α-Synuclein Tertiary Contact Dynamics

Lee, Jennifer C.; Lai, Bert; Kozak, John J.; Gray, Harry B.

doi:10.1021/jp068604y

Cited by 60 publications

(102 citation statements)

References 40 publications

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“…Lee et al measured rates of Trp triplet quenching by nitrotryosine of 1.6-5.3 × 10 5 s −1 for various loops, similar to our k obs (36). This quenching mechanism is likely not diffusion-limited, but reaction-limited rates were not determined.…”

Section: Discussionsupporting

confidence: 80%

Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion

Ahmad

Chen

Lapidus

2012

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

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We hypothesize that the first step of aggregation of disordered proteins, such as α-synuclein, is controlled by the rate of backbone reconfiguration. When reconfiguration is fast, bimolecular association is not stable, but as reconfiguration slows, association is more stable and subsequent aggregation is faster. To investigate this hypothesis, we have measured the rate of intramolecular diffusion in α-synuclein, a protein involved in Parkinson's disease, under solvent conditions that accelerate or decelerate aggregation. Using the method of tryptophan-cysteine (Trp-Cys) quenching, the rate of intramolecular contact is measured in four different loops along the chain length. This intrinsically disordered protein is highly diffusive at low temperature at neutral pH, when aggregation is slow, and compacts and diffuses more slowly at high temperature or low pH, when aggregation is rapid. Diffusion also slows with the disease mutation A30P. This work provides unique insights into the earliest steps of α-synuclein aggregation pathway and should provide the basis for the development of drugs that can prevent aggregation at the initial stage.unfolded state | Alzheimer's disease | amyloid T he protein α-synuclein is the primary component of intracellular aggregants known as Lewy bodies, a hallmark of Parkinson's disease, and likely plays a central role in neuronal cell death (1). When recombinantly expressed and purified it is intrinsically disordered in solution and highly prone to aggregation (2). Recent work has shown that the native structure in human cells is likely a helical tetramer that is resistant to aggregation, but when this tetramer is denatured the monomers cannot autonomously refold and aggregate very quickly (3, 4). Thus it is likely that the aggregation pathway passes through the monomer. In vitro, the aggregation propensity of α-synuclein is very sensitive to solution conditions such as temperature, pH, salt concentration, and solution cofactors. There has been significant work to discover the structures that form in association with lipids, structures of final aggregates, and structures that may be the aggregation precursor (5-15). However, the underlying reason for why monomeric α-synuclein is so prone to aggregation is still unknown. We propose that a physical influence on aggregation is the internal dynamics of the disordered chain, that is, the rate of intramolecular diffusion.Over the past decade, a number of groups have measured intramolecular diffusion in a variety of sequences using measurements of intramolecular contact between two probes placed in the chain. All unstructured peptides, including fragments of α-synuclein, diffuse relatively rapidly, approximately 1-3 × 10 −6 cm 2 s −1 (16-18). These rates are less than 10 times slower than free diffusion of individual amino acids and about the same as translational diffusion of the entire chain, suggesting that the chain does not exert significant drag on the movement of individual segments (19), although there are measurable tail effects when ...

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Section: Discussionsupporting

confidence: 80%

Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion

Ahmad

Chen

Lapidus

2012

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

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“…Additionally, we note that a major contributor of the peak broadening observed in the histograms is shot noise in addition to other experimental contributions that are difficult to fully quantify (44), including a potential contribution from differential dye properties in the mixture of labeling isomers (D-A and A-D); hence, we instead use FCS-FRET measurements to evaluate the presence of additional conformational distributions (see SI Appendix for general discussion of peak broadening and comparisons of histogram data with shot noise simulations). Thus, although we have denoted the observed peaks as conformations, consistent with the thermodynamics of the system (22), we note that each of these ''conformations'' represents an ensemble, borne out by our FCS-FRET f luctuation data and previous data from time-resolved FRET and tertiary contact dynamics measurements (33,50).…”

Section: Structure and Dynamics Of ␣-Synuclein Conformational States supporting

confidence: 63%

Interplay of α-synuclein binding and conformational switching probed by single-molecule fluorescence

