α-Synuclein induces both positive mean curvature and negative Gaussian curvature in membranes

Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes

The prion-like spread of protein aggregates is a leading hypothesis for the propagation of neurofibrillary lesions in the brain, including the spread of tau inclusions associated with Alzheimer's disease. The mechanisms of cellular uptake of tau seeds and subsequent nucleated polymerization of cytosolic tau are major questions in the field, and the potential for coupling between the entry and nucleation mechanisms has been little explored. We found that in primary astrocytes and neurons, endocytosis of tau seeds leads to their accumulation in lysosomes. This in turn leads to lysosomal swelling, deacidification, and recruitment of ESCRT proteins, but not Galectin-3, to the lysosomal membrane. These observations are consistent with nanoscale damage of the lysosomal membrane. Live cell imaging and STORM superresolution microscopy further show that the nucleation of cytosolic tau occurs primarily at the lysosome membrane under these conditions. These data suggest that tau seeds escape from lysosomes via nanoscale damage rather than wholesale rupture and that nucleation of cytosolic tau commences as soon as tau fibril ends emerge from the lysosomal membrane.

Interplay of α-synuclein with Lipid Membranes: Cooperative Adsorption, Membrane Remodeling and Coaggregation

α-Synuclein is a small neuronal protein enriched at presynaptic termini. It is hypothesized to play a role in neurotransmitter release and synaptic vesicle cycling, while the formation of α-synuclein amyloid fibrils is associated with several neurodegenerative diseases, most notably Parkinson's Disease. The molecular mechanisms of both the physiological and pathological functions of α-synuclein remain to be fully understood, but in both cases, interactions with membranes play an important role. In this Perspective, we discuss several aspects of α-synuclein interactions with lipid membranes including cooperative adsorption, membrane remodeling and α-synuclein amyloid fibril formation in the presence of lipid membranes. We highlight the coupling between the different phenomena and their interplay in the context of physiological and pathological functions of α-synuclein.

Flanking Domains Modulate α-Synuclein Monomer Structure: A Molecular Dynamics Domain Deletion Study

Aggregates of misfolded α-synuclein proteins (asyn) are key markers of Parkinson's disease. Asyn proteins have three domains: an N-terminal domain, a hydrophobic NAC core implicated in aggregation, and a proline-rich C-terminal domain. Proteins with truncated C-terminal domains are known to be prone to aggregation and suggest that studying domain-domain interactions in asyn monomers could help elucidate the role of the flanking domains in modulating protein structure. To this end, we used Gaussian accelerated molecular dynamics (GAMD) to simulate wild-type (WT), N-terminal truncated (DN), C-terminal truncated (ΔC), and isolated NAC domain variants (isoNAC). Using clustering and contact analysis, we found that N- and C-terminal domains interact via electrostatic interactions, while the NAC and N-terminal domains interact through hydrophobic contacts. Our work also suggests that the C-terminal domain does not interact directly with the NAC domain but instead interacts with the N-terminal domain. Removal of the N-terminal domain led to increased contacts between NAC and C-terminal domains and the formation of interdomain β-sheets. Removal of either flanking domain also resulted in increased compactness of every domain. We also found that the contacts between flanking domains results in an electrostatic potential (ESP) that could possibly lead to favorable interactions with anionic lipid membranes. Removal of the C-terminal domain disrupts the ESP in a way that is likely to over-stabilize protein-membrane interactions. All of this suggests that one of the roles of the flanking domains may be to modulate the protein structure in a way that helps maintain elongation, hide hydrophobic residue from the solvent, and maintain an ESP that aids favorable interactions with the membrane.

Docosahexaenoic acid promotes vesicle clustering mediated by alpha-Synuclein via electrostatic interaction

α-Synuclein (α-Syn) is an intrinsically disordered protein whose aggregation is associated with Parkinson's disease, dementia, and other neurodegenerative diseases known as synucleinopathies. However, the functional role of α-Syn is still unclear, although it has been shown to be involved in the regulation of neurotransmitter release via the interaction with synaptic vesicles (SVs), vesicle clustering, and SNARE complex assembly. Fatty acids have significant occupancy in synaptic vesicles; and recent studies suggest the interaction of fatty acids with α-Syn affect the formation of (pathological) aggregates, but it is less clear how fatty acids affects the functional role of α-Syn including α-Syn-membrane interactions, in particular with (SV-like) vesicles. Here, we report the concentration dependent effect of docosahexaenoic acid (DHA) in synaptic-like vesicle clustering via α-Syn interaction. Through molecular dynamics simulation, we revealed that DHA promoted vesicle clustering is due to the electrostatic interaction between DHA in the membrane and the N-terminal region of α-Syn. Moreover, this increased electrostatic interaction arises from a change in the macroscopic properties of the protein-membrane interface induced by (preferential solvation of) DHA. Our results provide insight as to how DHA regulates vesicle clustering mediated by α-Syn and may further be useful to understand its physiological as well as pathological role. Description: In physiological environments, α-Synuclein (α-Syn) localizes at nerve termini and synaptic vesicles and interacts with anionic phospholipid membranes to promote vesicle clustering. Docosahexaenoic acid (DHA) increases binding affinity between α-Syn and lipid membranes by increasing electrostatic interaction energy through modulating the local and global membrane environment and conformational properties of α-Syn.

