-
1
-
-
0033214502
-
The study of protein mechanics with the atomic force microscope
-
Fisher T.E., Oberhauser A.F., Carrion-Vazquez M., Marszalek P.E., and Fernandez J.M. The study of protein mechanics with the atomic force microscope. Trends Biochem Sci 24 (1999) 379-384
-
(1999)
Trends Biochem Sci
, vol.24
, pp. 379-384
-
-
Fisher, T.E.1
Oberhauser, A.F.2
Carrion-Vazquez, M.3
Marszalek, P.E.4
Fernandez, J.M.5
-
4
-
-
33846940059
-
Mechanical unfolding of proteins: insights into biology, structure and folding
-
Forman J.R., and Clarke J. Mechanical unfolding of proteins: insights into biology, structure and folding. Curr Opin Struct Biol 17 (2007) 58-66
-
(2007)
Curr Opin Struct Biol
, vol.17
, pp. 58-66
-
-
Forman, J.R.1
Clarke, J.2
-
5
-
-
23744478437
-
Free energy surfaces from single-molecule force spectroscopy
-
Hummer G., and Szabo A. Free energy surfaces from single-molecule force spectroscopy. Accounts Chem Res 38 (2005) 504-513
-
(2005)
Accounts Chem Res
, vol.38
, pp. 504-513
-
-
Hummer, G.1
Szabo, A.2
-
6
-
-
0042287973
-
Single-molecule fluorescence spectroscopy of biomolecular folding
-
Haran G. Single-molecule fluorescence spectroscopy of biomolecular folding. J Phys Condens Matter 15 (2003) R1291-R1317
-
(2003)
J Phys Condens Matter
, vol.15
-
-
Haran, G.1
-
7
-
-
22444436718
-
Single-molecule fluorescence spectroscopy of protein folding
-
Schuler B. Single-molecule fluorescence spectroscopy of protein folding. Chemphyschem 6 (2005) 1206-1220
-
(2005)
Chemphyschem
, vol.6
, pp. 1206-1220
-
-
Schuler, B.1
-
8
-
-
33646937406
-
Single-molecule fluorescence studies of protein folding and conformational dynamics
-
Michalet X., Weiss S., and Jäger M. Single-molecule fluorescence studies of protein folding and conformational dynamics. Chem Rev 106 (2006) 1785-1813
-
(2006)
Chem Rev
, vol.106
, pp. 1785-1813
-
-
Michalet, X.1
Weiss, S.2
Jäger, M.3
-
9
-
-
0029987587
-
Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor
-
Ha T., Enderle T., Ogletree D.F., Chemla D.S., Selvin P.R., and Weiss S. Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc Natl Acad Sci U S A 93 (1996) 6264-6268
-
(1996)
Proc Natl Acad Sci U S A
, vol.93
, pp. 6264-6268
-
-
Ha, T.1
Enderle, T.2
Ogletree, D.F.3
Chemla, D.S.4
Selvin, P.R.5
Weiss, S.6
-
10
-
-
0033462513
-
Folding dynamics of single GCN4 peptides by fluorescence resonant energy transfer confocal microscopy
-
Jia Y.W., Talaga D.S., Lau W.L., Lu H.S.M., DeGrado W.F., and Hochstrasser R.M. Folding dynamics of single GCN4 peptides by fluorescence resonant energy transfer confocal microscopy. Chem Phys 247 (1999) 69-83
-
(1999)
Chem Phys
, vol.247
, pp. 69-83
-
-
Jia, Y.W.1
Talaga, D.S.2
Lau, W.L.3
Lu, H.S.M.4
DeGrado, W.F.5
Hochstrasser, R.M.6
-
11
-
-
1542501215
-
Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy
-
Talaga D.S., Lau W.L., Roder H., Tang J., Jia Y., DeGrado W.F., and Hochstrasser R.M. Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy. Proc Natl Acad Sci U S A 97 (2000) 13021-13026
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 13021-13026
-
-
Talaga, D.S.1
Lau, W.L.2
Roder, H.3
Tang, J.4
Jia, Y.5
DeGrado, W.F.6
Hochstrasser, R.M.7
-
12
-
-
0034625167
-
Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2
-
Deniz A.A., Laurence T.A., Beligere G.S., Dahan M., Martin A.B., Chemla D.S., Dawson P.E., Schultz P.G., and Weiss S. Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2. Proc Natl Acad Sci U S A 97 (2000) 5179-5184
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 5179-5184
-
-
Deniz, A.A.1
Laurence, T.A.2
Beligere, G.S.3
Dahan, M.4
Martin, A.B.5
Chemla, D.S.6
Dawson, P.E.7
Schultz, P.G.8
Weiss, S.9
-
13
-
-
3042538758
-
Using photoinduced charge transfer reactions to study conformational dynamics of biopolymers at the single-molecule level
-
Neuweiler H., and Sauer M. Using photoinduced charge transfer reactions to study conformational dynamics of biopolymers at the single-molecule level. Curr Pharm Biotechnol 5 (2004) 285-298
-
(2004)
Curr Pharm Biotechnol
, vol.5
, pp. 285-298
-
-
Neuweiler, H.1
Sauer, M.2
-
14
-
-
0036400525
-
