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Volumn 99, Issue 9, 2010, Pages 3029-3037

Characterizing protein energy landscape by self-learning multiscale simulations: Application to a designed β-hairpin

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EID: 78349252730     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.08.041     Document Type: Article
Times cited : (21)

References (56)
  • 2
    • 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
  • 3
    • 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
  • 5
    • 17044393884 scopus 로고    scopus 로고
    • Coarse-grained models for proteins
    • Tozzini, V. 2005. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15:144-150.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 6
    • 0016610491 scopus 로고
    • Computer simulation of protein folding
    • Levitt, M., and A. Warshel. 1975. Computer simulation of protein folding. Nature. 253:694-698.
    • (1975) Nature , vol.253 , pp. 694-698
    • Levitt, M.1    Warshel, A.2
  • 7
    • 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., H. Nymeyer, and J. N. Onuchic. 2000. 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. 298:937-953.
    • (2000) J. Mol. Biol. , vol.298 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.N.3
  • 8
    • 34547474332 scopus 로고    scopus 로고
    • The MARTINI force field: Coarse grained model for biomolecular simulations
    • Marrink, S. J., H. J. Risselada., A. H. de Vries. 2007. The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B. 111:7812-7824.
    • (2007) J. Phys. Chem. B. , vol.111 , pp. 7812-7824
    • Marrink, S.J.1    Risselada, H.J.2    De Vries, A.H.3
  • 9
    • 49649084492 scopus 로고    scopus 로고
    • Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms
    • Okazaki, K., and S. Takada. 2008. Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms. Proc. Natl. Acad. Sci. USA. 105:11182-11187.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 11182-11187
    • Okazaki, K.1    Takada, S.2
  • 10
    • 0347417009 scopus 로고    scopus 로고
    • Optimizing physical energy functions for protein folding
    • Fujitsuka, Y., S. Takada., P. G. Wolynes. 2004. Optimizing physical energy functions for protein folding. Proteins. 54:88-103.
    • (2004) Proteins , vol.54 , pp. 88-103
    • Fujitsuka, Y.1    Takada, S.2    Wolynes, P.G.3
  • 11
    • 0035424584 scopus 로고    scopus 로고
    • Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
    • Liwo, A., C. Czaplewski., H. Scheraga. 2001. Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field. J. Chem. Phys. 115:2323-2347.
    • (2001) J. Chem. Phys. , vol.115 , pp. 2323-2347
    • Liwo, A.1    Czaplewski, C.2    Scheraga, H.3
  • 12
    • 38549169978 scopus 로고    scopus 로고
    • Folding pathway of the b1 domain of protein G explored by multiscale modeling
    • Kmiecik, S., and A. Kolinski. 2008. Folding pathway of the b1 domain of protein G explored by multiscale modeling. Biophys. J. 94:726-736.
    • (2008) Biophys. J. , vol.94 , pp. 726-736
    • Kmiecik, S.1    Kolinski, A.2
  • 13
    • 0020972782 scopus 로고
    • Theoretical studies of protein folding
    • Go, N. 1983. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12:183-210.
    • (1983) Annu. Rev. Biophys. Bioeng. , vol.12 , pp. 183-210
    • Go, N.1
  • 14
    • 0034687712 scopus 로고    scopus 로고
    • Associative memory hamiltonians for structure prediction without homology: A-helical proteins
    • Hardin, C., M. P. Eastwood., P. G. Wolynes. 2000. Associative memory hamiltonians for structure prediction without homology: a-helical proteins. Proc. Natl. Acad. Sci. USA. 97:14235-14240.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 14235-14240
    • Hardin, C.1    Eastwood, M.P.2    Wolynes, P.G.3
  • 15
    • 33846213672 scopus 로고    scopus 로고
    • Mapping allatom models onto one-bead coarse grained models: General properties and applications to a minimal polypeptide model
    • Tozzini, V., W. Rocchia, and J. A. McCammon. 2006. Mapping allatom models onto one-bead coarse grained models: general properties and applications to a minimal polypeptide model. J. Chem. Theory Comput. 2:667-673.
    • (2006) J. Chem. Theory Comput. , vol.2 , pp. 667-673
    • Tozzini, V.1    Rocchia, W.2    McCammon, J.A.3
  • 16
    • 33646123091 scopus 로고    scopus 로고
    • Coarse-grained modeling of the actin filament derived from atomistic-scale simulations
    • Chu, J. W., and G. A. Voth. 2006. Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys. J. 90:1572-1582.
