메뉴 건너뛰기




Volumn 343, Issue 1, 2004, Pages 235-248

Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: How far can a minimalist model go?

Author keywords

circular permutation; minimalist model; molecular dynamics simulations; protein folding; value analysis

Indexed keywords

PROTEIN S6;

EID: 4644340168     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.08.006     Document Type: Article
Times cited : (67)

References (77)
  • 1
    • 0033613255 scopus 로고    scopus 로고
    • Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
    • E. Alm, and D. Baker Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures Proc. Natl Acad. Sci. USA 96 1999 11305 11310
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 11305-11310
    • Alm, E.1    Baker, D.2
  • 4
    • 0033613165 scopus 로고    scopus 로고
    • A simple model for calculating the kinetics of protein folding from three-dimensional structures
    • V. Munoz, and W. Eaton A simple model for calculating the kinetics of protein folding from three-dimensional structures Proc. Natl Acad. Sci. USA 96 1999 11311 11316
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 11311-11316
    • Munoz, V.1    Eaton, W.2
  • 5
    • 0033951366 scopus 로고    scopus 로고
    • Protein folding mechanisms: New methods and emerging ideas
    • D. Brockwell, D. Smith, and S. Radford Protein folding mechanisms: new methods and emerging ideas Curr. Opin. Struct. Biol. 10 2000 16 25
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 16-25
    • Brockwell, D.1    Smith, D.2    Radford, S.3
  • 7
    • 0033117763 scopus 로고    scopus 로고
    • Matching theory and experiments in protein folding
    • E. Alm, and D. Baker Matching theory and experiments in protein folding Curr. Opin. Struct. Biol. 9 1999 189 196
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 189-196
    • Alm, E.1    Baker, D.2
  • 8
    • 0036183221 scopus 로고    scopus 로고
    • Im7 folding mechanism: Misfolding on a path to the native state
    • A. Capaldi, C. Kleanthous, and S. Radford Im7 folding mechanism: misfolding on a path to the native state Nature Struct. Biol. 9 2002 209 216
    • (2002) Nature Struct. Biol. , vol.9 , pp. 209-216
    • Capaldi, A.1    Kleanthous, C.2    Radford, S.3
  • 10
    • 0346727128 scopus 로고    scopus 로고
    • Therapeutic approaches to protein-misfolding diseases
    • F. Cohen, and J. Kelly Therapeutic approaches to protein-misfolding diseases Nature 426 2003 905 909
    • (2003) Nature , vol.426 , pp. 905-909
    • Cohen, F.1    Kelly, J.2
  • 11
    • 0344702698 scopus 로고    scopus 로고
    • Simulation of the folding equilibrium of alpha-helical peptides: A comparison of the generalized born approximation with explicit solvent
    • H. Nymeyer, and A. Garcia Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized born approximation with explicit solvent Proc. Natl Acad. Sci. USA 100 2003 13934 13939
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 13934-13939
    • Nymeyer, H.1    Garcia, A.2
  • 12
    • 0029963345 scopus 로고    scopus 로고
    • Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
    • A. Li, and V. Dagget Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations J. Mol. Biol. 256 1996 412 429
    • (1996) J. Mol. Biol. , vol.256 , pp. 412-429
    • Li, A.1    Dagget, V.2
  • 13
    • 0029981188 scopus 로고    scopus 로고
    • Structure of the transition state for folding of a protein derived from experiment and simulation
    • V. Dagget, L. Itzhaki, D. Otzen, and A. Fersht Structure of the transition state for folding of a protein derived from experiment and simulation J. Mol. Biol. 257 1996 430 440
    • (1996) J. Mol. Biol. , vol.257 , pp. 430-440
    • Dagget, V.1    Itzhaki, L.2    Otzen, D.3    Fersht, A.4
  • 14
    • 0028143603 scopus 로고
    • Characterization of the transition state of protein unfolding by unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2
    • A. Li, and V. Dagget Characterization of the transition state of protein unfolding by unfolding by use of molecular dynamics: chymotrypsin inhibitor 2 Proc. Natl Acad. Sci. USA 91 1994 10430 10434
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 10430-10434
