-
1
-
-
0028024928
-
Specific nucleus as the transition state for protein folding: evidence from the lattice model
-
Abkevich VI, Gutin AM et al (1994) Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 33(33): 10026-10036.
-
(1994)
Biochemistry
, vol.33
, Issue.33
, pp. 10026-10036
-
-
Abkevich, V.I.1
Gutin, A.M.2
-
2
-
-
0029155772
-
Impact of local and non-local interactions on thermodynamics and kinetics of protein folding
-
Abkevich VI, Gutin AM et al (1995) Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J Mol Biol 252(4): 460-471.
-
(1995)
J Mol Biol
, vol.252
, Issue.4
, pp. 460-471
-
-
Abkevich, V.I.1
Gutin, A.M.2
-
3
-
-
0016411482
-
Experimental and theoretical aspects of protein folding
-
Anfinsen CB, Scheraga HA (1975) Experimental and theoretical aspects of protein folding. Adv Protein Chem 29: 205-300.
-
(1975)
Adv Protein Chem
, vol.29
, pp. 205-300
-
-
Anfinsen, C.B.1
Scheraga, H.A.2
-
4
-
-
27744452242
-
Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing
-
Anil B, Sato S et al (2005) Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing. J Mol Biol 354(3): 693-705.
-
(2005)
J Mol Biol
, vol.354
, Issue.3
, pp. 693-705
-
-
Anil, B.1
Sato, S.2
-
5
-
-
0031038377
-
Local interactions in protein folding: lessons from the alpha-helix
-
Aurora R, Creamer TP et al (1997) Local interactions in protein folding: lessons from the alpha-helix. J Biol Chem 272(3): 1413-1416.
-
(1997)
J Biol Chem
, vol.272
, Issue.3
, pp. 1413-1416
-
-
Aurora, R.1
Creamer, T.P.2
-
6
-
-
0029643523
-
Protein folding intermediates: native-state hydrogen exchange
-
Bai Y, Sosnick TR et al (1995) Protein folding intermediates: native-state hydrogen exchange. Science 269(5221): 192-197.
-
(1995)
Science
, vol.269
, Issue.5221
, pp. 192-197
-
-
Bai, Y.1
Sosnick, T.R.2
-
7
-
-
0032972986
-
Is protein folding hierarchic? I. Local structure and peptide folding
-
Baldwin RL, Rose GD (1999a) Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci 24(1): 26-33.
-
(1999)
Trends Biochem Sci
, vol.24
, Issue.1
, pp. 26-33
-
-
Baldwin, R.L.1
Rose, G.D.2
-
8
-
-
0033080081
-
Is protein folding hierarchic? II. Folding intermediates and transition states
-
Baldwin RL, Rose GD (1999b) Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem Sci 24(2): 77-83.
-
(1999)
Trends Biochem Sci
, vol.24
, Issue.2
, pp. 77-83
-
-
Baldwin, R.L.1
Rose, G.D.2
-
9
-
-
0024675910
-
Simultaneous determination of intramolecular distance distributions and conformational dynamics by global analysis of energy transfer measurements
-
Beechem JM, Haas E (1989) Simultaneous determination of intramolecular distance distributions and conformational dynamics by global analysis of energy transfer measurements. Biophys J 55(6): 1225-1236.
-
(1989)
Biophys J
, vol.55
, Issue.6
, pp. 1225-1236
-
-
Beechem, J.M.1
Haas, E.2
-
10
-
-
84865756639
-
An instrument for fast acquisition of fluorescence decay curves at picosecond resolution designed for "double kinetics" experiments: Application to FRET study of protein folding
-
Ben Ishay E, Hazan G, et al (2012a) An instrument for fast acquisition of fluorescence decay curves at picosecond resolution designed for "double kinetics" experiments: Application to FRET study of protein folding. Rev Sci Instruments 83(8): 084301.
-
(2012)
Rev Sci Instruments
, vol.83
, Issue.8
, pp. 084301
-
-
Ben Ishay, E.1
Hazan, G.2
-
11
-
-
84867258888
-
Fast subdomain folding prior to the global refolding transition of E. coli adenylate kinase: a double kinetics study
-
Ben Ishay E, Rahamim G et al (2012b) Fast subdomain folding prior to the global refolding transition of E. coli adenylate kinase: a double kinetics study. J Mol Biol 423(4): 613-623.
-
(2012)
J Mol Biol
, vol.423
, Issue.4
, pp. 613-623
-
-
Ben Ishay, E.1
Rahamim, G.2
-
12
-
-
0036937817
-
Closed loops: persistence of the protein chain returns
-
Berezovsky IN, Kirzhner VM et al (2002) Closed loops: persistence of the protein chain returns. Protein Eng 15(12): 955-957.
-
(2002)
Protein Eng
, vol.15
, Issue.12
, pp. 955-957
-
-
Berezovsky, I.N.1
Kirzhner, V.M.2
-
13
-
-
0034892923
-
Loop fold nature of globular proteins
-
Berezovsky IN, Trifonov EN (2001) Loop fold nature of globular proteins. Protein Eng 14(6): 403-407.
-
(2001)
Protein Eng
, vol.14
, Issue.6
, pp. 403-407
-
-
Berezovsky, I.N.1
Trifonov, E.N.2
-
14
-
-
0036933205
-
Flowering buds of globular proteins: transpiring simplicity of protein organization
-
Berezovsky IN, Trifonov EN (2002) Flowering buds of globular proteins: transpiring simplicity of protein organization. Comp Funct Genomics 3(6): 525-534.
