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Volumn 99, Issue 10, 2010, Pages 3374-3384

Folding network of villin headpiece subdomain

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EID: 78649309080     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.08.081     Document Type: Article
Times cited : (16)

References (51)
  • 1
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • Bryngelson, J. D., J. N. Onuchic, ., P. G. Wolynes. 1995. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 21:167-195.
    • (1995) Proteins. , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 2
    • 17044382925 scopus 로고    scopus 로고
    • Free-energy landscape of the villin headpiece in an all-atom force field
    • Herges, T., and W. Wenzel. 2005. Free-energy landscape of the villin headpiece in an all-atom force field. Structure. 13:661-668.
    • (2005) Structure. , vol.13 , pp. 661-668
    • Herges, T.1    Wenzel, W.2
  • 3
    • 60349085890 scopus 로고    scopus 로고
    • A one-dimensional free energy surface does not account for two-probe folding kinetics of protein a D-3
    • Liu, F., C. Dumont, ., M. Gruebele. 2009. A one-dimensional free energy surface does not account for two-probe folding kinetics of protein a D-3. J. Chem. Phys. 130:061101.
    • (2009) J. Chem. Phys. , vol.130 , pp. 061101
    • Liu, F.1    Dumont, C.2    Gruebele, M.3
  • 4
    • 0036428782 scopus 로고    scopus 로고
    • Simulation of folding of a small α-helical protein in atomistic detail using worldwide-distributed computing
    • Zagrovic, B., C. D. Snow,., V. S. Pande. 2002. Simulation of folding of a small α-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323:927-937.
    • (2002) J. Mol. Biol. , vol.323 , pp. 927-937
    • Zagrovic, B.1    Snow., C.D.2    Pande, V.S.3
  • 5
    • 67749127393 scopus 로고    scopus 로고
    • Molecular dynamics (MD) simulations of VIP and PACAP27
    • Corcho, F. J., P. Mokoena, ., J. J. Perez. 2009. Molecular dynamics (MD) simulations of VIP and PACAP27. Biopolymers. 91:391-400.
    • (2009) Biopolymers. , vol.91 , pp. 391-400
    • Corcho, F.J.1    Mokoena, P.2    Perez, J.J.3
  • 6
    • 34249298006 scopus 로고    scopus 로고
    • Two-stage folding of HP-35 from ab initio simulations
    • Lei, H., and Y. Duan. 2007. Two-stage folding of HP-35 from ab initio simulations. J. Mol. Biol. 370:196-206.
    • (2007) J. Mol. Biol. , vol.370 , pp. 196-206
    • Lei, H.1    Duan, Y.2
  • 7
    • 34249807361 scopus 로고    scopus 로고
    • Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation
    • Lei, H., and Y. Duan. 2007. Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. J. Phys. Chem. B. 111:5458-5463.
    • (2007) J. Phys. Chem. B. , vol.111 , pp. 5458-5463
    • Lei, H.1    Duan, Y.2
  • 8
    • 34247639441 scopus 로고    scopus 로고
    • Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations
    • Lei, H., C. Wu, ., Y. Duan. 2007. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 104:4925-4930.
    • (2007) Proc. Natl. Acad. Sci. USA. , vol.104 , pp. 4925-4930
    • Lei, H.1    Wu, C.2    Duan, Y.3
  • 9
    • 72049130584 scopus 로고    scopus 로고
    • Dual folding pathways of an α/β protein from all-atom ab initio folding simulations
    • Lei, H. X., Z. X.Wang,., Y. Duan. 2009. Dual folding pathways of an α/β protein from all-atom ab initio folding simulations. J. Chem. Phys. 131:165105.
    • (2009) J. Chem. Phys. , vol.131 , pp. 165105
    • Lei, H.X.1    Wang, Z.X.2    Duan, Y.3
  • 10
    • 47249119770 scopus 로고    scopus 로고
    • Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations
    • Lei, H. X., C. Wu, ., Y. Duan. 2008. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations. J. Chem. Phys. 128:235105.
