-
1
-
-
34347375915
-
The protein folding problem: when will it be solved?
-
DOI 10.1016/j.sbi.2007.06.001, PII S0959440X07000772, Nucleic acids / Sequences and topology
-
K. A. Dill, B. Ozkan, T. R. Weikl, J. D. Chodera, and V. A. Voelz, Curr. Opin. Struct. Biol. COSBEF 0959-440X 17, 342 (2007). 10.1016/j.sbi.2007.06.001 (Pubitemid 47021366)
-
(2007)
Current Opinion in Structural Biology
, vol.17
, Issue.3
, pp. 342-346
-
-
Dill, K.A.1
Ozkan, S.B.2
Weikl, T.R.3
Chodera, J.D.4
Voelz, V.A.5
-
2
-
-
49449100900
-
-
SCIEAS 0036-8075,. 10.1126/science.321.5890.784
-
R. F. Service, Science SCIEAS 0036-8075 321, 784 (2008). 10.1126/science.321.5890.784
-
(2008)
Science
, vol.321
, pp. 784
-
-
Service, R.F.1
-
3
-
-
0031815749
-
How do small single-domain proteins fold?
-
DOI 10.1016/S1359-0278(98)00033-9
-
S. E. Jackson, Folding Des. FODEFH 1359-0278 3, R81 (1998). 10.1016/S1359-0278(98)00033-9 (Pubitemid 28366044)
-
(1998)
Folding and Design
, vol.3
, Issue.4
-
-
Jackson, S.E.1
-
4
-
-
0032993447
-
-
PRCIEI 0961-8368,. 10.1110/ps.8.6.1166
-
K. A. Dill, Protein Sci. PRCIEI 0961-8368 8, 1166 (1999). 10.1110/ps.8.6.1166
-
(1999)
Protein Sci.
, vol.8
, pp. 1166
-
-
Dill, K.A.1
-
6
-
-
69949190305
-
-
(Oxford University Press, Oxford), Cha
-
S. Berry, S. A. Rice, and J. Ross, Physical and Chemical Kinetics (Oxford University Press, Oxford, 2002), Chap..
-
(2002)
Physical and Chemical Kinetics
-
-
Berry, S.1
Rice, S.A.2
Ross, J.3
-
7
-
-
1542319916
-
Cooperativity Principles in Protein Folding
-
DOI 10.1016/S0076-6879(04)80016-8
-
H. S. Chan, S. Shimizu, and H. Kaya, Methods Enzymol. MENZAU 0076-6879 380, 350 (2004). 10.1016/S0076-6879(04)80016-8 (Pubitemid 38297503)
-
(2004)
Methods in Enzymology
, vol.380
, pp. 350-379
-
-
Chan, H.S.1
Shimizu, S.2
Kaya, H.3
-
8
-
-
0030322669
-
-
FODEFH 1359-0278,. 10.1016/S1359-0278(96)00060-0
-
J. N. Onuchic, N. D. Socci, Z. Luthey-Schulten, and P. G. Wolynes, Folding Des. FODEFH 1359-0278 1, 441 (1996). 10.1016/S1359-0278(96)00060-0
-
(1996)
Folding Des.
, vol.1
, pp. 441
-
-
Onuchic, J.N.1
Socci, N.D.2
Luthey-Schulten, Z.3
Wolynes, P.G.4
-
11
-
-
0028868995
-
-
JMOBAK 0022-2836,. 10.1006/jmbi.1995.0616
-
L. S. Itzhaki, D. E. Otzen, and A. R. Fersht, J. Mol. Biol. JMOBAK 0022-2836 254, 260 (1995). 10.1006/jmbi.1995.0616
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 260
-
-
Itzhaki, L.S.1
Otzen, D.E.2
Fersht, A.R.3
-
12
-
-
70349584103
-
-
JCOMEL 0953-8984,. 10.1088/0953-8984/21/37/373102
-
P. F. N. Faísca, J. Phys.: Condens. Matter JCOMEL 0953-8984 21, 373102 (2009). 10.1088/0953-8984/21/37/373102
-
(2009)
J. Phys.: Condens. Matter
, vol.21
, pp. 373102
-
-
Faísca, P.F.N.1
-
13
-
-
51349086269
-
-
JCPSA6 0021-9606,. 10.1063/1.2973624
-
P. F. N. Faísca, R. D. M. Travasso, R. C. Ball, and E. I. Shakhnovich, J. Chem. Phys. JCPSA6 0021-9606 129, 095108 (2008). 10.1063/1.2973624
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 095108
-
-
Faísca, P.F.N.1
Travasso, R.D.M.2
Ball, R.C.3
Shakhnovich, E.I.4
-
14
-
-
0001563395
-
-
JCPSA6 0021-9606,. 10.1063/1.475393
-
R. Du, V. S. Pande, A. Y. Grosberg, T. Tanaka, and E. S. Shakhnovich, J. Chem. Phys. JCPSA6 0021-9606 108, 334 (1998). 10.1063/1.475393
