-
1
-
-
0015040916
-
Theoretical and experimental studies of conformations of polypeptides
-
Scheraga HA (1971) Theoretical and experimental studies of conformations of polypeptides. Chem Rev 71:195-217.
-
(1971)
Chem Rev
, vol.71
, pp. 195-217
-
-
Scheraga, H.A.1
-
2
-
-
0022423920
-
Theory for the folding and stability of globular proteins
-
Dill KA (1985) Theory for the folding and stability of globular proteins. Biochemistry 24:1501-1509.
-
(1985)
Biochemistry
, vol.24
, pp. 1501-1509
-
-
Dill, K.A.1
-
3
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: A synthesis
-
Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 21:167-195.
-
(1995)
Proteins
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
4
-
-
1842298212
-
From Levinthal to pathways to funnels
-
Dill KA, Chan HS (1997) From Levinthal to pathways to funnels. Nat Struct Biol 4:10-19.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
5
-
-
3142782241
-
Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates
-
Chavez LL, Onuchic JN, Clementi C (2004) Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates. J Am Chem Soc 126:8426-8432.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 8426-8432
-
-
Chavez, L.L.1
Onuchic, J.N.2
Clementi, C.3
-
6
-
-
34547949340
-
Protein dynamics and function: Insights from the energy landscape and solvent slaving
-
Frauenfelder H, Fenimore PW, Young RD (2007) Protein dynamics and function: Insights from the energy landscape and solvent slaving. IUBMB Life 59:506-512.
-
(2007)
IUBMB Life
, vol.59
, pp. 506-512
-
-
Frauenfelder, H.1
Fenimore, P.W.2
Young, R.D.3
-
7
-
-
0034646218
-
Mechanisms and kinetics of β-hairpin formation
-
Klimov DK, Thirumalai D (2000) Mechanisms and kinetics of β-hairpin formation. Proc Natl Acad Sci USA 97:2544-2549.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 2544-2549
-
-
Klimov, D.K.1
Thirumalai, D.2
-
8
-
-
0037079586
-
Is there a unique melting temperature for two-state proteins?
-
Klimov DK, Thirumalai D (2002) Is there a unique melting temperature for two-state proteins? J Comput Chem 23:161-165.
-
(2002)
J Comput Chem
, vol.23
, pp. 161-165
-
-
Klimov, D.K.1
Thirumalai, D.2
-
9
-
-
0001804089
-
Aspects of protein reaction dynamics: Deviations from simple behavior
-
Karplus M (2000) Aspects of protein reaction dynamics: Deviations from simple behavior. J Phys Chem B 104:11-27.
-
(2000)
J Phys Chem B
, vol.104
, pp. 11-27
-
-
Karplus, M.1
-
10
-
-
0024745242
-
Theory of cooperative transitions in protein molecules. II Phase diagram for a protein molecule in solution
-
Finkelstein AV, Shakhnovich EI (1989) Theory of cooperative transitions in protein molecules. II Phase diagram for a protein molecule in solution. Biopolymers 28:1681-1694.
-
(1989)
Biopolymers
, vol.28
, pp. 1681-1694
-
-
Finkelstein, A.V.1
Shakhnovich, E.I.2
-
11
-
-
0033871781
-
Protein folding intermediates and pathways studied by hydrogen exchange
-
Englander SW (2000) Protein folding intermediates and pathways studied by hydrogen exchange. Annu Rev Biophys Biomol Struct 29:213-238.
-
(2000)
Annu Rev Biophys Biomol Struct
, vol.29
, pp. 213-238
-
-
Englander, S.W.1
-
12
-
-
0029975396
-
Motional dynamics of a buried tryptophan reveals the presence of partially structured forms during denaturation of barstar
-
Swaminathan R, Nath U, Udgaonkar JB, Periasamy N, Krishnamoorthy G (1996) Motional dynamics of a buried tryptophan reveals the presence of partially structured forms during denaturation of barstar. Biochemistry 35:9150-9157.
-
(1996)
Biochemistry
, vol.35
, pp. 9150-9157
-
-
Swaminathan, R.1
Nath, U.2
Udgaonkar, J.B.3
Periasamy, N.4
Krishnamoorthy, G.5
-
15
-
-
33644767158
-
Single-molecule FRET study of denaturant induced unfolding of RNase H
-
Kuzmenkina EV, Heyes CD, Nienhaus GU (2006) Single-molecule FRET study of denaturant induced unfolding of RNase H. J Mol Biol 357:313-324.
-
(2006)
J Mol Biol
, vol.357
, pp. 313-324
-
-
Kuzmenkina, E.V.1
Heyes, C.D.2
Nienhaus, G.U.3
-
16
-
-
33746102627
-
Atom-by-atom analysis of global downhill protein folding
-
Sadqi M, Fushman D, Munoz V (2006) Atom-by-atom analysis of global downhill protein folding. Nature 442:317-321.
