-
1
-
-
0023449962
-
Spin glasses and the statistical mechanics of protein folding
-
J.D. Bryngelson, and P.G. Wolynes Spin glasses and the statistical mechanics of protein folding Proc. Natl. Acad. Sci. USA 84 1987 7524 7528
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 7524-7528
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
2
-
-
84869761071
-
The protein-folding problem, 50 years on
-
K.A. Dill, and J.L. MacCallum The protein-folding problem, 50 years on Science 338 2012 1042 1046
-
(2012)
Science
, vol.338
, pp. 1042-1046
-
-
Dill, K.A.1
Maccallum, J.L.2
-
3
-
-
69949124663
-
Protein dynamics from single-molecule fluorescence intensity correlation functions
-
I.V. Gopich, and D. Nettels A. Szabo Protein dynamics from single-molecule fluorescence intensity correlation functions J. Chem. Phys. 131 2009 095102
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 095102
-
-
Gopich, I.V.1
Nettels, D.2
Szabo, A.3
-
4
-
-
34547275473
-
Brownian motion in a field of force and the diffusion model of chemical reactions
-
H.A. Kramers Brownian motion in a field of force and the diffusion model of chemical reactions Physica 7 1940 284 304
-
(1940)
Physica
, vol.7
, pp. 284-304
-
-
Kramers, H.A.1
-
5
-
-
67749147584
-
Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories
-
H.S. Chung, J.M. Louis, and W.A. Eaton Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories Proc. Natl. Acad. Sci. USA 106 2009 11837 11844
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 11837-11844
-
-
Chung, H.S.1
Louis, J.M.2
Eaton, W.A.3
-
6
-
-
77956250820
-
A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements
-
S. Chaudhury, and D.E. Makarov A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements J. Chem. Phys. 133 2010 034118
-
(2010)
J. Chem. Phys.
, vol.133
, pp. 034118
-
-
Chaudhury, S.1
Makarov, D.E.2
-
7
-
-
36749116443
-
First passage time approach to diffusion controlled reactions
-
A. Szabo, K. Schulten, and Z. Schulten First passage time approach to diffusion controlled reactions J. Chem. Phys. 72 1980 4350 4357
-
(1980)
J. Chem. Phys.
, vol.72
, pp. 4350-4357
-
-
Szabo, A.1
Schulten, K.2
Schulten, Z.3
-
8
-
-
0029964867
-
Diffusion-limited contact formation in unfolded cytochrome c: Estimating the maximum rate of protein folding
-
S.J. Hagen, and J. Hofrichter W.A. Eaton Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding Proc. Natl. Acad. Sci. USA 93 1996 11615 11617
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 11615-11617
-
-
Hagen, S.J.1
Hofrichter, J.2
Eaton, W.A.3
-
9
-
-
0028800425
-
Analysis of the structure of ribonuclease A in native and partially denatured states by time-resolved nonradiative dynamic excitation energy transfer between site-specific extrinsic probes
-
D.R. Buckler, E. Haas, and H.A. Scheraga Analysis of the structure of ribonuclease A in native and partially denatured states by time-resolved nonradiative dynamic excitation energy transfer between site-specific extrinsic probes Biochemistry 34 1995 15965 15978
-
(1995)
Biochemistry
, vol.34
, pp. 15965-15978
-
-
Buckler, D.R.1
Haas, E.2
Scheraga, H.A.3
-
10
-
-
0034691198
-
Measuring the rate of intramolecular contact formation in polypeptides
-
L.J. Lapidus, W.A. Eaton, and J. Hofrichter Measuring the rate of intramolecular contact formation in polypeptides Proc. Natl. Acad. Sci. USA 97 2000 7220 7225
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 7220-7225
-
-
Lapidus, L.J.1
Eaton, W.A.2
Hofrichter, J.3
-
11
-
-
33747623305
-
End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation
-
A. Möglich, K. Joder, and T. Kiefhaber End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation Proc. Natl. Acad. Sci. USA 103 2006 12394 12399
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 12394-12399
-
-
Möglich, A.1
Joder, K.2
Kiefhaber, T.3
-
12
-
-
33847254454
-
Ultrafast dynamics of protein collapse from single-molecule photon statistics
-
D. Nettels, and I.V. Gopich B. Schuler Ultrafast dynamics of protein collapse from single-molecule photon statistics Proc. Natl. Acad. Sci. USA 104 2007 2655 2660
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 2655-2660
-
-
Nettels, D.1
Gopich, I.V.2
Schuler, B.3
-
13
-
-
84863116610
-
Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion
-
B. Ahmad, Y. Chen, and L.J. Lapidus Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion Proc. Natl. Acad. Sci. USA 109 2012 2336 2341
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 2336-2341
-
-
Ahmad, B.1
Chen, Y.2
Lapidus, L.J.3
-
15
-
-
75749153687
-
Coordinate-dependent diffusion in protein folding
-
R.B. Best, and G. Hummer Coordinate-dependent diffusion in protein folding Proc. Natl. Acad. Sci. USA 107 2010 1088 1093
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 1088-1093
-
-
Best, R.B.1
Hummer, G.2
-
16
-
-
84870835154
-
Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy
-
A. Borgia, and B.G. Wensley B. Schuler Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy Nat. Commun. 3 2012 1195
-
(2012)
Nat. Commun.
