Peptide models of protein folding initiation sites. 2. The G-H turn region of myoglobin acts as a helix stop signal

Shin, Hang-Cheol; Merutka, Gene; Waltho, Jonathan P.; Wright, Peter E.; Dyson, H. Jane

doi:10.1021/bi00076a007

Cited by 83 publications

(68 citation statements)

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“…This would not be consistent with our data, except in the region of the Cterminal four residues, which are disordered in our structures. Our demonstration that a peptide fragment corresponding to the C-terminus of murine IL-6 is clearly able to adopt a helical structure in solution makes it likely that the same region of the intact protein is also helical (Dyson et al, 1992;Shin et al, 1993).…”

Section: Discussionmentioning

confidence: 88%

Solution structure of synthetic peptides corresponding to the C‐terminal helix of interleukin‐6

Morton

Simpson

Norton³

1994

European Journal of Biochemistry

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Parkville, AustraliaTwo synthetic peptides corresponding to the C-terminal 19 residues of human and murine interleukin-6, respectively, have been synthesized and their structures in solution investigated using high-resolution 'H-NMR spectroscopy. Both peptides show a marked dependence of chemical-shift dispersion on pH, with a greater degree of structure apparent above pH 4.5, where their glutamate carboxyl groups are ionised. In purely aqueous solution, neither peptide adopts a well-defined structure, although the murine peptide has characteristics of a nascent helix. Titration of the murine peptide with trifluoroethanol produced a significant increase in structure, which was then investigated using two-dimensional NMR. In 50% (by vol.) trifluoroethanol the murine peptide consists of a well-defined central helix of 12 residues with unstructured N-terminal and C-terminal regions. These observations lend experimental support to the current model of the interleukin-6 structure, which proposes a four-helical bundle with the last helix encompassing the C-terminal 20-30 residues. Furthermore, the fact that synthetic peptides corresponding to part of the putative receptorbinding surface of interleukin-6 are able to adopt a similar conformation in solution to that proposed for the intact protein suggests that such peptide analogues should be useful starting points in the design of peptide agonists and antagonists of interleukin-6.

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Section: Discussionmentioning

confidence: 88%

Solution structure of synthetic peptides corresponding to the C‐terminal helix of interleukin‐6

Morton

Simpson

Norton³

1994

European Journal of Biochemistry

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“…Part of the apomyoglobin molecule, consisting of the A, G, and H helices and part of the B helix, folds rapidly to form an on-pathway intermediate, with the remainder of the polypeptide chain folding at a slower rate, of the order of seconds (21,25). Peptide fragments of apomyoglobin corresponding to the G and H helices showed a propensity for helical structure (26)(27)(28), whereas peptides corresponding to the remainder of the protein showed far lower propensity for helix formation (29). Yet an experiment in which the H helix of myoglobin was mutated to decrease its helical propensity (30) showed very little influence on the folding rate of the protein.…”

Section: Experimental Verification Of Modelsmentioning

confidence: 99%

The role of hydrophobic interactions in initiation and propagation of protein folding

Dyson

Wright

Scheraga

2006

Proc. Natl. Acad. Sci. U.S.A.

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282

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Globular proteins fold by minimizing the nonpolar surface that is exposed to water, while simultaneously providing hydrogenbonding interactions for buried backbone groups, usually in the form of secondary structures such as ␣-helices, ␤-sheets, and tight turns. A primary thermodynamic driving force for the formation of globular structure is thus the sequestration of nonpolar groups, but the correlation between the parts of proteins that are observed to fold first (termed folding initiation sites) and the ''hydrophobicity'' (as customarily defined) of the amino acids in these regions has been quite weak. It has previously been noted that many amino acid side chains contain considerable nonpolar sections, even if they also contain polar or charged groups. For example, a lysine side chain contains four methylenes, which may undergo hydrophobic interactions if the charged -NH 3 ؉ group is saltbridged or hydrogen-bonded. Folding initiation sites might therefore contain not only accepted ''hydrophobic'' amino acids, but also larger charged side chains. Recent experiments on the folding of mutant apomyoglobins provides corroboration for models based on the hypothesis that folding initiation sites arise from hydrophobic interactions. A near-perfect correlation was observed between the areas of the molecule that are present in the burstphase kinetic intermediate and both the free energy of formation of hydrophobic initiation sites and the parameter ''average area buried upon folding,'' which pinpoints large side chains, even those containing charged or polar portions. These results provide a putative mechanism for the control of protein-folding initiation and growth by polar͞nonpolar sequence propensity alone.folding pathways ͉ myoglobin ͉ ribonuclease F reed of the ribosome, and in the absence of chaperones, a newly synthesized protein exists in an ensemble of states, the so-called statistical coil, the nature of which is a subject of much recent investigation (1). It subsequently folds to the native biologically active structure whose free energy is considered to be a minimum under appropriate solution conditions (2). Since the seminal work of Anfinsen (2), the kinetics of the folding process and the final structure have been considered to be determined by the physical interactions among the amino acid residues to attain the thermodynamically favored state.A major question has involved the exact mechanism by which the interresidue interactions specify the initiation of folding in the unfolded polypeptide chain under folding conditions. Because nonpolar groups are not soluble in water, attention has been focused on the hydrophobic interactions between nonpolar side chains to achieve their sequestration from aqueous solvent. A model has been proposed in which nearby nonpolar groups in the chain participate in hydrophobic interactions with minimal loss of entropy of the chain because of the proximity of the interacting side chains in the amino acid sequence (3).Yet the chemical nature of the polypeptide chain complicates ...