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 334
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, E.S.5
-
15
-
-
33745744079
-
Kinetic definition of protein folding transition state ensembles and reaction coordinates
-
DOI 10.1529/biophysj.105.075689
-
C. Snow and V. S. Pande, Biophys. J. BIOJAU 0006-3495 91, 14 (2006). 10.1529/biophysj.105.075689 (Pubitemid 44015305)
-
(2006)
Biophysical Journal
, vol.91
, Issue.1
, pp. 14-24
-
-
Snow, C.D.1
Young, M.R.2
Pande, V.S.3
-
18
-
-
63649158574
-
-
JCPSA6 0021-9606,. 10.1063/1.3099705
-
S. Muff and A. Caflisch, J. Chem. Phys. JCPSA6 0021-9606 130, 125104 (2009). 10.1063/1.3099705
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 125104
-
-
Muff, S.1
Caflisch, A.2
-
20
-
-
0024742246
-
-
BIPMAA 0006-3525,. 10.1002/bi360281003
-
E. I. Shakhnovich and A. V. Finkelstein, Biopolymers BIPMAA 0006-3525 28, 1667 (1989). 10.1002/bip.360281003
-
(1989)
Biopolymers
, vol.28
, pp. 1667
-
-
Shakhnovich, E.I.1
Finkelstein, A.V.2
-
21
-
-
0000630681
-
-
PRLTAO 0031-9007,. 10.1103/PhysRevLett.67.1665
-
E. Shakhnovich, G. Farztdinov, A. M. Gutin, and M. Karplus, Phys. Rev. Lett. PRLTAO 0031-9007 67, 1665 (1991). 10.1103/PhysRevLett.67.1665
-
(1991)
Phys. Rev. Lett.
, vol.67
, pp. 1665
-
-
Shakhnovich, E.1
Farztdinov, G.2
Gutin, A.M.3
Karplus, M.4
-
22
-
-
0028174310
-
-
NATUAS 0028-0836,. 10.1038/369248a0
-
A. Sali, E. Shakhnovich, and M. Karplus, Nature (London) NATUAS 0028-0836 369, 248 (1994). 10.1038/369248a0
-
(1994)
Nature (London)
, vol.369
, pp. 248
-
-
Sali, A.1
Shakhnovich, E.2
Karplus, M.3
-
23
-
-
0026723063
-
-
PNASA6 0027-8424,. 10.1073/pnas.89.18.8721
-
P. E. Leopold, M. Montal, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 89, 8721 (1992). 10.1073/pnas.89.18.8721
-
(1992)
Proc. Natl. Acad. Sci. U.S.A.
, vol.89
, pp. 8721
-
-
Leopold, P.E.1
Montal, M.2
Onuchic, J.N.3
-
24
-
-
0037230925
-
Efficient RMSD measures for the comparison of two molecular ensembles
-
DOI 10.1002/prot.10250
-
R. Brüschweiler, Proteins 18PLAF 0887-3585 50, 26 (2003). 10.1002/prot.10250 (Pubitemid 36090605)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.50
, Issue.1
, pp. 26-34
-
-
Bruschweiler, R.1
-
26
-
-
31444452031
-
P versus Q: Structural reaction coordinates capture protein folding on smooth landscapes
-
DOI 10.1073/pnas.0509768103
-
S. S. Cho, Y. Levy, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 103, 586 (2006). 10.1073/pnas.0509768103 (Pubitemid 43153069)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.3
, pp. 586-591
-
-
Cho, S.S.1
Levy, Y.2
Wolynes, P.G.3
-
27
-
-
0034681133
-
Landscape approaches for determining the ensemble of folding transition states: Success and failure hinge on the degree of frustration
-
DOI 10.1073/pnas.97.2.634
-
H. Nymeyer, N. D. Socci, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 97, 634 (2000). 10.1073/pnas.97.2.634 (Pubitemid 30070361)
-
(2000)
Proceedings of the National Academy of Sciences of the United States of America
, vol.97
, Issue.2
, pp. 634-639
-
-
Nymeyer, H.1
Socci, N.D.2
Onuchic, J.N.3
-
28
-
-
77957745274
-
-
BIOJAU 0006-3495
-
C. Clementi, M. Cheung, H. Nymeyer, and J. N. Onuchic, Biophys. J. BIOJAU 0006-3495 78, 46A (2000).
-
(2000)
Biophys. J.