What fluorescence correlation spectroscopy can tell us about unfolded proteins
-
Frieden C., Chattopadhyay K., and Elson E.L. What fluorescence correlation spectroscopy can tell us about unfolded proteins. Adv Protein Chem 62 (2002) 91-109
-
(2002)
Adv Protein Chem
, vol.62
, pp. 91-109
-
-
Frieden, C.1
Chattopadhyay, K.2
Elson, E.L.3
-
16
-
-
33644986099
-
Mechanisms of protein assembly: lessons from minimalist models
-
Levy Y., and Onuchic J.N. Mechanisms of protein assembly: lessons from minimalist models. Acc Chem Res 39 (2006) 135-142
-
(2006)
Acc Chem Res
, vol.39
, pp. 135-142
-
-
Levy, Y.1
Onuchic, J.N.2
-
18
-
-
33747592347
-
The experimental survey of protein-folding energy landscapes
-
Oliveberg M., and Wolynes P.G. The experimental survey of protein-folding energy landscapes. Q Rev Biophys 38 (2005) 245-288
-
(2005)
Q Rev Biophys
, vol.38
, pp. 245-288
-
-
Oliveberg, M.1
Wolynes, P.G.2
-
19
-
-
0037154980
-
Protein folding and unfolding at atomic resolution
-
Fersht A.R., and Daggett V. Protein folding and unfolding at atomic resolution. Cell 108 (2002) 573-582
-
(2002)
Cell
, vol.108
, pp. 573-582
-
-
Fersht, A.R.1
Daggett, V.2
-
20
-
-
8644232696
-
Combinatorial modeling of protein folding kinetics: free energy profiles and rates
-
Henry E.R., and Eaton W.A. Combinatorial modeling of protein folding kinetics: free energy profiles and rates. Chem Phys 307 (2004) 163-185
-
(2004)
Chem Phys
, vol.307
, pp. 163-185
-
-
Henry, E.R.1
Eaton, W.A.2
-
21
-
-
84981779372
-
Zwischenmolekulare Energiewanderung und Fluoreszenz
-
Förster T. Zwischenmolekulare Energiewanderung und Fluoreszenz. Annalen der Physik 6 (1948) 55-75
-
(1948)
Annalen der Physik
, vol.6
, pp. 55-75
-
-
Förster, T.1
-
22
-
-
14544283620
-
Polyproline and the "spectroscopic ruler" revisited with single molecule fluorescence
-
Schuler B., Lipman E.A., Steinbach P.J., Kumke M., and Eaton W.A. Polyproline and the "spectroscopic ruler" revisited with single molecule fluorescence. Proc Natl Acad Sci U S A 102 (2005) 2754-2759
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 2754-2759
-
-
Schuler, B.1
Lipman, E.A.2
Steinbach, P.J.3
Kumke, M.4
Eaton, W.A.5
-
24
-
-
33646416480
-
Quantitative single-molecule conformational distributions: a case study with poly-(l-proline)
-
Watkins L.P., Chang H.Y., and Yang H. Quantitative single-molecule conformational distributions: a case study with poly-(l-proline). J Phys Chem A 110 (2006) 5191-5203
-
(2006)
J Phys Chem A
, vol.110
, pp. 5191-5203
-
-
Watkins, L.P.1
Chang, H.Y.2
Yang, H.3
-
25
-
-
36849083388
-
Probing polyproline structure and dynamics by photoinduced electron transfer provides evidence for deviations from a regular polyproline type II helix
-
Doose S., Neuweiler H., Barsch H., and Sauer M. Probing polyproline structure and dynamics by photoinduced electron transfer provides evidence for deviations from a regular polyproline type II helix. Proc Natl Acad Sci U S A 104 (2007) 17400-17405
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 17400-17405
-
-
Doose, S.1
Neuweiler, H.2
Barsch, H.3
Sauer, M.4
-
26
-
-
37649015345
-
-
Best R, Merchant K, Gopich IV, Schuler B, Bax A, Eaton WA: Effect of flexibility and cis residues in single molecule FRET studies of polyproline. Proc Natl Acad Sci U S A 2007, 104:18964-18969.
-
Best R, Merchant K, Gopich IV, Schuler B, Bax A, Eaton WA: Effect of flexibility and cis residues in single molecule FRET studies of polyproline. Proc Natl Acad Sci U S A 2007, 104:18964-18969. A combination of single-molecule intensity and subpopulation lifetime measurements, NMR, and molecular dynamics simulations of polyproline, including the dyes and their linkers to the polypeptide, shows that that the kinks arising from internal cis-prolines are primarily responsible for a mean FRET efficiency higher than predicted for a rigid-rod all-trans polyproline. Theoretical analysis also shows that the width in excess of shot noise in the observed efficiency histograms and distributions of donor fluorescence lifetimes are explained by the presence of multiple species with efficiencies consistent with the simulations and the populations from NMR.
