-
2
-
-
0028387381
-
Finding intermediates in protein folding
-
Baldwin RL: Finding intermediates in protein folding. Bioessays 1994, 16:207-210.
-
(1994)
Bioessays
, vol.16
, pp. 207-210
-
-
Baldwin, R.L.1
-
3
-
-
0028917296
-
Structures of folding intermediates
-
Ptitsyn OB: Structures of folding intermediates. Curr Opin Struct Biol 1995, 5:74-78. A discussion of the characteristics of both kinetic and equilibrium partially folded states, and the nature of the barriers that separate these conformations from denatured and fully native species.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 74-78
-
-
Ptitsyn, O.B.1
-
4
-
-
0014278035
-
High resolution mixer for the study of rapid reactions in solution
-
Berger RL, Backo B, Chapman HF: High resolution mixer for the study of rapid reactions in solution. Rev Sei Instr 1968, 39:493-498.
-
(1968)
Rev Sei Instr
, vol.39
, pp. 493-498
-
-
Berger, R.L.1
Backo, B.2
Chapman, H.F.3
-
5
-
-
0028082357
-
Probing the structure of folding intermediates
-
Evans PA, Radford SE: Probing the structure of folding intermediates. Curr Opin Struct Biol 1994, 4:100-106.
-
(1994)
Curr Opin Struct Biol
, vol.4
, pp. 100-106
-
-
Evans, P.A.1
Radford, S.E.2
-
6
-
-
0028902628
-
Microsecond generation of oxygen-bound cytochrome c oxidase by rapid solution mixing
-
Takahashi S, Ching Y-L, Wang J, Rousseau DL: Microsecond generation of oxygen-bound cytochrome c oxidase by rapid solution mixing. J Biol Chem 1995, 270:8405-8407. A recent (but nonfolding) example of a continuous-flow freejet mixing device with a deadtime in the tens of microseconds range. The use of a laser light source and continuous flow, which provides long signal integration times, highlights the requirement for very sensitive detection methods to achieve good time resolution.
-
(1995)
J Biol Chem
, vol.270
, pp. 8405-8407
-
-
Takahashi, S.1
Ching, Y.-L.2
Wang, J.3
Rousseau, D.L.4
-
7
-
-
0027131947
-
Fast events in protein folding initiated by nanosecond laser photolysis
-
Jones CM, Henry ER, Hu U, Chan C-K, Luck SD, Bhuyan A, Roder H, Hofrichter J, Eaton WA: Fast events in protein folding initiated by nanosecond laser photolysis. Proc Nail Acad Sei USA 1993,90:11860-11864.
-
(1993)
Proc Nail Acad Sei USA
, vol.90
, pp. 11860-11864
-
-
Jones, C.M.1
Henry, E.R.2
Hu, U.3
Chan, C.-K.4
Luck, S.D.5
Bhuyan, A.6
Roder, H.7
Hofrichter, J.8
Eaton, W.A.9
-
8
-
-
0030584652
-
Protein folding triggered by electron transfer
-
Pascher T, Chesick JP, Winkler JR, Gray HB: Protein folding triggered by electron transfer. Science 1996, 271:1558-1560. The optically triggered reduction of oxidized, denatured cytochrome c initiates refolding in less than one microsecond. Time-resolved heme absorbance measurements suggest a rapid collapse (time constant 40 us in 4.6 M guanidine hydrochloride at 40°C) followed by slow progression to the native conformation.
-
(1996)
Science
, vol.271
, pp. 1558-1560
-
-
Pascher, T.1
Chesick, J.P.2
Winkler, J.R.3
Gray, H.B.4
-
9
-
-
0028889435
-
Submillisecond events in protein folding
-
Molting B, Golbik R, Fersht AR: Submillisecond events in protein folding. Proc Natl Acad Sei USA 1995, 92:10668-10672. The refolding of barstar is initiated in ∼10μs by rapidly heating the cold-denatured protein. Tryptophan fluorescence is used to identify a rapid phase (time constant 320 μs at 10°C) that is attributable to the formation of a relatively solvent exposed and unconsolidated folding intermediate.