-
(2006)
Nature
, vol.442
, pp. 317-321
-
-
Sadqi, M.1
Fushman, D.2
Munoz, V.3
-
18
-
-
23944522022
-
Downhill protein folding: Evolution meets physics
-
Gruebele M (2005) Downhill protein folding: Evolution meets physics. C R Biol 328:701-712.
-
(2005)
C R Biol
, vol.328
, pp. 701-712
-
-
Gruebele, M.1
-
19
-
-
26244466045
-
Dependence of the size of the initially collapsed form during the refolding of barstar on denaturant concentration: Evidence for a continuous transition
-
Sinha KK, Udgaonkar JB (2005) Dependence of the size of the initially collapsed form during the refolding of barstar on denaturant concentration: Evidence for a continuous transition. J Mol Biol 353:704-718.
-
(2005)
J Mol Biol
, vol.353
, pp. 704-718
-
-
Sinha, K.K.1
Udgaonkar, J.B.2
-
20
-
-
45849127598
-
Barrierless evolution of structure during the submillisecond refolding reaction of a small protein
-
Sinha KK, Udgaonkar JB (2008) Barrierless evolution of structure during the submillisecond refolding reaction of a small protein. Proc Natl Acad Sci USA 105:7998-8003.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 7998-8003
-
-
Sinha, K.K.1
Udgaonkar, J.B.2
-
21
-
-
0030916895
-
Picosecond fluorescence decay curves collected on millisecond time scale: Direct measurement of hydrodynamic radii, local/global mobility, and intramolecular distances during protein-folding reactions
-
Beechem JM (1997) Picosecond fluorescence decay curves collected on millisecond time scale: Direct measurement of hydrodynamic radii, local/global mobility, and intramolecular distances during protein-folding reactions. Methods Enzymol 278:24-49.
-
(1997)
Methods Enzymol
, vol.278
, pp. 24-49
-
-
Beechem, J.M.1
-
22
-
-
0034705335
-
Determination of intramolecular distance distribution during protein folding on the millisecond timescale
-
Ratner V, Sinev M, Haas E (2000) Determination of intramolecular distance distribution during protein folding on the millisecond timescale. J Mol Biol 299:1363-1371.
-
(2000)
J Mol Biol
, vol.299
, pp. 1363-1371
-
-
Ratner, V.1
Sinev, M.2
Haas, E.3
-
24
-
-
1542358783
-
Increasing stability reduces conformational heterogeneity in a protein folding intermediate ensemble
-
Sridevi K, Lakshmikanth GS, Krishnamoorthy G, Udgaonkar JB (2004) Increasing stability reduces conformational heterogeneity in a protein folding intermediate ensemble. J Mol Biol 337:699-711.
-
(2004)
J Mol Biol
, vol.337
, pp. 699-711
-
-
Sridevi, K.1
Lakshmikanth, G.S.2
Krishnamoorthy, G.3
Udgaonkar, J.B.4
-
25
-
-
48249140760
-
Multiple routes and structural heterogeneity in protein folding
-
Udgaonkar JB (2008) Multiple routes and structural heterogeneity in protein folding. Annu Rev Biophy 37:489-510.
-
(2008)
Annu Rev Biophy
, vol.37
, pp. 489-510
-
-
Udgaonkar, J.B.1
-
26
-
-
14544272814
-
Specific collapse followed by slow hydrogen-bond formation of β-sheet in the folding of single-chain monellin
-
Kimura T, et al. (2005) Specific collapse followed by slow hydrogen-bond formation of β-sheet in the folding of single-chain monellin. Proc Natl Acad Sci USA 102:2748-2753.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 2748-2753
-
-
Kimura, T.1
-
27
-
-
35448932093
-
Characterization of the folding and unfolding reactions of single-chain monellin: Evidence for multiple intermediates and competing pathways
-
Patra AK, Udgaonkar JB (2007) Characterization of the folding and unfolding reactions of single-chain monellin: Evidence for multiple intermediates and competing pathways. Biochemistry 46:11727-11743.
-
(2007)
Biochemistry
, vol.46
, pp. 11727-11743
-
-
Patra, A.K.1
Udgaonkar, J.B.2
-
28
-
-
51649090393
-
Dehydration of main-chain amides in the final folding step of single-chain monellin revealed by time-resolved infrared spectroscopy
-
Kimura T, et al. (2008) Dehydration of main-chain amides in the final folding step of single-chain monellin revealed by time-resolved infrared spectroscopy. Proc Natl Acad Sci USA 105:13391-13396.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 13391-13396
-
-
Kimura, T.1
-
30
-
-
33646171099
-
Characterization of intra-molecular distances and site-specific dynamics in chemically unfolded barstar: Evidence for denaturant-dependent non-random structure
-
Saxena AM, Udgaonkar JB, Krishnamoorthy G (2006) Characterization of intra-molecular distances and site-specific dynamics in chemically unfolded barstar: Evidence for denaturant-dependent non-random structure. J Mol Biol 359:174-189.