-
(2002)
Comp Funct Genomics
, vol.3
, Issue.6
, pp. 525-534
-
-
Berezovsky, I.N.1
Trifonov, E.N.2
-
15
-
-
32344442512
-
Molecular dimensions and their distributions in early folding intermediates
-
Bilsel O, Matthews CR (2006) Molecular dimensions and their distributions in early folding intermediates. Curr Opin Struct Biol 16(1): 86-93.
-
(2006)
Curr Opin Struct Biol
, vol.16
, Issue.1
, pp. 86-93
-
-
Bilsel, O.1
Matthews, C.R.2
-
16
-
-
46449109015
-
Structure and energetics of the hydrogen-bonded backbone in protein folding
-
Bolen DW, Rose GD (2008) Structure and energetics of the hydrogen-bonded backbone in protein folding. Annu Rev Biochem 77: 339-362.
-
(2008)
Annu Rev Biochem
, vol.77
, pp. 339-362
-
-
Bolen, D.W.1
Rose, G.D.2
-
17
-
-
0028328263
-
An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function
-
Bowie JU, Eisenberg D (1994) An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci USA 91(10): 4436-4440.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, Issue.10
, pp. 4436-4440
-
-
Bowie, J.U.1
Eisenberg, D.2
-
18
-
-
0041735179
-
Kinetics of intramolecular contact formation in a denatured protein
-
Buscaglia M, Schuler B et al (2003) Kinetics of intramolecular contact formation in a denatured protein. J Mol Biol 332(1): 9-12.
-
(2003)
J Mol Biol
, vol.332
, Issue.1
, pp. 9-12
-
-
Buscaglia, M.1
Schuler, B.2
-
19
-
-
0029028698
-
Modeling the role of disulfide bonds in protein folding: entropic barriers and pathways
-
Camacho CJ, Thirumalai D (1995) Modeling the role of disulfide bonds in protein folding: entropic barriers and pathways. Proteins 22(1): 27-40.
-
(1995)
Proteins
, vol.22
, Issue.1
, pp. 27-40
-
-
Camacho, C.J.1
Thirumalai, D.2
-
20
-
-
79953747234
-
Cooperativity, local-non-local coupling, and nonnative interactions: principles of protein folding from coarse-grained models
-
Chan HS, Zhang Z et al (2011) Cooperativity, local-non-local coupling, and nonnative interactions: principles of protein folding from coarse-grained models. Annu Rev Phys Chem 62: 301-326.
-
(2011)
Annu Rev Phys Chem
, vol.62
, pp. 301-326
-
-
Chan, H.S.1
Zhang, Z.2
-
21
-
-
33644760365
-
Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study
-
Chikenji G, Fujitsuka Y et al (2006) Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study. Proc Natl Acad Sci USA 103(9): 3141-3146.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.9
, pp. 3141-3146
-
-
Chikenji, G.1
Fujitsuka, Y.2
-
22
-
-
78149421274
-
Closed loop folding units from structural alignments: experimental foldons revisited
-
Chintapalli SV, Yew BK et al (2010) Closed loop folding units from structural alignments: experimental foldons revisited. J Comput Chem 31(15): 2689-2701.
-
(2010)
J Comput Chem
, vol.31
, Issue.15
, pp. 2689-2701
-
-
Chintapalli, S.V.1
Yew, B.K.2
-
23
-
-
0033253913
-
Folding initiation sites and protein folding
-
Dadlez M (1999) Folding initiation sites and protein folding. Acta Biochim Pol 46(3): 487-508.
-
(1999)
Acta Biochim Pol
, vol.46
, Issue.3
, pp. 487-508
-
-
Dadlez, M.1
-
24
-
-
0037221599
-
Is there a unifying mechanism for protein folding?
-
Daggett V, Fersht AR (2003) Is there a unifying mechanism for protein folding? Trends Biochem Sci 28(1): 18-25.
-
(2003)
Trends Biochem Sci
, vol.28
, Issue.1
, pp. 18-25
-
-
Daggett, V.1
Fersht, A.R.2
-
25
-
-
0027405357
-
Cooperativity in protein-folding kinetics
-
Dill KA, Fiebig KM et al (1993) Cooperativity in protein-folding kinetics. Proc Natl Acad Sci USA 90(5): 1942-1946.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, Issue.5
, pp. 1942-1946
-
-
Dill, K.A.1
Fiebig, K.M.2
-
26
-
-
48249134448
-
The protein folding problem
-
Dill KA, Ozkan SB et al (2008) The protein folding problem. Annu Rev Biophys 37: 289-316.
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 289-316
-
-
Dill, K.A.1
Ozkan, S.B.2
-
27
-
-
0034628914
-
Identifying the protein folding nucleus using molecular dynamics
-
Dokholyan NV, Buldyrev SV et al (2000) Identifying the protein folding nucleus using molecular dynamics. J Mol Biol 296(5): 1183-1188.
-
(2000)
J Mol Biol
, vol.296
, Issue.5
, pp. 1183-1188
-
-
Dokholyan, N.V.1
Buldyrev, S.V.2
-
28
-
-
42449151176
-
Protein folding and misfolding: mechanism and principles
-
Englander SW, Mayne L et al (2007) Protein folding and misfolding: mechanism and principles. Q Rev Biophys 40(4): 287-326.