    • Li, A.1    Dagget, V.2
  • 15
    • 0030982583 scopus 로고    scopus 로고
    • A molecular dynamics simulation study of segment B1 of protein G
    • F. Sheinerman, and C. Brooks A molecular dynamics simulation study of segment B1 of protein G Proteins: Struct. Funct. Genet. 29 1997 193 202
    • (1997) Proteins: Struct. Funct. Genet. , vol.29 , pp. 193-202
    • Sheinerman, F.1    Brooks, C.2
  • 16
    • 0037059017 scopus 로고    scopus 로고
    • Evidence of turn and salt bridge contributions to beta-hairpin stability:MD simulations of C-terminal fragment from the B1 domain of protein G
    • J. Tsai, and M. Levitt Evidence of turn and salt bridge contributions to beta-hairpin stability:MD simulations of C-terminal fragment from the B1 domain of protein G Biophys. Chem. 101 2002 187 201
    • (2002) Biophys. Chem. , vol.101 , pp. 187-201
    • Tsai, J.1    Levitt, M.2
  • 17
    • 0037058992 scopus 로고    scopus 로고
    • Probing the folding free energy landscape of the src-SH3 protein domain
    • J.E. Shea, J.N. Onuchic, and C.L. Brooks 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
  • 18
    • 0034743155 scopus 로고    scopus 로고
    • From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
    • J. Shea, and C. Brooks III From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding Annu. Rev. Phys. Chem. 52 2001 499 535
    • (2001) Annu. Rev. Phys. Chem. , vol.52 , pp. 499-535
    • Shea, J.1    Brooks III, C.2
  • 19
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • M. Karplus, and J.A. Mccammon Molecular dynamics simulations of biomolecules Nature Struct. Biol. 9 2002 646 652
    • (2002) Nature Struct. Biol. , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 20
    • 1042279571 scopus 로고    scopus 로고
    • Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints
    • E. Paci, C. Friel, K. Lindorff-Larsen, S. Radford, M. Karplus, and M. Vendruscolo Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints Proteins: Struct. Funct. Genet. 54 2004 513 525
    • (2004) Proteins: Struct. Funct. Genet. , vol.54 , pp. 513-525
    • Paci, E.1    Friel, C.2    Lindorff-Larsen, K.3    Radford, S.4    Karplus, M.5    Vendruscolo, M.6
  • 21
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Y. Duan, and P.A. Kollman Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution Science 282 1998 740 744
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 22
    • 0035865992 scopus 로고    scopus 로고
    • Exploring the energy landscape of a beta hairpin in explicit solvent
    • A. Garcia, and K. Sanbonmatsu Exploring the energy landscape of a beta hairpin in explicit solvent Proteins: Struct. Funct. Genet. 42 2001 345 354
    • (2001) Proteins: Struct. Funct. Genet. , vol.42 , pp. 345-354
    • Garcia, A.1    Sanbonmatsu, K.2
  • 23
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • C. Snow, H. Nguyen, V. Pande, and M. Gruebele Absolute comparison of simulated and experimental protein-folding dynamics Nature 420 2002 102 106
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.1    Nguyen, H.2    Pande, V.3    Gruebele, M.4
  • 24
    • 0035850758 scopus 로고    scopus 로고
    • Beta-hairpin folding simulations in atomistic detail using an implicit solvent model
    • B. Zagrovic, E. Sorin, and V. Pande beta-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.2    Pande, V.3
  • 25
    • 0037235952 scopus 로고    scopus 로고
    • Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
    • V. Pande, I. Baker, J. Chapman, S. Elmer, S. Khaliq, and S. Larson Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing Biopolymers 68 2003 91 109
    • (2003) Biopolymers , vol.68 , pp. 91-109
    • Pande, V.1    Baker, I.2    Chapman, J.3    Elmer, S.4    Khaliq, S.5    Larson, S.6
  • 26
    • 0036428782 scopus 로고    scopus 로고
    • Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
    • B. Zagrovic, C. Snow, M. Shirts, and V. Pande Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing J. Mol. Biol. 323 2002 927 937
    • (2002) J. Mol. Biol. , vol.323 , pp. 927-937
    • Zagrovic, B.1    Snow, C.2    Shirts, M.3    Pande, V.4
  • 27
    • 0037456298 scopus 로고    scopus 로고