The Effects of Lipids on α-Synuclein Aggregation In Vitro

The small neuronal protein α-synuclein (αS) is found in pre-synaptic terminals and plays a role in vesicle recycling and neurotransmission. Fibrillar aggregates of αS are the hallmark of Parkinson's disease and related neurodegenerative disorders. In both health and disease, interactions with lipids influence αS's structure and function, prompting much study of the effects of lipids on αS aggregation. A comprehensive collection (126 examples) of aggregation rate data for various αS/lipid combinations was presented, including combinations of lipid variations and mutations or post-translational modifications of αS. These data were interpreted in terms of lipid structure to identify general trends. These tabulated data serve as a resource for the community to help in the interpretation of aggregation experiments with lipids and to be potentially used as inputs for computational models of lipid effects on aggregation.

GM1 oligosaccharide efficacy against α-synuclein aggregation and toxicity in vitro

Fibrillary aggregated α-synuclein represents the neurologic hallmark of Parkinson's disease and is considered to play a causative role in the disease. Although the causes leading to α-synuclein aggregation are not clear, the GM1 ganglioside interaction is recognized to prevent this process. How GM1 exerts these functions is not completely clear, although a primary role of its soluble oligosaccharide (GM1-OS) is emerging. Indeed, we recently identified GM1-OS as the bioactive moiety responsible for GM1 neurotrophic and neuroprotective properties, specifically reverting the parkinsonian phenotype both in in vitro and in vivo models. Here, we report on GM1-OS efficacy against the α-synuclein aggregation and toxicity in vitro. By amyloid seeding aggregation assay and NMR spectroscopy, we demonstrated that GM1-OS was able to prevent both the spontaneous and the prion-like α-synuclein aggregation. Additionally, circular dichroism spectroscopy of recombinant monomeric α-synuclein showed that GM1-OS did not induce any change in α-synuclein secondary structure. Importantly, GM1-OS significantly increased neuronal survival and preserved neurite networks of dopaminergic neurons affected by α-synuclein oligomers, together with a reduction of microglia activation. These data further demonstrate that the ganglioside GM1 acts through its oligosaccharide also in preventing the α-synuclein pathogenic aggregation in Parkinson's disease, opening a perspective window for GM1-OS as drug candidate.

Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes

The prion-like spread of protein aggregates is a leading hypothesis for the propagation of neurofibrillary lesions in the brain, including the spread of tau inclusions associated with Alzheimer's disease. The mechanisms of cellular uptake of tau seeds and subsequent nucleated polymerization of cytosolic tau are major questions in the field, and the potential for coupling between the entry and nucleation mechanisms has been little explored. We found that in primary astrocytes, endocytosis of tau seeds leads to their accumulation in lysosomes. This in turn leads to lysosomal swelling, deacidification and recruitment of ESCRT proteins, but not Galectin-3, to the lysosomal membrane. These observations are consistent with nanoscale damage of the lysosomal membrane. Using live cell and STORM, imaging, nucleation of cytosolic tau occurs primarily at the lysosome membrane under these conditions. These data suggest that tau seeds escape from lysosomes via nanoscale damage rather than wholesale rupture, and that nucleation of cytosolic tau commences as soon as tau fibril ends emerge from the lysosomal membrane.

Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes

The accelerated acquisition of multidimensional NMR spectra using sparse non-uniform sampling (NUS) has been widely adopted in recent years. The key concept in NUS is that a major part of the data is omitted during measurement, and then reconstructed using, for example, compressed sensing (CS) methods. CS requires spectra to be compressible, that is, they should contain relatively few "significant" points. The more compressible the spectrum, the fewer experimental NUS points needed in order for it to be accurately reconstructed. In this paper we show that the CS processing of similar spectra can be enhanced by reconstructing only the differences between them. Accurate reconstruction can be obtained at lower sampling levels as the difference is sparser than the spectrum itself. In many situations this method is superior to "conventional" compressed sensing. We exemplify the concept of "difference CS" with one such case-the study of alpha-synuclein binding to liposomes and its dependence on temperature. To obtain information on temperature-dependent transitions between different states, we need to acquire several dozen spectra at various temperatures, with and without the presence of liposomes. Our detailed investigation reveals that changes in the binding modes of the alpha-synuclein ensemble are not only temperature-dependent but also show non-linear behavior in their transitions. Our proposed CS processing approach dramatically reduces the number of NUS points required and thus significantly shortens the experimental time.

Membrane-Active Peptides Attack Cell Membranes in a Lipid-Regulated Curvature-Generating Mode

Membrane-active peptides (MAPs) exhibit great potential in biomedical applications due to their unique ability to overcome the cell membrane barrier. However, the interactions between MAPs and membranes are complex, and little is known about the possibility of MAP action being specific to certain types of membranes. In this study, a combination of molecular dynamics simulations and theoretical analysis was utilized to investigate the interactions between typical MAPs and realistic cell membrane systems. Remarkably, the simulations revealed that MAPs can attack membranes by generating and sensing positive mean curvature, which is dependent on lipid composition. Furthermore, theoretical calculations demonstrated that this lipid-regulated curvature-based membrane attack mechanism is an integrated result of multiple effects, including peptide-induced membrane wedge and softening effects, the lipid shape effect, the area-difference elastic effect, and the boundary edge effect of formed peptide-lipid nanodomains. This study enhances our comprehension of MAP-membrane interactions and highlights the potential for developing membrane-specific MAP-based agents.

Intrinsic Disorder in α-Synuclein Regulates the Exocytotic Fusion Pore Transition

Today, it is widely accepted that intrinsic disorder is strongly related to the cell cycle, during mitosis, differentiation, and apoptosis. Of particular interest are hybrid proteins possessing both structured and unstructured domains that are critical in human health and disease, such as α-synuclein. In this work, we describe how α-synuclein interacts with the nascent fusion pore as it evolves toward expansion. We unveil the key role played by its intrinsically disordered region as a thermodynamic regulator of the nucleation-expansion energy barrier. By analyzing a truncated variant of α-synuclein that lacks the disordered region, we find that the landscape of protein interactions with PIP₂ and POPS lipids is highly altered, ultimately increasing the energy cost for the fusion pore to transit from nucleation to expansion. We conclude that the intrinsically disordered region in full-length α-synuclein recognizes and allocates pivotal protein:lipid interactions during membrane remodeling in the first stages of the fusion pore.

Amyloids on Membrane Interfaces: Implications for Neurodegeneration

Membrane interfaces are vital for various cellular processes, and their involvement in neurodegenerative disorders such as Alzheimer's and Parkinson's disease has taken precedence in recent years. The amyloidogenic proteins associated with neurodegenerative diseases interact with the neuronal membrane through various means, which has implications for both the onset and progression of the disease. The parameters that regulate the interaction between the membrane and the amyloids remain poorly understood. The review focuses on the various aspects of membrane interactions of amyloids, particularly amyloid-β (Aβ) peptides and Tau involved in Alzheimer's and α-synuclein involved in Parkinson's disease. The genetic, cell biological, biochemical, and biophysical studies that form the basis for our current understanding of the membrane interactions of Aβ peptides, Tau, and α-synuclein are discussed.

Insights into Membrane Curvature Sensing and Membrane Remodeling by Intrinsically Disordered Proteins and Protein Regions

Cellular membranes are highly dynamic in shape. They can rapidly and precisely regulate their shape to perform various cellular functions. The protein’s ability to sense membrane curvature is essential in various biological events such as cell signaling and membrane trafficking. As they are bound, these curvature-sensing proteins may also change the local membrane shape by one or more curvature driving mechanisms. Established curvature-sensing/driving mechanisms rely on proteins with specific structural features such as amphipathic helices and intrinsically curved shapes. However, the recent discovery and characterization of many proteins have shattered the protein structure–function paradigm, believing that the protein functions require a unique structural feature. Typically, such structure-independent functions are carried either entirely by intrinsically disordered proteins or hybrid proteins containing disordered regions and structured domains. It is becoming more apparent that disordered proteins and regions can be potent sensors/inducers of membrane curvatures. In this article, we outline the basic features of disordered proteins and regions, the motifs in such proteins that encode the function, membrane remodeling by disordered proteins and regions, and assays that may be employed to investigate curvature sensing and generation by ordered/disordered proteins.