-
(2007)
Q Rev Biophys
, vol.40
, Issue.4
, pp. 287-326
-
-
Englander, S.W.1
Mayne, L.2
-
29
-
-
44049097465
-
Modeling transient collapsed states of an unfolded protein to provide insights into early folding events
-
Felitsky DJ, Lietzow MA et al (2008) Modeling transient collapsed states of an unfolded protein to provide insights into early folding events. Proc Natl Acad Sci USA 105(17): 6278-6283.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.17
, pp. 6278-6283
-
-
Felitsky, D.J.1
Lietzow, M.A.2
-
30
-
-
0028856785
-
Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications
-
Fersht AR (1995) Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc Natl Acad Sci USA 92(24): 10869-10873.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, Issue.24
, pp. 10869-10873
-
-
Fersht, A.R.1
-
31
-
-
0031043161
-
Nucleation mechanisms in protein folding
-
Fersht AR (1997) Nucleation mechanisms in protein folding. Curr Opin Struct Biol 7(1): 3-9.
-
(1997)
Curr Opin Struct Biol
, vol.7
, Issue.1
, pp. 3-9
-
-
Fersht, A.R.1
-
32
-
-
0034652206
-
Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism
-
Fersht AR (2000) Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. Proc Natl Acad Sci USA 97(4): 1525-1529.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.4
, pp. 1525-1529
-
-
Fersht, A.R.1
-
33
-
-
0037154980
-
Protein folding and unfolding at atomic resolution
-
Fersht AR, Daggett V (2002) Protein folding and unfolding at atomic resolution. Cell 108(4): 573-582.
-
(2002)
Cell
, vol.108
, Issue.4
, pp. 573-582
-
-
Fersht, A.R.1
Daggett, V.2
-
34
-
-
0024745242
-
Theory of cooperative transitions in protein molecules. II. Phase diagram for a protein molecule in solution
-
Finkelstein AV, Shakhnovich EI (1989) Theory of cooperative transitions in protein molecules. II. Phase diagram for a protein molecule in solution. Biopolymers 28(10): 1681-1694.
-
(1989)
Biopolymers
, vol.28
, Issue.10
, pp. 1681-1694
-
-
Finkelstein, A.V.1
Shakhnovich, E.I.2
-
35
-
-
0032812796
-
Mapping the interactions present in the transition state for unfolding/folding of FKBP12
-
Fulton KF, Main ER et al (1999) Mapping the interactions present in the transition state for unfolding/folding of FKBP12. J Mol Biol 291(2): 445-461.
-
(1999)
J Mol Biol
, vol.291
, Issue.2
, pp. 445-461
-
-
Fulton, K.F.1
Main, E.R.2
-
36
-
-
5144220785
-
Comparison of the transition states for folding of two Ig-like proteins from different superfamilies
-
Geierhaas CD, Paci E et al (2004) Comparison of the transition states for folding of two Ig-like proteins from different superfamilies. J Mol Biol 343(4): 1111-1123.
-
(2004)
J Mol Biol
, vol.343
, Issue.4
, pp. 1111-1123
-
-
Geierhaas, C.D.1
Paci, E.2
-
37
-
-
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(2): 559-563.
-
(1978)
Proc Natl Acad Sci USA
, vol.75
, Issue.2
, pp. 559-563
-
-
Go, N.1
Taketomi, H.2
-
38
-
-
0026663720
-
Optimal protein-folding codes from spin-glass theory
-
Goldstein RA, Luthey-Schulten ZA et al (1992) Optimal protein-folding codes from spin-glass theory. Proc Natl Acad Sci USA 89(11): 4918-4922.
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, Issue.11
, pp. 4918-4922
-
-
Goldstein, R.A.1
Luthey-Schulten, Z.A.2
-
39
-
-
0035967862
-
Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: 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 proteins: application of long-range order to folding rate prediction. J Mol Biol 310(1): 27-32.
-
(2001)
J Mol Biol
, vol.310
, Issue.1
, pp. 27-32
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
40
-
-
0035339911
-
Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape
-
Gulotta M, Gilmanshin R et al (2001) Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape. Biochemistry 40(17): 5137-5143.
-
(2001)
Biochemistry
, vol.40
, Issue.17
, pp. 5137-5143
-
-
Gulotta, M.1
Gilmanshin, R.2
-
41
-
-
18744389451
-
The study of protein folding and dynamics by determination of intramolecular distance distributions and their fluctuations using ensemble and single-molecule FRET measurements
-
Haas E (2005) The study of protein folding and dynamics by determination of intramolecular distance distributions and their fluctuations using ensemble and single-molecule FRET measurements. Chemphyschem 6(5): 858-870.
-
(2005)
Chemphyschem
, vol.6
, Issue.5
, pp. 858-870
-
-
Haas, E.1
-
42
-
-
0001756859
-
Is there a single pathway for the folding of a polypeptide chain?
-
Harrison SC, Durbin R (1985) Is there a single pathway for the folding of a polypeptide chain? Proc Natl Acad Sci USA 82(12): 4028-4030.
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, Issue.12
, pp. 4028-4030
-
-
Harrison, S.C.1
Durbin, R.2
-
43
-
-
0345701546
-
Hierarchical protein folding pathways: a computational study of protein fragments
-
Haspel N, Tsai CJ et al (2003a) Hierarchical protein folding pathways: a computational study of protein fragments. Proteins 51(2): 203-215.
