-
1
-
-
33646931471
-
Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
-
DOI 10.1021/cr040425u
-
E. Shakhnovich, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 106, 1559 (2006). 10.1021/cr040425u (Pubitemid 43792772)
-
(2006)
Chemical Reviews
, vol.106
, Issue.5
, pp. 1559-1588
-
-
Shakhnovich, E.1
-
2
-
-
48249134448
-
-
10.1146/annurev.biophys.37.092707.153558
-
K. A. Dill, S. B. Ozkan, M. S. Shell, and T. R. Weikl, Annu. Rev. Biophys. 37, 289 (2008). 10.1146/annurev.biophys.37.092707.153558
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 289
-
-
Dill, K.A.1
Ozkan, S.B.2
Shell, M.S.3
Weikl, T.R.4
-
3
-
-
33747592347
-
The experimental survey of protein-folding energy landscapes
-
DOI 10.1017/S0033583506004185, PII S0033583506004185
-
M. Oliveberg and P. G. Wolynes, Q. Rev. Biophys. QURBAW 0033-5835 38, 245 (2005). 10.1017/S0033583506004185 (Pubitemid 44268537)
-
(2005)
Quarterly Reviews of Biophysics
, vol.38
, Issue.3
, pp. 245-288
-
-
Oliveberg, M.1
Wolynes, P.G.2
-
5
-
-
57449090161
-
-
PNASA6 0027-8424,. 10.1073/pnas.0806154105
-
T. Cellmer, E. R. Henry, J. Hofrichter, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 105, 18320 (2008). 10.1073/pnas.0806154105
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 18320
-
-
Cellmer, T.1
Henry, E.R.2
Hofrichter, J.3
Eaton, W.A.4
-
6
-
-
33747623305
-
End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation
-
DOI 10.1073/pnas.0604748103
-
A. Möglich, K. Joder, and T. Kiefhaber, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 103, 12394 (2006). 10.1073/pnas.0604748103 (Pubitemid 44267270)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.33
, pp. 12394-12399
-
-
Moglich, A.1
Joder, K.2
Kiefhaber, T.3
-
7
-
-
59049097904
-
-
PNASA6 0027-8424,. 10.1073/pnas.0808581106
-
B. Fierz, A. Reiner, and T. Kiefhaber, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 106, 1057 (2009). 10.1073/pnas.0808581106
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 1057
-
-
Fierz, B.1
Reiner, A.2
Kiefhaber, T.3
-
8
-
-
8844247109
-
Two-state folding observed in individual protein molecules
-
DOI 10.1021/ja046209k
-
E. Rhoades, M. Cohen, B. Schuler, and G. Haran, J. Am. Chem. Soc. JACSAT 0002-7863 126, 14686 (2004). 10.1021/ja046209k (Pubitemid 39532128)
-
(2004)
Journal of the American Chemical Society
, vol.126
, Issue.45
, pp. 14686-14687
-
-
Rhoades, E.1
Cohen, M.2
Schuler, B.3
Haran, G.4
-
9
-
-
67749147584
-
-
PNASA6 0027-8424,. 10.1073/pnas.0901178106
-
H. S. Chung, M. Louis, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 106, 11837 (2009). 10.1073/pnas.0901178106
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 11837
-
-
Chung, H.S.1
Louis, M.2
Eaton, W.A.3
-
12
-
-
58549088131
-
-
PNASA6 0027-8424,. 10.1073/pnas.0802986106
-
P. Li, F. Y. Oliva, A. N. Naganathan, and V. Munoz, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 106, 103 (2009). 10.1073/pnas.0802986106
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 103
-
-
Li, P.1
Oliva, F.Y.2
Naganathan, A.N.3
Munoz, V.4
-
13
-
-
70349524994
-
-
PNASA6 0027-8424,. 10.1073/pnas.0909126106
-
F. Huang, L. Ying, and A. R. Fersht, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 106, 16239 (2009). 10.1073/pnas.0909126106
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 16239
-
-
Huang, F.1
Ying, L.2
Fersht, A.R.3
-
15
-
-
0000050196
-
-
JPGCE8 1155-4304,. 10.1051/jp1:1995209
-
D. Thirumalai, J. Phys. I JPGCE8 1155-4304 5, 1457 (1995). 10.1051/jp1:1995209
-
(1995)
J. Phys. i
, vol.5
, pp. 1457
-
-
Thirumalai, D.1
-
16
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
DOI 10.1006/jmbi.1998.1645
-
K. W. Plaxco, K. T. Simons, and D. Baker, J. Mol. Biol. JMOBAK 0022-2836 277, 985 (1998). 10.1006/jmbi.1998.1645 (Pubitemid 28195995)
-
(1998)
Journal of Molecular Biology
, vol.277
, Issue.4
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
17
-
-
36749119688
-
-
JCPSA6 0021-9606,. 10.1063/1.445988
-
N. Agmon and J. J. Hopfield, J. Chem. Phys. JCPSA6 0021-9606 79, 2042 (1983). 10.1063/1.445988
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 2042
-
-
Agmon, N.1
Hopfield, J.J.2
-
18
-
-
0000710672
-
-
JCPSA6 0021-9606,. 10.1063/1.471317
-
N. D. Socci, J. N. Onuchic, and P. G. Wolynes, J. Chem. Phys. JCPSA6 0021-9606 104, 5860 (1996). 10.1063/1.471317
-
(1996)