    • (2006) Biophys. J. , vol.90 , pp. 1572-1582
    • Chu, J.W.1    Voth, G.A.2
  • 17
    • 33746606875 scopus 로고    scopus 로고
    • The multiscale challenge for biomolecular systems: Coarse-grained modeling
    • Chu, J. W., S. Izvekov, and G. A. Voth. 2006. The multiscale challenge for biomolecular systems: coarse-grained modeling. Mol. Simul. 32:211-218.
    • (2006) Mol. Simul , vol.32 , pp. 211-218
    • Chu, J.W.1    Izvekov, S.2    Voth, G.A.3
  • 18
    • 14544291957 scopus 로고    scopus 로고
    • A multiscale coarse-graining method for biomolecular systems
    • Izvekov, S., and G. A. Voth. 2005. A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B. 109:2469-2473.
    • (2005) J. Phys. Chem. B. , vol.109 , pp. 2469-2473
    • Izvekov, S.1    Voth, G.A.2
  • 19
    • 24144478280 scopus 로고    scopus 로고
    • Exploring global motions and correlations in the ribosome
    • Trylska, J., V. Tozzini, and J. A. McCammon. 2005. Exploring global motions and correlations in the ribosome. Biophys. J. 89:1455-1463.
    • (2005) Biophys. J. , vol.89 , pp. 1455-1463
    • Trylska, J.1    Tozzini, V.2    McCammon, J.A.3
  • 20
    • 33947421578 scopus 로고    scopus 로고
    • Emerging methods for multiscale simulation of biomolecular systems
    • Chu, J. W., G. S. Ayton., G. A. Voth. 2007. Emerging methods for multiscale simulation of biomolecular systems. Mol. Phys. 105:167-175.
    • (2007) Mol. Phys. , vol.105 , pp. 167-175
    • Chu, J.W.1    Ayton, G.S.2    Voth, G.A.3
  • 21
    • 41049093757 scopus 로고    scopus 로고
    • Multiscale simulation of soft matter: From scale bridging to adaptive resolution
    • Praprotnik, M., L. D. Site, and K. Kremer. 2008. Multiscale simulation of soft matter: from scale bridging to adaptive resolution. Annu. Rev. Phys. Chem. 59:545-571.
    • (2008) Annu. Rev. Phys. Chem. , vol.59 , pp. 545-571
    • Praprotnik, M.1    Site, L.D.2    Kremer, K.3
  • 22
    • 36549005182 scopus 로고    scopus 로고
    • Coarse-grained biomolecular simulation with REACH: Realistic extension algorithm via covariance Hessian
    • Moritsugu, K., and J. C. Smith. 2007. Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. Biophys. J. 93:3460-3469.
    • (2007) Biophys. J. , vol.93 , pp. 3460-3469
    • Moritsugu, K.1    Smith, J.C.2
  • 24
    • 34547926023 scopus 로고    scopus 로고
    • Multigraining: An algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems
    • Christen, M., and W. F. van Gunsteren. 2006. Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems. J. Chem. Phys. 124:154106.
    • (2006) J. Chem. Phys. , vol.124 , pp. 154106
    • Christen, M.1    Van Gunsteren, W.F.2
  • 25
    • 33749672504 scopus 로고    scopus 로고
    • Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations
    • Harmandaris, V. A., N. P. Adhikari., K. Kremer. 2006. Hierarchical modeling of polystyrene: from atomistic to coarse-grained simulations. Macromolecules. 39:6708-6719.
    • (2006) Macromolecules , vol.39 , pp. 6708-6719
    • Harmandaris, V.A.1    Adhikari, N.P.2    Kremer, K.3
  • 26
    • 0042783950 scopus 로고    scopus 로고
    • Deriving effective mesoscale potentials from atomistic simulations
    • Reith, D., M. Pütz, and F. Müller-Plathe. 2003. Deriving effective mesoscale potentials from atomistic simulations. J. Comput. Chem. 24:1624-1636.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1624-1636
    • Reith, D.1    Pütz, M.2    Müller-Plathe, F.3
  • 27
    • 0037120092 scopus 로고    scopus 로고
    • Coarse-graining in polymer simulation: From the atomistic to the mesoscopic scale and back
    • Müller-Plathe, F. 2002. Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back. ChemPhysChem. 3:755-769.