-
(2003)
Proteins
, vol.51
, Issue.2
, pp. 203-215
-
-
Haspel, N.1
Tsai, C.J.2
-
44
-
-
0037907566
-
Reducing the computational complexity of protein folding via fragment folding and assembly
-
Haspel N, Tsai CJ et al (2003b) Reducing the computational complexity of protein folding via fragment folding and assembly. Protein Sci 12(6): 1177-1187.
-
(2003)
Protein Sci
, vol.12
, Issue.6
, pp. 1177-1187
-
-
Haspel, N.1
Tsai, C.J.2
-
45
-
-
0038786578
-
Folding units govern the cytochrome c alkaline transition
-
Hoang L, Maity H et al (2003) Folding units govern the cytochrome c alkaline transition. J Mol Biol 331(1): 37-43.
-
(2003)
J Mol Biol
, vol.331
, Issue.1
, pp. 37-43
-
-
Hoang, L.1
Maity, H.2
-
46
-
-
18844459862
-
Nucleation and the transition state of the SH3 domain
-
Hubner IA, Edmonds KA et al (2005) Nucleation and the transition state of the SH3 domain. J Mol Biol 349(2): 424-434.
-
(2005)
J Mol Biol
, vol.349
, Issue.2
, pp. 424-434
-
-
Hubner, I.A.1
Edmonds, K.A.2
-
47
-
-
2942590388
-
Simulation, experiment, and evolution: understanding nucleation in protein S6 folding
-
Hubner IA, Oliveberg M et al (2004a) Simulation, experiment, and evolution: understanding nucleation in protein S6 folding. Proc Natl Acad Sci USA 101(22): 8354-8359.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.22
, pp. 8354-8359
-
-
Hubner, I.A.1
Oliveberg, M.2
-
48
-
-
0842332830
-
Commitment and nucleation in the protein G transition state
-
Hubner IA, Shimada J et al (2004b) Commitment and nucleation in the protein G transition state. J Mol Biol 336(3): 745-761.
-
(2004)
J Mol Biol
, vol.336
, Issue.3
, pp. 745-761
-
-
Hubner, I.A.1
Shimada, J.2
-
50
-
-
0028936789
-
Non-local interactions stabilize long range loops in the initial folding intermediates of reduced bovine pancreatic trypsin inhibitor
-
Ittah V, Haas E (1995) Non-local interactions stabilize long range loops in the initial folding intermediates of reduced bovine pancreatic trypsin inhibitor. Biochemistry 34(13): 4493-4506.
-
(1995)
Biochemistry
, vol.34
, Issue.13
, pp. 4493-4506
-
-
Ittah, V.1
Haas, E.2
-
51
-
-
0042510944
-
Contact order revisited: influence of protein size on the folding rate
-
Ivankov DN, Garbuzynskiy SO et al (2003) Contact order revisited: influence of protein size on the folding rate. Protein Sci 12(9): 2057-2062.
-
(2003)
Protein Sci
, vol.12
, Issue.9
, pp. 2057-2062
-
-
Ivankov, D.N.1
Garbuzynskiy, S.O.2
-
52
-
-
27144464106
-
Predicting reactivities of protein surface cysteines as part of a strategy for selective multiple labeling
-
Jacob MH, Amir D et al (2005) Predicting reactivities of protein surface cysteines as part of a strategy for selective multiple labeling. Biochemistry 44(42): 13664-13672.
-
(2005)
Biochemistry
, vol.44
, Issue.42
, pp. 13664-13672
-
-
Jacob, M.H.1
Amir, D.2
-
53
-
-
33750468665
-
Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
-
Juraszek J, Bolhuis PG (2006) Sampling the multiple folding mechanisms of Trp-cage in explicit solvent. Proc Natl Acad Sci USA 103(43): 15859-15864.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.43
, pp. 15859-15864
-
-
Juraszek, J.1
Bolhuis, P.G.2
-
54
-
-
0017251893
-
Protein-folding dynamics
-
Karplus M, Weaver DL (1976) Protein-folding dynamics. Nature 260(5550): 404-406.
-
(1976)
Nature
, vol.260
, Issue.5550
, pp. 404-406
-
-
Karplus, M.1
Weaver, D.L.2
-
55
-
-
77249159354
-
non-local interactions are responsible for tertiary structure formation in staphylococcal nuclease
-
Kato S, Kamikubo H et al (2010) non-local interactions are responsible for tertiary structure formation in staphylococcal nuclease. Biophys J 98(4): 678-686.
-
(2010)
Biophys J
, vol.98
, Issue.4
, pp. 678-686
-
-
Kato, S.1
Kamikubo, H.2
-
56
-
-
23644456329
-
The effect of long-range interactions on the secondary structure formation of proteins
-
Kihara D (2005) The effect of long-range interactions on the secondary structure formation of proteins. Protein Sci 14(8): 1955-1963.
-
(2005)
Protein Sci
, vol.14
, Issue.8
, pp. 1955-1963
-
-
Kihara, D.1
-
57
-
-
0020024242
-
Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding
-
Kim PS, Baldwin RL (1982) Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem 51: 459-489.
