Mapping Long-range Contacts in a Highly Unfolded Protein

Lietzow, Michael A.; Jamin, Marc; Dyson, H. Jane; Wright, Peter E.

doi:10.1016/s0022-2836(02)00847-1

Cited by 142 publications

(197 citation statements)

References 25 publications

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“…Indeed, broadening in NMR spectra of the aciddenatured state of apoMb specifically predicts s-ms contacts between the N-terminal portion of the protein, where Alexa 488 is located, and a stretch of amino acids that makes up the G-helix in the folded protein (33). More specifically, a second NMR study found native-like interactions between the N-terminal A-helix region and the C-terminal G-H-helix region of acidunfolded apoMb, indicating the transient formation of compact states in the denatured protein (37).…”

Section: Discussionmentioning

confidence: 97%

Dynamics of equilibrium structural fluctuations of apomyoglobin measured by fluorescence correlation spectroscopy

Chen

Rhoades

Butler

et al. 2007

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

101

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The spectra of equilibrium chain conformation fluctuations of apomyoglobin (apoMb) as a function of folding, from the aciddenatured state at pH 2.6 through the stable molten globule state pH Ϸ 4.1 to the folded state at pH 6.3, are reported, as measured by fluorescence correlation spectroscopy. The conformational fluctuations, which are detected by quenching of an N-terminal fluorescent label by contact with various amino acids, can be represented by superpositions of decaying exponentials with time scales ranging from Ϸ3 to Ϸ200 s. Both the time scales and amplitudes of the fluctuations increase with the degree of acid denaturation, with principal shifts associated with the transition across the molten globule state. Measurements of the diffusion of apoMb confirm theoretical values showing a Ϸ40% increase in the hydrodynamic radius upon acid denaturation. This study uses the model protein apoMb to illustrate the complex scope of foldingassociated structural dynamics.

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Section: Discussionmentioning

confidence: 97%

Dynamics of equilibrium structural fluctuations of apomyoglobin measured by fluorescence correlation spectroscopy

Chen

Rhoades

Butler

et al. 2007

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

101

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“…The function J(0) informs on s-ms time-scale motions and suggested that, for apomyoglobin at pH 2.3, the A and G helices were making transient contacts (34). This exciting result, later validated by spin-label NMR studies (37), provided definitive evidence of native-like long-range contacts in an unfolded protein. Even more intriguingly, the function J( N ), which informs on ps-ns time-scale motion, showed sequence-dependent variation, which could be correlated with variation in a calculated parameter, the ''average area buried upon folding'' (AABUF) (10).…”

Section: Experimental Verification Of Modelsmentioning

confidence: 89%

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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“…[40][41][42] PRE measurements can readily detect interactions between residues up to $25 Å from the spin label. We measured PRE in aS at pH 3.0 using a number of single cysteine mutants (S9C, G31C, E61C, A85C, E110C, and E130C) conjugated to MTSL (see Fig.…”

Section: Paramagnetic Relaxation Enhancementmentioning

confidence: 99%

Charge neutralization and collapse of the C‐terminal tail of alpha‐synuclein at low pH

2009

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Alpha-synuclein (aS) is the primary component of Lewy bodies, the pathological hallmark of Parkinson's Disease. Aggregation of aS is thought to proceed from a primarily disordered state with nascent secondary structure through intermediate conformations to oligomeric forms and finally to mature amyloid fibrils. Low pH conditions lead to conformational changes associated with increased aS fibril formation. Here we characterize these structural and dynamic changes using solution state NMR measurements of secondary chemical shifts, relaxation parameters, residual dipolar couplings, and paramagnetic relaxation enhancement. We find that the neutralization of negatively charged side-chains eliminates electrostatic repulsion in the C-terminal tail of aS and leads to a collapse of this region at low pH. Hydrophobic contacts between the compact C-terminal tail and the NAC (non-amyloid-b component) region are maintained and may lead to the formation of a globular domain. Transient long-range contacts between the C-terminus of the protein and regions N-terminal to the NAC region are also preserved. Thus, the release of long-range contacts does not play a role in the increased aggregation of aS at low pH, which we instead attribute to the increased hydrophobicity of the protein.

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Mapping Long-range Contacts in a Highly Unfolded Protein

Cited by 142 publications

References 25 publications

Dynamics of equilibrium structural fluctuations of apomyoglobin measured by fluorescence correlation spectroscopy

Dynamics of equilibrium structural fluctuations of apomyoglobin measured by fluorescence correlation spectroscopy

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

Charge neutralization and collapse of the C‐terminal tail of alpha‐synuclein at low pH

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