α-Synuclein-induced deformation of small unilamellar vesicles

α-Synuclein is a small neuronal protein that reversibly associates with lipid membranes. The membrane interactions are believed to be central to the healthy function of this protein involved in synaptic plasticity and neurotransmitter release. α-Synuclein has been speculated to induce vesicle fusion as well as fission, processes which are analogous to each other but proceed in different directions and involve different driving forces. In the current work, we analyse α-synuclein-induced small unilamellar vesicle deformation from a thermodynamics point of view. We show that the structures interpreted in the literature as fusion intermediates are in fact a stable deformed state and neither fusion nor vesicle clustering occurs. We speculate on the driving force for the observed deformation and put forward a hypothesis that α-synuclein self-assembly on the lipid membrane precedes and induces membrane remodelling.

Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides

Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.

Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR

α-Synuclein (αS) is a presynaptic protein that binds to cell membranes and is linked to Parkinson's disease (PD). Binding of αS to membranes is a likely first step in the molecular pathophysiology of PD. The αS molecule can adopt multiple conformations, being largely disordered in water, adopting a β-sheet conformation when present in amyloid fibrils, and forming a dynamic multiplicity of α-helical conformations when bound to lipid bilayers and related membrane-mimetic surfaces. Multiscale molecular dynamics simulations in conjunction with nuclear magnetic resonance (NMR) and cross-linking mass spectrometry (XLMS) measurements are used to explore the interactions of αS with an anionic lipid bilayer. The simulations and NMR measurements together reveal a break in the helical structure of the central non-amyloid-β component (NAC) region of αS in the vicinity of residues 65-70, which may facilitate subsequent oligomer formation. Coarse-grained simulations of αS starting from the structure of αS when bound to a detergent micelle reveal the overall pattern of protein contacts to anionic lipid bilayers, while subsequent all-atom simulations provide details of conformational changes upon membrane binding. In particular, simulations and NMR data for liposome-bound αS indicate incipient β-strand formation in the NAC region, which is supported by intramolecular contacts seen via XLMS and simulations. Markov state models based on the all-atom simulations suggest a mechanism of conformational change of membrane-bound αS via a dynamic helix break in the region of residue 65 in the NAC region. The emergent dynamic model of membrane-interacting αS advances our understanding of the mechanism of PD, potentially aiding the design of novel therapeutic approaches.

Mutations in membrane-fusion subunit of spike glycoprotein play crucial role in the recent outbreak of COVID-19

Coronavirus disease‐2019 (COVID‐19), the ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a major threat to the entire human race. It is reported that SARS‐CoV‐2 seems to have relatively low pathogenicity and higher transmissibility than previously outbroke SARS‐CoV. To explore the reason of the increased transmissibility of SARS‐CoV‐2 compared with SARS‐CoV, we have performed a comparative analysis on the structural proteins (spike, envelope, membrane, and nucleoprotein) of two viruses. Our analysis revealed that extensive substitutions of hydrophobic to polar and charged amino acids in spike glycoproteins of SARS‐CoV2 creates an intrinsically disordered region (IDR) at the beginning of membrane‐fusion subunit and intrinsically disordered residues in fusion peptide. IDR provides a potential site for proteolysis by furin and enriched disordered residues facilitate prompt fusion of the SARS‐CoV2 with host membrane by recruiting molecular recognition features. Here, we have hypothesized that mutation‐driven accumulation of intrinsically disordered residues in spike glycoproteins play dual role in enhancing viral transmissibility than previous SARS‐coronavirus. These analyses may help in epidemic surveillance and preventive measures against COVID‐19.

Spike glycoprotein of SARS‐CoV2 experiences higher synonymous and non‐synonymous substitution rates than other three structural (E, M, N) proteins.

Extensive hydrophobic to polar and charged amino acid substitutions in S proteins during evolution from SARS‐CoV generate intrinsically disordered residues in the membrane fusion subunit (S2) of S protein.

Intrinsically disordered region at the beginning of S2 offers cleavage site of furin protease and by virtue of their flexible nature, they provide sensitive site for efficient proteolysis to activate the fusion peptide.

Enrichment of intrinsically disordered residues in fusion peptide prompts rapid fusion of viral envelop with host membrane by recruiting several MoRFs.

Intrinsic disorderness in spike glycoproteins in SARS‐CoV2 play dual role in enhancing their transmissibility than previous SARS‐corona virus.

