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Volumn 21, Issue 1, 2011, Pages 4-11

Taming the complexity of protein folding

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL TRANSITION; HIDDEN MARKOV MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; REVIEW; STRUCTURE ANALYSIS;

EID: 79551682100     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2010.10.006     Document Type: Review
Times cited : (156)

References (74)
  • 1
    • 67349189383 scopus 로고
    • The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain
    • Anfinsen C.B., Haber E., Sela M., White F.H. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci USA 1961, 47:1309-1314.
    • (1961) Proc Natl Acad Sci USA , vol.47 , pp. 1309-1314
    • Anfinsen, C.B.1    Haber, E.2    Sela, M.3    White, F.H.4
  • 2
    • 69149103558 scopus 로고    scopus 로고
    • Intrinsic disorder in proteins associated with neurodegenerative diseases
    • Uversky V.N. Intrinsic disorder in proteins associated with neurodegenerative diseases. Front Biosci 2009, 14:5188-5238.
    • (2009) Front Biosci , vol.14 , pp. 5188-5238
    • Uversky, V.N.1
  • 3
    • 0000573002 scopus 로고    scopus 로고
    • A direct approach to conformational dynamics based on hybrid Monte Carlo
    • Schütte C., Fischer A., Huisinga W., Deuflhard P. A direct approach to conformational dynamics based on hybrid Monte Carlo. J Comput Phys 1999, 151:146-168.
    • (1999) J Comput Phys , vol.151 , pp. 146-168
    • Schütte, C.1    Fischer, A.2    Huisinga, W.3    Deuflhard, P.4
  • 4
    • 77953285974 scopus 로고    scopus 로고
    • Network models for molecular kinetics and their initial applications to human health
    • Bowman G.R., Huang X., Pande V.S. Network models for molecular kinetics and their initial applications to human health. Cell Res 2010, 20:622-630.
    • (2010) Cell Res , vol.20 , pp. 622-630
    • Bowman, G.R.1    Huang, X.2    Pande, V.S.3
  • 5
    • 42149175435 scopus 로고    scopus 로고
    • Transition networks for modeling the kinetics of conformational change in macromolecules
    • Noe F., Fischer S. Transition networks for modeling the kinetics of conformational change in macromolecules. Curr Opin Struct Biol 2008, 18:154-162.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 154-162
    • Noe, F.1    Fischer, S.2
  • 6
    • 3142707288 scopus 로고    scopus 로고
    • Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin
    • Singhal N., Snow C.D., Pande V.S. Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. J. Chem. Phys. 2004, 121:415-425.
    • (2004) J. Chem. Phys. , vol.121 , pp. 415-425
    • Singhal, N.1    Snow, C.D.2    Pande, V.S.3
  • 7
    • 25444493142 scopus 로고    scopus 로고
    • Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water
    • Elmer S.P., Park S., Pande V.S. Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water. J Chem Phys 2005, 123:114902.
    • (2005) J Chem Phys , vol.123 , pp. 114902
    • Elmer, S.P.1    Park, S.2    Pande, V.S.3
  • 8
    • 2942567954 scopus 로고    scopus 로고
    • Describing protein folding kinetics by molecular dynamics simulations. 1. Theory
    • Swope W.C., Pitera J.W., Suits F. Describing protein folding kinetics by molecular dynamics simulations. 1. Theory. J Phys Chem B 2004, 108:6571-6581.
    • (2004) J Phys Chem B , vol.108 , pp. 6571-6581
    • Swope, W.C.1    Pitera, J.W.2    Suits, F.3
  • 9
    • 34247339716 scopus 로고    scopus 로고
    • Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states
    • Noe F., Horenko I., Schutte C., Smith J.C. Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states. J Chem Phys 2007, 126:155102.
    • (2007) J Chem Phys , vol.126 , pp. 155102
    • Noe, F.1    Horenko, I.2    Schutte, C.3    Smith, J.C.4
  • 10
    • 34247338100 scopus 로고    scopus 로고
    • Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
    • Chodera J.D., Singhal N., Pande V.S., Dill K.A., Swope W.C. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys 2007, 126:155101.
