-
1
-
-
34347375915
-
The protein folding problem: When will it be solved?
-
Dill KA, Ozkan B, Weikl TR, Chodera JD, Voelz VA (2007) The protein folding problem: when will it be solved? Curr Opin Struc Biol 17:342-346.
-
(2007)
Curr Opin Struc Biol
, vol.17
, pp. 342-346
-
-
Dill, K.A.1
Ozkan, B.2
Weikl, T.R.3
Chodera, J.D.4
Voelz, V.A.5
-
2
-
-
49449100900
-
Problem solved (*sort of)
-
Service RF (2008) Problem solved (*sort of). Science 321:784-786.
-
(2008)
Science
, vol.321
, pp. 784-786
-
-
Service, R.F.1
-
3
-
-
33846901901
-
Intermediates: Ubiquitous species on folding energy landscapes?
-
Brockwell DJ, Radford SE (2007) Intermediates: ubiquitous species on folding energy landscapes? Curr Opin Struct Biol 17:30-37.
-
(2007)
Curr Opin Struct Biol
, vol.17
, pp. 30-37
-
-
Brockwell, D.J.1
Radford, S.E.2
-
4
-
-
0031815749
-
How do small single-domain proteins fold?
-
Jackson SE (1998) How do small single-domain proteins fold? Fold Des 3:R81-R91.
-
(1998)
Fold des
, vol.3
-
-
Jackson, S.E.1
-
5
-
-
0038581260
-
Hidden intermediates and Levinthal paradox in the folding of small proteins
-
Bai Y (2003) Hidden intermediates and Levinthal paradox in the folding of small proteins. Biochem Biophys Res Commun 305:785-788.
-
(2003)
Biochem Biophys Res Commun
, vol.305
, pp. 785-788
-
-
Bai, Y.1
-
6
-
-
0033871781
-
Protein folding intermediates and pathways studied by hydrogen exchange
-
Englander SW (2000) Protein folding intermediates and pathways studied by hydrogen exchange. Annu Rev Biophys Biomol Struct 29:213-238.
-
(2000)
Annu Rev Biophys Biomol Struct
, vol.29
, pp. 213-238
-
-
Englander, S.W.1
-
7
-
-
0031662891
-
Evidence for an unfolding and refolding pathway in cytochrome c
-
DOI 10.1038/1810
-
Xu Y, Mayne L, Englander SW (1998) Evidence for an unfolding and refolding pathway in cytochrome c. Nature Struct Biol 5:774-778. (Pubitemid 28402079)
-
(1998)
Nature Structural Biology
, vol.5
, Issue.9
, pp. 774-778
-
-
Xu, Y.1
Mayne, L.2
Englander, S.W.3
-
8
-
-
4644359012
-
How cytochrome c folds, and why: Submolecular foldon units and their stepwise sequential stabilization
-
DOI 10.1016/j.jmb.2004.08.005, PII S0022283604009726
-
Maity H, Maity M, Englander SW (2004) How cytochrome c folds, and why: submolecular foldon units and their stepwise sequential stabilization. J Mol Biol 343:223-233. (Pubitemid 39277460)
-
(2004)
Journal of Molecular Biology
, vol.343
, Issue.1
, pp. 223-233
-
-
Maity, H.1
Maity, M.2
Walter Englander, S.3
-
9
-
-
39149087014
-
Protein folding studied by single molecule FRET
-
Schuler B, Eaton WA (2008) Protein folding studied by single molecule FRET. Curr Opin Struct Biol 18:16-26.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 16-26
-
-
Schuler, B.1
Eaton, W.A.2
-
10
-
-
0029987587
-
Probing the interaction between two single molecules: Fluorescence resonance energy transfer between a single donor and a single acceptor
-
DOI 10.1073/pnas.93.13.6264
-
Ha T, Enderle T, Ogletree DF, Chemla DA, Selvin PR, Weiss S (1996) Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc Natl Acad Sci USA 93:6264-6268. (Pubitemid 26230293)
-
(1996)
Proceedings of the National Academy of Sciences of the United States of America
, vol.93
, Issue.13
, pp. 6264-6268
-
-
Ha, T.1
Enderle, Th.2
Ogletree, D.F.3
Chemla, D.S.4
Selvin, P.R.5
Weiss, S.6
-
11
-
-
0037126290
-
Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
-
Schuler B, Lipman EA, Eaton WA (2000) Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature 419:743-747.