J. Chem. Phys.
, vol.104
, pp. 5860
-
-
Socci, N.D.1
Onuchic, J.N.2
Wolynes, P.G.3
-
19
-
-
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
-
21
-
-
5244325378
-
-
JCPSA6 0021-9606,. 10.1063/1.462993
-
R. Zwanzig, J. Chem. Phys. JCPSA6 0021-9606 97, 3587 (1992). 10.1063/1.462993
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 3587
-
-
Zwanzig, R.1
-
22
-
-
63149145440
-
-
PRLTAO 0031-9007,. 10.1103/PhysRevLett.102.108101
-
N. A. Denesyuk and J. D. Weeks, Phys. Rev. Lett. PRLTAO 0031-9007 102, 108101 (2009). 10.1103/PhysRevLett.102.108101
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 108101
-
-
Denesyuk, N.A.1
Weeks, J.D.2
-
23
-
-
68649085948
-
-
PRLTAO 0031-9007,. 10.1103/PhysRevLett.103.028102
-
A. Alexander-Katz, H. Wada, and R. R. Netz, Phys. Rev. Lett. PRLTAO 0031-9007 103, 028102 (2009). 10.1103/PhysRevLett.103.028102
-
(2009)
Phys. Rev. Lett.
, vol.103
, pp. 028102
-
-
Alexander-Katz, A.1
Wada, H.2
Netz, R.R.3
-
24
-
-
33744952224
-
Diffusive model of protein folding dynamics with Kramers turnover in rate
-
DOI 10.1103/PhysRevLett.96.228104
-
R. B. Best and G. Hummer, Phys. Rev. Lett. PRLTAO 0031-9007 96, 228104 (2006). 10.1103/PhysRevLett.96.228104 (Pubitemid 43855967)
-
(2006)
Physical Review Letters
, vol.96
, Issue.22
, pp. 228104
-
-
Best, R.B.1
Hummer, G.2
-
25
-
-
35548963462
-
Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding
-
DOI 10.1073/pnas.0606506104
-
J. Chahine, R. J. Oliveira, V. B. P. Leite, and J. Wang, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 104, 14646 (2007). 10.1073/pnas.0606506104 (Pubitemid 350010648)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.37
, pp. 14646-14651
-
-
Chahine, J.1
Oliveira, R.J.2
Leite, V.B.P.3
Wang, J.4
-
27
-
-
34548273698
-
Folding Time Predictions from All-atom Replica Exchange Simulations
-
DOI 10.1016/j.jmb.2007.07.010, PII S0022283607009242
-
S. Yang, J. N. Onuchic, A. E. Garcia, and H. Levine, J. Mol. Biol. JMOBAK 0022-2836 372, 756 (2007). 10.1016/j.jmb.2007.07.010 (Pubitemid 47321796)
-
(2007)
Journal of Molecular Biology
, vol.372
, Issue.3
, pp. 756-763
-
-
Yang, S.1
Onuchic, J.N.2
Garcia, A.E.3
Levine, H.4
-
29
-
-
54249126941
-
-
JACSAT 0002-7863,. 10.1021/ja805562g
-
J. Dzubiella, J. Am. Chem. Soc. JACSAT 0002-7863 130, 14000 (2008). 10.1021/ja805562g
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 14000
-
-
Dzubiella, J.1
-
30
-
-
33750970551
-
Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid
-
DOI 10.1126/science.1133601
-
M. T. Woodside, P. C. Anthony, W. M. Behnke-Parks, K. Larizadeh, D. Herschlag, and S. M. Block, Science SCIEAS 0036-8075 314, 1001 (2006). 10.1126/science.1133601 (Pubitemid 44749947)