-
-
-
-
27
-
-
33751349660
-
Shot-noise limited single-molecule FRET histograms: comparison between theory and experiments
-
Nir E., Michalet X., Hamadani K.M., Laurence T.A., Neuhauser D., Kovchegov Y., and Weiss S. Shot-noise limited single-molecule FRET histograms: comparison between theory and experiments. J Phys Chem B 110 (2006) 22103-22124
-
(2006)
J Phys Chem B
, vol.110
, pp. 22103-22124
-
-
Nir, E.1
Michalet, X.2
Hamadani, K.M.3
Laurence, T.A.4
Neuhauser, D.5
Kovchegov, Y.6
Weiss, S.7
-
28
-
-
33646377416
-
Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysis
-
Antonik M., Felekyan S., Gaiduk A., and Seidel C.A.M. Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysis. J Phys Chem B 110 (2006) 6970-6978
-
(2006)
J Phys Chem B
, vol.110
, pp. 6970-6978
-
-
Antonik, M.1
Felekyan, S.2
Gaiduk, A.3
Seidel, C.A.M.4
-
29
-
-
2942650138
-
Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules
-
Kapanidis A.N., Lee N.K., Laurence T.A., Doose S., Margeat E., and Weiss S. Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules. Proc Natl Acad Sci U S A 101 (2004) 8936-8941
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 8936-8941
-
-
Kapanidis, A.N.1
Lee, N.K.2
Laurence, T.A.3
Doose, S.4
Margeat, E.5
Weiss, S.6
-
30
-
-
22144492905
-
Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation
-
Lee N.K., Kapanidis A.N., Wang Y., Michalet X., Mukhopadhyay J., Ebright R.H., and Weiss S. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys J 88 (2005) 2939-2953
-
(2005)
Biophys J
, vol.88
, pp. 2939-2953
-
-
Lee, N.K.1
Kapanidis, A.N.2
Wang, Y.3
Michalet, X.4
Mukhopadhyay, J.5
Ebright, R.H.6
Weiss, S.7
-
31
-
-
33846839535
-
Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations
-
The unfolded subpopulations of protein L and CspTm are compared over a range of denaturant concentrations from FRET efficiencies determined from both intensity and lifetime measurements. The interpretation is guided by Langevin simulations of a simplified representation of the polypeptide, which also suggest that collapse can result either from increased inter-residue attraction or from decreased excluded volume.
-
Merchant K.A., Best R.B., Louis J.M., Gopich I.V., and Eaton W.A. Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations. Proc Natl Acad Sci U S A 104 (2007) 1528-1533. The unfolded subpopulations of protein L and CspTm are compared over a range of denaturant concentrations from FRET efficiencies determined from both intensity and lifetime measurements. The interpretation is guided by Langevin simulations of a simplified representation of the polypeptide, which also suggest that collapse can result either from increased inter-residue attraction or from decreased excluded volume.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 1528-1533
-
-
Merchant, K.A.1
Best, R.B.2
Louis, J.M.3
Gopich, I.V.4
Eaton, W.A.5
-
32
-
-
33644767158
-
Single-molecule FRET study of denaturant induced unfolding of RNase H
-
Kuzmenkina E.V., Heyes C.D., and Nienhaus G.U. Single-molecule FRET study of denaturant induced unfolding of RNase H. J Mol Biol 357 (2006) 313-324
-
(2006)
J Mol Biol
, vol.357
, pp. 313-324
-
-
Kuzmenkina, E.V.1
Heyes, C.D.2
Nienhaus, G.U.3
-
33
-
-
0037566231
-
Single-macromolecule fluorescence resonance energy transfer and free-energy profiles
-
Gopich I.V., and Szabo A. Single-macromolecule fluorescence resonance energy transfer and free-energy profiles. J Phys Chem B 107 (2003) 5058-5063
-
(2003)
J Phys Chem B
, vol.107
, pp. 5058-5063
-
-
Gopich, I.V.1
Szabo, A.2
-
34
-
-
34548096938
-
Theory of photon statistics in single-molecule Förster resonance energy transfer
-
Gopich I.V., and Szabo A. Theory of photon statistics in single-molecule Förster resonance energy transfer. J Chem Phys 122 (2005) 1-18
-
(2005)
J Chem Phys
, vol.122
, pp. 1-18
-
-
Gopich, I.V.1
Szabo, A.2
-
35
-
-
36249028655
-
Single-molecule FRET with diffusion and conformational dynamics
-
A comprehensive theory is presented for the analysis of single-molecule FRET measurements on freely diffusing and immobilized molecules, including the contribution of various processes to the distribution and variance in FRET efficiency.
-
Gopich I.V., and Szabo A. Single-molecule FRET with diffusion and conformational dynamics. J Phys Chem B 111 (2007) 12925-12932. A comprehensive theory is presented for the analysis of single-molecule FRET measurements on freely diffusing and immobilized molecules, including the contribution of various processes to the distribution and variance in FRET efficiency.