Optimizing Gō-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane

Coarse-grained (CG) molecular dynamics (MD) simulations allow us to access much larger length and time scales than atomistic MD simulations, providing an attractive alternative to the conventional simulations. Based on the well-known MARTINI CG force field, the recently developed Gō-MARTINI model for proteins describes large-amplitude structural dynamics, which has not been possible with the commonly used elastic network model. Using the Gō-MARTINI model, we conduct MD simulations of the F-BAR Pacsin1 protein on lipid membrane. We observe that structural changes of the non-globular protein are largely dependent on the definition of the native contacts in the Gō model. To address this issue, we introduced a simple cutoff scheme and tuned the cutoff distance of the native contacts and the interaction strength of the Lennard-Jones potentials in the Gō-MARTINI model. With the optimized Gō-MARTINI model, we show that it reproduces structural fluctuations of the Pacsin1 dimer from atomistic simulations. We also show that two Pacsin1 dimers properly assemble through lateral interaction on the lipid membrane. Our work presents a first step towards describing membrane remodeling processes in the Gō-MARTINI CG framework by simulating a crucial step of protein assembly on the membrane.

Polyunsaturated Fatty Acid Modulates Membrane-Bound Monomeric α-Synuclein by Modulating Membrane Microenvironment through Preferential Interactions

There is ample evidence that both native functions and pathogenic aggregation of α-synuclein are intimately dependent on lipid interactions and fatty acid type; the regulatory mechanism however remains unclear. In the present work, using extensive atomistic molecular dynamics simulations and enhanced-sampling, we have focused on exploring the mechanism of fatty acid dependent regulation of monomeric α-Syn₁₀₀ in a native synaptic vesicle-like membrane. Our results show that α-Syn₁₀₀ spontaneously binds to the membrane through its N-terminal region (residues 1-34), where the depth of membrane insertion, the structure, and orientation of the membrane-bound α-Syn₁₀₀ and its impact on membrane structure are modulated by docosahexaenoic acid (DHA). DHA is a polyunsaturated fatty acid abundantly found in the brain and known to promote the oligomerization of α-synuclein. We found that DHA exhibits marked propensity to interact with monomeric α-Syn₁₀₀ and modulates the microenvironment of the protein by preferentially sorting DHA-containing phospholipids, depleting other phospholipids and cholesterol as well as increasing the proportion of anionic to neutral lipids in the immediate vicinity of the protein. Owing to the unique conformational flexibility, DHA chains form more lipid-packing defects in the membrane and efficiently coat the membrane-embedded surface of the protein, compared to the saturated and monounsaturated fatty acids. DHA thus makes the bilayer more amiable to protein adsorption and less prone to α-synuclein-induced perturbation associated with cytotoxicity. Indeed, in the absence of DHA, we observed significant thinning of the local bilayer membrane induced by α-Syn₁₀₀. Though α-Syn₁₀₀ is predominantly α-helical in membranes studied here, in the presence of DHA we observe formation of β-sheet/β-strands in the C-terminal region (residues 35-100) of α-Syn₁₀₀, which is extended out from the membrane surface. Notably, DHA induces β structure in the NAC domain of α-Syn₁₀₀ and promotes extended conformations as well as large solvent exposure of this hydrophobic domain, properties that are known to facilitate self-assembly of α-synuclein. To the best of our knowledge, this study for the first time provides the atomistic insights into DHA-induced regulatory mechanism of monomeric α-synuclein, having implications in protein structure and its physiological/pathological functions.

In situ kinetic measurements of α-synuclein aggregation reveal large population of short-lived oligomers

Knowledge of the mechanisms of assembly of amyloid proteins into aggregates is of central importance in building an understanding of neurodegenerative disease. Given that oligomeric intermediates formed during the aggregation reaction are believed to be the major toxic species, methods to track such intermediates are clearly needed. Here we present a method, electron paramagnetic resonance (EPR), by which the amount of intermediates can be measured over the course of the aggregation, directly in the reacting solution, without the need for separation. We use this approach to investigate the aggregation of α-synuclein (αS), a synaptic protein implicated in Parkinson’s disease and find a large population of oligomeric species. Our results show that these are primary oligomers, formed directly from monomeric species, rather than oligomers formed by secondary nucleation processes, and that they are short-lived, the majority of them dissociates rather than converts to fibrils. As demonstrated here, EPR offers the means to detect such short-lived intermediate species directly in situ. As it relies only on the change in size of the detected species, it will be applicable to a wide range of self-assembling systems, making accessible the kinetics of intermediates and thus allowing the determination of their rates of formation and conversion, key processes in the self-assembly reaction.