-
(2000)
Nature
, vol.419
, pp. 743-747
-
-
Schuler, B.1
Lipman, E.A.2
Eaton, W.A.3
-
12
-
-
33745955427
-
Specificity of the Initial Collapse in the Folding of the Cold Shock Protein
-
DOI 10.1016/j.jmb.2006.05.073, PII S0022283606006917
-
Magg C, Kubelka J, Holtermann G, Haas E, Schmid FX (2006) Specificity of the initial collapse in the folding of the cold shock protein. J Mol Biol 360:1067-1080. (Pubitemid 44062520)
-
(2006)
Journal of Molecular Biology
, vol.360
, Issue.5
, pp. 1067-1080
-
-
Magg, C.1
Kubelka, J.2
Holtermann, G.3
Haas, E.4
Schmid, F.X.5
-
14
-
-
0041735179
-
Kinetics of intramolecular contact formation in a denatured protein
-
Buscaglia M, Schuler B, Lapidus LJ, Eaton WA, Hofrichter J (2005) Kinetics of intramolecular contact formation in a denatured protein. J Mol Biol 332:9-12.
-
(2005)
J Mol Biol
, vol.332
, pp. 9-12
-
-
Buscaglia, M.1
Schuler, B.2
Lapidus, L.J.3
Eaton, W.A.4
Hofrichter, J.5
-
15
-
-
0030334626
-
Universality and diversity of the protein folding scenarios: A comprehensive analysis with the aid of a lattice model
-
Mirny LA, Abkevich V, Shakhnovich EI (1996) Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model. Fold Des 1:103-116. (Pubitemid 126748165)
-
(1996)
Folding and Design
, vol.1
, Issue.2
, pp. 103-116
-
-
Mirny, L.A.1
Abkevich, V.2
Shakhnovich, E.I.3
-
16
-
-
0034319711
-
Sequencing of folding events in Go-type proteins
-
Hoang TX, Cieplak M (2000) Sequencing of folding events in Go-type proteins. J Chem Phys 113:8319-8328.
-
(2000)
J Chem Phys
, vol.113
, pp. 8319-8328
-
-
Hoang, T.X.1
Cieplak, M.2
-
17
-
-
0035793713
-
Native topology or specific interactions: What is more important for protein folding?
-
Ferrara P, Caflisch A (2001) Native topology or specific interactions: what is more important for protein folding? J Mol Biol 306:837-850.
-
(2001)
J Mol Biol
, vol.306
, pp. 837-850
-
-
Ferrara, P.1
Caflisch, A.2
-
18
-
-
0037414650
-
Weak cooperativity in the core causes a switch in folding mechanism between two proteins of the cks family
-
Seeliger MA, Brewadr SE, Itzhaki LS (2005) Weak cooperativity in the core causes a switch in folding mechanism between two proteins of the cks family. J Mol Biol 325:189-199.
-
(2005)
J Mol Biol
, vol.325
, pp. 189-199
-
-
Seeliger, M.A.1
Brewadr, S.E.2
Itzhaki, L.S.3
-
19
-
-
33745712768
-
Sequence of events in folding mechanism: Beyond the Go model
-
Sutto L, Tiana G, Broglia R (2006) Sequence of events in folding mechanism: beyond the Go model. Protein Sci 15:1638-1652.
-
(2006)
Protein Sci
, vol.15
, pp. 1638-1652
-
-
Sutto, L.1
Tiana, G.2
Broglia, R.3
-
20
-
-
33646812860
-
Substructural cooperativity and parallel versus sequential events during protein unfolding
-
DOI 10.1002/prot.20966
-
Reich L, Weikl TR (2006) Substructural cooperativity and parallel versus sequential events during protein unfolding. Proteins 63:1052-1058. (Pubitemid 43765155)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.63
, Issue.4
, pp. 1052-1058
-
-
Reich, L.1
Weikl, T.R.2
-
21
-
-
10844267966
-
Explicit-chain model of native-state hydrogen exchange: Implications for event ordering and cooperativity in protein folding
-
DOI 10.1002/prot.20286
-
Kaya H, Chan HS (2005) Explicit-chain model of native-state hydrogen exchange: implications for event ordering and cooperativity in protein folding. Proteins 58:31-44. (Pubitemid 39665614)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.58
, Issue.1
, pp. 31-44
-
-
Kaya, H.1
Chan, H.S.2
-
22
-
-
35248828677
-
Pathways to folding, nucleation events, and native geometry
-
Travasso RDM, Telo de Gama MM, Faisca PFN (2007) Pathways to folding, nucleation events, and native geometry. J Chem Phys 127:145106.
