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Accumulation of α-synuclein resulting in the formation of oligomers and protofibrils has been linked to Parkinson's disease and Lewy body dementia. In contrast, β-synuclein (β-syn), a close homologue, does not aggregate and reduces α-synuclein (α-syn)-related pathology. Although considerable information is available about the conformation of α-syn at the initial and end stages of fibrillation, less is known about the dynamic process of α-syn conversion to oligomers and how interactions with antiaggregation chaperones such as β-synuclein might occur. Molecular modeling and molecular dynamics simulations based on the micelle-derived structure of α-syn showed that α-syn homodimers can adopt nonpropagating (head-to-tail) and propagating (head-to-head) conformations. Propagating α-syn dimers on the membrane incorporate additional α-syn molecules, leading to the formation of pentamers and hexamers forming a ring-like structure. In contrast, β-syn dimers do not propagate and block the aggregation of α-syn into ring-like oligomers. Under in vitro cell-free conditions, α-syn aggregates formed ring-like structures that were disrupted by β-syn. Similarly, cells expressing α-syn displayed increased ion current activity consistent with the formation of Zn2+-sensitive nonselective cation channels. These results support the contention that in Parkinson's disease and Lewy body dementia, α-syn oligomers on the membrane might form pore-like structures, and that the beneficial effects of β-synuclein might be related to its ability to block the formation of pore-like structures.
In recent years, new hope for understanding the pathogenesis of Parkinson's disease (PD) and Lewy body dementia (LBD) has emerged with the discovery of mutations and duplications in the α-synuclein (α-syn) gene that are associated with rare familial forms of Parkinsonism [1–3]. Moreover, it has been shown that α-syn is centrally involved in the pathogenesis of both sporadic and inherited forms of PD and LBD because this molecule accumulates in Lewy bodies (LBs) [4–6], synapses, and axons, and its expression in transgenic (tg) mice [7–9] and Drosophila  mimics several aspects of PD.
The mechanisms through which α-syn leads to neurodegeneration and the characteristic symptoms of LBD are unclear. However, recent evidence indicates that abnormal accumulation of misfolded α-syn in the synaptic terminals and axons plays an important role [11–14]. These studies suggest that α-syn oligomers and protofibrils rather than fibrils might be the neurotoxic species .
α-syn is an abundant presynaptic molecule  that probably plays a role in modulating vesicular synaptic release . Synucleins belong to a family of related proteins including α-, β-, and γ-synucleins. α-syn belongs to a class of so-called ‘naturally unfolded proteins’[13,18]. Such proteins do not have a stable tertiary structure and during their existence change their conformations. Human α-syn is a 140-amino acid (aa) protein, and β-syn is a 134-aa protein. Each of the synucleins is composed of an N-terminal lipid-binding domain containing 11 residue repeats and a C-terminal acidic domain that has been proposed to be involved in protein–protein interactions. It has been shown [19–22] that at the lipid–protein interface, α-syn has a conformation characterized by two helical domains interrupted by a short nonhelical turn. α-syn contains a highly amyloidogenic hydrophobic domain in the N-terminus region (aa 60–95), which is partially absent in β-syn and might explain why β-syn has a reduced ability to self-aggregate and form oligomers and fibrils [23,24]. Interestingly, although under physiological conditions β-syn is nonamyloidogenic, a recent study demonstrated that certain factors, namely, particular metals and pesticides, can cause rapid fibrillation of this molecule and of mixtures of α- and β-syn  under in vitro cell-free conditions. However, previous studies have shown that in the absence of metals, β-syn interacts with α-syn and is capable of preventing α-syn aggregation and related deficits both in vitro and in vivo[23,24].