-
(2007)
J Phys Chem B
, vol.111
, pp. 12925-12932
-
-
Gopich, I.V.1
Szabo, A.2
-
36
-
-
28444431959
-
Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins
-
This work contains the first use of subpopulation-specific fluorescence lifetime analysis for the investigation of distance distributions in unfolded proteins and infers the presence of transient unfolded state structure in CI2 and ACBP.
-
Laurence T.A., Kong X.X., Jäger M., and Weiss S. Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins. Proc Natl Acad Sci U S A 102 (2005) 17348-17353. This work contains the first use of subpopulation-specific fluorescence lifetime analysis for the investigation of distance distributions in unfolded proteins and infers the presence of transient unfolded state structure in CI2 and ACBP.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 17348-17353
-
-
Laurence, T.A.1
Kong, X.X.2
Jäger, M.3
Weiss, S.4
-
37
-
-
0037126290
-
Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
-
Schuler B., Lipman E.A., and Eaton W.A. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature 419 (2002) 743-747
-
(2002)
Nature
, vol.419
, pp. 743-747
-
-
Schuler, B.1
Lipman, E.A.2
Eaton, W.A.3
-
38
-
-
33846099514
-
Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy
-
By varying the position of donor and acceptor in the chain, different segments of unfolded CspTm are probed, indicating isotropic collapse and good agreement with Gaussian-chain behavior even in the collapsed unfolded state. Synchrotron circular dichroism spectroscopy reveals the formation of some β-structure concomitant with collapse.
-
Hoffmann A., Kane A., Nettels D., Hertzog D.E., Baumgärtel P., Lengefeld J., Reichardt G., Horsley D.A., Seckler R., Bakajin O., and Schuler B. Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy. Proc Natl Acad Sci U S A 104 (2007) 105-110. By varying the position of donor and acceptor in the chain, different segments of unfolded CspTm are probed, indicating isotropic collapse and good agreement with Gaussian-chain behavior even in the collapsed unfolded state. Synchrotron circular dichroism spectroscopy reveals the formation of some β-structure concomitant with collapse.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 105-110
-
-
Hoffmann, A.1
Kane, A.2
Nettels, D.3
Hertzog, D.E.4
Baumgärtel, P.5
Lengefeld, J.6
Reichardt, G.7
Horsley, D.A.8
Seckler, R.9
Bakajin, O.10
Schuler, B.11
-
39
-
-
27344452885
-
Single-molecule Förster resonance energy transfer study of protein dynamics under denaturing conditions
-
Folding/unfolding trajectories are obtained from FRET efficiency measurements on surface-immobilized RNase H, and suggest unfolded state dynamics on time scales from microseconds to seconds.
-
Kuzmenkina E.V., Heyes C.D., and Nienhaus G.U. Single-molecule Förster resonance energy transfer study of protein dynamics under denaturing conditions. Proc Natl Acad Sci U S A 102 (2005) 15471-15476. Folding/unfolding trajectories are obtained from FRET efficiency measurements on surface-immobilized RNase H, and suggest unfolded state dynamics on time scales from microseconds to seconds.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 15471-15476
-
-
Kuzmenkina, E.V.1
Heyes, C.D.2
Nienhaus, G.U.3
-
40
-
-
33746823043
-
Coil-globule transition in the denatured state of a small protein
-
The mean FRET efficiency and hydrodynamic radius from FCS indicate collapse of the unfolded protein L subpopulation upon decreasing denaturant concentration. The collapse is analyzed in terms of a coil-globule transition to obtain information about the solvation properties of the unfolded state.
