NMR Structural and Dynamic Characterization of the Acid-Unfolded State of Apomyoglobin Provides Insights into the Early Events in Protein Folding<sup>,</sup>

Yao, Jian; Chung, John Y. L.; Eliezer, David; Wright, Peter E.; Dyson, H. Jane

doi:10.1021/bi002776i

Cited by 210 publications

(315 citation statements)

References 51 publications

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Section: Experimental Verification Of Modelsmentioning

confidence: 92%

“…Thus, it has been possible to define the conformational propensities of unfolded and partly folded apomyoglobin by NMR (32)(33)(34)(35). Interestingly, acid-unfolded apomyoglobin shows a propensity for non-native helical structure in a region that connects the D and E helices, as well as the native-like structure observed in the A and H helices, which had been predicted in the kinetic studies (34). The NMR studies of the conformational propensities of the various forms of apomyoglobin (32)(33)(34)(35) included determination of the relaxation parameters of the polypeptide chain to site-specifically determine the backbone dynamics in each of the states of the protein.…”

Section: Experimental Verification Of Modelsmentioning

confidence: 99%

See 1 more Smart Citation

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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283

217

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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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Section: Experimental Verification Of Modelsmentioning

confidence: 92%

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.

Self Cite

283

217

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“…States-Residual helicity is retained even under denaturing conditions because it was also observed in a highly polar region (E52-AEMKA-S58) in acid-unfolded and in urea-denatured apomyoglobin (45,50). Remarkably, this sequence, which includes helix D of apomyoglobin, has an even higher content of residual helix than helix H of apomyoglobin, which has been shown to have a very high intrinsic helix propensity in peptide studies.…”

Section: The Interactions Rendering Prp Helix 1 Stable Are Responsiblmentioning

confidence: 96%

“…It has been shown that i,iϩ4 hydrophobic interactions stabilize helices (28,45,46). PrP helix 1 contains a pair of i,iϩ4-spaced tyrosine residues in positions 145 and 149, respectively.…”

Section: [De]-x-x-a-[rk]-x-x-[rk]-[de] Modeling the D147a Mutation Anmentioning

confidence: 99%

CD and NMR Studies of Prion Protein (PrP) Helix 1

Ziegler

Sticht

Marx

et al. 2003

Journal of Biological Chemistry

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The conversion of prion helix 1 from an ␣-helical into an extended conformation is generally assumed to be an essential step in the conversion of the cellular isoform PrP C of the prion protein to the pathogenic isoform PrP Sc . Peptides encompassing helix 1 and flanking sequences were analyzed by nuclear magnetic resonance and circular dichroism. Our results indicate a remarkably high instrinsic helix propensity of the helix 1 region. In particular, these peptides retain significant helicity under a wide range of conditions, such as high salt, pH variation, and presence of organic co-solvents. As evidenced by a data base search, the pattern of charged residues present in helix 1 generally favors helical structures over alternative conformations. Because of its high stability against environmental changes, helix 1 is unlikely to be involved in the initial steps of the pathogenic conformational change. Our results implicate that interconversion of helix 1 is rather representing a barrier than a nucleus for the PrP C 3 PrP Sc conversion.Prion protein, PrP, 1 is probably the disease-causing agent of transmissible spongiform encephalopathies such as bovine spongiform encephalopathy in cattle or Creutzfeldt-Jakob disease in man (1). Its cellular form, PrP C , is a highly conserved cell surface glycoprotein of 230 amino acids expressed in all of the mammals studied so far as well as in several species of fish and birds (2, 3). The physiological function of PrP C is not yet fully understood. PrP C seems to be involved in the maintenance of proper presynaptic copper levels as well as in protecting neurons from oxidative stress (4, 5). In addition, the physiological function of PrP C could be associated with higher neurological functions such as learning and memory (5). According to the protein-only hypothesis, disease is caused by accumulation of a misfolded pathogenic isoform, PrP Sc , which is the result of an irreversible large scale conformational change of PrP C . Although PrP C is largely ␣-helical and soluble in polar solvents and sensitive to protease K digestion, PrP Sc consists mostly of ␤-sheets, is soluble only in nonpolar, denaturing solvents, and is resistant to digestion with protease K (6). PrP Sc forms fibrillar aggregates similar to other amyloid fibrils (7). Accumulation of PrP Sc aggregates is accompanied by astrocytosis and gliosis in central nervous tissue, which in turn result in vacuoles in the brains of patients.The solution structures of human PrP-(23-230), huPrP (8), mouse PrP-(121-231) (9), bovine PrP-(23-230) (10), and Syrian hamster PrP-(29 -231) (11) have been determined by NMR spectroscopy. They possess a high degree of structural conservation consistent with the high sequence identity of these proteins. Prion proteins consist of a flexible NH 2 -terminal domain spanning residues 23-124 (huPrP C -numbering scheme), which is largely disordered. This region includes an octapeptide sequence that is repeated four times from residues 60 to 92 and that is likely to bind copper (4). This part al...

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“…Denatured proteins contain considerable amounts of native and non-native structure, both of which may provide information about early folding events [8–10]. Spectroscopic techniques such as nuclear magnetic resonance (NMR) allow the observation of residual structure in the denatured state of a number of proteins [11,12].…”

Section: Introductionmentioning

confidence: 99%

Thermodynamic characterization for the denatured state of bovine prion protein and the BSE Associated variant E211K

Hwang

Nicholson

2018

Prion

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Propagation of transmissible spongiform encephalopathies involves the conversion of cellular prion protein, PrPC, into a misfolded oligomeric form, PrPSc. The most common hereditary prion disease is a genetic form of Creutzfeldt-Jakob disease in humans, in which a mutation in the prion gene results in a glutamic acid to lysine substitution at position 200 (E200K) in PrP. In cattle, the analogous amino acid substitution is found at residue 211 (E211K) and has been associated with a case of bovine spongiform encephalopathy. Here, we have compared the secondary structure of E211K to that of wild type using circular dichroism and completed a thermodynamic analysis of the folding of recombinant wild type and E211K variants of the bovine prion protein. The secondary structure of the E211K variant was essentially indistinguishable from that of wild type. The thermodynamic stability of E211K substitution showed a slight destabilization relative to the wild type consistent with results reported for recombinant human prion protein and its mutant E200K. In addition, the E211K variant exhibits a similarly compact denatured state to that of wild type based upon similar m-value and change in heat capacity of unfolding for the proteins. Together these results indicate that residual structure in the denatured state of bPrP is present in both the wild type protein and BSE associated variant E211K. Given this observation, as well as folding similarities reported for other disease associated variants of PrP it is worth consideration that functional aspects of PrP conformation may play a role in the misfolding process.

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NMR Structural and Dynamic Characterization of the Acid-Unfolded State of Apomyoglobin Provides Insights into the Early Events in Protein Folding^,

Cited by 210 publications

References 51 publications

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

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

CD and NMR Studies of Prion Protein (PrP) Helix 1

Thermodynamic characterization for the denatured state of bovine prion protein and the BSE Associated variant E211K

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NMR Structural and Dynamic Characterization of the Acid-Unfolded State of Apomyoglobin Provides Insights into the Early Events in Protein Folding,

Cited by 210 publications

References 51 publications

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

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

CD and NMR Studies of Prion Protein (PrP) Helix 1

Thermodynamic characterization for the denatured state of bovine prion protein and the BSE Associated variant E211K

Contact Info

Product

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NMR Structural and Dynamic Characterization of the Acid-Unfolded State of Apomyoglobin Provides Insights into the Early Events in Protein Folding^,