-
(2007)
J Chem Phys
, vol.127
, pp. 145106
-
-
Travasso, R.D.M.1
Telo De Gama, M.M.2
Faisca, P.F.N.3
-
23
-
-
55549109717
-
On the relation between native geometry and conformational plasticity
-
Faisca PFN, Gomes CM (2008) On the relation between native geometry and conformational plasticity. Biophys Chem 138:99-106.
-
(2008)
Biophys Chem
, vol.138
, pp. 99-106
-
-
Faisca, P.F.N.1
Gomes, C.M.2
-
24
-
-
0034823503
-
Statistical analysis of native contact formation in the folding of designed model proteins
-
DOI 10.1063/1.1337041
-
Tiana G, Broglia RA (2001) Statistical analysis of native contact formation in the folding of designed model proteins. J Chem Phys 114:2503-2510. (Pubitemid 32873126)
-
(2001)
Journal of Chemical Physics
, vol.114
, Issue.5
, pp. 2503-2510
-
-
Tiana, G.1
Broglia Ricardo, A.2
-
25
-
-
0035932720
-
Hierarchy of events in the folding of model proteins
-
DOI 10.1063/1.1361076
-
Broglia RA, Tiana G (2001) Hierarchy of events in the folding of model proteins. J Chem Phys 114:7267-7273. (Pubitemid 32445505)
-
(2001)
Journal of Chemical Physics
, vol.114
, Issue.16
, pp. 7267-7273
-
-
Broglia, R.A.1
Tiana, G.2
-
26
-
-
30344481686
-
Folding pathway dependence on energetic frustration and interaction heterogeneity for a three-dimensional hydrophobic protein model
-
Garcia LG, Araujo AFP (2006) Folding pathway dependence on energetic frustration and interaction heterogeneity for a three-dimensional hydrophobic protein model. Proteins 62:46-63.
-
(2006)
Proteins
, vol.62
, pp. 46-63
-
-
Garcia, L.G.1
Araujo, A.F.P.2
-
27
-
-
67749130905
-
The limited role of nonnative contacts in the folding pathways of a lattice protein
-
Gin BC, Garrahan JP, Geissler PL (2009) The limited role of nonnative contacts in the folding pathways of a lattice protein. J Mol Biol 392:1303-1314.
-
(2009)
J Mol Biol
, vol.392
, pp. 1303-1314
-
-
Gin, B.C.1
Garrahan, J.P.2
Geissler, P.L.3
-
28
-
-
70349584103
-
The nucleation mechanism of protein folding: A survey of computer simulation studies
-
Faisca PFN (2009) The nucleation mechanism of protein folding: a survey of computer simulation studies. J Phys Condens Matter 21:373102.
-
(2009)
J Phys Condens Matter
, vol.21
, pp. 373102
-
-
Faisca, P.F.N.1
-
29
-
-
0028024928
-
Specific nucleus as the transition state for protein folding: Evidence from the lattice model
-
Abkevich VI, Gutin AM, Shakhnovich EI (1994) Specific nucleus as the transition state for protein folding: evidence from lattice model. Biochemistry 33:10026-10036. (Pubitemid 24286081)
-
(1994)
Biochemistry
, vol.33
, Issue.33
, pp. 10026-10036
-
-
Abkevich, V.I.1
Gutin, A.M.2
Shakhnovich, E.I.3
-
30
-
-
36449000646
-
Transition states and folding dynamics of proteins and heteropolymers
-
Chan HS, Dill KA (1994) Transition states and folding dynamics of proteins and heteropolymers. J Chem Phys 100:9238-9257.
-
(1994)
J Chem Phys
, vol.100
, pp. 9238-9257
-
-
Chan, H.S.1
Dill, K.A.2
-
31
-
-
0034112774
-
Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
-
DOI 10.1038/74111
-
Li L, Mirny LA, Shakhnovich EI (2000) Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat Struct Biol 7:336-342. (Pubitemid 30194459)
-
(2000)
Nature Structural Biology
, vol.7
, Issue.4
, pp. 336-342
-
-
Li, L.1
Mirny, L.A.2
Shakhnovich, E.I.3
-
32
-
-
3042677501
-
The effects of nonnative interactions on protein folding rates: Theory and simulation
-
DOI 10.1110/ps.03580104
-
Clementi C, Plotkin S (2003) The effects of nonnative interactions on protein folding rates: theory and simulation. Protein Sci 13:1750-1766. (Pubitemid 38822115)
-
(2004)
Protein Science
, vol.13
, Issue.7
, pp. 1750-1766
-
-
Clementi, C.1
Plotkin, S.S.2
-
33
-
-
0022098302
-
Kinetics of collapse for a flexible coil
-
de Gennes PG (1985) Kinetics of collapse for a flexible coil. J Phys Lett 46:L-639-L-642.