, vol.78
-
-
Clementi, C.1
Cheung, M.2
Nymeyer, H.3
Onuchic, J.N.4
-
29
-
-
0037459035
-
Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling?
-
DOI 10.1016/S0022-2836(02)01434-1
-
H. Kaya and H. S. Chan, J. Mol. Biol. JMOBAK 0022-2836 326, 911 (2003). 10.1016/S0022-2836(02)01434-1 (Pubitemid 36279329)
-
(2003)
Journal of Molecular Biology
, vol.326
, Issue.3
, pp. 911-931
-
-
Kaya, H.1
Chan, H.S.2
-
30
-
-
0037459022
-
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein L
-
DOI 10.1016/S0022-2836(02)01379-7
-
C. Clementi, A. E. Garcia, and J. N. Onuchic, J. Mol. Biol. JMOBAK 0022-2836 326, 933 (2003). 10.1016/S0022-2836(02)01379-7 (Pubitemid 36284722)
-
(2003)
Journal of Molecular Biology
, vol.326
, Issue.3
, pp. 933-954
-
-
Clementi, C.1
Garcia, A.E.2
Onuchic, J.N.3
-
31
-
-
0037974485
-
-
BIOJAU 0006-3495,. 10.1016/S0006-3495(03)74454-3
-
W. Guo, S. Lampoudi, and J. E. Shea, Biophys. J. BIOJAU 0006-3495 85, 61 (2003). 10.1016/S0006-3495(03)74454-3
-
(2003)
Biophys. J.
, vol.85
, pp. 61
-
-
Guo, W.1
Lampoudi, S.2
Shea, J.E.3
-
32
-
-
0003166498
-
-
18PLAF 0887-3585,. 10.1002/(SICI)1097-0134(19980101)30:1<2::AID- PROT2>3.0.CO;2-R
-
H. S. Chan and K. A. Dill, Proteins 18PLAF 0887-3585 30, 2 (1998). 10.1002/(SICI)1097-0134(19980101)30:1<2::AID-PROT2>3.0.CO;2-R
-
(1998)
Proteins
, vol.30
, pp. 2
-
-
Chan, H.S.1
Dill, K.A.2
-
33
-
-
33846071499
-
Using the histogram test to quantify reaction coordinate error
-
DOI 10.1063/1.2409924
-
B. Peters, J. Chem. Phys. JCPSA6 0021-9606 125, 241101 (2006). 10.1063/1.2409924 (Pubitemid 46058257)
-
(2006)
Journal of Chemical Physics
, vol.125
, Issue.24
, pp. 241101
-
-
Peters, B.1
-
34
-
-
0036927818
-
-
BIOJAU 0006-3495,. 10.1016/S0006-3495(02)75352-6
-
F. Ding, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich, Biophys. J. BIOJAU 0006-3495 83, 3525 (2002). 10.1016/S0006- 3495(02)75352-6
-
(2002)
Biophys. J.