-
(1982)
Annu Rev Biochem
, vol.51
, pp. 459-489
-
-
Kim, P.S.1
Baldwin, R.L.2
-
58
-
-
33846041173
-
Site-specific collapse dynamics guide the formation of the cytochrome c' four-helix bundle
-
Kimura T, Lee JC et al (2007) Site-specific collapse dynamics guide the formation of the cytochrome c' four-helix bundle. Proc Natl Acad Sci USA 104(1): 117-122.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.1
, pp. 117-122
-
-
Kimura, T.1
Lee, J.C.2
-
59
-
-
1442348207
-
Discerning the structure and energy of multiple transition states in protein folding using psi-analysis
-
Krantz BA, Dothager RS et al (2004) Discerning the structure and energy of multiple transition states in protein folding using psi-analysis. J Mol Biol 337(2): 463-475.
-
(2004)
J Mol Biol
, vol.337
, Issue.2
, pp. 463-475
-
-
Krantz, B.A.1
Dothager, R.S.2
-
60
-
-
0036440985
-
Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding
-
Krantz BA, Mayne L et al (2002) Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J Mol Biol 324(2): 359-371.
-
(2002)
J Mol Biol
, vol.324
, Issue.2
, pp. 359-371
-
-
Krantz, B.A.1
Mayne, L.2
-
61
-
-
0043237588
-
Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding
-
Krieger F, Fierz B et al (2003) Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. J Mol Biol 332(1): 265-274.
-
(2003)
J Mol Biol
, vol.332
, Issue.1
, pp. 265-274
-
-
Krieger, F.1
Fierz, B.2
-
62
-
-
0034691198
-
Measuring the rate of intramolecular contact formation in polypeptides
-
Lapidus LJ, Eaton WA et al (2000) Measuring the rate of intramolecular contact formation in polypeptides. Proc Natl Acad Sci USA 97(13): 7220-7225.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.13
, pp. 7220-7225
-
-
Lapidus, L.J.1
Eaton, W.A.2
-
63
-
-
34447292770
-
Protein hydrophobic collapse and early folding steps observed in a microfluidic mixer
-
Lapidus LJ, Yao S et al (2007) Protein hydrophobic collapse and early folding steps observed in a microfluidic mixer. Biophys J 93(1): 218-224.
-
(2007)
Biophys J
, vol.93
, Issue.1
, pp. 218-224
-
-
Lapidus, L.J.1
Yao, S.2
-
64
-
-
36549027487
-
Plasticity within the obligatory folding nucleus of an immunoglobulin-like domain
-
Lappalainen I, Hurley MG et al (2008) Plasticity within the obligatory folding nucleus of an immunoglobulin-like domain. J Mol Biol 375(2): 547-559.
-
(2008)
J Mol Biol
, vol.375
, Issue.2
, pp. 547-559
-
-
Lappalainen, I.1
Hurley, M.G.2
-
65
-
-
0033514939
-
Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
-
Lee J, Liwo A et al (1999) Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. Proc Natl Acad Sci USA 96(5): 2025-2030.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, Issue.5
, pp. 2025-2030
-
-
Lee, J.1
Liwo, A.2
-
66
-
-
0026754015
-
Accurate modeling of protein conformation by automatic segment matching
-
Levitt M (1992) Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 226(2): 507-533.
-
(1992)
J Mol Biol
, vol.226
, Issue.2
, pp. 507-533
-
-
Levitt, M.1
-
67
-
-
11844289547
-
Protein folding and the organization of the protein topology universe
-
Lindorff-Larsen K, Rogen P et al (2005) Protein folding and the organization of the protein topology universe. Trends Biochem Sci 30(1): 13-19.
-
(2005)
Trends Biochem Sci
, vol.30
, Issue.1
, pp. 13-19
-
-
Lindorff-Larsen, K.1
Rogen, P.2
-
68
-
-
2342451295
-
Transition states for protein folding have native topologies despite high structural variability
-
Lindorff-Larsen K, Vendruscolo M et al (2004) Transition states for protein folding have native topologies despite high structural variability. Nat Struct Mol Biol 11(5): 443-449.
-
(2004)
Nat Struct Mol Biol
, vol.11
, Issue.5
, pp. 443-449
-
-
Lindorff-Larsen, K.1
Vendruscolo, M.2
-
69
-
-
77950803518
-
Prediction of stability upon point mutation in the context of the folding nucleus
-
Lonquety M, Chomilier J et al (2009) Prediction of stability upon point mutation in the context of the folding nucleus. OMICS 14(2): 151-156.
-
(2009)
Omics
, vol.14
, Issue.2
, pp. 151-156
-
-
Lonquety, M.1
Chomilier, J.2
-
70
-
-
4544273743
-
Fast folding of a helical protein initiated by the collision of unstructured chains
-
Meisner WK, Sosnick TR (2004) Fast folding of a helical protein initiated by the collision of unstructured chains. Proc Natl Acad Sci USA 101(37): 13478-13482.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.37
, pp. 13478-13482
-
-
Meisner, W.K.1
Sosnick, T.R.2
-
71
-
-
0034984144
-
Protein folding theory: from lattice to all-atom models
-
Mirny L, Shakhnovich E (2001) Protein folding theory: from lattice to all-atom models. Annu Rev Biophys Biomol Struct 30: 361-396.
-
(2001)
Annu Rev Biophys Biomol Struct
, vol.30
, pp. 361-396
-
-
Mirny, L.1
Shakhnovich, E.2
-
72
-
-
0025906759
-
An analysis of protein folding pathways
-
Moult J, Unger R (1991) An analysis of protein folding pathways. Biochemistry 30(16): 3816-3824.