-
(1995)
Proc Natl Acad Sei USA
, vol.92
, pp. 10668-10672
-
-
Molting, B.1
Golbik, R.2
Fersht, A.R.3
-
10
-
-
0029973119
-
Direct observation of fast protein folding: The initial collapse of apomyoglobin
-
Ballew RM, Sabelko J, Gruebele M: Direct observation of fast protein folding: the initial collapse of apomyoglobin. Proc Natl Acad Sei USA 1996, 93:5759-5764. The laser-induced T-jump initiation of refolding is used to probe the extremely rapid initial stages of the refolding of apomyoglobin. Analysis of fluorescence changes upon initiation with -15ns time resolution indicates that a partially solvent-excluded collapsed state is achieved in a rapid reaction with a time constant of -7 (as at 22'C. The solvent viscosity dependence of this rate suggests that the formation of this state is limited by large-scale protein motions during the initial collapse.
-
(1996)
Proc Natl Acad Sei USA
, vol.93
, pp. 5759-5764
-
-
Ballew, R.M.1
Sabelko, J.2
Gruebele, M.3
-
11
-
-
0029864379
-
Collapse and cooperativity in protein folding
-
Miranker AD, Dobson CM: Collapse and cooperativity in protein folding. Curr Opin Struct Biol 1996, 6:31 -42. An overview of the evidence for and implications of the occurrence of a highly cooperative collapse during the refolding of globular proteins.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 31-42
-
-
Miranker, A.D.1
Dobson, C.M.2
-
12
-
-
0028917484
-
Nature of the early folding intermediate of ribonuclease a
-
Udgaonkar JB, Baldwin RL: Nature of the early folding intermediate of ribonuclease A. Biochemistry 1995, 34:4088-4096. A variety of discrete intermediates have been described on the folding pathway of RNase A, in part on the basis of the ultraviolet absorbance characteristics of tyrosine side chains. In this paper, the properties of an early folding intermediate of RNase A are characterized by tyrosine absorbance, inhibitor binding (also monitored by absorbance) and pulse-labelling hydrogen exchange.
-
(1995)
Biochemistry
, vol.34
, pp. 4088-4096
-
-
Udgaonkar, J.B.1
Baldwin, R.L.2
-
13
-
-
0030342725
-
Experimental investigation of side chain interactions in early folding intermediates
-
Engelhard M, Evans PA: Experimental investigation of side chain interactions in early folding intermediates. Fold Des 1996, 1:31-37. A comprehensive and up-to-date review of techniques available to monitor the evolution of side chain interactions during refolding, as a measure of both hydrophobic core organization and overall collapse of the polypeptide chain.
-
(1996)
Fold Des
, vol.1
, pp. 31-37
-
-
Engelhard, M.1
Evans, P.A.2
-
14
-
-
0029115374
-
Kinetics of interaction of partially folded proteins with a hydrophobic dye: Evidence that molten globule character is maximal in early folding intermediates
-
Engelhard M, Evans PA: Kinetics of interaction of partially folded proteins with a hydrophobic dye: evidence that molten globule character is maximal in early folding intermediates. Protein Sei 1996, 4:1553-1562. Binding of the hydrophobic dye ANS is considered the hallmark of the formation of a class of collapsed and loosely packed intermediates termed molten globules. In this paper, ANS is used in a carefully controlled manner to probe the evolution of this species during the folding of several proteins. A significant perturbative effected is noted, and a manner of avoiding this pitfall demonstrated.
-
(1996)
Protein Sei
, vol.4
, pp. 1553-1562
-
-
Engelhard, M.1
Evans, P.A.2
-
15
-
-
0027391299
-
Characterization of an intermediate in the folding pathway of phosphoglycerate kinase: Chemical reactivity of genetically introduced cysteinyl residues during the folding process
-
Ballery N, Desmadril M, Minard P, Yon JM: Characterization of an intermediate in the folding pathway of phosphoglycerate kinase: chemical reactivity of genetically introduced cysteinyl residues during the folding process. Biochemistry 1993, 33:708-714.