-
Sherman E., and Haran G. Coil-globule transition in the denatured state of a small protein. Proc Natl Acad Sci U S A 103 (2006) 11539-11543. The mean FRET efficiency and hydrodynamic radius from FCS indicate collapse of the unfolded protein L subpopulation upon decreasing denaturant concentration. The collapse is analyzed in terms of a coil-globule transition to obtain information about the solvation properties of the unfolded state.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 11539-11543
-
-
Sherman, E.1
Haran, G.2
-
41
-
-
33846073474
-
Distinguishing between cooperative and unimodal downhill protein folding
-
Huang F., Sato S., Sharpe T.D., Ying L.M., and Fersht A.R. Distinguishing between cooperative and unimodal downhill protein folding. Proc Natl Acad Sci U S A 104 (2007) 123-127
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 123-127
-
-
Huang, F.1
Sato, S.2
Sharpe, T.D.3
Ying, L.M.4
Fersht, A.R.5
-
42
-
-
33748460691
-
Urea-induced unfolding of the immunity protein Im9 monitored by spFRET
-
Tezuka-Kawakami T., Gell C., Brockwell D.J., Radford S.E., and Smith D.A. Urea-induced unfolding of the immunity protein Im9 monitored by spFRET. Biophys J 91 (2006) L42-L44
-
(2006)
Biophys J
, vol.91
-
-
Tezuka-Kawakami, T.1
Gell, C.2
Brockwell, D.J.3
Radford, S.E.4
Smith, D.A.5
-
43
-
-
0041321045
-
Single-molecule measurement of protein folding kinetics
-
Lipman E.A., Schuler B., Bakajin O., and Eaton W.A. Single-molecule measurement of protein folding kinetics. Science 301 (2003) 1233-1235
-
(2003)
Science
, vol.301
, pp. 1233-1235
-
-
Lipman, E.A.1
Schuler, B.2
Bakajin, O.3
Eaton, W.A.4
-
44
-
-
34347218159
-
Conformational dynamics and ensembles in protein folding
-
Muñoz V. Conformational dynamics and ensembles in protein folding. Annu Rev Biophys Biomol Struct 36 (2007) 395-412
-
(2007)
Annu Rev Biophys Biomol Struct
, vol.36
, pp. 395-412
-
-
Muñoz, V.1
-
46
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: a synthesis
-
Bryngelson J.D., Onuchic J.N., Socci N.D., and Wolynes P.G. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21 (1995) 167-195
-
(1995)
Proteins
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
47
-
-
33847324863
-
A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures
-
The prion-determining NM domain of the yeast prion protein Sup35 is shown to undergo a continuous expansion rather than a cooperative unfolding transition upon addition of denaturant. Fluorescence intensity fluctuations in the submicrosecond range are assigned to chain dynamics resulting in rapid intramolecular quenching by tyrosine.
-
Mukhopadhyay S., Krishnan R., Lemke E.A., Lindquist S., and Deniz A.A. A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. Proc Natl Acad Sci U S A 104 (2007) 2649-2654. The prion-determining NM domain of the yeast prion protein Sup35 is shown to undergo a continuous expansion rather than a cooperative unfolding transition upon addition of denaturant. Fluorescence intensity fluctuations in the submicrosecond range are assigned to chain dynamics resulting in rapid intramolecular quenching by tyrosine.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 2649-2654
-
-
Mukhopadhyay, S.1
Krishnan, R.2
Lemke, E.A.3
Lindquist, S.4
Deniz, A.A.5
-
48
-
-
4344716256
-
Random-coil behavior and the dimensions of chemically unfolded proteins
-
Kohn J.E., Millett I.S., Jacob J., Zagrovic B., Dillon T.M., Cingel N., Dothager R.S., Seifert S., Thiyagarajan P., Sosnick T.R., et al. Random-coil behavior and the dimensions of chemically unfolded proteins. Proc Natl Acad Sci U S A 101 (2004) 12491-12496
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 12491-12496
-
-
Kohn, J.E.1
Millett, I.S.2
Jacob, J.3
Zagrovic, B.4
Dillon, T.M.5
Cingel, N.6
Dothager, R.S.7
Seifert, S.8
Thiyagarajan, P.9
Sosnick, T.R.10
-
49
-
-
0037039440
-
Equilibrium collapse and the kinetic 'foldability' of proteins
-
Millet I.S., Townsley L.E., Chiti F., Doniach S., and Plaxco K.W. Equilibrium collapse and the kinetic 'foldability' of proteins. Biochemistry 41 (2002) 321-325
-
(2002)
Biochemistry
, vol.41
, pp. 321-325
-
-
Millet, I.S.1
Townsley, L.E.2
Chiti, F.3
Doniach, S.4
Plaxco, K.W.5
-
50
-
-
0032978994
-
Chain collapse can occur concomitantly with the rate-limiting step in protein folding
-
Plaxco K.W., Millett I.S., Segel D.J., Doniach S., and Baker D. Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nat Struct Biol 6 (1999) 554-556
-
(1999)
Nat Struct Biol
, vol.6
, pp. 554-556
-
-
Plaxco, K.W.1
Millett, I.S.2
Segel, D.J.3
Doniach, S.4
Baker, D.5
-
51
-
-
0038370011
-
The molecular basis for the chemical denaturation of proteins by urea
-
Bennion B.J., and Daggett V. The molecular basis for the chemical denaturation of proteins by urea. Proc Natl Acad Sci U S A 100 (2003) 5142-5147
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 5142-5147
-
-
Bennion, B.J.1
Daggett, V.2
-
52
-
-
33745955427
-
Specificity of the initial collapse in the folding of the cold shock protein
-
Magg C., Kubelka J., Holtermann G., Haas E., and Schmid F.X. Specificity of the initial collapse in the folding of the cold shock protein. J Mol Biol 360 (2006) 1067-1080
-
(2006)
J Mol Biol
, vol.360
, pp. 1067-1080
-
-
Magg, C.1
Kubelka, J.2
Holtermann, G.3
Haas, E.4
Schmid, F.X.5
-
53
-
-
24044462641
-
Site-specific dimensions across a highly denatured protein; a single molecule study
-
McCarney E.R., Werner J.H., Bernstein S.L., Ruczinski I., Makarov D.E., Goodwin P.M., and Plaxco K.W. Site-specific dimensions across a highly denatured protein; a single molecule study. J Mol Biol 352 (2005) 672-682
-
(2005)
J Mol Biol
, vol.352
, pp. 672-682
-
-
McCarney, E.R.1
Werner, J.H.2
Bernstein, S.L.3
Ruczinski, I.4
Makarov, D.E.5
Goodwin, P.M.6
Plaxco, K.W.7
-
54
-
-
0036400715
-
Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance
-
Dyson H.J., and Wright P.E. Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance. Adv Protein Chem 62 (2002) 311-340
-
(2002)
Adv Protein Chem
, vol.62
, pp. 311-340
-
-
Dyson, H.J.1
Wright, P.E.2
-
55
-
-
0036401140
-
Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins
-
Millett I.S., Doniach S., and Plaxco K.W. Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. Adv Protein Chem 62 (2002) 241-262
-
(2002)
Adv Protein Chem
, vol.62
, pp. 241-262
-
-
Millett, I.S.1
Doniach, S.2
Plaxco, K.W.3
-
56
-
-
0036400325
-
Is polyproline II a major backbone conformation in unfolded proteins?
