-
1
-
-
0009586942
-
Understanding protein folding via free-energy surfaces from theory and experiment
-
DOI 10.1016/S0968-0004(00)01610-8, PII S0968000400016108
-
A. R. Dinner, A. Šali, L. J. Smith, C. M. Dobson, and M. Karplus, Trends Biochem. Sci. 0968-0004 10.101 (Pubitemid 30421099)
-
(2000)
Trends in Biochemical Sciences
, vol.25
, Issue.7
, pp. 331-339
-
-
Dinner, A.R.1
Salib, A.2
Smitha, L.J.3
Dobsona, C.M.4
Karplus, M.5
-
3
-
-
0344301982
-
Protein folding: A perspective from theory and experiment
-
DOI 10.1002/(SICI)1521-3773(19980420)37:7<868::AID-ANIE868>3.0. CO;2-H
-
C. M. Dobson, A. Šali, and M. Karplus, Angew. Chem., Int. Ed. Engl. ARPLAP 1433-7851 10.1002/(SICI)1521-3773(19980420)37:7<868::AID- ANIE868>3.0.CO;2-H 37, 868 (1998). (Pubitemid 28228882)
-
(1998)
Angewandte Chemie - International Edition
, vol.37
, Issue.7
, pp. 868-893
-
-
Dobson, C.M.1
Sali, A.2
Karplus, M.3
-
4
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
DOI 10.1146/annurev.physchem.52.1.499
-
J.-E. Shea and C. L. Brooks III, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.52.1.499 52, 499 (2001). (Pubitemid 33655131)
-
(2001)
Annual Review of Physical Chemistry
, vol.52
, pp. 499-535
-
-
Shea, J.-E.1
Brooks III, C.L.2
-
5
-
-
48249134448
-
-
ARPLAP 1936-122X 10.1146/annurev.biophys.37.092707.153558
-
K. A. Dill, S. B. Ozkan, M. S. Shell, and T. R. Weikl, Annu. Rev. Biophys. ARPLAP 1936-122X 10.1146/annurev.biophys.37.092707.153558 37, 289 (2008).
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 289
-
-
Dill, K.A.1
Ozkan, S.B.2
Shell, M.S.3
Weikl, T.R.4
-
9
-
-
33645806992
-
-
PHTOAD 0031-9228 10.1063/1.2207037
-
G. Falkovich and K. R. Sreenivasan, Phys. Today PHTOAD 0031-9228 10.1063/1.2207037 59 (4), 43 (2006).
-
(2006)
Phys. Today
, vol.59
, pp. 43
-
-
Falkovich, G.1
Sreenivasan, K.R.2
-
12
-
-
68349106928
-
-
JLTPAC 0022-2291 10.1007/s10909-009-9894-y
-
V. B. Efimov, A. N. Ganshin, G. V. Kolmakov, P. V. E. McClintock, and L. P. Mezhov-Deglin, J. Low Temp. Phys. JLTPAC 0022-2291 10.1007/s10909-009-9894-y 156, 95 (2009).
-
(2009)