-
(1985)
J Phys Lett
, vol.46
-
-
De Gennes, P.G.1
-
34
-
-
0029155772
-
Impact of local and non-local interactions on thermodynamics and kinetics of protein folding
-
Abkevich VI, Gutin AM, Shakhnovich EI (1995) Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J Mol Biol 252:460-471.
-
(1995)
J Mol Biol
, vol.252
, pp. 460-471
-
-
Abkevich, V.I.1
Gutin, A.M.2
Shakhnovich, E.I.3
-
35
-
-
14744273112
-
Native geometry and the dynamics of protein folding
-
DOI 10.1016/j.bpc.2004.12.022
-
Faisca PFN, Telo de Gama MM (2005) Native geometry and the dynamics of protein folding. Biophys Chem 115:169-175. (Pubitemid 40327053)
-
(2005)
Biophysical Chemistry
, vol.115
, Issue.2-3 SPEC. ISS
, pp. 169-175
-
-
Faisca, P.F.N.1
Telo Da Gama, M.M.2
-
36
-
-
0037156117
-
Thermodynamic control and dynamical regimes in protein folding
-
Faisca PFN, Ball RC (2002) Thermodynamic control and dynamical regimes in protein folding. J Chem Phys 116:7231-7238.
-
(2002)
J Chem Phys
, vol.116
, pp. 7231-7238
-
-
Faisca, P.F.N.1
Ball, R.C.2
-
37
-
-
0037044965
-
Topological complexity, contact order and protein folding rates
-
Faisca PFN, Ball RC (2002) Topological complexity, contact order and protein folding rates. J Chem Phys 117:8587-8591.
-
(2002)
J Chem Phys
, vol.117
, pp. 8587-8591
-
-
Faisca, P.F.N.1
Ball, R.C.2
-
38
-
-
0034687123
-
Topology, stability, sequence and length: Defining the determinants of two-state protein folding kinetics
-
Plaxco KW, Simmons KT, Ruczinski I, Baker D (2000) Topology, stability, sequence and length: defining the determinants of two-state protein folding kinetics. Biochemistry 39:11177-11183.
-
(2000)
Biochemistry
, vol.39
, pp. 11177-11183
-
-
Plaxco, K.W.1
Simmons, K.T.2
Ruczinski, I.3
Baker, D.4
-
39
-
-
0035967862
-
Comparison between long-range interactions and contact order in determining the folding rate of two-state folders: Application of long-range order to folding rate prediction
-
Gromiha MM, Selvaraj S (2001) Comparison between long-range interactions and contact order in determining the folding rate of two-state folders: application of long-range order to folding rate prediction. J Mol Biol 310:27-32.
-
(2001)
J Mol Biol
, vol.310
, pp. 27-32
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
40
-
-
0000355428
-
Respective roles of short- And long-range interactions in protein folding
-
Go N, Taketomi H (1978) Respective roles of short- and long-range interactions in protein folding. Proc Natl Acad Sci USA 75:559-563.
-
(1978)
Proc Natl Acad Sci USA
, vol.75
, pp. 559-563
-
-
Go, N.1
Taketomi, H.2
-
41
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S, Jernigan RL (1985) Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
42
-
-
0027234766
-
Engineering of stable and fast-folding sequences of model proteins
-
Shakhnovich EI, Gutin AM (1993) Engineering of stable and fast-folding sequences of model proteins. Proc Natl Acad Sci USA 90:7195-7199.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 7195-7199
-
-
Shakhnovich, E.I.1
Gutin, A.M.2
-
43
-
-
0031709922
-
Optimizing potentials for the inverse protein folding problem
-
Chiu TL, Goldstein RA (1998) Optimizing potentials for the inverse protein folding problem. Protein Eng 11:749-752.