    • (2007) J Chem Phys , vol.126 , pp. 155101
    • Chodera, J.D.1    Singhal, N.2    Pande, V.S.3    Dill, K.A.4    Swope, W.C.5
  • 11
    • 44949178407 scopus 로고    scopus 로고
    • Coarse master equations for peptide folding dynamics
    • Buchete N.V., Hummer G. Coarse master equations for peptide folding dynamics. J Phys Chem B 2008, 112:6057-6069.
    • (2008) J Phys Chem B , vol.112 , pp. 6057-6069
    • Buchete, N.V.1    Hummer, G.2
  • 12
    • 49849097184 scopus 로고    scopus 로고
    • Building Markov state models along pathways to determine free energies and rates of transitions
    • Pan A.C., Roux B. Building Markov state models along pathways to determine free energies and rates of transitions. J Chem Phys 2008, 129:064107.
    • (2008) J Chem Phys , vol.129 , pp. 064107
    • Pan, A.C.1    Roux, B.2
  • 13
    • 62649161772 scopus 로고    scopus 로고
    • Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories
    • Yang S., Banavali N.K., Roux B. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc Natl Acad Sci U S A 2009, 106:3776-3781.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 3776-3781
    • Yang, S.1    Banavali, N.K.2    Roux, B.3
  • 14
    • 18744366086 scopus 로고    scopus 로고
    • Protein folding pathways from replica exchange simulations and a kinetic network model
    • Andrec M., Felts A.K., Gallicchio E., Levy R.M. Protein folding pathways from replica exchange simulations and a kinetic network model. Proc Natl Acad Sci U S A 2005, 102:6801-6806.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 6801-6806
    • Andrec, M.1    Felts, A.K.2    Gallicchio, E.3    Levy, R.M.4
  • 16
    • 63449118443 scopus 로고    scopus 로고
    • Using generalized ensemble simulations and Markov state models to identify conformational states
    • Bowman G.R., Huang X., Pande V.S. Using generalized ensemble simulations and Markov state models to identify conformational states. Methods 2009, 49:197-201.
    • (2009) Methods , vol.49 , pp. 197-201
    • Bowman, G.R.1    Huang, X.2    Pande, V.S.3
  • 17
    • 70349631761 scopus 로고    scopus 로고
    • Progress and challenges in the automated construction of Markov state models for full protein systems
    • Bowman G.R., Beauchamp K.A., Boxer G., Pande V.S. Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys 2009, 131:124101.
    • (2009) J Chem Phys , vol.131 , pp. 124101
    • Bowman, G.R.1    Beauchamp, K.A.2    Boxer, G.3    Pande, V.S.4
  • 18
    • 76149136021 scopus 로고    scopus 로고
    • Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)
    • Voelz V.A., Bowman G.R., Beauchamp K.A., Pande V.S. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J Am Chem Soc 2010, 132:1526-1528.
    • (2010) J Am Chem Soc , vol.132 , pp. 1526-1528
    • Voelz, V.A.1    Bowman, G.R.2    Beauchamp, K.A.3    Pande, V.S.4
  • 19
    • 70450255797 scopus 로고    scopus 로고
    • Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
    • Noe F., Schutte C., Vanden-Eijnden E., Reich L., Weikl T.R. Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proc Natl Acad Sci U S A 2009, 106:19011-19016.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 19011-19016
    • Noe, F.1    Schutte, C.2    Vanden-Eijnden, E.3    Reich, L.4    Weikl, T.R.5
  • 20
    • 77954635393 scopus 로고    scopus 로고
    • Protein folded states are kinetic hubs
    • Bowman G.R., Pande V.S. Protein folded states are kinetic hubs. Proc Natl Acad Sci U S A 2010, 107:10890-10895.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 10890-10895
    • Bowman, G.R.1    Pande, V.S.2
  • 21
    • 79551684741 scopus 로고    scopus 로고
    • Atomistic folding simulations of the five helix bundle protein λ6-85. submitted for publication
    • A landmark simulation study demonstrating the ability of MSMs to capture ten millisecond timescales for relatively large systems (80 residues). This study shows that even large systems have a native hub and provides an alternative explanation for appar
    • Bowman GR, Voelz VA, Pande VS: Atomistic folding simulations of the five helix bundle protein λ6-85. submitted for publication. A landmark simulation study demonstrating the ability of MSMs to capture ten millisecond timescales for relatively large systems (80 residues). This study shows that even large systems have a native hub and provides an alternative explanation for apparent " downhill" folding in addition to yielding a number of other hypotheses that warrant further experimental investigation.