The Localization of Alpha-synuclein in the Endocytic Pathway

Alpha-synuclein (αS) is an intrinsically disordered protein (IDP) that is abundantly present in the brain and is associated with Parkinson's disease (PD). In spite of its abundance and its contribution to PD pathogenesis, the exact cellular function of αS remains largely unknown. The ability of αS to remodel phospholipid model membranes combined with biochemical and cellular studies suggests that αS is involved in endocytosis. To unravel with which route(s) and stage(s) of the endocytic pathway αS is associated, we quantified the colocalization between αS and endocytic marker proteins in differentiated SH-SY5Y neuronal cells, using an object based colocalization analysis. Comparison with randomized data allowed us to discriminate between structural and coincidental colocalizations. A large fraction of the αS positive vesicles colocalizes with caveolin positive vesicles, a smaller fraction colocalizes with EEA1 and Rab7. We find no structural colocalization between αS and clathrin and Rab11 positive vesicles. We conclude that in a physiological context, αS is structurally associated with caveolin dependent membrane vesiculation and is found further along the endocytic pathway, in decreasing amounts, on early and late endosomes. Our results not only shed new light on the function of αS, they also provide a possible link between αS function and vesicle trafficking malfunction in PD.

α-Synuclein and neuronal membranes: Conformational flexibilities in health and disease

Parkinson's disease (PD) is the second most common neurodegenerative disease. Currently, PD has no treatment. The neuronal protein α-synuclein (αS) plays an important role in PD. However, the molecular mechanisms governing its physiological and pathological roles are not fully understood. It is becoming widely acknowledged that the biological roles of αS involve interactions with biological membranes. In these biological processes there is a fine-tuned interplay between lipids affecting the properties of αS and αS affecting lipid metabolism, αS binding to membranes, and membrane damage. In this review, the intricate interactions between αS and membranes will be reviewed and a discussion of the relationship between αS and neuronal membrane structural plasticity in health and disease will be made. It is proposed that in healthy neurons the conformational flexibilities of αS and the neuronal membranes are coupled to assist the physiological roles of αS. However, in circumstances where their conformational flexibilities are decreased or uncoupled, there is a shift toward cell toxicity. Strategies to modulate toxic αS-membrane interactions are potential approaches for the development of new therapies for PD. Future work using specific αS molecular species as well as membranes with specific physicochemical properties should widen our understanding of the intricate biological roles of αS which, in turn, would propel the development of new strategies for the treatment of PD.

Protein crowding mediates membrane remodeling in upstream ESCRT-induced formation of intraluminal vesicles

As part of the lysosomal degradation pathway, the endosomal sorting complexes required for transport (ESCRT-0 to -III/VPS4) sequester receptors at the endosome and simultaneously deform the membrane to generate intraluminal vesicles (ILVs). Whereas ESCRT-III/VPS4 have an established function in ILV formation, the role of upstream ESCRTs (0 to II) in membrane shape remodeling is not understood. Combining experimental measurements and electron microscopy analysis of ESCRT-III-depleted cells with a mathematical model, we show that upstream ESCRT-induced alteration of the Gaussian bending rigidity and their crowding in concert with the transmembrane cargo on the membrane induce membrane deformation and facilitate ILV formation: Upstream ESCRT-driven budding does not require ATP consumption as only a small energy barrier needs to be overcome. Our model predicts that ESCRTs do not become part of the ILV, but localize with a high density at the membrane neck, where the steep decline in the Gaussian curvature likely triggers ESCRT-III/VPS4 assembly to enable neck constriction and scission.

Single-vesicle imaging reveals lipid-selective and stepwise membrane disruption by monomeric α-synuclein

Neurodegenerative diseases are increasing among the world's population, but there are no cures. These disorders all involve proteins that assemble into amyloid fibers which results in brain cell death. Evidence suggests that association of these proteins with lipid membranes is crucial for both functional and pathological roles. In Parkinson's disease, the involved protein, α-synuclein, is thought to function in trafficking of lipid vesicles in the brain. In search of mechanistic origins, increasing focus is put on identifying neurotoxic reactions induced by membrane interactions. To contribute new clues to this question, we here employed a new surface-sensitive scattering microscopy technique. With this approach, we discovered that α-synuclein perturbs vesicles in a stepwise and lipid-dependent fashion already at very low protein coverage.