    • (2002) ChemPhysChem , vol.3 , pp. 755-769
    • Müller-Plathe, F.1
  • 28
    • 0010523548 scopus 로고    scopus 로고
    • Multiscale problems in polymer science: Simulation approaches
    • Kremer, K., and F. Muller-Plathe. 2001. Multiscale problems in polymer science: simulation approaches. MRS Bull. 26:205-210.
    • (2001) MRS Bull. , vol.26 , pp. 205-210
    • Kremer, K.1    Muller-Plathe, F.2
  • 29
    • 67249145514 scopus 로고    scopus 로고
    • Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously
    • Li, W., and S. Takada. 2009. Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously. J. Chem. Phys. 130:214108.
    • (2009) J. Chem. Phys. , vol.130 , pp. 214108
    • Li, W.1    Takada, S.2
  • 30
    • 77956203531 scopus 로고    scopus 로고
    • Multiscale methods for protein folding simulations
    • Li, W., H. Yoshii., S. Takada. 2010. Multiscale methods for protein folding simulations. Methods. 52:106-114.
    • (2010) Methods , vol.52 , pp. 106-114
    • Li, W.1    Yoshii, H.2    Takada, S.3
  • 31
    • 34447515841 scopus 로고    scopus 로고
    • From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
    • Heath, A. P., L. E. Kavraki, and C. Clementi. 2007. From coarse-grain to all-atom: toward multiscale analysis of protein landscapes. Proteins. 68:646-661.
    • (2007) Proteins , vol.68 , pp. 646-661
    • Heath, A.P.1    Kavraki, L.E.2    Clementi, C.3
  • 32
    • 55149087047 scopus 로고    scopus 로고
    • Peptide folding using multiscale coarse-grained models
    • Thorpe, I. F., J. Zhou, and G. A. Voth. 2008. Peptide folding using multiscale coarse-grained models. J. Phys. Chem. B. 112:13079-13090.
    • (2008) J. Phys. Chem. B. , vol.112 , pp. 13079-13090
    • Thorpe, I.F.1    Zhou, J.2    Voth, G.A.3
  • 33
    • 64749106745 scopus 로고    scopus 로고
    • Systematic multiscale simulation of membrane protein systems
    • Ayton, G. S., and G. A. Voth. 2009. Systematic multiscale simulation of membrane protein systems. Curr. Opin. Struct. Biol. 19:138-144.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 138-144
    • Ayton, G.S.1    Voth, G.A.2
  • 35
    • 33846204007 scopus 로고    scopus 로고
    • Resolution exchange simulation with incremental coarsening
    • Lyman, E., and D. M. Zuckerman. 2006. Resolution exchange simulation with incremental coarsening. J. Chem. Theory Comput. 2:656-666.
    • (2006) J. Chem. Theory Comput. , vol.2 , pp. 656-666
    • Lyman, E.1    Zuckerman, D.M.2
  • 36
    • 33847717840 scopus 로고    scopus 로고
    • Smart resolution replica exchange: An efficient algorithm for exploring complex energy landscapes
    • Liu, P., and G. A. Voth. 2007. Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. J. Chem. Phys. 126:045106.
    • (2007) J. Chem. Phys. , vol.126 , pp. 045106
    • Liu, P.1    Voth, G.A.2
  • 38
    • 0043245780 scopus 로고    scopus 로고
    • Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
    • Gohlke, H., C. Kiel, and D. A. Case. 2003. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol. 330:891-913.
    • (2003) J. Mol. Biol. , vol.330 , pp. 891-913
    • Gohlke, H.1    Kiel, C.2    Case, D.A.3
  • 39
    • 56449088089 scopus 로고    scopus 로고
    • Crystal structure of a tenamino acid protein
    • Honda, S., T. Akiba., K. Harata. 2008. Crystal structure of a tenamino acid protein. J. Am. Chem. Soc. 130:15327-15331.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 15327-15331
    • Honda, S.1    Akiba, T.2    Harata, K.3
  • 40
    • 34249821932 scopus 로고    scopus 로고
    • Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
    • Gront, D., S. Kmiecik, and A. Kolinski. 2007. Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. J. Comput. Chem. 28:1593-1597.
    • (2007) J. Comput. Chem. , vol.28 , pp. 1593-1597
    • Gront, D.1    Kmiecik, S.2    Kolinski, A.3
  • 41
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu, A. A., A. A. Shelenkov, and R. L. Dunbrack, Jr. 2003. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12:2001-2014.