, vol.3
, pp. 1195
-
-
Borgia, A.1
Wensley, B.G.2
Schuler, B.3
-
18
-
-
84873525793
-
Force as a single molecule probe of multidimensional protein energy landscapes
-
G. Zoldák, and M. Rief Force as a single molecule probe of multidimensional protein energy landscapes Curr. Opin. Struct. Biol. 23 2013 48 57
-
(2013)
Curr. Opin. Struct. Biol.
, vol.23
, pp. 48-57
-
-
Zoldák, G.1
Rief, M.2
-
20
-
-
84864661883
-
Transition path times for nucleic acid folding determined from energy-landscape analysis of single-molecule trajectories
-
K. Neupane, and D.B. Ritchie M.T. Woodside Transition path times for nucleic acid folding determined from energy-landscape analysis of single-molecule trajectories Phys. Rev. Lett. 109 2012 068102
-
(2012)
Phys. Rev. Lett.
, vol.109
, pp. 068102
-
-
Neupane, K.1
Ritchie, D.B.2
Woodside, M.T.3
-
21
-
-
84865987083
-
Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates
-
H. Yu, and A.N. Gupta M.T. Woodside Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates Proc. Natl. Acad. Sci. USA 109 2012 14452 14457
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 14452-14457
-
-
Yu, H.1
Gupta, A.N.2
Woodside, M.T.3
-
22
-
-
84875438723
-
Force-clamp experiments reveal the free-energy profile and diffusion coefficient of the collapse of protein molecules
-
H. Lannon, and J.S. Haghpanah J. Brujic Force-clamp experiments reveal the free-energy profile and diffusion coefficient of the collapse of protein molecules Phys. Rev. Lett. 110 2013 128301
-
(2013)
Phys. Rev. Lett.
, vol.110
, pp. 128301
-
-
Lannon, H.1
Haghpanah, J.S.2
Brujic, J.3
-
23
-
-
84901982914
-
Reconstructing folding energy landscapes by single-molecule force spectroscopy
-
M.T. Woodside, and S.M. Block Reconstructing folding energy landscapes by single-molecule force spectroscopy Annu Rev Biophys 43 2014 19 39
-
(2014)
Annu Rev Biophys
, vol.43
, pp. 19-39
-
-
Woodside, M.T.1
Block, S.M.2
-
24
-
-
79960978673
-
Reconstructing free energy profiles from nonequilibrium relaxation trajectories
-
Q. Zhang, J. Brujic, and E. Vanden-Eijnden Reconstructing free energy profiles from nonequilibrium relaxation trajectories J. Stat. Phys. 144 2011 344 366
-
(2011)
J. Stat. Phys.
, vol.144
, pp. 344-366
-
-
Zhang, Q.1
Brujic, J.2
Vanden-Eijnden, E.3
-
25
-
-
80052423145
-
Direct quantification of the attempt frequency determining the mechanical unfolding of ubiquitin protein
-
I. Popa, J.M. Fernández, and S. Garcia-Manyes Direct quantification of the attempt frequency determining the mechanical unfolding of ubiquitin protein J. Biol. Chem. 286 2011 31072 31079
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 31072-31079
-
-
Popa, I.1
Fernández, J.M.2
Garcia-Manyes, S.3
-
26
-
-
33646587736
-
Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins
-
M.T. Woodside, and W.M. Behnke-Parks S.M. Block Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins Proc. Natl. Acad. Sci. USA 103 2006 6190 6195
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 6190-6195
-
-
Woodside, M.T.1
Behnke-Parks, W.M.2
Block, S.M.3
-
27
-
-
33750970551
-
Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid
-
M.T. Woodside, and P.C. Anthony S.M. Block Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid Science 314 2006 1001 1004
-
(2006)
Science
, vol.314
, pp. 1001-1004
-
-
Woodside, M.T.1
Anthony, P.C.2
Block, S.M.3
-
28
-
-
28844460238
-
Passive all-optical force clamp for high-resolution laser trapping
-
W.J. Greenleaf, and M.T. Woodside S.M. Block Passive all-optical force clamp for high-resolution laser trapping Phys. Rev. Lett. 95 2005 208102
-
(2005)
Phys. Rev. Lett.