-
(1993)
Biochemistry
, vol.33
, pp. 708-714
-
-
Ballery, N.1
Desmadril, M.2
Minard, P.3
Yon, J.M.4
-
16
-
-
0028925815
-
Local and global dynamics during the folding of E. coli dihydrofolate reductase by time-resolved fluorescence spectroscopy
-
Jones BE, Beechem JM, Matthews CR: Local and global dynamics during the folding of E. coli dihydrofolate reductase by time-resolved fluorescence spectroscopy. Biochemistry 1995, 34:1867-1877. Time-resolved fluorescence spectroscopy provides detailed information on the dynamics of tryptophan side chains and the bound reporter group ANS. This study of the refolding of dihydrofolate reductase suggests that an early intermediate, despite being collapsed to a near-native radius of gyration, maintains side chain mobilities similar to those of the denatured state.
-
(1995)
Biochemistry
, vol.34
, pp. 1867-1877
-
-
Jones, B.E.1
Beechem, J.M.2
Matthews, C.R.3
-
17
-
-
0028892701
-
Modification of a specific tyrosine enables tracing of the end-to-end distance during apomyoglobin folding
-
7. Rischel C, Poulsen FM: Modification of a specific tyrosine enables tracing of the end-to-end distance during apomyoglobin folding. FEBS Lett 1995, 374:105-109. An excellent example of data derived from fluorescence energy transfer experiments. Here, the normally vexing requirement of the covalent attachment of a suitable fluorophore is overcome by the chemical modification of a tyrosine side chain in situ. This study, like the SAXS studies discussed in [20], indicates that a collapsed intermediate with near-native separation of a specific tyrosine and tryptophan pair occurs early during the refolding of apomyoglobin.
-
(1995)
FEBS Lett
, vol.374
, pp. 105-109
-
-
Rischel, C.1
Poulsen, F.M.2
-
19
-
-
0027955639
-
Small angle scattering studies of protein folding
-
Lattman EE: Small angle scattering studies of protein folding. Curr Opin Struct Biol 1994, 4:87-92.
-
(1994)
Curr Opin Struct Biol
, vol.4
, pp. 87-92
-
-
Lattman, E.E.1
-
20
-
-
0028884580
-
The radius of gyration of an apomyoglobin folding intermediate
-
Eliezer D, Jennings PA, Wright PE, Doniach, S, Hodgson SK, Tsuruta H: The radius of gyration of an apomyoglobin folding intermediate. Science 1995, 270:487-488. Direct determination of the radius of gyration of a putative molten-globule intermediate during the refolding of apomyoglobin with < 100ms time resolution. The value obtained suggests that apomyoglobin folds via a rapidly formed intermediate of near-native compactness.
-
(1995)
Science
, vol.270
, pp. 487-488
-
-
Eliezer, D.1
Jennings, P.A.2
Wright, P.E.3
Doniach, S.4
Hodgson, S.K.5
Tsuruta, H.6
-
21
-
-
0027301270
-
Evidence of an associative intermediate on the myoglobin refolding pathway
-
Eliezer D, Chiba K, Tsuruta H, Doniach S, Hodgson KO, Kihara H: Evidence of an associative intermediate on the myoglobin refolding pathway. Biophys J 1995, 65:912-917.
-
(1995)
Biophys J
, vol.65
, pp. 912-917
-
-
Eliezer, D.1
Chiba, K.2
Tsuruta, H.3
Doniach, S.4
Hodgson, K.O.5
Kihara, H.6
-
22
-
-
0027940515
-
Kinetics of compaction during lysozyme refolding studied by continuous-flow quasielastic light scattering
-
Feng H-P, Widom J: Kinetics of compaction during lysozyme refolding studied by continuous-flow quasielastic light scattering. Biochemistry 1994, 33:13382-13390.
-
(1994)
Biochemistry
, vol.33
, pp. 13382-13390
-
-
Feng, H.-P.1
Widom, J.2
-
23
-
-
0001547817
-
Nanosecond circular dichroism spectral measurements: Extension to the far-ultra violet range
-
Zhang C-F, Lewis JW, Cerpa R, Kuntz ID, Kliger D: Nanosecond circular dichroism spectral measurements: extension to the far-ultra violet range. J Phys Chem 1993, 97:5499-5505.
