Evidence for a molten globule state as a general intermediate in protein folding

Ptitsyn, Oleg B.; Pain, Roger H.; Semisotnov, Gennady V.; Žerovnik, Eva; Razgulyaev, O.I.

doi:10.1016/0014-5793(90)80143-7

Cited by 676 publications

(492 citation statements)

References 27 publications

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“…This distribution has been actually observed for equilibrium urea-induced unfolding of myoglobin [18] and of bovine serum albumin [19] at 25°C. The U -> MG transition usually takes place in a few seconds [4,7]. However, this transition takes much more time for some proteins in cool Gdm-HCI solutions.…”

Section: Resultsmentioning

confidence: 99%

“…It is almost as compact as the native state (N), has a pronounced secondary structure and differs from N mainly by the absence of ~ight packing of side chains in the protein core and by a substantial increase of fluctuations [1][2][3][4]. The molten globule state (MN) accumulates during the renaturation of globular proteins from the fully unfolded state (U) [1][2][3][4][5][6][7][8] and therefore may play a universal role in protein folding [7]. It has been also suggested [9] and shown experimentally that the molten globule is trapped by Gro-EL chaperons ( [10] and unpublished data of G.V.…”

Section: Introductionmentioning

confidence: 99%

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‘All‐or‐none’ mechanism of the molten globule unfolding

et al. 1992

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The Gdm-HCl-induced unfolding of bovine carbonic anhydrase B and S. at~ret~s fl-lactamase was studied at 4°C by a variety of methods. With the use of FPLC it has been shown that within the transition from the molten globule to the unfolded state the distribution function of molecular dimensions is bimodal. This means that equilibrium intermediates between the molten globule and the unfolded states are about, i.¢. the molten globule unfolding follows the "all-or-none' mechanism.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

‘All‐or‐none’ mechanism of the molten globule unfolding

et al. 1992

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“…The species (observed at equilibrium for a large number of proteins under mild denaturing conditions with properties of partially-folded states) made possible the study in real-time scale experiments. Such intermediates from different proteins of different structure types have some common characteristics, and are termed as "molten globule" to emphasize the possible occurrence of such an intermediate as a general physical state of globular proteins (Ptitsyn et al, 1990;Harding et al, 1991;Arai and Kuwajima, 1996).…”

Section: Introductionmentioning

confidence: 99%

Acid and Chemical Induced Conformational Changes of Ervatamin B. Presence of Partially Structured Multiple Intermediates

Sundd¹,

Kundu²,

Jagannadham³

2002

BMB Reports

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The structural and functional aspects of ervatamin B were studied in solution. Ervatamin B belongs to the α + β class of proteins. The intrinsic fluorescence emission maximum of the enzyme was at 350 nm under neutral conditions, and at 355 nm under denaturing conditions. Between pH 1.0-2.5 the enzyme exists in a partially unfolded state with minimum or no tertiary structure, and no proteolytic activity. At still lower pH, the enzyme regains substantial secondary structure, which is predominantly a β-sheet conformation and shows a strong binding to 8-anilino-1-napthalene-sulfonic acid (ANS). In the presence of salt, the enzyme attains a similar state directly from the native state. Under neutral conditions, the enzyme was stable in urea, while the guanidine hydrochloride (GuHCl) induced equilibrium unfolding was cooperative. The GuHCl induced unfolding transition curves at pH 3.0 and 4.0 were non-coincidental, indicating the presence of intermediates in the unfolding pathway. This was substantiated by strong ANS binding that was observed at low concentrations of GuHCl at both pH 3.0 and 4.0. The urea induced transition curves at pH 3.0 were, however, coincidental, but non-cooperative. This indicates that the different structural units of the enzyme unfold in steps through intermediates. This observation is further supported by two emission maxima in ANS binding assay during urea denaturation. Hence, denaturant induced equilibrium unfolding pathway of ervatamin B, which differs from the acid induced unfolding pathway, is not a simple two-state transition but involves intermediates which probably accumulate at different stages of protein folding and hence adds a new dimension to the unfolding pathway of plant proteases of the papain superfamily.

