisch, A.2
  • 9
    • 0042845840 scopus 로고    scopus 로고
    • Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations
    • Sorin E.J., Rhee Y.M., Nakatani B.J., Pande V.S. Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophys. J. 85:2003;790-803.
    • (2003) Biophys. J. , vol.85 , pp. 790-803
    • Sorin, E.J.1    Rhee, Y.M.2    Nakatani, B.J.3    Pande, V.S.4
  • 11
    • 0032750509 scopus 로고    scopus 로고
    • The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
    • Martínez J.C., Serrano L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nature Struct. Biol. 6:1999;1010-1016.
    • (1999) Nature Struct. Biol. , vol.6 , pp. 1010-1016
    • Martínez, J.C.1    Serrano, L.2
  • 13
    • 0035853564 scopus 로고    scopus 로고
    • Single-molecule studies of heterogeneous dynamics in polymer melts near the glass transition
    • Deschenes L.A., Vanden Bout D.A. Single-molecule studies of heterogeneous dynamics in polymer melts near the glass transition. Science. 292:2001;255-258.
    • (2001) Science , vol.292 , pp. 255-258
    • Deschenes, L.A.1    Vanden Bout, D.A.2
  • 15
    • 0037143694 scopus 로고    scopus 로고
    • The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation
    • Shimada J., Shakhnovich E.I. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc. Natl Acad. Sci. USA. 99:2002;11175-11180.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 11175-11180
    • Shimada, J.1    Shakhnovich, E.I.2
  • 16
    • 0035850758 scopus 로고    scopus 로고
    • β-Hairpin folding simulations in atomistic detail using an implicit solvent model
    • Zagrovic B., Sorin E.J., Pande V. β-Hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313:2001;151-169.
    • (2001) J. Mol. Biol. , vol.313 , pp. 151-169
    • Zagrovic, B.1    Sorin, E.J.2    Pande, V.3
  • 17
    • 0037235952 scopus 로고    scopus 로고
    • Atomistic protein folding simulations on the submillisecond timescale using worldwide distributed computing
    • Pande V.S., Baker I., Chapman J., Elmer S., Kaliq S., Larson S., et al. Atomistic protein folding simulations on the submillisecond timescale using worldwide distributed computing. Biopolymers. 68:2003;91-109.
    • (2003) Biopolymers , vol.68 , pp. 91-109
    • Pande, V.S.1    Baker, I.2    Chapman, J.3    Elmer, S.4    Kaliq, S.5    Larson, S.6
  • 18
    • 0036297661 scopus 로고    scopus 로고
    • RNA simulations: Probing hairpin unfolding and the dynamics of a GNRA tetraloop
    • Sorin E.J., Engelhardt M.A., Herschlag D., Pande V.S. RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. J. Mol. Biol. 317:2002;493-506.
    • (2002) J. Mol. Biol. , vol.317 , pp. 493-506
    • Sorin, E.J.1    Engelhardt, M.A.2    Herschlag, D.3    Pande, V.S.4
  • 21
    • 0017295709 scopus 로고
    • Conformational changes of transfer RNA. The role of magnesium(II)
    • Stein A., Crothers D.M. Conformational changes of transfer RNA. The role of magnesium(II). Biochemistry. 15:1976;160-168.
    • (1976) Biochemistry , vol.15 , pp. 160-168
    • Stein, A.1    Crothers, D.M.2
  • 23
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effects of specific amino acid sequence represented by specific inter-unit interactions
    • Ueda Y., Taketomi H., Go N. Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effects of specific amino acid sequence represented by specific inter-unit interactions. Int. J. Pept. Protein Res. 7:1975;445-459.
    • (1975) Int. J. Pept. Protein Res. , vol.7 , pp. 445-459
    • Ueda, Y.1    Taketomi, H.2    Go, N.3
  • 24
    • 0017842051 scopus 로고
    • Studies on protein folding, unfolding, and fluctuations by computer-simulation. 2. 3-dimensional lattice model of lysozyme
    • Ueda Y., Taketomi H., Go N. Studies on protein folding, unfolding, and fluctuations by computer-simulation. 2. 3-dimensional lattice model of lysozyme. Biopolymers. 17:1978;1531-1548.