    • The complete folding pathway of a protein from nanoseconds to microseconds
    • U. Mayor, N.R. Guydosh, C.M. Johnson, J.G. Grossmann, S. Sato, and G.S. Jas The complete folding pathway of a protein from nanoseconds to microseconds Nature 421 2003 863 867
    • (2003) Nature , vol.421 , pp. 863-867
    • Mayor, U.1    Guydosh, N.R.2    Johnson, C.M.3    Grossmann, J.G.4    Sato, S.5    Jas, G.S.6
  • 28
    • 0037154980 scopus 로고    scopus 로고
    • Protein folding and unfolding at atomic resolution
    • A.R. Fersht, and V. Daggett Protein folding and unfolding at atomic resolution Cell 108 2002 573 582
    • (2002) Cell , vol.108 , pp. 573-582
    • Fersht, A.R.1    Daggett, V.2
  • 29
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues form a critical contact network in a protein folding transition state
    • M. Vendruscolo, E. Paci, C. Dobson, and M. Karplus Three key residues form a critical contact network in a protein folding transition state Nature 409 2001 641 645
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.3    Karplus, M.4
  • 30
    • 0036435907 scopus 로고    scopus 로고
    • Determination of a transition state at atomic resolution from protein engineering data
    • E. Paci, M. Vendruscolo, C. Dobson, and M. Karplus Determination of a transition state at atomic resolution from protein engineering data J. Mol. Biol. 324 2002 151 163
    • (2002) J. Mol. Biol. , vol.324 , pp. 151-163
    • Paci, E.1    Vendruscolo, M.2    Dobson, C.3    Karplus, M.4
  • 31
    • 0345598912 scopus 로고    scopus 로고
    • Structures and relative free energies of partially folded states of proteins
    • M. Vendruscolo, E. Paci, M. Karplus, and C. Dobson Structures and relative free energies of partially folded states of proteins Proc. Natl Acad. Sci. USA 25 2003 14817 14821
    • (2003) Proc. Natl Acad. Sci. USA , vol.25 , pp. 14817-14821
    • Vendruscolo, M.1    Paci, E.2    Karplus, M.3    Dobson, C.4
  • 32
    • 0032708771 scopus 로고    scopus 로고
    • Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
    • F. Chiti, N. Taddei, P. White, M. Bucciantini, F. Magherini, M. Stefani, and C.M. Dobson Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding Nature Struct. Biol. 6 1999 1005 1009
    • (1999) Nature Struct. Biol. , vol.6 , pp. 1005-1009
    • Chiti, F.1    Taddei, N.2    White, P.3    Bucciantini, M.4    Magherini, F.5    Stefani, M.6    Dobson, C.M.7
  • 33
    • 4644259872 scopus 로고    scopus 로고
    • Three-body interactions improve prediction of rate and mechanism in protein folding models
    • In press.
    • Ejtehadi, M. R, Avall, S. P & Plotkin, S. S. (2004). Three-body interactions improve prediction of rate and mechanism in protein folding models. Proc. Natl Acad. Sci. USA. In press.
    • (2004) Proc. Natl. Acad. Sci. USA.
    • Ejtehadi, M.R.1    Avall, S.P.2    Plotkin, S.S.3
  • 34
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potential? a new approach to an old problem
    • L.A. Mirny, and E.I. Shakhnovich How to derive a protein folding potential? A new approach to an old problem J. Mol. Biol. 264 1996 1164 1179
    • (1996) J. Mol. Biol. , vol.264 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 36
    • 0000636216 scopus 로고    scopus 로고
    • Determination of interaction potentials of amino acids from native protein structures: Tests on simple lattice models
    • J. Van Mourik, C. Clementi, A. Maritan, F. Seno, and J. Banavar Determination of interaction potentials of amino acids from native protein structures: tests on simple lattice models J. Chem. Phys. 110 1998 10123 10133
    • (1998) J. Chem. Phys. , vol.110 , pp. 10123-10133
    • Van Mourik, J.1    Clementi, C.2    Maritan, A.3    Seno, F.4    Banavar, J.5
  • 39
    • 0036733958 scopus 로고    scopus 로고
    • Statistical mechanical refinement of protein prediction schemes: Cumulant expansion approach
    • M.P. Eastwood, C. Hardin, Z. Luthey-Schulten, and P.G. Wolynes Statistical mechanical refinement of protein prediction schemes: cumulant expansion approach J. Chem. Phys. 117 2002 4602 4615
    • (2002) J. Chem. Phys. , vol.117 , pp. 4602-4615