-
(2006)
J Mol Biol
, vol.359
, pp. 174-189
-
-
Saxena, A.M.1
Udgaonkar, J.B.2
Krishnamoorthy, G.3
-
33
-
-
70049095180
-
-
Dua A, Adhikari R (2008) Non-Markovian fluctuations in Markovian models of protein dynamics. arXiv:0810.2232v1.
-
Dua A, Adhikari R (2008) Non-Markovian fluctuations in Markovian models of protein dynamics. arXiv:0810.2232v1.
-
-
-
-
34
-
-
4344704080
-
Reassessing random-coil statistics in unfolded proteins
-
Fitzkee NC, Rose GD (2004) Reassessing random-coil statistics in unfolded proteins. Proc Natl Acad Sci USA 101:12497-12502.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 12497-12502
-
-
Fitzkee, N.C.1
Rose, G.D.2
-
35
-
-
0032519183
-
Dynamics of the swelling or collapse of a homopolymer
-
Pitard E, Orland H (1998) Dynamics of the swelling or collapse of a homopolymer. Europhys Lett 41:467-472.
-
(1998)
Europhys Lett
, vol.41
, pp. 467-472
-
-
Pitard, E.1
Orland, H.2
-
37
-
-
0024121530
-
Diffusion in a rough potential
-
Zwanzig R (1988) Diffusion in a rough potential. Proc Natl Acad Sci USA 85:2029-2030.
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 2029-2030
-
-
Zwanzig, R.1
-
38
-
-
0037235662
-
Exponential decay kinetics in "downhill" protein folding
-
Hagen SJ (2003) Exponential decay kinetics in "downhill" protein folding. Proteins 50:1-4.
-
(2003)
Proteins
, vol.50
, pp. 1-4
-
-
Hagen, S.J.1
-
39
-
-
0029001090
-
Direct NMR evidence for an intermediate preceding the rate-limiting step in the unfolding of ribonuclease A
-
Kiefhaber T, Labhardt AM, Baldwin RL (1995) Direct NMR evidence for an intermediate preceding the rate-limiting step in the unfolding of ribonuclease A. Nature 375:513-515.
-
(1995)
Nature
, vol.375
, pp. 513-515
-
-
Kiefhaber, T.1
Labhardt, A.M.2
Baldwin, R.L.3
-
40
-
-
0029079665
-
19F-tryptophan-labeled Escherichia coli dihydrofolate reductase
-
19F-tryptophan-labeled Escherichia coli dihydrofolate reductase. Proc Natl Acad Sci USA 92:9318-9322.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 9318-9322
-
-
Hoeltzli, S.D.1
Frieden, C.2
-
41
-
-
0037065672
-
Mechanism of formation of a productive molten globule form of barstar
-
Rami BR, Udgaonkar JB (2002) Mechanism of formation of a productive molten globule form of barstar. Biochemistry 41:1710-1716.
-
(2002)
Biochemistry
, vol.41
, pp. 1710-1716
-
-
Rami, B.R.1
Udgaonkar, J.B.2
-
42
-
-
55949131241
-
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding
-
Hua L, Zhou R, Thirumalai D, Berne BJ (2008) Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc Natl Acad Sci USA 105:16928-16933.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 16928-16933
-
-
Hua, L.1
Zhou, R.2
Thirumalai, D.3
Berne, B.J.4
-
43
-
-
28444454101
-
Amyloid fibril formation can proceed from different conformations of a partially unfolded protein
-
Calamai M, Chiti F, Dobson CM (2005) Amyloid fibril formation can proceed from different conformations of a partially unfolded protein. Biophys J 89:4201-4210.
-
(2005)
Biophys J
, vol.89
, pp. 4201-4210
-
-
Calamai, M.1
Chiti, F.2
Dobson, C.M.3
-
44
-
-
0027985340
-
Similarity of fluorescence lifetime distributions for single tryptophan proteins in the random coil state
-
Swaminathan R, Krishnamoorthy G, Periasamy N (1994) Similarity of fluorescence lifetime distributions for single tryptophan proteins in the random coil state. Biophys J 67:2013-2023.
-
(1994)
Biophys J
, vol.67
, pp. 2013-2023
-
-
Swaminathan, R.1
Krishnamoorthy, G.2
Periasamy, N.3
-
45
-
-
0030087307
-
Analysis of fluorescence decay by maximum entropy method: Influence of noise and analysis parameters on the width of the distribution of lifetimes
-
Swaminathan R, Periasamy N (1996) Analysis of fluorescence decay by maximum entropy method: Influence of noise and analysis parameters on the width of the distribution of lifetimes. Proc Indian Acad Sci Chem Sci 108:39-49.
-
(1996)
Proc Indian Acad Sci Chem Sci
, vol.108
, pp. 39-49
-
-
Swaminathan, R.1
Periasamy, N.2
|