, vol.95
, pp. 208102
-
-
Greenleaf, W.J.1
Woodside, M.T.2
Block, S.M.3
-
29
-
-
84880316740
-
A simple and effective Verlet-type algorithm for simulating Langevin dynamics
-
N. Gronbech-Jensen, and O. Farago A simple and effective Verlet-type algorithm for simulating Langevin dynamics Mol. Phys. 111 2013 983 991
-
(2013)
Mol. Phys.
, vol.111
, pp. 983-991
-
-
Gronbech-Jensen, N.1
Farago, O.2
-
30
-
-
0347193736
-
Reaction-rate theory - 50 years after Kramers
-
P. Hanggi, P. Talkner, and M. Borkovec Reaction-rate theory - 50 years after Kramers Rev. Mod. Phys. 62 1990 251 341
-
(1990)
Rev. Mod. Phys.
, vol.62
, pp. 251-341
-
-
Hanggi, P.1
Talkner, P.2
Borkovec, M.3
-
31
-
-
0034934258
-
Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins
-
A. Ansari, S.V. Kuznetsov, and Y. Shen Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins Proc. Natl. Acad. Sci. USA 98 2001 7771 7776
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 7771-7776
-
-
Ansari, A.1
Kuznetsov, S.V.2
Shen, Y.3
-
32
-
-
1642576003
-
Kinetics of end-to-end collision in short single-stranded nucleic acids
-
X. Wang, and W.M. Nau Kinetics of end-to-end collision in short single-stranded nucleic acids J. Am. Chem. Soc. 126 2004 808 813
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 808-813
-
-
Wang, X.1
Nau, W.M.2
-
33
-
-
54849437727
-
Relative stability of helices determines the folding landscape of adenine riboswitch aptamers
-
J.-C. Lin, and D. Thirumalai Relative stability of helices determines the folding landscape of adenine riboswitch aptamers J. Am. Chem. Soc. 130 2008 14080 14081
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 14080-14081
-
-
Lin, J.-C.1
Thirumalai, D.2
-
34
-
-
84875249565
-
From mechanical folding trajectories to intrinsic energy landscapes of biopolymers
-
M. Hinczewski, and J.C.M. Gebhardt D. Thirumalai From mechanical folding trajectories to intrinsic energy landscapes of biopolymers Proc. Natl. Acad. Sci. USA 110 2013 4500 4505
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 4500-4505
-
-
Hinczewski, M.1
Gebhardt, J.C.M.2
Thirumalai, D.3
-
35
-
-
84880340824
-
Rigid DNA beams for high-resolution single-molecule mechanics
-
E. Pfitzner, and C. Wachauf H. Dietz Rigid DNA beams for high-resolution single-molecule mechanics Angew. Chem. Int. Ed. Engl. 52 2013 7766 7771
-
(2013)
Angew. Chem. Int. Ed. Engl.
, vol.52
, pp. 7766-7771
-
-
Pfitzner, E.1
Wachauf, C.2
Dietz, H.3
-
37
-
-
34247640029
-
Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results
-
J.-D. Wen, and M. Manosas I. Tinoco Jr. Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results Biophys. J. 92 2007 2996 3009
-
(2007)
Biophys. J.
, vol.92
, pp. 2996-3009
-
-
Wen, J.-D.1
Manosas, M.2
Tinoco, I.3
-
38
-
-
84873050143
-
Effect of handle length and microsphere size on transition kinetics in single-molecule experiments
-
J.-C. Chang, M. de Messieres, and A. La Porta Effect of handle length and microsphere size on transition kinetics in single-molecule experiments Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 87 2013 012721
-
(2013)
Phys. Rev. e Stat. Nonlin. Soft Matter Phys.
, vol.87
, pp. 012721
-
-
Chang, J.-C.1
De Messieres, M.2
La Porta, A.3
-
39
-
-
79959671944
-
Improving signal/noise resolution in single-molecule experiments using molecular constructs with short handles
-
N. Forns, and S. de Lorenzo F. Ritort Improving signal/noise resolution in single-molecule experiments using molecular constructs with short handles Biophys. J. 100 2011 1765 1774
-
(2011)
Biophys. J.
, vol.100
, pp. 1765-1774
-
-
Forns, N.1
De Lorenzo, S.2
Ritort, F.3
-
40
-
-
34247609813
-
Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments
-
M. Manosas, and J.-D. Wen F. Ritort Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments Biophys. J. 92 2007 3010 3021
-
(2007)
Biophys. J.
, vol.92
, pp. 3010-3021
-
-
Manosas, M.1
Wen, J.-D.2
Ritort, F.3
-
41
-
-
84867004600
-
Limitations of constant-force-feedback experiments
-
P.J. Elms, and J.D. Chodera S. Marqusee Limitations of constant-force-feedback experiments Biophys. J. 103 2012 1490 1499
-
(2012)
Biophys. J.
, vol.103
, pp. 1490-1499
-
-
Elms, P.J.1
Chodera, J.D.2
Marqusee, S.3
|