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“…Concentration and pH of solutions: AB-domain peptide 0.5 mM (methanol); B-helix peptide 1 mM pH 4.3; BC-turn peptide 7.5 mM pH 5.0; CCD-domain peptide 4 mM pH 5.0; D-helix peptide 4 mM pH 4.3; E-helix peptide 2 mM pH 5.0; EF-turn peptide 7.5 mM pH 4.5; F-helix peptide 2 mM pH 4.3; FG-turn peptide 7.5 mM pH 4.3. studies of peptide fragments corresponding to the G-and H-helices of myoglobin clearly implicate long-range packing interactions, presumably involving the A-helix, in stabilization of helical structure in the AGH molten globule (Shin et al, 1993b). The intrinsic conformational propensities of the A-helix region are therefore of great interest.…”

Section: Implications For Initiation Of Apomyoglobin Foldingmentioning

confidence: 99%

“…We present here the continuation of these studies with the aim of examining peptide fragments that together constitute the complete sequence of apomyoglobin to obtain insights into the location of potential folding initiation sites. A series of peptides was synthesized to span the entire myoglobin sequence from the A helix to the FG turn, residues 4 to 99 (Table I), complementing our earlier work on the GH helical hairpin region (Shin et al, 1993a(Shin et al, , 1993bWaltho et al, 1993). As in previous studies (Dyson et al, 1992a(Dyson et al, , 1992b, the peptides were designed to represent elements of secondary structure and their conformational preferences were examined by nuclear magnetic resonance (NMR) spectroscopy and circular dichroism (CD) spectroscopy.…”

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confidence: 99%

Folding propensities of peptide fragments of myoglobin

et al. 1997

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Myoglobin has been studied extensively as a paradigm for protein folding. As part of an ongoing study of potential folding initiation sites in myoglobin, we have synthesized a series of peptides covering the entire sequence of sperm whale myoglobin. We report here on the conformational preferences of a series of peptides that cover the region from the A helix to the FG turn. Structural propensities were determined using circular dichroism and nuclear magnetic resonance spectroscopy in aqueous solution, trifluoroethanol, and methanol. Peptides corresponding to helical regions in the native protein, namely the B, C, D, and E helices, populate the a region of (c#J,$) space in water solution but show no measurable helix formation except in the presence of trifluoroethanol. The F-helix sequence has a much lower propensity to populate helical conformations even in TFE. Despite several attempts, we were not successful in synthesizing a peptide corresponding to the A-helix region that was soluble in water. A peptide termed the AB domain was constructed spanning the A-and B-helix sequences. The AB domain is not soluble in water, but shows extensive helix formation throughout the peptide when dissolved in methanol, with a break in the helix at a site close to the A-B helix junction in the intact folded myoglobin protein. With the exception of one local preference for a turn conformation stabilized by hydrophobic interactions, the peptides corresponding to turns in the folded protein do not measurably populate p-turn conformations in water, and the addition of trifluoroethanol does not enhance the formation of either helical or turn structure. In contrast to the series of peptides described here, earlier studies of peptides from the GH region of myoglobin show a marked tendency to populate helical structures (H), nascent helical structures (G), or turn conformations (GH peptide) in water solution. This region, together with the A-helix and part of the B-helix, has been shown to participate in an early folding intermediate. The complete analysis of conformational properties of isolated myoglobin peptides supports the hypothesis that spontaneous secondary structure formation in local regions of the polypeptide may play an important role in the initiation of protein folding.Keywords: myoglobin; nuclear magnetic resonance; peptide conformation; protein folding; reverse turn; secondary structureThe mechanism by which proteins fold into their native conformations remains one of the central unsolved problems in molecular biology. One view is that folding occurs along defined pathways, often with structured intermediates (for reviews, see Creighton,

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Peptide models of protein folding initiation sites. 2. The G-H turn region of myoglobin acts as a helix stop signal

Cited by 83 publications

References 50 publications

Solution structure of synthetic peptides corresponding to the C‐terminal helix of interleukin‐6

Solution structure of synthetic peptides corresponding to the C‐terminal helix of interleukin‐6

The role of hydrophobic interactions in initiation and propagation of protein folding

Folding propensities of peptide fragments of myoglobin

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