-
Shi Z., Woody R.W., and Kallenbach N.R. Is polyproline II a major backbone conformation in unfolded proteins?. Adv Protein Chem 62 (2002) 163-240
-
(2002)
Adv Protein Chem
, vol.62
, pp. 163-240
-
-
Shi, Z.1
Woody, R.W.2
Kallenbach, N.R.3
-
57
-
-
0034743156
-
Ratiometric single-molecule studies of freely diffusing biomolecules
-
Deniz A.A., Laurence T.A., Dahan M., Chemla D.S., Schultz P.G., and Weiss S. Ratiometric single-molecule studies of freely diffusing biomolecules. Annu Rev Phys Chem 52 (2001) 233-253
-
(2001)
Annu Rev Phys Chem
, vol.52
, pp. 233-253
-
-
Deniz, A.A.1
Laurence, T.A.2
Dahan, M.3
Chemla, D.S.4
Schultz, P.G.5
Weiss, S.6
-
58
-
-
33847254454
-
Ultrafast dynamics of protein collapse from single-molecule photon statistics
-
Global chain reconfiguration dynamics on a 50 ns time scale are measured for unfolded CspTm in subpopulation-specific correlation experiments. Increased internal friction causes the dynamics to slow down in the more compact denatured state at low denaturant concentrations. This finding may explain the flat chevron observed for an ultrafast-folding protein [65] and raises the possibility of related effects on the folding kinetics of other proteins.
-
Nettels D., Gopich I.V., Hoffmann A., and Schuler B. Ultrafast dynamics of protein collapse from single-molecule photon statistics. Proc Natl Acad Sci U S A 104 (2007) 2655-2660. Global chain reconfiguration dynamics on a 50 ns time scale are measured for unfolded CspTm in subpopulation-specific correlation experiments. Increased internal friction causes the dynamics to slow down in the more compact denatured state at low denaturant concentrations. This finding may explain the flat chevron observed for an ultrafast-folding protein [65] and raises the possibility of related effects on the folding kinetics of other proteins.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 2655-2660
-
-
Nettels, D.1
Gopich, I.V.2
Hoffmann, A.3
Schuler, B.4
-
59
-
-
0037663777
-
Nanosecond dynamics of single polypeptide molecules revealed by photoemission statistics of fluorescence resonance energy transfer: a theoretical study
-
Wang Z.S., and Makarov D.E. Nanosecond dynamics of single polypeptide molecules revealed by photoemission statistics of fluorescence resonance energy transfer: a theoretical study. J Phys Chem B 107 (2003) 5617-5622
-
(2003)
J Phys Chem B
, vol.107
, pp. 5617-5622
-
-
Wang, Z.S.1
Makarov, D.E.2
-
60
-
-
34547554494
-
Theory of the statistics of kinetic transitions with application to single-molecule enzyme catalysis
-
Gopich I.V., and Szabo A. Theory of the statistics of kinetic transitions with application to single-molecule enzyme catalysis. J Chem Phys 124 (2006) 154712
-
(2006)
J Chem Phys
, vol.124
, pp. 154712
-
-
Gopich, I.V.1
Szabo, A.2
-
61
-
-
36749116443
-
1st passage time approach to diffusion controlled reactions
-
Szabo A., Schulten K., and Schulten Z. 1st 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
-
62
-
-
0000710672
-
Diffusive dynamics of the reaction coordinate for protein folding funnels
-
Socci N.D., Onuchic J.N., and Wolynes P.G. Diffusive dynamics of the reaction coordinate for protein folding funnels. J Chem Phys 104 (1996) 5860-5868
-
(1996)
J Chem Phys
, vol.104
, pp. 5860-5868
-
-
Socci, N.D.1
Onuchic, J.N.2
Wolynes, P.G.3
-
63
-
-
33744952224
-
Diffusive model of protein folding dynamics with Kramers turnover in rate
-
Best R.B., and Hummer G. Diffusive model of protein folding dynamics with Kramers turnover in rate. Phys Rev Lett 96 (2006) 228104
-
(2006)
Phys Rev Lett
, vol.96
, pp. 228104
-
-
Best, R.B.1
Hummer, G.2
-
64
-
-
35548963462
-
Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding
-
Chahine J., Oliveira R.J., Leite V.B.P., and Wang J. Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding. Proc Natl Acad Sci U S A 104 (2007) 14646-14651
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 14646-14651
-
-
Chahine, J.1
Oliveira, R.J.2
Leite, V.B.P.3
Wang, J.4
-
65
-
-
36749012371
-
-
Cellmer T, Henry ER, Kubelka J, Hofrichter J, Eaton WA: Relaxation rate for an ultrafast folding protein is independent of chemical denaturant concentration. J Am Chem Soc 2007, 129:14564-14566.