J. Low Temp. Phys.
, vol.156
, pp. 95
-
-
Efimov, V.B.1
Ganshin, A.N.2
Kolmakov, G.V.3
McClintock, P.V.E.4
Mezhov-Deglin, L.P.5
-
13
-
-
0029949064
-
Turbulent cascades in foreign exchange markets
-
DOI 10.1038/381767a0
-
S. Ghashghaie, W. Breymann, J. Peinke, P. Talkner, and Y. Dodge, Nature NATUAS 0028-0836 10.1038/381767a0 381, 767 (1996). (Pubitemid 26243111)
-
(1996)
Nature
, vol.381
, Issue.6585
, pp. 767-770
-
-
Ghashghaie, S.1
Breymann, W.2
Peinke, J.3
Talkner, P.4
Dodge, Y.5
-
14
-
-
40749090023
-
Hydrodynamic description of protein folding
-
DOI 10.1103/PhysRevLett.100.018107
-
S. F. Chekmarev, A. Yu. Palyanov, and M. Karplus, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.018107 100, 018107 (2008). (Pubitemid 351388443)
-
(2008)
Physical Review Letters
, vol.100
, Issue.1
, pp. 018107
-
-
Chekmarev, S.F.1
Palyanov, A.Yu.2
Karplus, M.3
-
16
-
-
0028485085
-
High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides
-
DOI 10.1038/nsb0894-546
-
A. Musacchio, M. Saraste, and M. Wilmanns, Nat. Struct. Biol. NSBIEW 1072-8368 10.1038/nsb0894-546 1, 546 (1994). (Pubitemid 2110677)
-
(1994)
Nature Structural Biology
, vol.1
, Issue.8
, pp. 546-551
-
-
Musacchio, A.1
Saraste, M.2
Wilmanns, M.3
-
17
-
-
0031444104
-
Folding dynamics of the src SH3 domain
-
DOI 10.1021/bi971786p
-
V. P. Grantcharova and D. Baker, Biochemistry NSBIEW 0006-2960 10.1021/bi971786p 36, 15685 (1997). (Pubitemid 28027367)
-
(1997)
Biochemistry
, vol.36
, Issue.50
, pp. 15685-15692
-
-
Grantcharova, V.P.1
Baker, D.2
-
18
-
-
0031853167
-
Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain
-
DOI 10.1038/1412
-
V. P. Grantcharova, D. S. Riddle, J. V. Santiago, and D. Baker, Nat. Struct. Biol. NSBIEW 1072-8368 10.1038/1412 5, 714 (1998). (Pubitemid 28359808)
-
(1998)
Nature Structural Biology
, vol.5
, Issue.8
, pp. 714-720
-
-
Grantcharova, V.P.1
Riddle, D.S.2
Santiago, J.V.3
Baker, D.4
-
19
-
-
0032734515
-
Experiment and theory highlight role of native state topology in SH3 folding
-
DOI 10.1038/14901
-
D. S. Riddle, V. P. Grantcharova, J. V. Santiago, E. Alm, I. Ruczinski, and D. Baker, Nat. Struct. Biol. NSBIEW 1072-8368 10.1038/14901 6, 1016 (1999). (Pubitemid 29519594)
-
(1999)
Nature Structural Biology
, vol.6
, Issue.11
, pp. 1016-1024
-
-
Riddle, D.S.1
Grantcharova, V.P.2
Santiago, J.V.3
Aim, E.4
Ruczinski, I.5
Baker, D.6
-
20
-
-
0032562182
-
The folding kinetics and thermodynamics of the Fyn-SH3 domain
-
DOI 10.1021/bi972075u
-
K. W. Plaxco, J. I. Guijarro, C. J. Morton, M. Pitkeathly, I. D. Campbell, and C. M. Dobson, Biochemistry NSBIEW 0006-2960 10.1021/bi972075u 37, 2529 (1998). (Pubitemid 28119329)
-
(1998)
Biochemistry
, vol.37
, Issue.8
, pp. 2529-2537
-
-
Plaxco, K.W.1
Guijarro, J.I.2
Morton, C.J.3
Pitkeathly, M.4
Campbell, I.D.5
Dobson, C.M.6
-
21
-
-
0039726624
-
Thermodynamic analysis of α-spectrin SH3 and two of its circular permutants with different loop lengths: Discerning the reasons for rapid folding in proteins
-
DOI 10.1021/bi981515u
-
J. C. Martinez, A. R. Viguera, R. Berisio, M. Wilmanns, P. L. Mateo, V. V. Filimonov, and L. Serrano, Biochemistry NSBIEW 0006-2960 10.1021/bi981515u 38, 549 (1999). (Pubitemid 29058139)
-
(1999)
Biochemistry
, vol.38
, Issue.2
, pp. 549-559
-
-
Martinez, J.C.1
Viguera, A.R.2
Berisio, R.3
Wilmanns, M.4
Mateo, P.L.5
Filimonov, V.V.6
Serrano, L.7
-
22
-
-
0029643950
-
-
STRUE6 0969-2126 10.1016/S0969-2126(01)00151-4
-
X. D. Wu, B. Knudsen, S. M. Feller, J. Zheng, A. Šali, D. Cowburn, H. Hanafusa, and J. Kuriyan, Structure STRUE6 0969-2126 10.1016/S0969-2126(01) 00151-4 3, 215 (1995).