-
(2006)
Science
, vol.314
, Issue.5801
, pp. 1001-1004
-
-
Woodside, M.T.1
Anthony, P.C.2
Behnke-Parks, W.M.3
Larizadeh, K.4
Herschlag, D.5
Block, S.M.6
-
31
-
-
76649093956
-
-
PNASA6 0027-8424,. 10.1073/pnas.0909854107
-
J. C. M. Gebhardt, T. Bornschlögl, and M. Rief, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 107, 2013 (2010). 10.1073/pnas.0909854107
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 2013
-
-
Gebhardt, J.C.M.1
Bornschlögl, T.2
Rief, M.3
-
32
-
-
38949165395
-
Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins
-
DOI 10.1021/ja0771641
-
C. Hyeon and D. Thirumalai, J. Am. Chem. Soc. JACSAT 0002-7863 130, 1538 (2008). 10.1021/ja0771641 (Pubitemid 351214055)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.5
, pp. 1538-1539
-
-
Hyeon, C.1
Thirumalai, D.2
-
33
-
-
0036424048
-
Transition path sampling: Throwing ropes over rough mountain passes, in the dark
-
DOI 10.1146/annurev.physchem.53.082301.113146
-
P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 53, 291 (2002). 10.1146/annurev.physchem.53.082301. 113146 (Pubitemid 35336255)
-
(2002)
Annual Review of Physical Chemistry
, vol.53
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
35
-
-
33746255471
-
String method in collective variables: Minimum free energy paths and isocommittor surfaces
-
DOI 10.1063/1.2212942
-
L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, J. Chem. Phys. JCPSA6 0021-9606 125, 024106 (2006). 10.1063/1.2212942 (Pubitemid 44088333)
-
(2006)
Journal of Chemical Physics
, vol.125
, Issue.2
, pp. 024106
-
-
Maragliano, L.1
Fischer, A.2
Vanden-Eijnden, E.3
Ciccotti, G.4
-
36
-
-
34548728544
-
Quantitative protein dynamics from dominant folding pathways
-
DOI 10.1103/PhysRevLett.99.118102
-
M. Sega, P. Faccioli, F. Pederiva, G. Garberoglio, and H. Orland, Phys. Rev. Lett. PRLTAO 0031-9007 99, 118102 (2007). 10.1103/PhysRevLett.99.118102 (Pubitemid 47429438)
-
(2007)
Physical Review Letters
, vol.99
, Issue.11
, pp. 118102
-
-
Sega, M.1
Faccioli, P.2
Pederiva, F.3
Garberoglio, G.4
Orland, H.5
-
37
-
-
70450255797
-
-
PNASA6 0027-8424,. 10.1073/pnas.0905466106
-
F. Noe, C. Schütte, E. Vanden-Eijnden, L. Reich, and T. R. Weikl, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 106, 19011 (2009). 10.1073/pnas.0905466106
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 19011
-
-
Noe, F.1
Schütte, C.2
Vanden-Eijnden, E.3
Reich, L.4
Weikl, T.R.5
-
38
-
-
0242385345
-
-
BIOJAU 0006-3495,. 10.1016/S0006-3495(03)74736-5
-
T. Ghosh, S. Garde, and A. E. Garcia, Biophys. J. BIOJAU 0006-3495 85, 3187 (2003). 10.1016/S0006-3495(03)74736-5
-
(2003)
Biophys. J.