    • Eastwood, M.P.1    Hardin, C.2    Luthey-Schulten, Z.3    Wolynes, P.G.4
  • 40
    • 0034687712 scopus 로고    scopus 로고
    • Associative memory Hamiltonians for structure prediction without homology: Alpha-helical proteins
    • C. Hardin, M.P. Eastwood, Z. Luthey-Schulten, and P.G. Wolynes Associative memory Hamiltonians for structure prediction without homology: alpha-helical proteins Proc. Natl Acad. Sci. USA 97 2000 14235 14240
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 14235-14240
    • Hardin, C.1    Eastwood, M.P.2    Luthey-Schulten, Z.3    Wolynes, P.G.4
  • 41
    • 0034333083 scopus 로고    scopus 로고
    • How to generate improved potentials for proteins tertiary structure prediction: A lattice model study
    • C. Ting-Lan, and R.A. Goldstein How to generate improved potentials for proteins tertiary structure prediction: a lattice model study Proteins: Struct. Funct. Genet. 41 2000 157 163
    • (2000) Proteins: Struct. Funct. Genet. , vol.41 , pp. 157-163
    • Ting-Lan, C.1    Goldstein, R.A.2
  • 42
    • 0034337368 scopus 로고    scopus 로고
    • Simulating folding of helical proteins with coarse grained models
    • S. Takada Simulating folding of helical proteins with coarse grained models Prog. Theor. Phys. Suppl. 132 2000 366 371
    • (2000) Prog. Theor. Phys. Suppl. , vol.132 , pp. 366-371
    • Takada, S.1
  • 44
    • 0035797727 scopus 로고    scopus 로고
    • Optimization of parameters in macromolecular potential energy functions by conformational space annealing
    • J. Lee, D. Ripoll, C. Czaplewski, J. Pillardy, W. Wedemeyer, and H. Scheraga Optimization of parameters in macromolecular potential energy functions by conformational space annealing J. Phys. Chem. B 105 2001 7291 7298
    • (2001) J. Phys. Chem. B , vol.105 , pp. 7291-7298
    • Lee, J.1    Ripoll, D.2    Czaplewski, C.3    Pillardy, J.4    Wedemeyer, W.5    Scheraga, H.6
  • 45
    • 33645078713 scopus 로고
    • Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
    • A.P. Lyubartsen, and A. Laaksonen Calculation of effective interaction potentials from radial distribution functions: a reverse Monte Carlo approach Phys. Rev. E 52 1995 3730 3737
    • (1995) Phys. Rev. e , vol.52 , pp. 3730-3737
    • Lyubartsen, A.P.1    Laaksonen, A.2
  • 47
    • 33646987405 scopus 로고
    • Optimized Monte-Carlo data-analysis
    • A. Ferrenberg, and R. Swendsen Optimized Monte-Carlo data-analysis Phys. Rev. Letters 63 1989 1195 1198
    • (1989) Phys. Rev. Letters , vol.63 , pp. 1195-1198
    • Ferrenberg, A.1    Swendsen, R.2
  • 48
    • 4243819810 scopus 로고
    • New Monte-Carlo technique for studying phase-transitions
    • A. Ferrenberg, and R. Swendsen New Monte-Carlo technique for studying phase-transitions Phys. Rev. 61 1988 2635 2638
    • (1988) Phys. Rev. , vol.61 , pp. 2635-2638
    • Ferrenberg, A.1    Swendsen, R.2
  • 49
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method
    • S. Kumar, D. Bouzida, R.H. Swendsen, P. Kollman, and J. Rosenberg The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method J. Comput. Chem. 13 1992 1011 1021
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.4    Rosenberg, J.5
  • 50
    • 0001692244 scopus 로고    scopus 로고
    • λ-dynamics: A new approach to free energy calculations
    • X. Kong, and C. Brooks III λ-dynamics: a new approach to free energy calculations J. Chem. Phys. 105 1996 2414 2423
    • (1996) J. Chem. Phys. , vol.105 , pp. 2414-2423
    • Kong, X.1    Brooks III, C.2
  • 51
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. I. Nonpolar gases
    • R.W. Zwanzig High-temperature equation of state by a perturbation method. I. Nonpolar gases J. Chem. Phys. 22 1954 1420 1426
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 52
    • 36149029495 scopus 로고
    • Learning algorithms with optimal stability in neural networks
    • W. Krauth, and M. Mezard Learning algorithms with optimal stability in neural networks J. Phys. A 20 1987 L745 L752
    • (1987) J. Phys. a , vol.20
    • Krauth, W.1    Mezard, M.2
  • 53
    • 0036293485 scopus 로고    scopus 로고
    • Conformational plasticity in folding of the split beta-alpha-beta protein S6: Evidence for burst-phase disruption of the native state