-
(1995)
Structure
, vol.3
, pp. 215
-
-
Wu, X.D.1
Knudsen, B.2
Feller, S.M.3
Zheng, J.4
Šali, A.5
Cowburn, D.6
Hanafusa, H.7
Kuriyan, J.8
-
24
-
-
1842584557
-
Temperature Dependence of the Free Energy Landscape of the src-SH3 Protein Domain
-
DOI 10.1002/prot.20053
-
W. Guo, S. Lampoudi, and J.-E. Shea, Proteins: Struct., Funct., Bioinformatics 18PLAF 0887-3585 10.1002/prot.20053 55, 395 (2004). (Pubitemid 38437496)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.2
, pp. 395-406
-
-
Guo, W.1
Lampoudi, S.2
Shea, J.-E.3
-
25
-
-
1342268048
-
Cooperativity in two-state protein folding kinetics
-
DOI 10.1110/ps.03403604
-
T. R. Weikl, M. Palassini, and K. A. Dill, Protein Science PRCIEI 0961-8368 10.1110/ps.03403604 13, 822 (2004). (Pubitemid 38252578)
-
(2004)
Protein Science
, vol.13
, Issue.3
, pp. 822-829
-
-
Weikl, T.R.1
Palassini, M.2
Dill, K.A.3
-
26
-
-
33748474227
-
Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model
-
DOI 10.1002/prot.21069
-
D. Mitomo, H. Nakamura, K. Ikeda, A. Yamagishi, and J. Higo, Proteins: Struct., Funct., Bioinformatics 18PLAF 0887-3585 10.1002/prot.21069 64, 883 (2006). (Pubitemid 44420930)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.64
, Issue.4
, pp. 883-894
-
-
Mitomo, D.1
Nakamura, H.K.2
Ikeda, K.3
Yamagishi, A.4
Higo, J.5
-
27
-
-
0034319711
-
-
JCPSA6 0021-9606 10.1063/1.1314868
-
T. X. Hoang and M. Cieplak, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1314868 113, 8319 (2001).
-
(2001)
J. Chem. Phys.
, vol.113
, pp. 8319
-
-
Hoang, T.X.1
Cieplak, M.2
-
28
-
-
0036308818
-
Thermodynamics and folding kinetics analysis of the SH3 domain from discrete molecular dynamics
-
DOI 10.1016/S0022-2836(02)00136-5
-
J. M. Borreguero, N. V. Dokholyan, S. V. Buldyrev, E. I. Shakhnovich, and H. E. Stanley, J. Mol. Biol. JMOBAK 0022-2836 10.1016/S0022-2836(02)00136-5 318, 863 (2002). (Pubitemid 34729375)
-
(2002)
Journal of Molecular Biology
, vol.318
, Issue.3
, pp. 863-876
-
-
Borreguero, J.M.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Shakhnovich, E.I.4
Eugene Stanley, H.5
-
29
-
-
3042857533
-
Multiple folding pathways of the SH3 domain
-
DOI 10.1529/biophysj.104.039529
-
J. M. Borreguero, F. Ding, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.104.039529 87, 521 (2004). (Pubitemid 38880105)
-
(2004)
Biophysical Journal
, vol.87
, Issue.1
, pp. 521-533
-
-
Borreguero, J.M.1
Ding, F.2
Buldyrev, S.V.3
Stanley, H.E.4
Dokholyan, N.V.5
-
30
-
-
6944250414
-
Sparsely populated folding intermediates of the Fyn SH3 domain: Matching native-centric essential dynamics and experiment
-
DOI 10.1073/pnas.0404436101
-
J. E. Ollerenshaw, H. Kaya, H. S. Chan, and L. E. Kay, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0404436101 101, 14748 (2004). (Pubitemid 39410746)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.41