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“…Side-chain packing may also be important to the kinetics of folding. Ptitsyn (1987) and Ptitsyn et al (1990) is critical. Rey and Skolnick (1993) have shown that the addition of model side chains to a model main chain in a computer simulation of protein folding reduces the number of pathways that lead to the native state, and Handel et al (1993) have shown that it is not easy to design sequences that can fold to conformations with immobilized side chains.…”

Section: Introductionmentioning

confidence: 99%

“…Side-chain packing may also be important to the kinetics of folding. Ptitsyn (1987) and Ptitsyn et al (1990) have suggested that the slow rate of protein folding may be due to the process of packing core side chains. Recent computer simulation and protein design results also suggest that the packing of side chains Reprint requests to: Ken A. Dill, Department of Pharmaceutical Chemistry, Box 1204, University of California, San Francisco, California 94143-1204; e-mail: dill@maxwell.ucsf.edu.…”

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Side‐chain entropy and packing in proteins

1994

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What role does side-chain packing play in protein stability and structure? To address this question, we compare a lattice model with side chains (SCM) to a linear lattice model without side chains (LCM). Self-avoiding configurations are enumerated in 2 and 3 dimensions exhaustively for short chains and by Monte Carlo sampling for chains up to 50 main-chain monomers long. This comparison shows that (1) side-chain degrees of freedom increase the entropy of open conformations, but side-chain steric exclusion decreases the entropy of compact conformations, thus producing a substantial entropy that opposes folding; (2) there is a side-chain "freezing" or ordering, Le., a sharp decrease in entropy, near maximum compactness; and (3) the different types of contacts among side chains (s) and main-chain elements ( m ) have different frequencies, and the frequencies have different dependencies on compactness. m m contacts contribute significantly only at high densities, suggesting that mainchain hydrogen bonding in proteins may be promoted by compactness. The distributions of mrn, ms, and ss contacts in compact SCM configurations are similar to the distributions in protein structures in the Brookhaven Protein Data Bank. We propose that packing in proteins is more like the packing of nuts and bolts in a jar than like the pairwise matching of jigsaw puzzle pieces.Keywords: conformational entropy; lattice model; protein stability; side-chain freezing; side-chain packing When a polymer becomes compact, as when a protein folds to its native state, the main chain loses degrees of freedom, incurring a large loss of entropy. Main-chain configurational entropy is a strong force opposing the stability of native proteins (Dill, 1985(Dill, , 1990. How do side chains contribute to the configurational entropy of protein conformations? Is there "side-chain freezing," i.e., a large sharp loss of degrees of freedom as the side chains pack into compact native conformations? We explore these issues with a simple model that can be studied rigorously.The inference that side-chain packing is important to protein stability has been drawn from several lines of evidence. Side chains in the hydrophobic cores of proteins are tightly packed (Richards, 1974(Richards, , 1977Richards & Lim, 1994) and proteins have low compressibilities (Klapper, 1971;Eden et al., 1982;Gavish et al., 1983;Kundrot & Richards, 1987). Many core side-chain motions are hindered or eliminated in native proteins (Gurd & Rothgeb, 1979;Wagner, 1983;McCammon & Harvey, 1987). Side-chain packing may also be important to the kinetics of folding. Ptitsyn (1987) and Ptitsyn et al. (1990) is critical. Rey and Skolnick (1993) have shown that the addition of model side chains to a model main chain in a computer simulation of protein folding reduces the number of pathways that lead to the native state, and Handel et al. (1993) have shown that it is not easy to design sequences that can fold to conformations with immobilized side chains.We can imagine a range of models of how sid...

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Evidence for a molten globule state as a general intermediate in protein folding

Cited by 676 publications

References 27 publications

‘All‐or‐none’ mechanism of the molten globule unfolding

‘All‐or‐none’ mechanism of the molten globule unfolding

Acid and Chemical Induced Conformational Changes of Ervatamin B. Presence of Partially Structured Multiple Intermediates

Side‐chain entropy and packing in proteins

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