-
(1993)
J Phys Chem
, vol.97
, pp. 5499-5505
-
-
Zhang, C.-F.1
Lewis, J.W.2
Cerpa, R.3
Kuntz, I.D.4
Kliger, D.5
-
24
-
-
0027394285
-
Pulsed H/D-exchange studies of folding intermediates
-
Baldwin RL: Pulsed H/D-exchange studies of folding intermediates. Curr Opin Struct Biol 1993, 3:84-91.
-
(1993)
Curr Opin Struct Biol
, vol.3
, pp. 84-91
-
-
Baldwin, R.L.1
-
25
-
-
0030027339
-
Investigation of protein folding by mass spectrometry
-
Miranker A, Robinson, CV, Radford SE, Dobson CM: Investigation of protein folding by mass spectrometry. FASEB J 1996, 10:93-101. A review of recent developments in the analysis of equilibrium and pulselabelling hydrogen-exchange data by MS. Particular attention is paid to the ability of these techniques to resolve individual components from heterogeneous folding populations.
-
(1996)
FASEB J
, vol.10
, pp. 93-101
-
-
Miranker, A.1
Robinson, C.V.2
Radford, S.E.3
Dobson, C.M.4
-
26
-
-
0000715233
-
The mass spectrometry of helical unfolding in peptides
-
Anderegg RJ, Wagner DS, Stevenson CL, Borchardt RT: The mass spectrometry of helical unfolding in peptides. J Am Soc Mass Spectrom 1994, 5:425-433.
-
(1994)
J Am Soc Mass Spectrom
, vol.5
, pp. 425-433
-
-
Anderegg, R.J.1
Wagner, D.S.2
Stevenson, C.L.3
Borchardt, R.T.4
-
27
-
-
0029769671
-
An isotope labelling strategy for the assignment of protein fragments generated for mass spectrometry
-
Miranker A, Kruppa GH, Robinson CV, Aplin RT, Dobson CM: An isotope labelling strategy for the assignment of protein fragments generated for mass spectrometry. J Am Chem Soc 1996, in press. This paper reports the use of isotope labelled proteins to aid in the identification of lysozyme fragments produced by chemically induced dissociation. This technique makes possible the identification of many of the small peptides produced by gas-phase dissociation and suggests that MS-derived sequence-specific hydrogen-protection studies may be possible.
-
(1996)
J Am Chem Soc
-
-
Miranker, A.1
Kruppa, G.H.2
Robinson, C.V.3
Aplin, R.T.4
Dobson, C.M.5
-
28
-
-
0027315969
-
A reexamination of the folding mechanism of dihydrofolate reductase from Escherichi'a coli: Verification and refinement of a four-channel model
-
Jennings PA, Finn BE, Jones BE, Mathews CR: A reexamination of the folding mechanism of dihydrofolate reductase from Escherichi'a coli: verification and refinement of a four-channel model. Biochemistry 1993, 32:3783-3789.
-
(1993)
Biochemistry
, vol.32
, pp. 3783-3789
-
-
Jennings, P.A.1
Finn, B.E.2
Jones, B.E.3
Mathews, C.R.4
-
29
-
-
0021113912
-
Mechanism of folding of ribonuclease A. Slow refolding is a sequential reaction via structural intermediates
-
Schmid FX: Mechanism of folding of ribonuclease A. Slow refolding is a sequential reaction via structural intermediates. Biochemistry 1983, 22:4690-4696.
-
(1983)
Biochemistry
, vol.22
, pp. 4690-4696
-
-
Schmid, F.X.1
-
30
-
-
0027385015
-
The refolding of cis- And transpeptidylprolyl isomers of barstar
-
Schreiber G, Fersht AR: The refolding of cis- and transpeptidylprolyl isomers of barstar. Biochemistry 1993, 32:11195-11203.