    • (2008) J. Chem. Phys. , vol.128 , pp. 235105
    • Lei, H.X.1    Wu, C.2    Duan, Y.3
  • 11
    • 77049109643 scopus 로고    scopus 로고
    • Folding simulations of a de novo designed protein with a bab fold
    • Qi, Y. F., Y. Q. Huang, ., L. Lai. 2010. Folding simulations of a de novo designed protein with a bab fold. Biophys. J. 98:321-329.
    • (2010) Biophys. J. , vol.98 , pp. 321-329
    • Qi, Y.F.1    Huang, Y.Q.2    Lai., L.3
  • 12
    • 0037115811 scopus 로고    scopus 로고
    • Free energy disconnectivity graphs: Application to peptide models
    • Krivov, S. V., and M. Karplus. 2002. Free energy disconnectivity graphs: application to peptide models. J. Chem. Phys. 117:10894-10903.
    • (2002) J. Chem. Phys. , vol.117 , pp. 10894-10903
    • Krivov, S.V.1    Karplus, M.2
  • 13
    • 6944235051 scopus 로고    scopus 로고
    • Hidden complexity of free energy surfaces for peptide (protein) folding
    • Krivov, S. V., and M. Karplus. 2004. Hidden complexity of free energy surfaces for peptide (protein) folding. Proc. Natl. Acad. Sci. USA. 101:14766-14770.
    • (2004) Proc. Natl. Acad. Sci. USA. , vol.101 , pp. 14766-14770
    • Krivov, S.V.1    Karplus, M.2
  • 14
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • Palla, G., I. Derényi, ., T. Vicsek. 2005. Uncovering the overlapping community structure of complex networks in nature and society. Nature. 435:814-818.
    • (2005) Nature. , vol.435 , pp. 814-818
    • Palla, G.1    Derényi, I.2    Vicsek, T.3
  • 15
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan, Y., and P. A. Kollman. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:740-744.
    • (1998) Science. , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 16
    • 4143090730 scopus 로고    scopus 로고
    • The protein folding network
    • Rao, F., and A. Caflisch. 2004. The protein folding network. J. Mol. Biol. 342:299-306.
    • (2004) J. Mol. Biol. , vol.342 , pp. 299-306
    • Rao, F.1    Caflisch, A.2
  • 17
    • 32344450229 scopus 로고    scopus 로고
    • Network and graph analyses of folding free energy surfaces
    • Caflisch, A. 2006. Network and graph analyses of folding free energy surfaces. Curr. Opin. Struct. Biol. 16:71-78.
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 71-78
    • Caflisch, A.1
  • 18
    • 39749156392 scopus 로고    scopus 로고
    • Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a β-sheet miniprotein
    • Muff, S., and A. Caflisch. 2008. Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a β-sheet miniprotein. Proteins. 70:1185-1195.
    • (2008) Proteins. , vol.70 , pp. 1185-1195
    • Muff, S.1    Caflisch, A.2
  • 19
    • 37649029819 scopus 로고    scopus 로고
    • Simulations of a small protein in a specifically designed generalized ensemble
    • Hansmann, U. H. 2004. Simulations of a small protein in a specifically designed generalized ensemble. Phys. Rev. E. 70:012902.
    • (2004) Phys. Rev. E. , vol.70 , pp. 012902
    • Hansmann, U.H.1
  • 20
    • 0000032263 scopus 로고    scopus 로고
    • Generalized-ensemble Monte Carlo method for systems with rough energy landscape
    • Hansmann, U. H. E., and Y. Okamoto. 1997. Generalized-ensemble Monte Carlo method for systems with rough energy landscape. Phys. Rev. E. 56:2228-2233.