-
Cellmer T, Henry ER, Kubelka J, Hofrichter J, Eaton WA: Relaxation rate for an ultrafast folding protein is independent of chemical denaturant concentration. J Am Chem Soc 2007, 129:14564-14566.
-
-
-
-
66
-
-
0033613165
-
A simple model for calculating the kinetics of protein folding from three-dimensional structures
-
Muñoz V., and Eaton W.A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc Natl Acad Sci U S A 96 (1999) 11311-11316
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 11311-11316
-
-
Muñoz, V.1
Eaton, W.A.2
-
67
-
-
0242330738
-
The importance of explicit chain representation in protein folding models: an examination of Ising-like models
-
Karanicolas J., and Brooks C.L. The importance of explicit chain representation in protein folding models: an examination of Ising-like models. Proteins 53 (2003) 740-747
-
(2003)
Proteins
, vol.53
, pp. 740-747
-
-
Karanicolas, J.1
Brooks, C.L.2
-
68
-
-
0034743155
-
From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding
-
Shea J.E., and Brooks C.L. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu Rev Phys Chem 52 (2001) 499-535
-
(2001)
Annu Rev Phys Chem
, vol.52
, pp. 499-535
-
-
Shea, J.E.1
Brooks, C.L.2
-
70
-
-
8844247109
-
Two-state folding observed in individual protein molecules
-
Rhoades E., Cohen M., Schuler B., and Haran G. Two-state folding observed in individual protein molecules. J Am Chem Soc 126 (2004) 14686-14687
-
(2004)
J Am Chem Soc
, vol.126
, pp. 14686-14687
-
-
Rhoades, E.1
Cohen, M.2
Schuler, B.3
Haran, G.4
-
71
-
-
1842607369
-
Biofunctionalized, ultrathin coatings of cross-linked star-shaped poly(ethylene oxide) allow reversible folding of immobilized proteins
-
Groll J., Amirgoulova E.V., Ameringer T., Heyes C.D., Röcker C., Nienhaus G.U., and Möller M. Biofunctionalized, ultrathin coatings of cross-linked star-shaped poly(ethylene oxide) allow reversible folding of immobilized proteins. J Am Chem Soc 126 (2004) 4234-4239
-
(2004)
J Am Chem Soc
, vol.126
, pp. 4234-4239
-
-
Groll, J.1
Amirgoulova, E.V.2
Ameringer, T.3
Heyes, C.D.4
Röcker, C.5
Nienhaus, G.U.6
Möller, M.7
-
72
-
-
0030961780
-
The kinetic folding intermediate of ribonuclease H resembles the acid molten globule and partially unfolded molecules detected under native conditions
-
Raschke T.M., and Marqusee S. The kinetic folding intermediate of ribonuclease H resembles the acid molten globule and partially unfolded molecules detected under native conditions. Nat Struct Biol 4 (1997) 298-304
-
(1997)
Nat Struct Biol
, vol.4
, pp. 298-304
-
-
Raschke, T.M.1
Marqusee, S.2
-
73
-
-
0035807849
-
Protein folding pathways of adenylate kinase from E. coli: hydrostatic pressure and stopped-flow studies
-
Ruan Q., Ruan K., Balny C., Glaser M., and Mantulin W.W. Protein folding pathways of adenylate kinase from E. coli: hydrostatic pressure and stopped-flow studies. Biochemistry 40 (2001) 14706-14714
-
(2001)
Biochemistry
, vol.40
, pp. 14706-14714
-
-
Ruan, Q.1
Ruan, K.2
Balny, C.3
Glaser, M.4
Mantulin, W.W.5
-
74
-
-
33645223271
-
Suppressing Brownian motion of individual biomolecules in solution
-
Cohen A.E., and Moerner W.E. Suppressing Brownian motion of individual biomolecules in solution. Proc Natl Acad Sci U S A 103 (2006) 4362-4365
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 4362-4365
-
-
Cohen, A.E.1
Moerner, W.E.2
-
75
-
-
34547512144
-
Development of a technique for the investigation of folding dynamics of single proteins for extended time periods
-
Kinoshita M., Kamagata K., Maeda A., Goto Y., Komatsuzaki T., and Takahashi S. Development of a technique for the investigation of folding dynamics of single proteins for extended time periods. Proc Natl Acad Sci U S A 104 (2007) 10453-10458