, vol.83
, pp. 3525
-
-
Ding, F.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Stanley, H.E.4
Shakhnovich, E.I.5
-
35
-
-
2942590388
-
Simulation, experiment, and evolution: Understanding nucleation in protein S6 folding
-
DOI 10.1073/pnas.0401672101
-
I. A. Hubner, M. Oliveberg, and E. I. Shakhnovich, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 101, 8354 (2004). 10.1073/pnas.0401672101 (Pubitemid 38736579)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.22
, pp. 8354-8359
-
-
Hubner, I.A.1
Oliveberg, M.2
Shakhnovich, E.I.3
-
36
-
-
18844459862
-
Nucleation and the transition state of the SH3 domain
-
DOI 10.1016/j.jmb.2005.03.050, PII S002228360500330X
-
I. A. Hubner, K. A. Edmonds, and E. I. Shakhnovich, J. Mol. Biol. JMOBAK 0022-2836 349, 424 (2005). 10.1016/j.jmb.2005.03.050 (Pubitemid 40693760)
-
(2005)
Journal of Molecular Biology
, vol.349
, Issue.2
, pp. 424-434
-
-
Hubner, I.A.1
Edmonds, K.A.2
Shakhnovich, E.I.3
-
37
-
-
21744452297
-
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations
-
DOI 10.1016/j.jmb.2005.05.017, PII S0022283605005486
-
F. Ding, W. Guo, N. V. Dokholyan, E. I. Shakhnovich, and J. -E. Shea, J. Mol. Biol. JMOBAK 0022-2836 350, 1035 (2005). 10.1016/j.jmb.2005.05.017 (Pubitemid 40943460)
-
(2005)
Journal of Molecular Biology
, vol.350
, Issue.5
, pp. 1035-1050
-
-
Ding, F.1
Guo, W.2
Dokholyan, N.V.3
Shakhnovich, E.I.4
Shea, J.-E.5
-
38
-
-
36549027538
-
fold-like calculations
-
DOI 10.1529/biophysj.106.100149
-
D. A. C. Beck and V. Daggett, Biophys. J. BIOJAU 0006-3495 93, 3382 (2007). 10.1529/biophysj.106.100149 (Pubitemid 350190803)
-
(2007)
Biophysical Journal
, vol.93
, Issue.10
, pp. 3382-3391
-
-
Beck, D.A.C.1
Daggett, V.2
-
40
-
-
5744249209
-
-
JCPSA6 0021-9606,. 10.1063/1.1699114
-
N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. JCPSA6 0021-9606 21, 1087 (1953). 10.1063/1.1699114
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
42
-
-
36449008575
-
-
JCPSA6 0021-9606,. 10.1063/1.465277
-
H. S. Chan and K. A. Dill, J. Chem. Phys. JCPSA6 0021-9606 99, 2116 (1993). 10.1063/1.465277
-
(1993)
J. Chem. Phys.
, vol.99
, pp. 2116
-
-
Chan, H.S.1
Dill, K.A.2
-
43
-
-
36449000646
-
-
JCPSA6 0021-9606,. 10.1063/1.466677
-
H. S. Chan and K. A. Dill, J. Chem. Phys. JCPSA6 0021-9606 100, 9238 (1994). 10.1063/1.466677
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9238
-
-
Chan, H.S.1
Dill, K.A.2
-
44
-
-
77957737480
-
-
BICHAW 0006-2960
-
K. W. Plaxco, K. T. Simmons, I. Ruczinski, and D. Baker, Biochemistry BICHAW 0006-2960 39, 1117783 (2002).
-
(2002)
Biochemistry
, vol.39
, pp. 1117783
-
-
Plaxco, K.W.1
Simmons, K.T.2
Ruczinski, I.3
Baker, D.4
-
45
-
-
0031578972
-
-
CHPLBC 0009-2614,. 10.1016/S0009-2614(97)01198-6
-
U. H. E. Hansmann, Chem. Phys. Lett. CHPLBC 0009-2614 281, 140 (1997). 10.1016/S0009-2614(97)01198-6
-
(1997)
Chem. Phys. Lett.
, vol.281
, pp. 140
-
-
Hansmann, U.H.E.1
-
46
-
-
84986519238
-
-
JCCHDD 0192-8651,. 10.1002/jcc.540130812
-
S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, J. Comput. Chem. JCCHDD 0192-8651 13, 1011 (1992). 10.1002/jcc.540130812
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011
-
-
Kumar, S.1
Rosenberg, J.M.2
Bouzida, D.3
Swendsen, R.H.4
Kollman, P.A.5
-
47
-
-
33947398571
-
-
JCTCCE 1549-9618,. 10.1021/ct0502864
-
J. D. Chodera, W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill, J. Chem. Theory Comput. JCTCCE 1549-9618 3, 26 (2007). 10.1021/ct0502864
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 26
-
-
Chodera, J.D.1
Swope, W.C.2
Pitera, J.W.3
Seok, C.4
Dill, K.A.5
-
48
-
-
0842332830
-
Commitment and Nucleation in the Protein G Transition State