-
(1993)
Biochemistry
, vol.32
, pp. 11195-11203
-
-
Schreiber, G.1
Fersht, A.R.2
-
31
-
-
0029025915
-
Kinetic traps in lysozyme folding
-
Kiefhaber T: Kinetic traps in lysozyme folding. Biochemistry 1995,92:9029-9033. The refolding of lysozyme is monitored with 10ms time resolution (and a 20 ms deadtime) using an interrupted folding technique, in which transiently refolded protein is re-unfolded by the addition of dénaturant. The rate of formation of native material is quantified by assuming that the fraction of protein exhibiting a slow unfolding rate represents native protein. The observation of a biphasic rate of recovery for this slowly unfolding material supports the view that this protein refolds via at least two parallel pathways.
-
(1995)
Biochemistry
, vol.92
, pp. 9029-9033
-
-
Kiefhaber, T.1
-
32
-
-
0029653905
-
Mapping the structures of transition states and intermediates in folding: Delineation of pathways at high resolution
-
Fersht AR: Mapping the structures of transition states and intermediates in folding: delineation of pathways at high resolution. Philos Trans R Soc Lond 1995, 348:11 -1 5. A review of the application of site-directed mutagenesis techniques to the exploration of protein folding. Particular attention is paid to the characterization of the folding transition states of barnase and Cl2.
-
(1995)
Philos Trans R Soc Lond
, vol.348
, pp. 11-15
-
-
Fersht, A.R.1
-
33
-
-
0030347884
-
The development of tertiary interactions during the folding of a large protein
-
Parker MJ, Sessions RB, Badcoe IG, Clarke AR: The development of tertiary interactions during the folding of a large protein. Fold Des 1996, 1:145-156. Protein engineering is used to probe the formation of native contacts by the effect of mutations on the stability of a transient intermediate during the refolding of phosphoglycerate kinase.
-
(1996)
Fold Des
, vol.1
, pp. 145-156
-
-
Parker, M.J.1
Sessions, R.B.2
Badcoe, I.G.3
Clarke, A.R.4
-
34
-
-
0027370063
-
Characterization of a folding intermediate of apoplastocyanin trapped by proline isomerization
-
Koide S, Dyson HJ, Wright PE: Characterization of a folding intermediate of apoplastocyanin trapped by proline isomerization. Biochemistry 1993, 32:12299-12310.
-
(1993)
Biochemistry
, vol.32
, pp. 12299-12310
-
-
Koide, S.1
Dyson, H.J.2
Wright, P.E.3
-
35
-
-
0029123975
-
Following protein-folding in real-time using NMR-spectroscopy
-
Balbach J, Forge V, VanNuland NAJ, Winder SL. Höre RJ, Dobson CM: Following protein-folding in real-time using NMR-spectroscopy. Nat Struct Biol 1995, 2:865-870. The application of stopped flow NMR to the refolding of apo-lactalbumin demonstrates the existence of a rapidly formed kinetic molten-globule intermediate previously postulated from extrinsic fluorescence measurements and equilibrium studies. All spectra recorded after the 2 s deadtime can be reconstructed as linear combinations of the spectra of the initial, rapidly formed molten globule and native protein, suggesting that interconversion between the two occurs via a highly cooperative transition lacking significantly populated intermediates.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 865-870
-
-
Balbach, J.1
Forge, V.2
VanNuland, N.A.J.3
Winder, S.L.4
Höre, R.J.5
Dobson, C.M.6
-
36
-
-
0028981210
-
Negative activation enthalpies in the kinetics of protein folding
-
Oliveberg M, Tan YJ, Fersht AR: Negative activation enthalpies in the kinetics of protein folding. Proc Natl Acad Sei USA 1995, 92:8926-8929. Unlike many chemical reactions, protein folding tends to slow at higher (above physiological) temperatures. In this paper, data on the temperature dependence of the refolding rates of CI2 and barnase are used to determine the relative enthalpy and heat capacity contributions to the folding transition states of these proteins. The thermodynamic properties of the major folding intermediate in barnase are also investigated.
