Protein folding: Hypotheses and experiments

Ptitsyn, Oleg B.

doi:10.1007/bf00248050

Cited by 569 publications

(398 citation statements)

References 48 publications

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“…Molren Globule Model. The mutagenesis results obtained here, together with evidence that I retains substantial secondary structure (Griko et ai., 1988, Hughson et al, 1990 and is relatively compact (Griko et ai., 1988) and that its enthalpy is close to that of the unfolded state (Griko et al, 1988;Privalov et ai., 1989), strongly suggest that the AGH subdomain of I resembles a molten globule (Ohgushi & Wada, 1983;Dolgikh et al, 1985;Ptitsyn, 1987;Kuwajima, 1989). Our results suggest that I is flexible, accommodating mutation more readily than the native state.…”

Section: Acknowledgmentsmentioning

confidence: 98%

Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis

1991

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A partly folded form (I) of apomyoglobin has an a-helix content of about 35%; in an earlier study, hydrogen exchange revealed that the A, G, and H helices are folded, while much of the rest of the protein is not [Hughson, F. M., Wright, P. E., & Baldwin, R. L. (1990) Science 249, . Because A, G, and H form a compact subdomain in native myoglobin, we proposed that nativelike packing interactions among the three helices might be retained in the I form of apomyoglobin. To test this proposal, disruptive mutations were introduced into the A-H and G -H helix packing sites. These mutations destabilize native apomyoglobin relative to I. In contrast, the stability of I is relatively insensitive to mutation; in particular, side-chain volume alone does not appear to be important. These results indicate that the I form is not stabilized by nativelike A-H and G -H packing interactions. In support of this we show that partly helical peptides derived from the G and H helix regions of myoglobin do not pair in solution. Since the isolated G and H peptides are a t best only partly helical, some type of interaction must stabilize these helices in the I form. Small increases in the stability of I are seen when mutation introduces a side chain of increased nonpolar surface area. We suggest that I is stabilized by relatively nonspecific hydrophobic interactions that allow it to adapt easily to mutation. In this and other respects, I appears to conform to the "molten globule" model, with the caveat that only part of the polypeptide chain appears to participate in the globule.

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Section: Acknowledgmentsmentioning

confidence: 98%

Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis

1991

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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.…”

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confidence: 99%

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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“…This form is called molten globule (Ohgushi & Wada, 1983;Ptitsyn, 1987; Christensen & Pain, 1994). As described above, under mild denaturing conditions, oPL takes up a partially denatured conformation.…”

Section: Discussionmentioning

confidence: 99%

Detection and characterization of an ovine placental lactogen stable intermediate in the urea‐induced unfolding process

et al. 1996

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The urea-induced equilibrium unfolding of ovine placental lactogen, purified from ovine placenta, was followed by size-exclusion chromatography, far-UV CD, and intrinsic tryptophan fluorescence. The data obtained by each of these methods showed a poor fit to a two-state model involving only a native and an unfolded form. A satisfactory fit required, instead, a model that involved a stable, partially folded form in addition to the native and unfolded ones. The results obtained from the best-fitting theoretical curves for the three-state model indicated that this intermediate state, which is the predominant species in solution at 3.6 M of urea activity, is compact, largely a-helical, and changes considerably the native-like tertiary packing around its tryptophan residues. These findings suggest that this stable intermediate exhibits properties similar to those that characterize the molten globule state.

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Protein folding: Hypotheses and experiments

Cited by 569 publications

References 48 publications

Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis

Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis

Side‐chain entropy and packing in proteins

Detection and characterization of an ovine placental lactogen stable intermediate in the urea‐induced unfolding process

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