Various lines of evidence support the contention that abnormal aggregates arise from a partially folded intermediate precursor that contains hydrophobic patches. It has been proposed that the intermediate α-syn oligomers form annular protofibrils and pore-like structures [26–29]. The mechanism through which monomeric α-syn converts into a toxic oligomer and later into fibrils is currently under intense investigation. Recent reviews indicate that the kinetics of α-syn fibrillation are consistent with a nucleation-dependent mechanism for which a partially folded intermediate is needed in the early stages of aggregation . Factors leading to the formation of the folded intermediates include oxidation, phosphorylation, mutations, and lipids in the membrane [30–34]. α-syn oligomerization might occur on the membrane and involves interactions between hydrophobic residues of the amphipathic α-helices of α-syn . These studies indicate that the hydrophobic lipid binding domains in the N-terminal region might be important in modulating α-syn aggregation [13,36–38]. There are several studies describing the effects of membranes and membrane-like structure on aggregation [21,39,40], however, less is known about the effects of membrane lipids on β-syn structure. In this context, a recent study has analyzed by NMR the micelle-bound structure and dynamics of β- and γ-syn .
Thus, better understanding of the steps involved in the process of α-syn aggregation is important in order to develop intervention strategies that might prevent or reverse α-syn oligomerization and toxic conversion. The conformational state of α-syn at the initial and end stages of fibrillation have been characterized in some detail and recent studies have shown that early stage oligomers are globular structures with variable height (2–6 nm) that after prolonged incubation results in the formation of elongated protofibrils which disappear upon fibril formation .
However, less is known about the dynamic process of conversion of α-syn at earlier stages and how interactions with antiaggregation chaperones such as β-syn and heat-shock proteins might occur. This is in part due to the transient nature of the oligomers and the difficulties in crystallizing such conformers. Therefore, the use of computer-based molecular modeling techniques in combination with biochemical and cell based assays might facilitate understanding the dynamic characteristics and structure of the synuclein aggregates. In this context, the main objective was to develop a dynamical model for the early steps of α-syn aggregation using computer simulations that includes the process of membrane docking and the potential mechanisms through which β-syn blocks α-syn aggregation.
Our studies suggest that at early stages, propagating α-syn dimers immersed in the membrane lead to the formation of pentamers and hexamers with a pore-like structure. These ring-like aggregates might correspond to Zn2+-sensitive nonselective cation channels whose formation is blocked by β-syn. The inhibitory effect of β-syn may result from its interaction with α-syn, which prevents formation of functional α-syn channels.
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The present study showed by utilizing molecular modeling and molecular dynamics simulations, in combination with biochemical and ultrastructural analysis, that α-syn can arrange into homodimers that can adopt nonpropagating and propagating conformations. The evidence predicts that propagating α-syn dimers dock on the membrane surface and can incorporate additional α-syn molecules, leading to the formation of pore-like structures. In contrast, β-syn dimers do not propagate, and when interacting with α-syn aggregates block the propagation of α-syn into multimeric structures. Recent studies have suggested that the transformation of α-syn into a neurotoxic molecule might involve the sequential conversion of α-syn monomers into globular oligomers and then protofibrils . In contrast, α-syn fibrils, which are present in the LBs , might represent a mechanism for isolating toxic oligomers . Previous studies have investigated the conformation of α-syn either at the very initial stages of aggregation  or during the process of fibril formation . In micelles, α-syn monomers consist of two curved α-helices connected by a short linker in an antiparallel arrangement, followed by a short extended region and a predominantly unstructured mobile tail [21,48]. The molecular dynamics studies described here showed that this structure of α-syn displayed significant changes in the organization of the N-terminal helices from 2 to 3 helices over time, which might lead to more complex membrane interactions.
Computerized analysis predicted that these changes were accompanied over time by alterations in the secondary structure showing that a π-helical conformation appears in the N-terminus in addition to the α-helix. However, confirmation of this structural transformation awaits NMR analysis. Interestingly, molecular modeling of the misfolding of the Alzheimer's disease amyloid-β protein has shown a rapid transition of the N-terminal α-helix 1 into a π-helix . Such conformational changes, in combination with β-hairpin structures, might be essential to the aggregation process  and the subsequent formation of pore-like structures.