-
(1995)
Proc Natl Acad Sei USA
, vol.92
, pp. 8926-8929
-
-
Oliveberg, M.1
Tan, Y.J.2
Fersht, A.R.3
-
37
-
-
0028905560
-
Evidence for a molten globule-like transition state in protein folding from determination of activation volumes
-
Vidugiris GJA, Markley JL, Royer CA: Evidence for a molten globule-like transition state in protein folding from determination of activation volumes. Biochemistry 1995, 34:4909-4912. Direct detection of the activation volume for the refolding of staphylococcal nuclease from the pressure dependence of its folding rate suggests that the transition state of this process exhibits a molten-globule-like degree of compactness. The solvent-excluded expansion of this transition state contributes to the rate-limiting step in the folding of the protein.
-
(1995)
Biochemistry
, vol.34
, pp. 4909-4912
-
-
Vidugiris, G.J.A.1
Markley, J.L.2
Royer, C.A.3
-
38
-
-
0026545583
-
Folding kinetics of T4 lysozyme and nine mutants at 12°C
-
Chen B-L, Baase WA, Nicholson H, Schellman JA: Folding kinetics of T4 lysozyme and nine mutants at 12°C. Biochemistry 1992, 31:1464-1476.
-
(1992)
Biochemistry
, vol.31
, pp. 1464-1476
-
-
Chen, B.-L.1
Baase, W.A.2
Nicholson, H.3
Schellman, J.A.4
-
39
-
-
0028227296
-
Tertiary interactions in the folding pathway of hen lysozyme: Kinetic studies using fluorescent probes
-
Itzhaki LS, Evans PA, Dobson CM, Radford SE: Tertiary interactions in the folding pathway of hen lysozyme: kinetic studies using fluorescent probes. Biochemistry 1994, 33:5212-5220.
-
(1994)
Biochemistry
, vol.33
, pp. 5212-5220
-
-
Itzhaki, L.S.1
Evans, P.A.2
Dobson, C.M.3
Radford, S.E.4
-
40
-
-
0029670343
-
Formation of electrostatic interactions on the protein-folding pathway
-
Oliveberg M, Fersht AR: Formation of electrostatic interactions on the protein-folding pathway. Biochemistry 1996, 35:2726-2737.
-
(1996)
Biochemistry
, vol.35
, pp. 2726-2737
-
-
Oliveberg, M.1
Fersht, A.R.2
-
41
-
-
0028037217
-
Single versus parallel pathways of protein folding and fractional formation of structure in the transition state
-
Fersht AR, Itzhaki LS, ElMasry NF, Matthews JM, Otzen DE: Single versus parallel pathways of protein folding and fractional formation of structure in the transition state. Proc Natl Acad Sei USA 1994, 91:10426-10429.
-
(1994)
Proc Natl Acad Sei USA
, vol.91
, pp. 10426-10429
-
-
Fersht, A.R.1
Itzhaki, L.S.2
ElMasry, N.F.3
Matthews, J.M.4
Otzen, D.E.5
-
42
-
-
0029653893
-
Insights into protein folding using physical techniques: Studies of lysozyme and ot-lactalbumin
-
Radford SE, Dobson CM: Insights into protein folding using physical techniques: studies of lysozyme and ot-lactalbumin. Philos Trans R Soc Lond Biol 1995, 348:1 7-25. A review of the experimental strategies used to produce the current, detailed model of the primary intermediates in the refolding of hen lysozyme. This paper provides a clear example of the power of multiple complementary probes to provide detailed insights into the nature of protein folding intermediates.
-
(1995)
Philos Trans R Soc Lond Biol
, vol.348
, pp. 17-25
-
-
Radford, S.E.1
Dobson, C.M.2
-
43
-
-
0029763434
-
Rapid folding of a proline rich all -sheet fibronectin type III domain
-
Plaxco KW, Spitzfaden C, Campbell ID, Dobson CM: Rapid folding of a proline rich all -sheet fibronectin type III domain. Proc Natl Acad Sei USA 1996, in press. Analysis of the folding of a fibronectin type III module by a battery of independent kinetic probes is shown to be necessary to demonstrate that the surprisingly rapid refolding of this domain reflects complete recovery of native backbone and core structure.