    • (1978) Biopolymers , vol.17 , pp. 1531-1548
    • Ueda, Y.1    Taketomi, H.2    Go, N.3
  • 25
    • 0037058992 scopus 로고    scopus 로고
    • Probing the folding free energy landscape of the src-SH3 protein domain
    • Shea J.E., Onuchic J.N., Brooks C.L. Probing the folding free energy landscape of the src-SH3 protein domain. Proc. Natl Acad. Sci. USA. 99:2002;16064-16068.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 16064-16068
    • Shea, J.E.1    Onuchic, J.N.2    Brooks, C.L.3
  • 26
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? an investigation for small globular proteins
    • Clementi C., Hugh Nymeyer H., Onuchic J.N. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? an investigation for small globular proteins. J. Mol. Biol. 298:2000;937-953.
    • (2000) J. Mol. Biol. , vol.298 , pp. 937-953
    • Clementi, C.1    Hugh Nymeyer, H.2    Onuchic, J.N.3
  • 27
    • 0032539684 scopus 로고    scopus 로고
    • Is the molten globule a third phase of proteins?
    • Pande V.S., Rokhsar D.S. Is the molten globule a third phase of proteins? Proc. Natl Acad. Sci. USA. 95:1998;1490-1494.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 1490-1494
    • Pande, V.S.1    Rokhsar, D.S.2
  • 28
    • 0037459022 scopus 로고    scopus 로고
    • Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein L
    • Clementi C., Garcia A.E., Onuchic J.N. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. J. Mol. Biol. 326:2003;933-954.
    • (2003) J. Mol. Biol. , vol.326 , pp. 933-954
    • Clementi, C.1    Garcia, A.E.2    Onuchic, J.N.3
  • 29
    • 0034641612 scopus 로고    scopus 로고
    • 2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering
    • 2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry. 39:2000;11107-11113.
    • (2000) Biochemistry , vol.39 , pp. 11107-11113
    • Fang, X.1    Littrell, K.2    Yang, X.-J.3    Henderson, S.J.4    Siefert, S.5    Thiyagarajan, P.6
  • 31
    • 0034934258 scopus 로고    scopus 로고
    • Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins
    • Ansari A., Kuznetsov S.V., Shen Y.Q. Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins. Proc. Natl Acad. Sci. USA. 98:2001;7771-7776.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 7771-7776
    • Ansari, A.1    Kuznetsov, S.V.2    Shen, Y.Q.3
  • 32
    • 0034338307 scopus 로고    scopus 로고
    • Heteropolymer freezing and design: Towards physical models of protein folding
    • Pande V.S., Grosberg A.Y., Tanaka T. Heteropolymer freezing and design: towards physical models of protein folding. Rev. Mod. Phys. 72:2000;259-314.
    • (2000) Rev. Mod. Phys. , vol.72 , pp. 259-314
    • Pande, V.S.1    Grosberg, A.Y.2    Tanaka, T.3
  • 33
    • 0037686252 scopus 로고    scopus 로고
    • The present view of the mechanism of protein folding
    • Daggett V., Fersht A. The present view of the mechanism of protein folding. Nature Rev. Mol. Cell Biol. 4:2003;497-502.
    • (2003) Nature Rev. Mol. Cell Biol. , vol.4 , pp. 497-502
    • Daggett, V.1    Fersht, A.2
  • 34
    • 0032568599 scopus 로고    scopus 로고
    • Folding funnels and frustration in off-lattice minimalist protein landscapes
    • Nymeyer H., Garcia A.E., Onuchic J.N. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc. Natl Acad. Sci. USA. 95:1998;5921-5928.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 5921-5928
    • Nymeyer, H.1    Garcia, A.E.2    Onuchic, J.N.3
  • 35
    • 0035818481 scopus 로고    scopus 로고
    • Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations
    • Li L., Shakhnovich E.I. Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc. Natl Acad. Sci. USA. 98:2001;13014-13018.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 13014-13018
    • Li, L.1    Shakhnovich, E.I.2
  • 36
    • 0029011701 scopus 로고
    • A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
    • Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Gould, I.R.4    Merz, K.M.5    Ferguson, D.M.6
  • 37
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E., Hess B., van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7:2001;306-317.
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.