    • D. Otzen, and M. Oliveberg Conformational plasticity in folding of the split beta-alpha-beta protein S6: evidence for burst-phase disruption of the native state J. Mol. Biol. 317 2002 613 627
    • (2002) J. Mol. Biol. , vol.317 , pp. 613-627
    • Otzen, D.1    Oliveberg, M.2
  • 54
    • 0033580679 scopus 로고    scopus 로고
    • Structural changes in the transition state of protein folding: Alternative interpretations of curved chevron plots
    • D.E. Otzen, O. Kristensen, M. Proctor, and M. Oliveberg Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots Biochemistry 38 1999 6499 6511
    • (1999) Biochemistry , vol.38 , pp. 6499-6511
    • Otzen, D.E.1    Kristensen, O.2    Proctor, M.3    Oliveberg, M.4
  • 55
    • 0036829967 scopus 로고    scopus 로고
    • Complete change of the protein folding transition state upon circular permutation
    • M. Lindberg, J. Tangrot, and M. Oliveberg Complete change of the protein folding transition state upon circular permutation Nature Struct. Biol. 9 2002 818 822
    • (2002) Nature Struct. Biol. , vol.9 , pp. 818-822
    • Lindberg, M.1    Tangrot, J.2    Oliveberg, M.3
  • 57
    • 0034612228 scopus 로고    scopus 로고
    • Investigation of routes and funnels in protein folding by free energy functional methods
    • S. Plotkin, and J. Onuchic Investigation of routes and funnels in protein folding by free energy functional methods Proc. Natl Acad. Sci. USA 97 2000 6509 6514
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 6509-6514
    • Plotkin, S.1    Onuchic, J.2
  • 58
    • 0037155413 scopus 로고    scopus 로고
    • Structural and energetic heterogeneity in protein folding I: Theory
    • S. Plotkin, and J. Onuchic Structural and energetic heterogeneity in protein folding I: theory J. Chem. Phys. 116 2002 5263 5283
    • (2002) J. Chem. Phys. , vol.116 , pp. 5263-5283
    • Plotkin, S.1    Onuchic, J.2
  • 59
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • D. Baker A surprising simplicity to protein folding Nature 405 2000 39 42
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 60
    • 0034687123 scopus 로고    scopus 로고
    • Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics
    • K. Plaxco, K. Simons, I. Ruczinski, and D. Baker 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.1    Simons, K.2    Ruczinski, I.3    Baker, D.4
  • 61
  • 62
    • 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
    • C. Clementi, H. Nymeyer, and J. Onuchic 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    Nymeyer, H.2    Onuchic, J.3
  • 63
    • 0034705115 scopus 로고    scopus 로고
    • How native state topology affects the folding of dihydrofolate reductase and interleukin-1β
    • C. Clementi, P. Jennings, and J. Onuchic How native state topology affects the folding of dihydrofolate reductase and interleukin-1β Proc. Natl Acad. Sci. USA 97 2000 5871 5876
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 5871-5876
    • Clementi, C.1    Jennings, P.2    Onuchic, J.3
  • 64
    • 0035943433 scopus 로고    scopus 로고
    • Prediction of folding mechanism for circular-permuted proteins
    • C. Clementi, P. Jennings, and J. Onuchic Prediction of folding mechanism for circular-permuted proteins J. Mol. Biol. 311 2001 879 890
    • (2001) J. Mol. Biol. , vol.311 , pp. 879-890
    • Clementi, C.1    Jennings, P.2    Onuchic, J.3
  • 65
    • 0037457892 scopus 로고    scopus 로고
    • Self-consistent determination of the transition state for protein folding: Application to a fibronectin type III domain
    • E. Paci, J. Clarke, A. Steward, M. Vendruscolo, and M. Karplus Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain Proc. Natl Acad. Sci. USA 100 2003 394 399
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 394-399
    • Paci, E.1    Clarke, J.2    Steward, A.3    Vendruscolo, M.4    Karplus, M.5
  • 66
    • 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
    • C. Clementi, A. García, and J. Onuchic 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    García, A.2    Onuchic, J.3
  • 67
    • 0033548553 scopus 로고    scopus 로고