Ferreon

Gambin²,

Lemke³

et al. 2009

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

381

449

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We studied the coupled binding and folding of ␣-synuclein, an intrinsically disordered protein linked with Parkinson's disease. Using single-molecule fluorescence resonance energy transfer and correlation methods, we directly probed protein membrane association, structural distributions, and dynamics. Results revealed an intricate energy landscape on which binding of ␣-synuclein to amphiphilic small molecules or membrane-like partners modulates conformational transitions between a natively unfolded state and multiple ␣-helical structures. ␣-Synuclein conformation is not continuously tunable, but instead partitions into 2 main classes of folding landscape structural minima. The switch between a broken and an extended helical structure can be triggered by changing the concentration of binding partners or by varying the curvature of the binding surfaces presented by micelles or bilayers composed of the lipid-mimetic SDS. Single-molecule experiments with lipid vesicles of various composition showed that a low fraction of negatively charged lipids, similar to that found in biological membranes, was sufficient to drive ␣-synuclein binding and folding, resulting here in the induction of an extended helical structure. Overall, our results imply that the 2 folded structures are preencoded by the ␣-synuclein amino acid sequence, and are tunable by small-molecule supramolecular states and differing membrane properties, suggesting novel control elements for biological and amyloid regulation of ␣-synuclein.A lpha-synuclein, a highly acidic 140-residue protein expressed at high levels in the human brain and enriched in presynaptic nerve termini, is a member of the growing class of intrinsically disordered proteins that adopt ordered structure upon interaction with cellular partners (1-5). This natively unfolded protein plays crucial roles in the pathogenesis of several neurodegenerative disorders including Parkinson's disease and Alzheimer's disease (6-9). Although several physiological functions have been proposed for the protein, including roles in the regulation of distinct pools of presynaptic vesicles (10, 11), maintenance of SNARE protein complexes (12), modulation of neural plasticity (13), control of dopamine neurotransmission (14), and ER-Golgi trafficking (15), its precise biological role remains unclear. Nevertheless, membrane interaction is generally believed to be a key modulator of ␣-synuclein function (16,17).Sequence analysis predicts ␣-synuclein interaction with lipid membranes through amphipathic ␣-helices encoded by 7 imperfect 11-residue repeats, approximately 4 of which are located in the highly basic N-terminal region of the protein, and 3 in the highly acidic and hydrophobic NAC region (non-A␤ component of Alzheimer's disease amyloid) (13, 18). Not surprisingly, the protein undergoes structural transitions upon binding to either brain-derived or synthetic acidic phospholipid vesicles, adopting ␣-helical conformations in the membrane-bound form (17)(18)(19). Similarly, ␣-synuclein assumes helical structu...

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“…The poorness of solvent can be established through quantitative studies of chain size in dilute solutions. Recent work of Lee et al on α-synuclein [60] and Mukhopadhyay et al [61] on the N-domain of Sup35 show that these molecules prefer an ensemble of collapsed states in aqueous milieus and this explains their propensity to phase-separate as concentration increases. We measured the scaling of hydrodynamic sizes for monomeric polyglutamine in aqueous solution at ca.…”

Section: Applicability Of Polymer Physics Concepts To Study Of Aggregmentioning

confidence: 99%

A polymer physics perspective on driving forces and mechanisms for protein aggregation

Pappu

Wang

Vitalis

et al. 2008

Archives of Biochemistry and Biophysics

156

174

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Protein aggregation is a commonly occurring problem in biology. Cells have evolved stress-response mechanisms to cope with problems posed by protein aggregation. Yet, these quality control mechanisms are overwhelmed by chronic aggregation-related stress and the resultant consequences of aggregation become toxic to cells. As a result, a variety of systemic and neurodegenerative diseases are associated with various aspects of protein aggregation and rational approaches to either inhibit aggregation or manipulate the pathways to aggregation might lead to an alleviation of disease phenotypes. To develop such approaches, one needs a rigorous and quantitative understanding of protein aggregation. Much work has been done in this area. However, several unanswered questions linger, and these pertain primarily to the actual mechanism of aggregation as well as to the types of intermolecular associations and intramolecular fluctuations realized at low protein concentrations. It has been suggested that the concepts underlying protein aggregation are similar to those used to describe the aggregation of synthetic polymers. Following this suggestion, the relevant concepts of polymer aggregation are introduced. The focus is on explaining the driving forces for polymer aggregation and how these driving forces vary with chain length and solution conditions. It is widely accepted that protein aggregation is a nucleation-dependent process. This view is based mainly on the presence of long times for the accumulation of aggregates and the elimination of these lag times with "seeds". In this sense, protein aggregation is viewed as being analogous to the aggregation of colloidal particles. The theories for polymer aggregation reviewed in this work suggest an alternative mechanism for the origin of long lag times in protein aggregation. The proposed mechanism derives from the recognition that polymers have unique dynamics that distinguish them from other aggregation-prone systems such as colloidal particles.

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α-Synuclein Tertiary Contact Dynamics

Cited by 60 publications

References 40 publications

Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion

Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion

Interplay of α-synuclein binding and conformational switching probed by single-molecule fluorescence

A polymer physics perspective on driving forces and mechanisms for protein aggregation

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