    • Bowman, G.R.1    Voelz, V.A.2    Pande, V.S.3
  • 22
    • 79551682518 scopus 로고    scopus 로고
    • Fine Structure in Protein Folding: Quantitative Comparison of HP35 Simulations and Triplet-Triplet Energy Transfer Experiments. submitted for publication.
    • Beauchamp KA, Ensign DL, Das R, Pande VS: Fine Structure in Protein Folding: Quantitative Comparison of HP35 Simulations and Triplet-Triplet Energy Transfer Experiments. submitted for publication.
    • Beauchamp, K.A.1    Ensign, D.L.2    Das, R.3    Pande, V.S.4
  • 23
    • 79551681839 scopus 로고    scopus 로고
    • A simple theory of protein folding kinetics. Phys Rev Lett, submitted for publication. Derivation of a simple theoretical model for protein folding that captures the native hub observed in simulation studies by accounting for non-native contacts.
    • Pande VS: A simple theory of protein folding kinetics. Phys Rev Lett, submitted for publication. Derivation of a simple theoretical model for protein folding that captures the native hub observed in simulation studies by accounting for non-native contacts.
    • Pande, V.S.1
  • 24
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: a synthesis
    • Bryngelson J.D., Onuchic J.N., Socci N.D., Wolynes P.G. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 1995, 21:167-195.
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 25
    • 0026723063 scopus 로고
    • Protein folding funnels: a kinetic approach to the sequence-structure relationship
    • Leopold P.E., Montal M., Onuchic J.N. Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc Natl Acad Sci U S A 1992, 89:8721-8725.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 8721-8725
    • Leopold, P.E.1    Montal, M.2    Onuchic, J.N.3
  • 26
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill K.A., Chan H.S. From Levinthal to pathways to funnels. Nat Struct Biol 1997, 4:10-19.
    • (1997) Nat Struct Biol , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 27
    • 0026345750 scopus 로고
    • Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
    • Jackson S.E., Fersht A.R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 1991, 30:10428-10435.
    • (1991) Biochemistry , vol.30 , pp. 10428-10435
    • Jackson, S.E.1    Fersht, A.R.2
  • 28
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco K.W., Simons K.T., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998, 277:985-994.
    • (1998) J Mol Biol , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 29
    • 63449129633 scopus 로고    scopus 로고
    • 3rd: Insights from coarse-grained go models for protein folding and dynamics
    • Hills R.D., Brooks C.L. 3rd: Insights from coarse-grained go models for protein folding and dynamics. Int J Mol Sci 2009, 10:889-905.
    • (2009) Int J Mol Sci , vol.10 , pp. 889-905
    • Hills, R.D.1    Brooks, C.L.2
  • 31
    • 39149100599 scopus 로고    scopus 로고
    • Coarse-grained models of protein folding: toy models or predictive tools?
    • Clementi C. Coarse-grained models of protein folding: toy models or predictive tools?. Curr Opin Struct Biol 2008, 18:10-15.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 10-15
    • Clementi, C.1
  • 32
    • 66749176784 scopus 로고    scopus 로고
    • The unfolded state of the C-terminal domain of the ribosomal protein L9 contains both native and non-native structure
    • Shan B., Eliezer D., Raleigh D.P. The unfolded state of the C-terminal domain of the ribosomal protein L9 contains both native and non-native structure. Biochemistry 2009, 48:4707-4719.
    • (2009) Biochemistry , vol.48 , pp. 4707-4719
    • Shan, B.1    Eliezer, D.2    Raleigh, D.P.3
  • 33
    • 77649264931 scopus 로고    scopus 로고
    • Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins
    • Zhang Z., Chan H.S. Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins. Proc Natl Acad Sci 2010, 107:2920-2925.
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 2920-2925
    • Zhang, Z.1    Chan, H.S.2
  • 34
    • 0347627528 scopus 로고    scopus 로고
    • Destabilization of the Escherichia coli RNase H kinetic intermediate: switching between a two-state and three-state folding mechanism
    • Spudich G.M., Miller E.J., Marqusee S. Destabilization of the Escherichia coli RNase H kinetic intermediate: switching between a two-state and three-state folding mechanism. J Mol Biol 2004, 335:609-618.