-
(1991)
Biochemistry
, vol.30
, Issue.16
, pp. 3816-3824
-
-
Moult, J.1
Unger, R.2
-
73
-
-
0024293117
-
Structure of the complex of adenylate kinase from Escherichia coli with the inhibitor P1, P5-di(adenosine-5′-)pentaphosphate
-
Muller CW, Schulz GE (1988) Structure of the complex of adenylate kinase from Escherichia coli with the inhibitor P1, P5-di(adenosine-5′-)pentaphosphate. J Mol Biol 202(4): 909-912.
-
(1988)
J Mol Biol
, vol.202
, Issue.4
, pp. 909-912
-
-
Muller, C.W.1
Schulz, G.E.2
-
74
-
-
0026544877
-
Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state
-
Muller CW, Schulz GE (1992) Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1. 9 A resolution. A model for a catalytic transition state. J Mol Biol 224(1): 159-177.
-
(1992)
J Mol Biol
, vol.224
, Issue.1
, pp. 159-177
-
-
Muller, C.W.1
Schulz, G.E.2
-
75
-
-
0030627747
-
Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude
-
Munson M, Anderson KS et al (1997) Speeding up protein folding: mutations that increase the rate at which Rop folds and unfolds by over four orders of magnitude. Fold Des 2(1): 77-87.
-
(1997)
Fold Des
, vol.2
, Issue.1
, pp. 77-87
-
-
Munson, M.1
Anderson, K.S.2
-
76
-
-
22444443996
-
Sequence determinants of a protein folding pathway
-
Nishimura C, Lietzow MA et al (2005) Sequence determinants of a protein folding pathway. J Mol Biol 351(2): 383-392.
-
(2005)
J Mol Biol
, vol.351
, Issue.2
, pp. 383-392
-
-
Nishimura, C.1
Lietzow, M.A.2
-
77
-
-
0016436058
-
Crystalline adenylate kinase from carp muscle
-
Noda L, Schulz GE et al (1975) Crystalline adenylate kinase from carp muscle. Eur J Biochem 51(1): 229-235.
-
(1975)
Eur J Biochem
, vol.51
, Issue.1
, pp. 229-235
-
-
Noda, L.1
Schulz, G.E.2
-
78
-
-
84873304972
-
Non local residue-residue contacts in proteins are more conserved than local ones
-
Noivirt-Brik O, Hazan G et al (2013) Non local residue-residue contacts in proteins are more conserved than local ones. Bioinformatics 29(3): 331-337.
-
(2013)
Bioinformatics
, vol.29
, Issue.3
, pp. 331-337
-
-
Noivirt-Brik, O.1
Hazan, G.2
-
79
-
-
0036172116
-
Hydrophobic core packing in the SH3 domain folding transition state
-
Northey JG, Di Nardo AA et al (2002) Hydrophobic core packing in the SH3 domain folding transition state. Nat Struct Biol 9(2): 126-130.
-
(2002)
Nat Struct Biol
, vol.9
, Issue.2
, pp. 126-130
-
-
Northey, J.G.1
Di Nardo, A.A.2
-
80
-
-
0034723140
-
Localized, stereochemically sensitive hydrophobic packing in an early folding intermediate of dihydrofolate reductase from Escherichia coli
-
O'Neill JC Jr, Robert Matthews C (2000) Localized, stereochemically sensitive hydrophobic packing in an early folding intermediate of dihydrofolate reductase from Escherichia coli. J Mol Biol 295(4): 737-744.
-
(2000)
J Mol Biol
, vol.295
, Issue.4
, pp. 737-744
-
-
O'Neill Jr., J.C.1
Robert Matthews, C.2
-
81
-
-
58149396567
-
Early closure of a long loop in the refolding of adenylate kinase: a possible key role of non-local interactions in the initial folding steps
-
Orevi T, Ben Ishay E et al (2009) Early closure of a long loop in the refolding of adenylate kinase: a possible key role of non-local interactions in the initial folding steps. J Mol Biol 385(4): 1230-1242.
-
(2009)
J Mol Biol
, vol.385
, Issue.4
, pp. 1230-1242
-
-
Orevi, T.1
Ben Ishay, E.2
-
82
-
-
34547551805
-
Protein folding by zipping and assembly
-
Ozkan SB, Wu GA et al (2007) Protein folding by zipping and assembly. Proc Natl Acad Sci USA 104(29): 11987-11992.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.29
, pp. 11987-11992
-
-
Ozkan, S.B.1
Wu, G.A.2
-
83
-
-
0037457892
-
Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain
-
Paci E, Clarke J et al (2003) Self-consistent determination of the transition state for protein folding: application to a fibronectin type III domain. Proc Natl Acad Sci USA 100(2): 394-399.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.2
, pp. 394-399
-
-
Paci, E.1
Clarke, J.2
-
84
-
-
11244343926
-
Universal positions in globular proteins
-
Papandreou N, Berezovsky IN et al (2004) Universal positions in globular proteins. Eur J Biochem 271(23-24): 4762-4768.
-
(2004)
Eur J Biochem
, vol.271
, Issue.23-24
, pp. 4762-4768
-
-
Papandreou, N.1
Berezovsky, I.N.2
-
85
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco KW, Simons KT et al (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277(4): 985-994.
-
(1998)
J Mol Biol
, vol.277
, Issue.4
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
-
86
-
-
73049092594
-
Prediction of the protein folding core: application to the immunoglobulin fold
-
Prudhomme N, Chomilier J (2009) Prediction of the protein folding core: application to the immunoglobulin fold. Biochimie 91(11-12): 1465-1474.