    • (1997) Phys. Rev. E. , vol.56 , pp. 2228-2233
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 21
    • 0038054301 scopus 로고    scopus 로고
    • Experimental tests of villin subdomain folding simulations
    • Kubelka, J.,W. A. Eaton, and J. Hofrichter. 2003. Experimental tests of villin subdomain folding simulations. J. Mol. Biol. 329:625-630.
    • (2003) J. Mol. Biol. , vol.329 , pp. 625-630
    • Kubelka, J.1    Eaton, W.A.2    Hofrichter, J.3
  • 22
    • 19644381706 scopus 로고    scopus 로고
    • High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein
    • Chiu, T. K., J. Kubelka, ., D. R. Davies. 2005. High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein. Proc. Natl. Acad. Sci. USA. 102:7517-7522.
    • (2005) Proc. Natl. Acad. Sci. USA. , vol.102 , pp. 7517-7522
    • Chiu, T.K.1    Kubelka, J.2    Davies, D.R.3
  • 23
    • 85031276237 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 24
    • 0032544002 scopus 로고    scopus 로고
    • The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fullysolvated molecular dynamics simulation
    • Duan, Y., L.Wang, and P. A. Kollman. 1998. The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fullysolvated molecular dynamics simulation. Proc. Natl. Acad. Sci. USA. 95:9897-9902.
    • (1998) Proc. Natl. Acad. Sci. USA. , vol.95 , pp. 9897-9902
    • Duan, Y.1    Wang, L.2    Kollman, P.A.3
  • 25
    • 11344285181 scopus 로고    scopus 로고
    • Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics
    • De Mori, G. M., G. Colombo, and C. Micheletti. 2005. Study of the villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Proteins. 58: 459-471.
    • (2005) Proteins. , vol.58 , pp. 459-471
    • De Mori, G.M.1    Colombo, G.2    Micheletti, C.3
  • 26
    • 0036892356 scopus 로고    scopus 로고
    • All-atom fast protein folding simulations: The villin headpiece
    • Shen, M. Y., and K. F. Freed. 2002. All-atom fast protein folding simulations: the villin headpiece. Proteins. 49:439-445.
    • (2002) Proteins. , vol.49 , pp. 439-445
    • Shen, M.Y.1    Freed, K.F.2
  • 27
    • 0036394906 scopus 로고    scopus 로고
    • Native-like mean structure in the unfolded ensemble of small proteins
    • Zagrovic, B., C. D. Snow, ., V. S. Pande. 2002. Native-like mean structure in the unfolded ensemble of small proteins. J. Mol. Biol. 323:153-164.
    • (2002) J. Mol. Biol. , vol.323 , pp. 153-164
    • Zagrovic, B.1    Snow, C.D.2    Pande, V.S.3
  • 28
    • 0037235952 scopus 로고    scopus 로고
    • Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
    • Pande, V. S., I. Baker,., B. Zagrovic. 2003. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers. 68:91-109.
    • (2003) Biopolymers. , vol.68 , pp. 91-109
    • Pande, V.S.1    Baker, I.2    Zagrovic, B.3
  • 29
    • 33748248896 scopus 로고    scopus 로고
    • Using massively parallel simulation and Markovian models to study protein folding: Examining the dynamics of the villin headpiece
    • Jayachandran, G., V. Vishal, and V. S. Pande. 2006. Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. J. Chem. Phys. 124:164902.
    • (2006) J. Chem. Phys. , vol.124 , pp. 164902
    • Jayachandran, G.1    Vishal, V.2    Pande, V.S.3
  • 30
    • 0345724787 scopus 로고    scopus 로고
    • Ab initio folding of helix bundle proteins using molecular dynamics simulations
    • Jang, S., E. Kim, ., Y. Pak. 2003. Ab initio folding of helix bundle proteins using molecular dynamics simulations. J. Am. Chem. Soc. 125:14841-14846.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 14841-14846
    • Jang, S.1    Kim, E.2    Pak, Y.3
  • 31
    • 2542462060 scopus 로고    scopus 로고
    • Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH
    • Ripoll, D. R., J. A. Vila, and H. A. Scheraga. 2004. Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH. J. Mol. Biol. 339:915-925.