, pp. 14748-14753
-
-
Ollerenshaw, J.E.1
Kaya, H.2
Chan, H.S.3
Kay, L.E.4
-
32
-
-
33845377127
-
-
MAMOBX 0024-9297 10.1021/ma00145a039
-
S. Miyazawa and R. L. Jernigan, Macromolecules MAMOBX 0024-9297 10.1021/ma00145a039 18, 534 (1985).
-
(1985)
Macromolecules
, vol.18
, pp. 534
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
33
-
-
0029964867
-
Diffusion-limited contact formation in unfolded cytochrome c: Estimating the maximum rate of protein folding
-
DOI 10.1073/pnas.93.21.11615
-
S. J. Hagen, J. Hofrichter, A. Szabo, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.93.21.11615 93, 11615 (1996). (Pubitemid 26347170)
-
(1996)
Proceedings of the National Academy of Sciences of the United States of America
, vol.93
, Issue.21
, pp. 11615-11617
-
-
Hagen, S.J.1
Hofrichter, J.2
Szabo, A.3
Eaton, W.A.4
-
34
-
-
0038502170
-
Folding dynamics and mechanism of β-hairpin formation
-
DOI 10.1038/36626
-
V. Muñoz, P. A. Thompson, J. Hofrichter, and W. A. Eaton, Nature (London) NATUAS 0028-0836 10.1038/36626 390, 196 (1997). (Pubitemid 27507992)
-
(1997)
Nature
, vol.390
, Issue.6656
, pp. 196-199
-
-
Munoz, V.1
Thompson, P.A.2
Hofrichter, J.3
Eaton, W.A.4
-
35
-
-
0033527768
-
Folding of a model three-helix bundle protein: A thermodynamic and kinetic analysis
-
DOI 10.1006/jmbi.1999.2936
-
Y. Zhou and M. Karplus, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1999.2936 293, 917 (1999). (Pubitemid 29527675)
-
(1999)
Journal of Molecular Biology
, vol.293
, Issue.4
, pp. 917-951
-
-
Zhou, Y.1
Karplus, M.2
-
37
-
-
79951689037
-
-
In Ref. [15], the fast and slow trajectories were separated by the time at which the decay curves for these trajectories intersected (t=3.5×103). In the present paper, to ensure that no fast trajectories were attributed to the slow ones, this point was moved to t=5.5×103, which decreased the number of the slow trajectories under consideration from 1200 to 1100
-
In Ref. [15], the fast and slow trajectories were separated by the time at which the decay curves for these trajectories intersected (t = 3.5 × 10 3). In the present paper, to ensure that no fast trajectories were attributed to the slow ones, this point was moved to t = 5.5 × 10 3, which decreased the number of the slow trajectories under consideration from 1200 to 1100.
-
-
-
-
39
-
-
0002534246
-
-
PRLTAO 0031-9007 10.1103/PhysRevLett.51.1265
-
Y. Termonia and Z. Alexandrowicz, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.51.1265 51, 1265 (1983).
-
(1983)
Phys. Rev. Lett.
, vol.51
, pp. 1265
-
-
Termonia, Y.1
Alexandrowicz, Z.2
-
45
-
-
0003595195
-
-
JCPSA6 1364-5021 10.1098/rspa.1991.0076
-
A. N. Kolmogorov, Proc. R. Soc. London, Ser. A JCPSA6 1364-5021 10.1098/rspa.1991.0076 434, 15 (1991).
-
(1991)
Proc. R. Soc. London, Ser. A
, vol.434
, pp. 15
-
-
Kolmogorov, A.N.1
-
47
-
-
84956238589
-
-
JFLSA7 0022-1120 10.1017/S0022112062000506
-
A. M. Obukhov, J. Fluid Mech. JFLSA7 0022-1120 10.1017/S0022112062000506 13, 77 (1962).
-
(1962)
J. Fluid Mech.
, vol.13
, pp. 77
-
-
Obukhov, A.M.1
-
48
-
-
36849114603
-
-
PHFLE6 1070-6631 10.1063/1.1762301
-
R. H. Kraichnan, Phys. Fluids PHFLE6 1070-6631 10.1063/1.1762301 10, 1417 (1967).
-
(1967)
Phys. Fluids
, vol.10
, pp. 1417
-
-
Kraichnan, R.H.1
-
50
-
-
0042283661
-
Scaling in three-dimensional and quasi-two-dimensional rotating turbulent flows
-
DOI 10.1063/1.1577120
-
C. N. Baroud, B. B. Plapp, H. L. Swinney, and Z.-S. She, Phys. Fluids PHFLE6 1070-6631 10.1063/1.1577120 15, 2091 (2003). (Pubitemid 37096632)
-
(2003)
Physics of Fluids
, vol.15
, Issue.8
, pp. 2091-2104
-
-
Baroud, C.N.1
Plapp, B.B.2
Swinney, H.L.3
She, Z.-S.4
-
52
-
-
79951717043
-
-
lll(l) are shown as multiplied by factors 1010 and 1015, respectively.