The interaction of the neuronal protein α-synuclein with lipid membranes appears crucial in the context of Parkinson’s disease, but the underlying mechanistic details, including the roles of different lipids in pathogenic protein aggregation and membrane disruption, remain elusive. Here, we used single-vesicle resolution fluorescence and label-free scattering microscopy to investigate the interaction kinetics of monomeric α-synuclein with surface-tethered vesicles composed of different negatively charged lipids. Supported by a theoretical model to account for structural changes in scattering properties of surface-tethered lipid vesicles, the data demonstrate stepwise vesicle disruption and asymmetric membrane deformation upon α-synuclein binding to phosphatidylglycerol vesicles at protein concentrations down to 10 nM (∼100 proteins per vesicle). In contrast, phosphatidylserine vesicles were only marginally affected. These insights into structural consequences of α-synuclein interaction with lipid vesicles highlight the contrasting roles of different anionic lipids, which may be of mechanistic relevance for both normal protein function (e.g., synaptic vesicle binding) and dysfunction (e.g., mitochondrial membrane interaction).

Deep mutational scanning reveals the structural basis for α-synuclein activity

Defining the biologically active structures of proteins in their cellular environments remains challenging for proteins with multiple conformations and functions, where only a minor conformer might be associated with a given function. Here, we use deep mutational scanning to probe the structure and dynamics of α-synuclein, a protein known to adopt disordered, helical and amyloid conformations. We examined the effects of 2,600 single-residue substitutions on the ability of intracellularly expressed α-synuclein to slow the growth of yeast. Computational analysis of the data showed that the conformation responsible for this phenotype is a long, uninterrupted, amphiphilic helix with increasing dynamics toward the C terminus. Deep mutational scanning can therefore determine biologically active conformations in cellular environments, even for a highly dynamic multi-conformational protein.

Discerning Dynamic Signatures of Membrane-Bound α-Synuclein Using Site-Specific Fluorescence Depolarization Kinetics

α-Synuclein is an intrinsically disordered protein that adopts an α-helical structure upon binding to the negatively charged lipid membrane. Binding-induced conformational change of α-synuclein plays a crucial role in the regulation of synaptic plasticity. In this work, we utilized the fluorescence depolarization kinetics methodology to gain the site-specific dynamical insights into the membrane-bound α-synuclein. We took advantage of the nonoccurrence of Cys in α-synuclein and created single-Cys variants at different sites for us to be able to label it with a thiol-active fluorophore. Our fluorescence depolarization results reveal the presence of three dynamically distinct types of motions of α-synuclein on POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol)) small unilamellar vesicles (SUVs): (i) the (local) wobbling-in-cone motion of the fluorophore on the subnanosecond timescale, (ii) the backbone segmental mobility on the nanosecond timescale, and (iii) a slow depolarization component with a characteristic long rotational correlation time (∼60 ns) that is independent of the residue position. This characteristic timescale could potentially arise due to global tumbling of the protein-membrane complex, the global reorientation of only the protein within the membrane, and/or the translation diffusion of the protein on the curved membrane surface that could result in fluorescence depolarization due to the angular displacement of the transition dipole. In order to discern the molecular origin of the characteristic long rotational correlation time, we then carried our depolarization experiments varying the curvature of the membrane and varying the binding affinity by changing the lipid headgroup. These experiments revealed that the long rotational correlation time primarily arises due to the translational diffusion of α-synuclein on the curved membrane surface with a diffusion coefficient of ∼8.7 × 10^-10 m²/s. The site-specific fluorescence depolarization methodology will find broad application in quantifying diffusion of a wide range of membrane-associated proteins involved in functions and diseases.

Order–disorder skewness in alpha-synuclein: a key mechanism to recognize membrane curvature

Currently, membrane curvature is understood as an active mechanism to control cells spatial organization and activity.

Synaptic vesicle mimics affect the aggregation of wild-type and A53T α-synuclein variants differently albeit similar membrane affinity

α-Synuclein misfolding results in the accumulation of amyloid fibrils in Parkinson's disease. Missense protein mutations (e.g. A53T) have been linked to early onset disease. Although α-synuclein interacts with synaptic vesicles in the brain, it is not clear what role they play in the protein aggregation process. Here, we compare the effect of small unilamellar vesicles (lipid composition similar to synaptic vesicles) on wild-type (WT) and A53T α-synuclein aggregation. Using biophysical techniques, we reveal that binding affinity to the vesicles is similar for the two proteins, and both interact with the helix long axis parallel to the membrane surface. Still, the vesicles affect the aggregation of the variants differently: effects on secondary processes such as fragmentation dominate for WT, whereas for A53T, fibril elongation is mostly affected. We speculate that vesicle interactions with aggregate intermediate species, in addition to monomer binding, vary between WT and A53T, resulting in different consequences for amyloid formation.