-
DOI 10.1016/j.jmb.2003.12.032
-
I. A. Hubner, J. Shimada, and E. I. Shakhnovich, J. Mol. Biol. JMOBAK 0022-2836 336, 745 (2004). 10.1016/j.jmb.2003.12.032 (Pubitemid 38183026)
-
(2004)
Journal of Molecular Biology
, vol.336
, Issue.3
, pp. 745-761
-
-
Hubner, I.A.1
Shimada, J.2
Shakhnovich, E.I.3
-
49
-
-
0001229818
-
-
JCPSA6 0021-9606,. 10.1063/1.476053
-
A. Gutin, A. Sali, V. Abkevich, M. Karplus, and E. I. Shakhnovich, J. Chem. Phys. JCPSA6 0021-9606 108, 6466 (1998). 10.1063/1.476053
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 6466
-
-
Gutin, A.1
Sali, A.2
Abkevich, V.3
Karplus, M.4
Shakhnovich, E.I.5
-
50
-
-
0037156117
-
Thermodynamic control and dynamical regimes in protein folding
-
DOI 10.1063/1.1466833
-
P. F. N. Faisca and R. C. Ball, J. Chem. Phys. JCPSA6 0021-9606 116, 7231 (2002). 10.1063/1.1466833 (Pubitemid 34537102)
-
(2002)
Journal of Chemical Physics
, vol.116
, Issue.16
, pp. 7231-7237
-
-
Faisca, P.F.N.1
Ball, R.C.2
-
51
-
-
14744273112
-
Native geometry and the dynamics of protein folding
-
DOI 10.1016/j.bpc.2004.12.022
-
P. F. N. Faisca and M. M. Telo da Gama, Biophys. Chem. BICIAZ 0301-4622 115, 169 (2005). 10.1016/j.bpc.2004.12.022 (Pubitemid 40327053)
-
(2005)
Biophysical Chemistry
, vol.115
, Issue.SPEC. ISS. 2-3
, pp. 169-175
-
-
Faisca, P.F.N.1
Telo Da Gama, M.M.2
-
52
-
-
0034581192
-
Problems and prospects in microcalorimetry of biological macromolecules
-
DOI 10.1016/S0076-6879(00)23360-0
-
G. P. Privalov and P. L. Privalov, Methods Enzymol. MENZAU 0076-6879 323, 31 (2000). 10.1016/S0076-6879(00)23360-0 (Pubitemid 34193272)
-
(2000)
Methods in Enzymology
, vol.323
, pp. 31-62
-
-
Privalov, G.P.1
Privalov, P.L.2
-
53
-
-
33745698759
-
-
PRCIEI 0961-8368,. 10.1110/ps.062180806
-
P. F. N. Faísca and K. W. Plaxco, Protein Sci. PRCIEI 0961-8368 15, 1608 (2006). 10.1110/ps.062180806
-
(2006)
Protein Sci.
, vol.15
, pp. 1608
-
-
Faísca, P.F.N.1
Plaxco, K.W.2
-
54
-
-
77957742044
-
-
See supplementary material at E-JCPSA6-133-002034 for Fig. S1 for heat capacity curve as function of temperature, Fig. S2 for the histogram for the different Q values, and a note for the practitioner for what should not be done in order to correctly construct an ensemble of conformations representative of the TSE
-
See supplementary material at http://dx.doi.org/10.1063/1.3485286 E-JCPSA6-133-002034 for Fig. S1 for heat capacity curve as function of temperature, Fig. S2 for the histogram for the different Q values, and a note for the practitioner for what should not be done in order to correctly construct an ensemble of conformations representative of the TSE.
-
-
-
-
55
-
-
35248828677
-
Pathways to folding, nucleation events, and native geometry
-
DOI 10.1063/1.2777150
-
R. D. M. Travasso, M. M. T. Gama, and P. F. N. Faisca, J. Chem. Phys. JCPSA6 0021-9606 127, 145106 (2007). 10.1063/1.2777150 (Pubitemid 47569059)
-
(2007)
Journal of Chemical Physics
, vol.127
, Issue.14
, pp. 145106
-
-
Travasso, R.D.M.1
Telo Da Gama, M.M.2
Faisca, P.F.N.3
-
56
-
-
0028024928
-
-
BICHAW 0006-2960,. 10.1021/bi00199a029
-
V. I. Abkevich, A. M. Gutin, and E. I. Shakhnovich, Biochemistry BICHAW 0006-2960 33, 10026 (1994). 10.1021/bi00199a029
-
(1994)
Biochemistry
, vol.33
, pp. 10026
-
-
Abkevich, V.I.1
Gutin, A.M.2
Shakhnovich, E.I.3
-
57
-
-
0034112774
-
Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
-
DOI 10.1038/74111
-
L. Li, L. A. Mirny, and E. I. Shakhnovich, Nat. Struct. Biol. NSBIEW 1072-8368 7, 336 (2000). 10.1038/74111 (Pubitemid 30194459)
-
(2000)
Nature Structural Biology
, vol.7
, Issue.4
, pp. 336-342
-
-
Li, L.1
Mirny, L.A.2
Shakhnovich, E.I.3
|