-
(2009)
Biochimie
, vol.91
, Issue.11-12
, pp. 1465-1474
-
-
Prudhomme, N.1
Chomilier, J.2
-
87
-
-
0015920746
-
Stages in the mechanism of self-organization of protein molecules
-
Ptitsyn OB (1973) Stages in the mechanism of self-organization of protein molecules. Dokl Akad Nauk SSSR 210(5): 1213-1215.
-
(1973)
Dokl Akad Nauk SSSR
, vol.210
, Issue.5
, pp. 1213-1215
-
-
Ptitsyn, O.B.1
-
88
-
-
24044490917
-
Fast collapse but slow formation of secondary structure elements in the refolding transition of E. coli adenylate kinase
-
Ratner V, Amir D et al (2005) Fast collapse but slow formation of secondary structure elements in the refolding transition of E. coli adenylate kinase. J Mol Biol 352(3): 683-699.
-
(2005)
J Mol Biol
, vol.352
, Issue.3
, pp. 683-699
-
-
Ratner, V.1
Amir, D.2
-
89
-
-
0034705335
-
Determination of intramolecular distance distribution during protein folding on the millisecond timescale
-
Ratner V, Sinev M et al (2000) Determination of intramolecular distance distribution during protein folding on the millisecond timescale. J Mol Biol 299(5): 1363-1371.
-
(2000)
J Mol Biol
, vol.299
, Issue.5
, pp. 1363-1371
-
-
Ratner, V.1
Sinev, M.2
-
90
-
-
0026447086
-
Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions
-
Rooman MJ, Kocher JP et al (1992) Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry 31(42): 10226-10238.
-
(1992)
Biochemistry
, vol.31
, Issue.42
, pp. 10226-10238
-
-
Rooman, M.J.1
Kocher, J.P.2
-
91
-
-
0028174310
-
How does a protein fold?
-
Sali A, Shakhnovich E et al (1994) How does a protein fold? Nature 369(6477): 248-251.
-
(1994)
Nature
, vol.369
, Issue.6477
, pp. 248-251
-
-
Sali, A.1
Shakhnovich, E.2
-
92
-
-
70349448685
-
How strong are side chain interactions in the folding intermediate?
-
Samatova EN, Katina NS et al (2009) How strong are side chain interactions in the folding intermediate? Protein Sci 18(10): 2152-2159.
-
(2009)
Protein Sci
, vol.18
, Issue.10
, pp. 2152-2159
-
-
Samatova, E.N.1
Katina, N.S.2
-
93
-
-
0037305938
-
Low free energy cost of very long loop insertions in proteins
-
Scalley-Kim M, Minard P et al (2003) Low free energy cost of very long loop insertions in proteins. Protein Sci 12(2): 197-206.
-
(2003)
Protein Sci
, vol.12
, Issue.2
, pp. 197-206
-
-
Scalley-Kim, M.1
Minard, P.2
-
94
-
-
0025340754
-
Induced-fit movements in adenylate kinases
-
Schulz GE, Muller CW et al (1990) Induced-fit movements in adenylate kinases. J Mol Biol 213(4): 627-630.
-
(1990)
J Mol Biol
, vol.213
, Issue.4
, pp. 627-630
-
-
Schulz, G.E.1
Muller, C.W.2
-
95
-
-
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(24): 3907-3910.
-
(1994)
Phys Rev Lett
, vol.72
, Issue.24
, pp. 3907-3910
-
-
Shakhnovich, E.I.1
-
96
-
-
0027234766
-
Engineering of stable and fast-folding sequences of model proteins
-
Shakhnovich EI, Gutin AM (1993a) Engineering of stable and fast-folding sequences of model proteins. Proc Natl Acad Sci USA 90(15): 7195-7199.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, Issue.15
, pp. 7195-7199
-
-
Shakhnovich, E.I.1
Gutin, A.M.2
-
97
-
-
0027438090
-
A new approach to the design of stable proteins
-
Shakhnovich EI, Gutin AM (1993b) A new approach to the design of stable proteins. Protein Eng 6(8): 793-800.
-
(1993)
Protein Eng
, vol.6
, Issue.8
, pp. 793-800
-
-
Shakhnovich, E.I.1
Gutin, A.M.2
-
98
-
-
61549140397
-
Blind test of physics-based prediction of protein structures
-
Shell MS, Ozkan SB et al (2009) Blind test of physics-based prediction of protein structures. Biophys J 96(3): 917-924.
-
(2009)
Biophys J
, vol.96
, Issue.3
, pp. 917-924
-
-
Shell, M.S.1
Ozkan, S.B.2
-
99
-
-
0024963569
-
Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitutions
-
Shortle D, Meeker AK (1989) Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitutions. Biochemistry 28(3): 936-944.
-
(1989)
Biochemistry
, vol.28
, Issue.3
, pp. 936-944
-
-
Shortle, D.1
Meeker, A.K.2
-
100
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons KT, Kooperberg C et al (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268(1): 209-225.
-
(1997)
J Mol Biol
, vol.268
, Issue.1
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
-
101
-
-
34249748424
-
Dissecting the non-specific and specific components of the initial folding reaction of barstar by multi-site FRET measurements
-
Sinha KK, Udgaonkar JB (2007) Dissecting the non-specific and specific components of the initial folding reaction of barstar by multi-site FRET measurements. J Mol Biol 370(2): 385-405.