    • (2003) Protein Sci. , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack Jr., R.L.3
  • 43
    • 33646987405 scopus 로고
    • Optimized Monte Carlo data analysis
    • Ferrenberg, A. M., and R. H. Swendsen. 1989. Optimized Monte Carlo data analysis. Phys. Rev. Lett. 63:1195-1198.
    • (1989) Phys. Rev. Lett. , vol.63 , pp. 1195-1198
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 44
    • 0037426218 scopus 로고    scopus 로고
    • Correlation between rate of folding, energy landscape, and topology in the folding of a model protein HP-36
    • Mukherjee, A., and B. Bagchi. 2003. Correlation between rate of folding, energy landscape, and topology in the folding of a model protein HP-36. J. Chem. Phys. 118:4733-4747.
    • (2003) J. Chem. Phys. , vol.118 , pp. 4733-4747
    • Mukherjee, A.1    Bagchi, B.2
  • 45
    • 37549009571 scopus 로고    scopus 로고
    • Coarse-grained models for simulations of multiprotein complexes: Application to ubiquitin binding
    • Kim, Y. C., and G. Hummer. 2008. Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J. Mol. Biol. 375:1416-1433.
    • (2008) J. Mol. Biol. , vol.375 , pp. 1416-1433
    • Kim, Y.C.1    Hummer, G.2
  • 46
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • Hornak, V., R. Abel., C. Simmerling. 2006. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 65:712-725.
    • (2006) Proteins , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Simmerling, C.3
  • 47
    • 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
  • 48
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita, Y., and Y. Okamoto. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314:141-151.
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 49
    • 33646940952 scopus 로고
    • Numerical integration of cartesian equation of motion of a system with constraintsmolecular dynamics of N-alkanes
    • Ryckaert, J., G. Ciccotti, and H. Berendsen. 1977. Numerical integration of cartesian equation of motion of a system with constraintsmolecular dynamics of N-alkanes. J. Comput. Phys. 23:327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.1    Ciccotti, G.2    Berendsen, H.3
  • 50
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules: 1
    • Kumar, S., D. Bouzida., J. Rosenberg. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules: 1. the method. J. Comput. Chem. 13:1011-1021.
    • (1992) The Method. J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Rosenberg, J.3
  • 51
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • 27-28
    • Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD: visual molecular dynamics. J. Mol. Graph. 14:33-38, 27-28.
    • (1996) J. Mol. Graph , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 52
    • 0018110116 scopus 로고
    • Prediction of the secondary structure of proteins from their amino acid sequence
    • Chou, P. Y., and G. D. Fasman. 1978. Prediction of the secondary structure of proteins from their amino acid sequence. Adv. Enzymol. Relat. Areas Mol. Biol. 47:45-148.
    • (1978) Adv. Enzymol. Relat. Areas Mol. Biol. , vol.47 , pp. 45-148
    • Chou, P.Y.1    Fasman, G.D.2
  • 53
    • 67650752138 scopus 로고    scopus 로고
    • The multiscale coarsegraining method. IV. Transferring coarse-grained potentials between temperatures
    • Krishna, V., W. G. Noid, and G. A. Voth. 2009. The multiscale coarsegraining method. IV. Transferring coarse-grained potentials between temperatures. J. Chem. Phys. 131:024103.
    • (2009) J. Chem. Phys. , vol.131 , pp. 024103
    • Krishna, V.1    Noid, W.G.2    Voth, G.A.3
  • 54
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley, P., K. M. Misura, and D. Baker. 2005. Toward high-resolution de novo structure prediction for small proteins. Science. 309:1868-1871.
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.2    Baker, D.3
  • 55
    • 46149109506 scopus 로고    scopus 로고
    • The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
    • Noid, W. G., J. W. Chu., H. C. Andersen. 2008. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J. Chem. Phys. 128:244114.
    • (2008) J. Chem. Phys. , vol.128 , pp. 244114
    • Noid, W.G.1    Chu, J.W.2    Andersen, H.C.3
  • 56
    • 52649162293 scopus 로고    scopus 로고
    • Reconstructing atomistic detail for coarse-grained models with resolution exchange
    • Liu, P., Q. Shi., G. A. Voth. 2008. Reconstructing atomistic detail for coarse-grained models with resolution exchange. J. Chem. Phys. 129:114103.
    • (2008) J. Chem. Phys. , vol.129 , pp. 114103
    • Liu, P.1    Shi, Q.2    Voth, G.A.3


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