    • Rapid folding with and without populated intermediates in homologous four-helix proteins Im7 and Im9
    • N. Ferguson, A.P. Capaldi, R. James, C. Kleanthous, and S.E. Radford Rapid folding with and without populated intermediates in homologous four-helix proteins Im7 and Im9 J. Mol. Biol. 286 1999 1597 1608
    • (1999) J. Mol. Biol. , vol.286 , pp. 1597-1608
    • Ferguson, N.1    Capaldi, A.P.2    James, R.3    Kleanthous, C.4    Radford, S.E.5
  • 68
    • 0034685619 scopus 로고    scopus 로고
    • A breakdown of symmetry in the folding transition state of protein L
    • D. Kim, C. Fisher, and D. Baker A breakdown of symmetry in the folding transition state of protein L J. Mol. Biol. 298 2000 971 984
    • (2000) J. Mol. Biol. , vol.298 , pp. 971-984
    • Kim, D.1    Fisher, C.2    Baker, D.3
  • 69
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • K. Plaxco, K. Simons, and D. Baker Contact order, transition state placement and the refolding rates of single domain proteins J. Mol. Biol. 277 1998 985 994
    • (1998) J. Mol. Biol. , vol.277 , pp. 985-994
    • Plaxco, K.1    Simons, K.2    Baker, D.3
  • 70
    • 0037375366 scopus 로고    scopus 로고
    • Prediction of folding rates and transition-state placement from native-state geometry
    • C. Micheletti Prediction of folding rates and transition-state placement from native-state geometry Proteins: Struct. Funct. Genet. 51 2003 74 84
    • (2003) Proteins: Struct. Funct. Genet. , vol.51 , pp. 74-84
    • Micheletti, C.1
  • 71
    • 3142782241 scopus 로고    scopus 로고
    • Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates
    • L. Chavez, J.N. Onuchic, and C. Clementi Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates J. Am. Chem. Soc. 126 2004 8426 8432
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 8426-8432
    • Chavez, L.1    Onuchic, J.N.2    Clementi, C.3
  • 72
    • 0037159944 scopus 로고    scopus 로고
    • Determination of the structures of distinct transition state ensembles for a beta-sheet peptide with parallel folding pathways
    • R. Davis, C.M. Dobson, and M. Vendruscolo Determination of the structures of distinct transition state ensembles for a beta-sheet peptide with parallel folding pathways J. Chem. Phys. 117 1999 9510 9517
    • (1999) J. Chem. Phys. , vol.117 , pp. 9510-9517
    • Davis, R.1    Dobson, C.M.2    Vendruscolo, M.3
  • 73
    • 0035824886 scopus 로고    scopus 로고
    • Folding of circular permutants with decreased contact order: General trend balanced by protein stability
    • M. Lindberg, J. Tangrot, D. Otzen, D. Dolgikh, A. Finkelstein, and M. Oliveberg Folding of circular permutants with decreased contact order: general trend balanced by protein stability J. Mol. Biol. 314 2001 891 900
    • (2001) J. Mol. Biol. , vol.314 , pp. 891-900
    • Lindberg, M.1    Tangrot, J.2    Otzen, D.3    Dolgikh, D.4    Finkelstein, A.5    Oliveberg, M.6
  • 74
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • S. Miyazawa, and R.L. Jernigan Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading J. Mol. Biol. 256 1996 623 644
    • (1996) J. Mol. Biol. , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 75
    • 0031559919 scopus 로고    scopus 로고
    • S6 permutein shows that the unusual target topology is not responsible for the absence of rigid tertiary structure in de novo protein albebetin
    • Z. Abdullaev, R. Latypov, A. Badretdinov, D. Dolgikh, A. Finkeistein, V. Uversky, and M. Kirpichnikov S6 permutein shows that the unusual target topology is not responsible for the absence of rigid tertiary structure in de novo protein albebetin FEBS Letters 414 1997 243 246
    • (1997) FEBS Letters , vol.414 , pp. 243-246
    • Abdullaev, Z.1    Latypov, R.2    Badretdinov, A.3    Dolgikh, D.4    Finkeistein, A.5    Uversky, V.6    Kirpichnikov, M.7
  • 76
    • 12944249776 scopus 로고
    • Discussion of solution for best rotation to relate 2 sets of vectors
    • W. Kabsch Discussion of solution for best rotation to relate 2 sets of vectors Acta Crystallog. sect. A 34 1978 827 828
    • (1978) Acta Crystallog. Sect. a , vol.34 , pp. 827-828
    • Kabsch, W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.