Under basal conditions, both nonpropagating and propagating dimers might exist, with a higher proportion of dimers exhibiting a nonpropagating conformation. In disorders with α-syn aggregation such as PD it is possible that an increased proportion of propagating dimers might be present. The conditions that might favor an increased ratio of propagating α-syn complexes are unclear, but given the conformational instability of the proteins implied by both experimental and modeling results, it may be highly sensitive to local environmental influences. In support of this, closer association with the membrane has been suggested to induce α-syn oligomerization . It has been reported that small oligomeric forms of α-syn preferentially associate with lipids and cell membranes , however, the conformations of α-syn multimers have been difficult to study due to the inability to crystallize the oligomeric form of this protein. Our molecular dynamics studies support the contention that oligomers of α-syn associate with membranes and suggest that propagating dimers might be thermodynamically stable on membranes in association with lipids. Moreover, the simulations and modeling suggest that anchoring of propagating α-syn dimers to the membrane facilitates the incorporation of additional α-syn monomers, leading to the formation of trimers, tetramers, pentamers, and hexamers, the latter oligomers forming ring-like structures.
Recent Raman and AFM studies showed that in vitro early stage oligomers have a globular structure that elongates over time to form protofibrils [42,51]. High-resolution ultrastructural and AFM have suggested that these aggregates might form pore-like structures that appear to be common to those produced by other molecules involved in neurodegeneration , including amyloid-β protein , British dementia peptide (ABri) , Danish dementia peptide (ADan), serum amyloid A, and amylin . In such studies, the dimension of the α-syn disc-like structure was 8–10 nm (outer diameter) with a central pore of 1–2 nm . Similarly, our theoretical studies show that the outer diameter of the α-syn multimers is 9–15 nm, with an inner diameter of 2–5 nm. Consistent with the possibility that these α-syn aggregates might represent active pores, cells transduced with α-syn displayed significant increases in Zn2+-sensitive ion channel activity that might correspond to Zn2+-sensitive nonselective cation channels. The Zn2+-sensitivity of the α-syn pore-like structures is likely to be a result of interactions between Zn2+ and cysteine, histidine or arginine residues, as has been previously shown in the case of Zn2+-sensitive Aβ-derived pore-like structures [56,57]. Specifically, the His residue located at position 50 in the α-syn monomer is a possible candidate for interaction with Zn2+ ions because it is situated near the putative pore region of the α-syn pentamer. The increased ion channel activity observed in the present study is in agreement with recent results showing that human neuronal cells expressing mutant α-syn have high plasma membrane ion permeability that was sensitive to calcium chelators . Taken together, these results support the contention that α-syn aggregates might form functional ion-permeable channels that in turn might play a role in the mechanisms of neurodegeneration in LBD.
Therefore, developing strategies that might prevent α-syn aggregation and subsequent oligomerization into pore-like structures, or compounds that might block such potential ion channels could represent a viable approach to treating disorders characterized by α-syn aggregation. As in other neurodegenerative disorders, such as AD similar pore-like structures are formed [58,59], it is possible that generic antioligomer antibodies that can recognize these assemblies might be useful [60,61]. The presence of the oligomers in the membrane might also facilitate recognition by antibodies that promote clearance of aggregated α-syn . Chaperone molecules such as heat sock proteins and β-syn might also be useful. Remarkably, in support of this possibility, we found that, via interactions with α-syn monomers and multimers, β-syn is capable of preventing further oligomerization. Moreover, we found that β-syn ameliorated the abnormal increase in plasma membrane ion permeability in cells expressing α-syn. These findings might help to explain previous in vitro and in vivo studies showing that β-syn is protective . Therefore, developing molecules that might mimic the effects of β-syn based on the molecular structure observations described here may help in the development of therapeutic strategies to reduce α-syn aggregation in disorders with parkinsonism.