    • (2004) J. Mol. Biol. , vol.339 , pp. 915-925
    • Ripoll, D.R.1    Vila, J.A.2    Scheraga, H.A.3
  • 32
    • 21644454399 scopus 로고    scopus 로고
    • Finding pathways between distant local minima
    • Carr, J. M., S. A. Trygubenko, and D. J.Wales. 2005. Finding pathways between distant local minima. J. Chem. Phys. 122:234903.
    • (2005) J. Chem. Phys. , vol.122 , pp. 234903
    • Carr, J.M.1    Trygubenko, S.A.2    Wales, D.J.3
  • 33
    • 1942455284 scopus 로고    scopus 로고
    • Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces
    • Wen, E. Z., M. J. Hsieh, ., R. Luo. 2004. Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces. J. Mol. Graph. Model. 22:415-424.
    • (2004) J. Mol. Graph. Model. , vol.22 , pp. 415-424
    • Wen, E.Z.1    Hsieh, M.J.2    Luo, R.3
  • 34
    • 72449198627 scopus 로고    scopus 로고
    • Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure
    • Lee, I. H., S. Y. Kim, and J. Lee. 2010. Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure. J. Comput. Chem. 31:57-65.
    • (2010) J. Comput. Chem. , vol.31 , pp. 57-65
    • Lee, I.H.1    Kim, S.Y.2    Lee., J.3
  • 35
  • 36
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensedphase quantum mechanical calculations
    • Duan, Y., C. Wu, ., P. Kollman. 2003. A point-charge force field for molecular mechanics simulations of proteins based on condensedphase quantum mechanical calculations. J. Comput. Chem. 24:1999-2012.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Kollman, P.3
  • 37
    • 1842479952 scopus 로고    scopus 로고
    • Exploring protein native states and large-scale conformational changes with a modified generalized Born model
    • Onufriev, A., D. Bashford, and D. A. Case. 2004. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins. 55:383-394.
    • (2004) Proteins. , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 38
    • 33750587438 scopus 로고
    • Moleculardynamics with coupling to an external bath
    • Berendsen, H. J. C., J. P. M. Postma, ., J. R. Haak. 1984. Moleculardynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
    • (1984) J. Chem. Phys. , vol.81 , pp. 3684-3690
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Haak, J.R.3
  • 39
    • 33646940952 scopus 로고
    • Numerical integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes. J. Comput. Phys. 23:327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 40
    • 0028327236 scopus 로고
    • Protein folding dynamics: The diffusion-collision model and experimental data
    • Karplus, M., and D. L. Weaver. 1994. Protein folding dynamics: the diffusion-collision model and experimental data. Protein Sci. 3: 650-668.
    • (1994) Protein Sci. , vol.3 , pp. 650-668
    • Karplus, M.1    Weaver, D.L.2
  • 41
    • 0028856785 scopus 로고
    • Optimization of rates of protein folding: The nucleation- condensation mechanism and its implications
    • Fersht, A. R. 1995. Optimization of rates of protein folding: the nucleation- condensation mechanism and its implications. Proc. Natl. Acad. Sci. USA. 92:10869-10873.
    • (1995) Proc. Natl. Acad. Sci. USA. , vol.92 , pp. 10869-10873
    • Fersht, A.R.1
  • 42
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill, K. A. 1990. Dominant forces in protein folding. Biochemistry. 29:7133-7155.
    • (1990) Biochemistry. , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 43
    • 54349127109 scopus 로고    scopus 로고
    • Using an amino acid fluorescence resonance energy transfer pair to probe protein unfolding: Application to the villin headpiece subdomain and the LysM domain
    • Glasscock, J. M., Y. Zhu, ., F. Gai. 2008. Using an amino acid fluorescence resonance energy transfer pair to probe protein unfolding: application to the villin headpiece subdomain and the LysM domain. Biochemistry. 47:11070-11076.