    • (2004) J Mol Biol , vol.335 , pp. 609-618
    • Spudich, G.M.1    Miller, E.J.2    Marqusee, S.3
  • 35
    • 0025345415 scopus 로고
    • Intermediates in the folding reactions of small proteins
    • Kim P.S., Baldwin R.L. Intermediates in the folding reactions of small proteins. Annu Rev Biochem 1990, 59:631-660.
    • (1990) Annu Rev Biochem , vol.59 , pp. 631-660
    • Kim, P.S.1    Baldwin, R.L.2
  • 36
    • 34948869804 scopus 로고    scopus 로고
    • The ultimate speed limit to protein folding is conformational searching
    • Ghosh K., Ozkan S.B., Dill K.A. The ultimate speed limit to protein folding is conformational searching. J Am Chem Soc 2007, 129:11920-11927.
    • (2007) J Am Chem Soc , vol.129 , pp. 11920-11927
    • Ghosh, K.1    Ozkan, S.B.2    Dill, K.A.3
  • 37
    • 46449120907 scopus 로고    scopus 로고
    • Predicting protein folding rates from geometric contact and amino acid sequence
    • Ouyang Z., Liang J. Predicting protein folding rates from geometric contact and amino acid sequence. Protein Sci 2008, 17:1256-1263.
    • (2008) Protein Sci , vol.17 , pp. 1256-1263
    • Ouyang, Z.1    Liang, J.2
  • 43
    • 44449093098 scopus 로고    scopus 로고
    • Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment
    • Huang X., Bowman G.R., Pande V.S. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. J Chem Phys 2008, 128:205106.
    • (2008) J Chem Phys , vol.128 , pp. 205106
    • Huang, X.1    Bowman, G.R.2    Pande, V.S.3
  • 44
    • 58149299971 scopus 로고    scopus 로고
    • Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
    • Laio A., Gervasio F. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep Prog Phys 2008, 71.
    • (2008) Rep Prog Phys , pp. 71
    • Laio, A.1    Gervasio, F.2
  • 45
    • 42349111182 scopus 로고    scopus 로고
    • Normal mode partitioning of Langevin dynamics for biomolecules
    • Sweet C.R., Petrone P., Pande V.S., Izaguirre J.A. Normal mode partitioning of Langevin dynamics for biomolecules. J Chem Phys 2008, 128:145101.
    • (2008) J Chem Phys , vol.128 , pp. 145101
    • Sweet, C.R.1    Petrone, P.2    Pande, V.S.3    Izaguirre, J.A.4
  • 46
    • 3142716857 scopus 로고    scopus 로고
    • Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules
    • Hamelberg D., Mongan J., McCammon J.A. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys 2004, 120:11919-11929.
    • (2004) J Chem Phys , vol.120 , pp. 11919-11929
    • Hamelberg, D.1    Mongan, J.2    McCammon, J.A.3
  • 47
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang J.M., Cieplak P., Kollman P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. J Comp Chem 2000, 21:1049-1074.
    • (2000) J Comp Chem , vol.21 , pp. 1049-1074
    • Wang, J.M.1    Cieplak, P.2    Kollman, P.A.3
  • 48
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 2006, 65:712-725.
    • (2006) Proteins , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 49
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
    • Sorin E.J., Pande V.S. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J 2005, 88:2472-2493.
    • (2005) Biophys J , vol.88 , pp. 2472-2493
    • Sorin, E.J.1    Pande, V.S.2
  • 50
    • 77955606360 scopus 로고    scopus 로고
    • Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water
    • Mittal J., Best R.B. Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water. Biophys J 2010, 99:L26-28.
    • (2010) Biophys J , vol.99
    • Mittal, J.1    Best, R.B.2
  • 52
    • 0036424048 scopus 로고    scopus 로고
    • Transition path sampling: throwing ropes over rough mountain passes, in the dark
    • Bolhuis P.G., Chandler D., Dellago C., Geissler P.L. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem 2002, 53:291-318.