-
(2007)
J Mol Biol
, vol.370
, Issue.2
, pp. 385-405
-
-
Sinha, K.K.1
Udgaonkar, J.B.2
-
102
-
-
10644261303
-
Differences in the folding transition state of ubiquitin indicated by phi and psi analyses
-
Sosnick TR, Dothager RS et al (2004) Differences in the folding transition state of ubiquitin indicated by phi and psi analyses. Proc Natl Acad Sci USA 101(50): 17377-17382.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.50
, pp. 17377-17382
-
-
Sosnick, T.R.1
Dothager, R.S.2
-
103
-
-
0028402689
-
The barriers in protein folding
-
Sosnick TR, Mayne L et al (1994) The barriers in protein folding. Nat Struct Biol 1(3): 149-156.
-
(1994)
Nat Struct Biol
, vol.1
, Issue.3
, pp. 149-156
-
-
Sosnick, T.R.1
Mayne, L.2
-
104
-
-
65549171633
-
Topology is the principal determinant in the folding of a complex all-alpha Greek key death domain from human FADD
-
Steward A, McDowell GS et al (2009) Topology is the principal determinant in the folding of a complex all-alpha Greek key death domain from human FADD. J Mol Biol 389(2): 425-437.
-
(2009)
J Mol Biol
, vol.389
, Issue.2
, pp. 425-437
-
-
Steward, A.1
McDowell, G.S.2
-
105
-
-
0016696599
-
Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions
-
Taketomi H, Ueda Y et al (1975) Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. Int J Pept Protein Res 7(6): 445-459.
-
(1975)
Int J Pept Protein Res
, vol.7
, Issue.6
, pp. 445-459
-
-
Taketomi, H.1
Ueda, Y.2
-
106
-
-
79955917231
-
Backbone-driven collapse in unfolded protein chains
-
Teufel DP, Johnson CM et al (2011) Backbone-driven collapse in unfolded protein chains. J Mol Biol 409(2): 250-262.
-
(2011)
J Mol Biol
, vol.409
, Issue.2
, pp. 250-262
-
-
Teufel, D.P.1
Johnson, C.M.2
-
107
-
-
46849118765
-
Hydrophobic condensation and modular assembly model of protein folding
-
Tsong TY, Hu CK et al (2008) Hydrophobic condensation and modular assembly model of protein folding. Biosystems 93(1-2): 78-89.
-
(2008)
Biosystems
, vol.93
, Issue.1-2
, pp. 78-89
-
-
Tsong, T.Y.1
Hu, C.K.2
-
108
-
-
0030604696
-
Local interactions dominate folding in a simple protein model
-
Unger R, Moult J (1996) Local interactions dominate folding in a simple protein model. J Mol Biol 259(5): 988-994.
-
(1996)
J Mol Biol
, vol.259
, Issue.5
, pp. 988-994
-
-
Unger, R.1
Moult, J.2
-
109
-
-
26244449482
-
Loop entropy and cytochrome c stability
-
Wang L, Rivera EV et al (2005) Loop entropy and cytochrome c stability. J Mol Biol 353(3): 719-729.
-
(2005)
J Mol Biol
, vol.353
, Issue.3
, pp. 719-729
-
-
Wang, L.1
Rivera, E.V.2
-
110
-
-
36749066113
-
Loop-closure principles in protein folding
-
Weikl TR (2008) Loop-closure principles in protein folding. Arch Biochem Biophys 469(1): 67-75.
-
(2008)
Arch Biochem Biophys
, vol.469
, Issue.1
, pp. 67-75
-
-
Weikl, T.R.1
-
111
-
-
0038630483
-
Folding rates and low-entropy-loss routes of two-state proteins
-
Weikl TR, Dill KA (2003) Folding rates and low-entropy-loss routes of two-state proteins. J Mol Biol 329(3): 585-598.
-
(2003)
J Mol Biol
, vol.329
, Issue.3
, pp. 585-598
-
-
Weikl, T.R.1
Dill, K.A.2
-
112
-
-
0015597839
-
Nucleation, rapid folding, and globular intrachain regions in proteins
-
Wetlaufer DB (1973) Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA 70(3): 697-701.
-
(1973)
Proc Natl Acad Sci USA
, vol.70
, Issue.3
, pp. 697-701
-
-
Wetlaufer, D.B.1
-
113
-
-
0024293204
-
Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding
-
Wright PE, Dyson HJ et al (1988) Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding. Biochemistry 27(19): 7167-7175.
-
(1988)
Biochemistry
, vol.27
, Issue.19
, pp. 7167-7175
-
-
Wright, P.E.1
Dyson, H.J.2
-
114
-
-
51649106422
-
Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein
-
Wu Y, Kondrashkina E et al (2008) Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein. Proc Natl Acad Sci USA 105(36): 13367-13372.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.36
, pp. 13367-13372
-
-
Wu, Y.1
Kondrashkina, E.2
-
115
-
-
84871375244
-
Transition paths, diffusive processes, and preequilibria of protein folding
-
Zhang Z, Chan HS (2013) Transition paths, diffusive processes, and preequilibria of protein folding. Proc Natl Acad Sci USA 109(51): 20919-20924.
-
(2013)
Proc Natl Acad Sci USA
, vol.109
, Issue.51
, pp. 20919-20924
-
-
Zhang, Z.1
Chan, H.S.2
|