, vol.85
, pp. 3187
-
-
Ghosh, T.1
Garde, S.2
Garcia, A.E.3
-
39
-
-
47949111745
-
-
University of California, San Francisco
-
D. A. Case, AMBER 9.0 software, University of California, San Francisco (2006).
-
(2006)
AMBER 9.0 software
-
-
Case, D.A.1
-
40
-
-
0020997912
-
-
BIPMAA 0006-3525,. 10.1002/bi360221211
-
W. Kabsch and D. Sander, Biopolymers BIPMAA 0006-3525 22, 2577 (1983). 10.1002/bip.360221211
-
(1983)
Biopolymers
, vol.22
, pp. 2577
-
-
Kabsch, W.1
Sander, D.2
-
41
-
-
0347193736
-
-
RMPHAT 0034-6861,. 10.1103/RevModPhys.62.251
-
P. Hänggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys. RMPHAT 0034-6861 62, 251 (1990). 10.1103/RevModPhys.62.251
-
(1990)
Rev. Mod. Phys.
, vol.62
, pp. 251
-
-
Hänggi, P.1
Talkner, P.2
Borkovec, M.3
-
42
-
-
23244438863
-
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
-
DOI 10.1088/1367-2630/7/1/034, PII S136726300587003X
-
G. Hummer, New J. Phys. NJOPFM 1367-2630 7, 34 (2005). 10.1088/1367-2630/7/1/034 (Pubitemid 41093480)
-
(2005)
New Journal of Physics
, vol.7
-
-
Hummer, G.1
-
43
-
-
0002278837
-
-
ADCPAA 0065-2385,. 10.1002/9780470140154.ch1
-
G. H. Weiss, Adv. Chem. Phys. ADCPAA 0065-2385 13, 1 (1966). 10.1002/9780470140154.ch1
-
(1966)
Adv. Chem. Phys.
, vol.13
, pp. 1
-
-
Weiss, G.H.1
-
45
-
-
17444378255
-
One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution
-
DOI 10.1021/jp045544s
-
Y. M. Rhee and V. S. Pande, J. Phys. Chem. B JPCBFK 1089-5647 109, 6780 (2005). 10.1021/jp045544s (Pubitemid 40538446)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.14
, pp. 6780-6786
-
-
Rhee, Y.M.1
Pande, V.S.2
-
47
-
-
77954187276
-
-
See supplementary material at E-JCPSA6-132-006022 for full details of the mapping between RCs and extracting the diffusivity profile through first-passage/Bayesian methods
-
See supplementary material at http://dx.doi.org/10.1063/1.3442716 E-JCPSA6-132-006022 for full details of the mapping between RCs and extracting the diffusivity profile through first-passage/Bayesian methods.
-
-
-
-
48
-
-
0037234367
-
-
BIPMAA 0006-3525,. 10.1002/bi10216
-
S. Chowdhury, W. Zhang, C. Wu, G. Xiong, and Y. Duan, Biopolymers BIPMAA 0006-3525 68, 63 (2003). 10.1002/bip.10216
-
(2003)
Biopolymers
, vol.68
, pp. 63
-
-
Chowdhury, S.1
Zhang, W.2
Wu, C.3
Xiong, G.4
Duan, Y.5
-
49
-
-
34247521430
-
Examination of the folding of a short alanine-based helical peptide with salt bridges using molecular dynamics simulation
-
DOI 10.1021/jp067637a
-
W. -Z. Wang, T. Lin, and Y. -C. Sun, J. Phys. Chem. B JPCBFK 1089-5647 111, 3508 (2007). 10.1021/jp067637a (Pubitemid 46652704)
-
(2007)
Journal of Physical Chemistry B
, vol.111
, Issue.13
, pp. 3508-3514
-
-
Wang, W.-Z.1
Lin, T.2
Sun, Y.-C.3
-
50
-
-
0141704162
-
Free energy landscape of protein folding in water: Explicit vs. implicit solvent
-
DOI 10.1002/prot.10483
-
R. Zhou, Proteins 18PLAF 0887-3585 53, 148 (2003). 10.1002/prot.10483 (Pubitemid 37193811)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.53
, Issue.2
, pp. 148-161
-
-
Zhou, R.1
-
51
-
-
2342448436
-
Simulations of the role of water in the protein-folding mechanism
-
DOI 10.1073/pnas.0307898101
-
Y. M. Rhee, E. J. Sorin, G. Jayachandran, E. Lindahl, and V. S. Pande, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 101, 6456 (2004). 10.1073/pnas.0307898101 (Pubitemid 38585995)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.17
, pp. 6456-6461
-
-
Rhee, Y.M.1
Sorin, E.J.2
Jayachandran, G.3
Lindahl, E.4
Pande, V.S.5
|