-
(1996)
Proc Natl Acad Sei USA
-
-
Plaxco, K.W.1
Spitzfaden, C.2
Campbell, I.D.3
Dobson, C.M.4
-
44
-
-
0029886030
-
Direct NMR measurement of the folding kinetics of a trimeric peptide
-
15N, the folding and association rate of trimeric collagen fibres is monitored using two-dimensional NMR with a time resolution of ∼3 min. These observations suggest that the peptide folds to a significantly populated trimeric intermediate with native-like helical structure at the C terminus before folding to the native structure.
-
(1996)
Biochemistry
, vol.35
, pp. 4306-4313
-
-
Liu, X.1
Siegel, D.L.2
Fan, P.3
Brodsky, B.4
Baum, J.5
-
45
-
-
0000749460
-
Toward a description of the conformations of denatured states of proteins
-
Fiebig KM, Schwalbe H, Buck M, Smith U, Dobson, CM: Toward a description of the conformations of denatured states of proteins. Comparison of a random coil model with NMR measurements. J Phys Chem 1996, 100:2661-2666. A model for the 'random coil' state of a polypeptide chain is developed using a Monte Carlo simulation based on an empirical sampling strategy derived from the protein structural database. While a generally good correlation between predicted and observed NOE and J-coupling constant data for lysozyme in urea suggests that the model is a reasonable representation of the distribution of structures involved, comparison of observed and predicted NOEs enables additional conformational preferences to be identified.
-
(1996)
Comparison of a Random Coil Model with NMR Measurements. J Phys Chem
, vol.100
, pp. 2661-2666
-
-
Fiebig, K.M.1
Schwalbe, H.2
Buck, M.3
Smith, U.4
Dobson, C.M.5
-
46
-
-
0029981188
-
Structure of the transition state for folding of a protein derived from experiment and simulation
-
Dagget V, Li A, Itzhaki LS, Otzen DE, Fersht AR: Structure of the transition state for folding of a protein derived from experiment and simulation. J Mol Biol 1996, 257:430-440. Molecular dynamics simulations are performed at elevated temperatures in water to characterize the unfolding/folding transition state of Cl2. Excellent correspondence between theoretically derived and experimental values suggests that the simulated transition state provides an accurate structural model of the experimentally observed transition state.
-
(1996)
J Mol Biol
, vol.257
, pp. 430-440
-
-
Dagget, V.1
Li, A.2
Itzhaki, L.S.3
De Otzen4
Fersht, A.R.5
-
47
-
-
0028949547
-
Theoretical studies of protein folding and unfolding
-
Karplus M, Sali A: Theoretical studies of protein folding and unfolding. Curr Opin Struct Biol 1995, 4:58-73. A comprehensive review of the contribution of molecular dynamics and lattice Monte Carlo simulations to the study of protein folding.
-
(1995)
Curr Opin Struct Biol
, vol.4
, pp. 58-73
-
-
Karplus, M.1
Sali, A.2
-
48
-
-
0029670994
-
Conserved residues and the mechanism of protein folding
-
Shakhnovich E, Abkevich V, Ptitsyn O: Conserved residues and the mechanism of protein folding. Nature 1996, 379:96-98. attice simulations of the folding of a series of 'homologous' sequences are used to define conserved elements in the transition state conformation of CI2. The predicted nucleus is very similar to the folding nucleus previously defined by protein-engineering experiments.
-
(1996)
Nature
, vol.379
, pp. 96-98
-
-
Shakhnovich, E.1
Abkevich, V.2
Ptitsyn, O.3
-
49
-
-
0028963362
-
Toward an outline of the topography of a realistic protein folding funnel
-
Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND: Toward an outline of the topography of a realistic protein folding funnel. Proc Natl Acad Sei USA 1995, 92:3626-3630. Helix-coil transition theory and experimental data are coupled in this paper to characterize the properties of a protein folding pathway. A law of corresponding states is developed that permits comparisons to be made between experimental results and the predictions of lattice simulations of protein folding.
-
(1995)
Proc Natl Acad Sei USA
, vol.92
, pp. 3626-3630
-
-
Onuchic, J.N.1
Wolynes, P.G.2
Luthey-Schulten, Z.3
Socci, N.D.4
|