-
lll (l) are shown as multiplied by factors 10 10 and 10 15, respectively.
-
-
-
-
53
-
-
79951718591
-
-
As previously, the folding fluxes are multiplied by a factor 105; correspondingly, the variance of folding fluxes has the factor 1010
-
As previously, the folding fluxes are multiplied by a factor 10 5; correspondingly, the variance of folding fluxes has the factor 10 10.
-
-
-
-
56
-
-
10844264077
-
Fractional Brownian dynamics in proteins
-
DOI 10.1063/1.1806134
-
G. R. Kneller and K. Hinsen, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1806134 121, 10278 (2004). (Pubitemid 40001680)
-
(2004)
Journal of Chemical Physics
, vol.121
, Issue.20
, pp. 10278-10283
-
-
Kneller, G.R.1
Hinsen, K.2
-
57
-
-
19744382497
-
-
PRLTAO 0031-9007 10.1103/PhysRevLett.93.180603
-
S. C. Kou and X. S. Xie, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.180603 93, 180603 (2004).
-
(2004)
Phys. Rev. Lett.
, vol.93
, pp. 180603
-
-
Kou, S.C.1
Xie, X.S.2
-
58
-
-
36849063768
-
Anomalous diffusion in folding dynamics of minimalist protein landscape
-
DOI 10.1103/PhysRevLett.99.238103
-
Y. Matsunaga, C.-B. Li, and T. Komatsuzaki, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.99.238103 99, 238103 (2007). (Pubitemid 350231894)
-
(2007)
Physical Review Letters
, vol.99
, Issue.23
, pp. 238103
-
-
Matsunaga, Y.1
Li, C.-B.2
Komatsuzaki, T.3
-
59
-
-
72149092396
-
-
JPCBFK 1520-6106 10.1021/jp907009r
-
A. K. Sangha and T. Keyes, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp907009r 113, 15886 (2009).
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 15886
-
-
Sangha, A.K.1
Keyes, T.2
-
60
-
-
43249110336
-
Subdiffusion in peptides originates from the fractal-like structure of configuration space
-
DOI 10.1103/PhysRevLett.100.188103
-
T. Neusius, I. Daidone, I. M. Sokolov, and J. C. Smith, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.188103 100, 188103 (2008). (Pubitemid 351656434)
-
(2008)
Physical Review Letters
, vol.100
, Issue.18
, pp. 188103
-
-
Neusius, T.1
Daidone, I.2
Sokolov, I.M.3
Smith, J.C.4
-
61
-
-
78049438869
-
-
PRLTAO 1553-734X 10.1371/journal.pcbi.1000921
-
S. V. Krivov, PLoS Comp. Biol. PRLTAO 1553-734X 10.1371/journal.pcbi. 1000921 6, e1000921 (2010).
-
(2010)
PLoS Comp. Biol.
, vol.6
, pp. 1000921
-
-
Krivov, S.V.1
-
63
-
-
0001250839
-
-
JFLSA7 0022-1120 10.1017/S0022112078001846
-
U. Frisch, P.-L. Sulem, and M. Nelkin, J. Fluid Mech. JFLSA7 0022-1120 10.1017/S0022112078001846 87, 719 (1978).
-
(1978)
J. Fluid Mech.
, vol.87
, pp. 719
-
-
Frisch, U.1
Sulem, P.-L.2
Nelkin, M.3
-
64
-
-
33745440760
-
-
JPCBFK 1520-6106 10.1021/jp057497p
-
G. Luo, I. Andricioaei, X. S. Xie, and M. Karplus, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp057497p 110, 9363 (2006).
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 9363
-
-
Luo, G.1
Andricioaei, I.2
Xie, X.S.3
Karplus, M.4
|