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 10453-10458
-
-
Kinoshita, M.1
Kamagata, K.2
Maeda, A.3
Goto, Y.4
Komatsuzaki, T.5
Takahashi, S.6
-
76
-
-
4143071283
-
Single-molecule three-color FRET
-
Hohng S., Joo C., and Ha T. Single-molecule three-color FRET. Biophys J 87 (2004) 1328-1337
-
(2004)
Biophys J
, vol.87
, pp. 1328-1337
-
-
Hohng, S.1
Joo, C.2
Ha, T.3
-
77
-
-
13444291091
-
Three-color single-molecule fluorescence resonance energy transfer
-
Clamme J.P., and Deniz A.A. Three-color single-molecule fluorescence resonance energy transfer. Chemphyschem 6 (2005) 74-77
-
(2005)
Chemphyschem
, vol.6
, pp. 74-77
-
-
Clamme, J.P.1
Deniz, A.A.2
-
78
-
-
33846028172
-
Three-color alternating-laser excitation of single molecules: monitoring multiple interactions and distances
-
Lee N.K., Kapanidis A.N., Koh H.R., Korlann Y., Ho S.O., Kim Y., Gassman N., Kim S.K., and Weiss S. Three-color alternating-laser excitation of single molecules: monitoring multiple interactions and distances. Biophys J 92 (2007) 303-312
-
(2007)
Biophys J
, vol.92
, pp. 303-312
-
-
Lee, N.K.1
Kapanidis, A.N.2
Koh, H.R.3
Korlann, Y.4
Ho, S.O.5
Kim, Y.6
Gassman, N.7
Kim, S.K.8
Weiss, S.9
-
79
-
-
0037461520
-
Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules
-
Kapanidis A.N., and Weiss S. Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules. J Chem Phys 117 (2002) 10953-10964
-
(2002)
J Chem Phys
, vol.117
, pp. 10953-10964
-
-
Kapanidis, A.N.1
Weiss, S.2
-
80
-
-
0033437006
-
Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions
-
Onuchic J.N., Wang J., and Wolynes P.G. Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions. Chem Phys 247 (1999) 175-184
-
(1999)
Chem Phys
, vol.247
, pp. 175-184
-
-
Onuchic, J.N.1
Wang, J.2
Wolynes, P.G.3
-
81
-
-
2442482377
-
GroEL mediates protein folding with a two successive timer mechanism
-
Ueno T., Taguchi H., Tadakuma H., Yoshida M., and Funatsu T. GroEL mediates protein folding with a two successive timer mechanism. Mol Cell 14 (2004) 423-434
-
(2004)
Mol Cell
, vol.14
, pp. 423-434
-
-
Ueno, T.1
Taguchi, H.2
Tadakuma, H.3
Yoshida, M.4
Funatsu, T.5
-
82
-
-
0033536619
-
Single molecular observation of the interaction of GroEL with substrate proteins
-
Yamasaki R., Hoshino M., Wazawa T., Ishii Y., Yanagida T., Kawata Y., Higurashi T., Sakai K., Nagai J., and Goto Y. Single molecular observation of the interaction of GroEL with substrate proteins. J Mol Biol 292 (1999) 965-972
-
(1999)
J Mol Biol
, vol.292
, pp. 965-972
-
-
Yamasaki, R.1
Hoshino, M.2
Wazawa, T.3
Ishii, Y.4
Yanagida, T.5
Kawata, Y.6
Higurashi, T.7
Sakai, K.8
Nagai, J.9
Goto, Y.10
-
83
-
-
35948935175
-
-
Hillger F, Nettels D, Dorsch S, Schuler B: Detection and analysis of protein aggregation with confocal single molecule fluorescence spectroscopy. J Fluoresc 2007, 17:759-765.
-
Hillger F, Nettels D, Dorsch S, Schuler B: Detection and analysis of protein aggregation with confocal single molecule fluorescence spectroscopy. J Fluoresc 2007, 17:759-765.
-
-
-
-
84
-
-
3042631531
-
Time-resolved confocal fluorescence imaging and spectroscopy system with single molecule sensitivity and sub-micrometer resolution
-
Wahl M., Koberling F., Patting M., Rahn H., and Erdmann R. Time-resolved confocal fluorescence imaging and spectroscopy system with single molecule sensitivity and sub-micrometer resolution. Curr Pharm Biotechnol 5 (2004) 299-308
-
(2004)
Curr Pharm Biotechnol
, vol.5
, pp. 299-308
-
-
Wahl, M.1
Koberling, F.2
Patting, M.3
Rahn, H.4
Erdmann, R.5
|