    • (2002) Annu Rev Phys Chem , vol.53 , pp. 291-318
    • Bolhuis, P.G.1    Chandler, D.2    Dellago, C.3    Geissler, P.L.4
  • 53
    • 3042545299 scopus 로고    scopus 로고
    • Computing time scales from reaction coordinates by milestoning
    • Faradjian A.K., Elber R. Computing time scales from reaction coordinates by milestoning. J Chem Phys 2004, 120:10880-10889.
    • (2004) J Chem Phys , vol.120 , pp. 10880-10889
    • Faradjian, A.K.1    Elber, R.2
  • 55
    • 79551687503 scopus 로고    scopus 로고
    • On the approximation quality of Markov state models
    • SIAM Multiscale Model Simul, in press.
    • Sarich M, Noe F, Schutte C: On the approximation quality of Markov state models. SIAM Multiscale Model Simul, in press.
    • Sarich, M.1    Noe, F.2    Schutte, C.3
  • 56
    • 33747589472 scopus 로고    scopus 로고
    • Toward a theory of transition paths
    • Vanden Eijnden E. Toward a theory of transition paths. J Stat Phys 2006, 123:503-523.
    • (2006) J Stat Phys , vol.123 , pp. 503-523
    • Vanden Eijnden, E.1
  • 57
    • 66849091890 scopus 로고    scopus 로고
    • Reactive flux and folding pathways in network models of coarse-grained protein dynamics
    • Berezhkovskii A., Hummer G., Szabo A. Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J Chem Phys 2009, 130:205102.
    • (2009) J Chem Phys , vol.130 , pp. 205102
    • Berezhkovskii, A.1    Hummer, G.2    Szabo, A.3
  • 58
    • 34547341247 scopus 로고    scopus 로고
    • Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics
    • Hinrichs N.S., Pande V.S. Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics. J Chem Phys 2007, 126:244101.
    • (2007) J Chem Phys , vol.126 , pp. 244101
    • Hinrichs, N.S.1    Pande, V.S.2
  • 59
    • 77950159292 scopus 로고    scopus 로고
    • Enhanced modeling via network theory: adaptive sampling of Markov state models
    • Bowman G.R., Ensign D.L., Pande V.S. Enhanced modeling via network theory: adaptive sampling of Markov state models. J Chem Theory Comput 2010, 6:787-794.
    • (2010) J Chem Theory Comput , vol.6 , pp. 787-794
    • Bowman, G.R.1    Ensign, D.L.2    Pande, V.S.3
  • 61
    • 2942560604 scopus 로고    scopus 로고
    • Describing protein folding kinetics by molecular dynamics simulations 2. Example applications to alanine dipeptide and beta-hairpin peptide
    • Swope W.C., Pitera J.W., Suits F., Pitman M., Eleftheriou M. Describing protein folding kinetics by molecular dynamics simulations 2. Example applications to alanine dipeptide and beta-hairpin peptide. J Phys Chem B 2004, 108:6582-6594.
    • (2004) J Phys Chem B , vol.108 , pp. 6582-6594
    • Swope, W.C.1    Pitera, J.W.2    Suits, F.3    Pitman, M.4    Eleftheriou, M.5
  • 62
    • 17444404720 scopus 로고    scopus 로고
    • Foldamer simulations: novel computational methods and applications to poly-phenylacetylene oligomers
    • Elmer S.P., Pande V.S. Foldamer simulations: novel computational methods and applications to poly-phenylacetylene oligomers. J Chem Phys 2004, 121:12760-12771.
    • (2004) J Chem Phys , vol.121 , pp. 12760-12771
    • Elmer, S.P.1    Pande, V.S.2
  • 63
    • 33644880643 scopus 로고    scopus 로고
    • Extracting markov models of peptide conformational dynamics from simulation data
    • Schultheis V., Hirschberger T., Carstens H., Tavan P. Extracting markov models of peptide conformational dynamics from simulation data. JCTC 2005, 1:515-526.
    • (2005) JCTC , vol.1 , pp. 515-526
    • Schultheis, V.1    Hirschberger, T.2    Carstens, H.3    Tavan, P.4
  • 64
    • 4143090730 scopus 로고    scopus 로고
    • The protein folding network
    • Rao F., Caflisch A. The protein folding network. J Mol Biol 2004, 342:299-306.