-
(1998)
Protein Eng
, vol.11
, pp. 749-752
-
-
Chiu, T.L.1
Goldstein, R.A.2
-
44
-
-
0028957666
-
Evolution-like selection of fast-folding model proteins
-
Shakhnovich EI, Gutin AM (1995) Evolution-like selection of fast-folding model proteins. Proc Natl Acad Sci USA 92:1282-1286.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 1282-1286
-
-
Shakhnovich, E.I.1
Gutin, A.M.2
-
45
-
-
21744452297
-
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations
-
Ding F, Guo W, Dokholyan NV, Shakhnovich EI, Shea JE (2005) Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. J Mol Biol 350:1035-1050.
-
(2005)
J Mol Biol
, vol.350
, pp. 1035-1050
-
-
Ding, F.1
Guo, W.2
Dokholyan, N.V.3
Shakhnovich, E.I.4
Shea, J.E.5
-
47
-
-
0000007199
-
On the role of conformational geometry in protein folding
-
Du R, Pande V, Shakhnovich EI (1999) On the role of conformational geometry in protein folding. J Chem Phys 111:10375-10380.
-
(1999)
J Chem Phys
, vol.111
, pp. 10375-10380
-
-
Du, R.1
Pande, V.2
Shakhnovich, E.I.3
-
48
-
-
48249138078
-
Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding
-
Zarrine-Afsar A, Wallin S, Mirela Neculai A, Neudecker P, Howell PL, Davidson AR, Chan HS (2008) Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding. Proc Natl Acad Sci USA 105:9999-10004.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 9999-10004
-
-
Zarrine-Afsar, A.1
Wallin, S.2
Mirela Neculai, A.3
Neudecker, P.4
Howell, P.L.5
Davidson, A.R.6
Chan, H.S.7
-
49
-
-
77649264931
-
Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins
-
Zhang Z, Chan HS (2010) Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins. Proc Natl Acad Sci USA 107:2920-2925.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 2920-2925
-
-
Zhang, Z.1
Chan, H.S.2
-
50
-
-
4243392673
-
Proteins with selected sequences fold into unique native conformation
-
Shakhnovich EI (1994) Proteins with selected sequences fold into unique native conformation. Phys Rev Lett 72:3907-3910.
-
(1994)
Phys Rev Lett
, vol.72
, pp. 3907-3910
-
-
Shakhnovich, E.I.1
-
51
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1958) Equation of state calculations by fast computing machines. J Chem Phys 21:1087-1092.
-
(1958)
J Chem Phys
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
53
-
-
0028981210
-
Negative activation enthalpies in the kinetics of protein folding
-
Oliveberg M, Tan Y, Fersht AR (1995) Negative activation enthalpies in the kinetics of protein folding. Proc Natl Acad Sci USA 92:8926-8929.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 8926-8929
-
-
Oliveberg, M.1
Tan, Y.2
Fersht, A.R.3
-
54
-
-
0001229818
-
Temperature dependence of the folding rate in a simple protein model: Search for a "glass" transition
-
Gutin A, Sali A, Abkevich V, Karplus M, Shakhnovich EI (1998) Temperature dependence of the folding rate in a simple protein model: search for a "glass" transition. J Chem Phys 108:6466-6483.
-
(1998)
J Chem Phys
, vol.108
, pp. 6466-6483
-
-
Gutin, A.1
Sali, A.2
Abkevich, V.3
Karplus, M.4
Shakhnovich, E.I.5
-
55
-
-
0000301323
-
Scaling of folding properties in simple models of proteins
-
Cieplak M, Hoang TX, Li MS (1999) Scaling of folding properties in simple models of proteins. Phys Rev Lett 83:1684-1687. (Pubitemid 129689805)
-
(1999)
Physical Review Letters
, vol.83
, Issue.8
, pp. 1684-1687
-
-
Cieplak, M.1
Hoang, T.X.2
Li, M.S.3
-
56
-
-
0842332830
-
Commitment and nucleation in the protein G transition state
-
Hubner IA, Shimada J, Shakhnovich EI (2004) Commitment and nucleation in the protein G transition state. J Mol Biol 336:745-761.
-
(2004)
J Mol Biol
, vol.336
, pp. 745-761
-
-
Hubner, I.A.1
Shimada, J.2
Shakhnovich, E.I.3
-
57
-
-
34547700512
-
Nucleation phenomena in protein folding: The modulating role of protein sequence
-
Travasso RDM, Faisca PFN, Telo da Gama MM (2007) Nucleation phenomena in protein folding: the modulating role of protein sequence. J Phys Condens Matter 19:285212.
-
(2007)
J Phys Condens Matter
, vol.19
, pp. 285212
-
-
Travasso, R.D.M.1
Faisca, P.F.N.2
Telo Da Gama, M.M.3
|