    • (2008) Biochemistry. , vol.47 , pp. 11070-11076
    • Glasscock, J.M.1    Zhu, Y.2    Gai, F.3
  • 44
    • 67650550291 scopus 로고    scopus 로고
    • Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis
    • Bunagan, M. R., J. Gao,., F. Gai. 2009. Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis. J. Am. Chem. Soc. 131:7470-7476.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 7470-7476
    • Bunagan, M.R.1    Gao., J.2    Gai, F.3
  • 45
    • 74849099434 scopus 로고    scopus 로고
    • Detection of a transient intermediate in a rapid protein folding process by solid-state nuclear magnetic resonance
    • Hu, K. N., W. M. Yau, and R. Tycko. 2010. Detection of a transient intermediate in a rapid protein folding process by solid-state nuclear magnetic resonance. J. Am. Chem. Soc. 132:24-25.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 24-25
    • Hu, K.N.1    Yau, W.M.2    Tycko., R.3
  • 46
    • 57449106823 scopus 로고    scopus 로고
    • Chemical, physical, and theoretical kinetics of an ultrafast folding protein
    • Kubelka, J., E. R. Henry, ., W. A. Eaton. 2008. Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc. Natl. Acad. Sci. USA. 105:18655-18662.
    • (2008) Proc. Natl. Acad. Sci. USA. , vol.105 , pp. 18655-18662
    • Kubelka, J.1    Henry, E.R.2    Eaton, W.A.3
  • 47
    • 44949236102 scopus 로고    scopus 로고
    • Estimating freeenergy barrier heights for an ultrafast folding protein from calorimetric and kinetic data
    • Godoy-Ruiz, R., E. R. Henry, ., W. A. Eaton. 2008. Estimating freeenergy barrier heights for an ultrafast folding protein from calorimetric and kinetic data. J. Phys. Chem. B. 112:5938-5949.
    • (2008) J. Phys. Chem. B. , vol.112 , pp. 5938-5949
    • Godoy-Ruiz, R.1    Henry, E.R.2    Eaton, W.A.3
  • 48
    • 77950388103 scopus 로고    scopus 로고
    • An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain
    • Reiner, A., P. Henklein, and T. Kiefhaber. An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain. Proc. Natl. Acad. Sci. USA 107:4955-4960.
    • Proc. Natl. Acad. Sci. USA , vol.107 , pp. 4955-4960
    • Reiner, A.1    Henklein, P.2    Kiefhaber, T.3
  • 49
    • 77957570449 scopus 로고    scopus 로고
    • Improvements of network approach for analysis of the folding free-energy surface of peptides and proteins
    • Jiang, X. W., C. J. Chen, and Y. Xiao. 2010. Improvements of network approach for analysis of the folding free-energy surface of peptides and proteins. J. Comput. Chem. 31:57-65.
    • (2010) J. Comput. Chem. , vol.31 , pp. 57-65
    • Jiang, X.W.1    Chen, C.J.2    Xiao., Y.3
  • 50
    • 77956298149 scopus 로고    scopus 로고
    • Going beyond clustering in MD trajectory analysis: An application to villin headpiece folding
    • Rajan, A., P. L. Freddolino, and K. Schulten. 2010. Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding. PLoS ONE. 5:e9890.
    • (2010) PLoS ONE. , vol.5
    • Rajan, A.1    Freddolino, P.L.2    Schulten., K.3
  • 51
    • 58549104541 scopus 로고    scopus 로고
    • Folding energy landscape and network dynamics of small globular proteins
    • Hori, N., G. Chikenji, ., S. Takada. 2009. Folding energy landscape and network dynamics of small globular proteins. Proc. Natl. Acad. Sci. USA. 106:73-78.
    • (2009) Proc. Natl. Acad. Sci. USA. , vol.106 , pp. 73-78
    • Hori, N.1    Chikenji, G.2    Takada, S.3


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