    • (2004) J Mol Biol , vol.342 , pp. 299-306
    • Rao, F.1    Caflisch, A.2
  • 65
    • 33748248896 scopus 로고    scopus 로고
    • Folding simulations of the villin headpiece in all-atom detail
    • Jayachandran G., Vishal V., Pande V.S. Folding simulations of the villin headpiece in all-atom detail. J Chem Phys 2006, 124:164902.
    • (2006) J Chem Phys , vol.124 , pp. 164902
    • Jayachandran, G.1    Vishal, V.2    Pande, V.S.3
  • 66
    • 35648943228 scopus 로고    scopus 로고
    • Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece
    • Ensign D.L., Kasson P.M., Pande V.S. Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. J Mol Biol 2007, 374:806-816.
    • (2007) J Mol Biol , vol.374 , pp. 806-816
    • Ensign, D.L.1    Kasson, P.M.2    Pande, V.S.3
  • 67
    • 33745137861 scopus 로고    scopus 로고
    • Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism
    • Krishna M.M., Maity H., Rumbley J.N., Lin Y., Englander S.W. Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism. J Mol Biol 2006, 359:1410-1419.
    • (2006) J Mol Biol , vol.359 , pp. 1410-1419
    • Krishna, M.M.1    Maity, H.2    Rumbley, J.N.3    Lin, Y.4    Englander, S.W.5
  • 68
    • 0026751786 scopus 로고
    • The folding of hen lysozyme involves partially structured intermediates and multiple pathways
    • Radford S.E., Dobson C.M., Evans P.A. The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature 1992, 358:302-307.
    • (1992) Nature , vol.358 , pp. 302-307
    • Radford, S.E.1    Dobson, C.M.2    Evans, P.A.3
  • 69
    • 0042887400 scopus 로고    scopus 로고
    • Multiple parallel-pathway folding of proline-free Staphylococcal nuclease
    • Kamagata K., Sawano Y., Tanokura M., Kuwajima K. Multiple parallel-pathway folding of proline-free Staphylococcal nuclease. J Mol Biol 2003, 332:1143-1153.
    • (2003) J Mol Biol , vol.332 , pp. 1143-1153
    • Kamagata, K.1    Sawano, Y.2    Tanokura, M.3    Kuwajima, K.4
  • 71
    • 77950789652 scopus 로고    scopus 로고
    • Unfolded state dynamics and structure of protein L characterized by simulation and experiment
    • Voelz V.A., Singh V.R., Wedemeyer W.J., Lapidus L.J., Pande V.S. Unfolded state dynamics and structure of protein L characterized by simulation and experiment. J Am Chem Soc 2010, 132:4702-4709.
    • (2010) J Am Chem Soc , vol.132 , pp. 4702-4709
    • Voelz, V.A.1    Singh, V.R.2    Wedemeyer, W.J.3    Lapidus, L.J.4    Pande, V.S.5
  • 72
    • 77950388103 scopus 로고    scopus 로고
    • An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain
    • Reiner A., Henklein P., Kiefhaber T. An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain. Proc Natl Acad Sci U S A 2010, 107:4955-4960.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 4955-4960
    • Reiner, A.1    Henklein, P.2    Kiefhaber, T.3
  • 73
    • 77956361829 scopus 로고    scopus 로고
    • Extremely slow intramolecular diffusion in unfolded protein L
    • Waldauer S.A., Bakajin O., Lapidus L.J. Extremely slow intramolecular diffusion in unfolded protein L. Proc Natl Acad Sci U S A 2010, 107:13713-13717.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 13713-13717
    • Waldauer, S.A.1    Bakajin, O.2    Lapidus, L.J.3
  • 74
    • 71449103005 scopus 로고    scopus 로고
    • Hidden alternative structures of proline isomerase essential for catalysis
    • Fraser J.S., Clarkson M.W., Degnan S.C., Erion R., Kern D., Alber T. Hidden alternative structures of proline isomerase essential for catalysis. Nature 2009, 462:669-673.
    • (2009) Nature , vol.462 , pp. 669-673
    • Fraser, J.S.1    Clarkson, M.W.2    Degnan, S.C.3    Erion, R.4    Kern, D.5    Alber, T.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.