Shaping membranes with disordered proteins

Membrane proteins control and shape membrane trafficking processes. The role of protein structure in shaping cellular membranes is well established. However, a significant fraction of membrane proteins is disordered or contains long disordered regions. It becomes more and more clear that these disordered regions contribute to the function of membrane proteins. While the fold of a structured protein is essential for its function, being disordered seems to be a crucial feature of membrane bound intrinsically disordered proteins and protein regions. Here we outline the motifs that encode function in disordered proteins and discuss how these functional motifs enable disordered proteins to modulate membrane properties. These changes in membrane properties facilitate and regulate membrane trafficking processes which are highly abundant in eukaryotes.

Membrane-mediated fibrillation and toxicity of the tau hexapeptide PHF6

The aggregation of the tau protein into neurofibrillary tangles is believed to correlate with cognitive decline in several neurodegenerative disorders, including Alzheimer's disease. Recent studies suggest that tau's interactions with the cell membrane could serve as a toxicity pathway and also enhance fibrillation into paired helical filaments (PHFs). Conformational changes associated with tau-membrane interactions are poorly understood, and their characterization could improve our understanding of tau pathogenicity. In this study, we investigated the molecular level structural changes associated with the interaction of the tau hexapeptide PHF6 with model lipid membranes and characterized the effects of these interactions on membrane stability and peptide fibrillation. We used two PHF6 forms, the aggregation-prone PHF6 with N-terminal acetylation (Ac-PHF6) and the non-aggregation prone PHF6 with a standard N terminus (NH₃ ⁺-PHF6). We found that both PHF6 peptides are neurotoxic and exhibit similar membrane-mediated changes, consisting of: 1) favorable interactions with anionic membranes, 2) membrane destabilization through lipid extraction, and 3) membrane-mediated fibrillation. The rate at which these changes occurred was the main difference between the two peptides. NH₃ ⁺-PHF6 displayed slow membrane-mediated fibrillation after 6 days of incubation, whereas Ac-PHF6 adopted a β-sheet conformation at the surface of the membrane within hours. Ac-PHF6 interactions with the membrane were also accompanied by membrane invagination and rapid membrane destabilization. Overall, our results reveal that membrane interactions could play a critical role in tau toxicity and fibrillation, and highlight that unraveling these interactions is important for significantly advancing the development of therapeutic strategies to manage tau-associated neurodegenerative diseases.

α-synuclein oligomers and fibrils: a spectrum of species, a spectrum of toxicities

This review article provides an overview of the different species that α-synuclein aggregates can populate. It also attempts to reconcile conflicting views regarding the cytotoxic roles of oligomers versus fibrils. α-synuclein, while highly dynamic in the monomeric state, can access a large number of different assembly states. Depending on assembly conditions, these states can interconvert over different timescales. The fibrillar state is the most thermodynamically favored due to the many stabilizing interactions formed between each monomeric unit, but different fibrillar types form at different rates. The end distribution is likely to reflect kinetic partitioning as much as thermodynamic equilibra. In addition, metastable oligomeric species, some of which are on-pathway and others off-pathway, can be populated for remarkably long periods of time. Chemical modifications (phosphorylation, oxidation, covalent links to ligands, etc.) perturb these physical interconversions and invariably destabilize the fibrillar state, leading to small prefibrillar assemblies which can coalesce into amorphous states. Both oligomeric and fibrillar species have been shown to be cytotoxic although firm conclusions require very careful evaluation of particle concentrations and is complicated by the great variety and heterogeneity of different experimentally observed states. The mechanistic relationship between oligomers and fibrils remains to be clarified, both in terms of assembly of oligomers into fibrils and potential dissolution of fibrils into oligomers. While oligomers are possibly implicated in the collapse of neuronal homeostasis, the fibrillar state(s) appears to be the most efficient at propagating itself both in vitro and in vivo, pointing to critical roles for multiple different aggregate species in the progression of Parkinson's disease (https://onlinelibrary.wiley.com/page/journal/14714159/homepage/virtual_issues.htm). This article is part of the Special Issue "Synuclein".

Computational Modeling of Realistic Cell Membranes

Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.

Interplay between α-synuclein amyloid formation and membrane structure

Amyloid formation is a pathological hallmark of many neurodegenerative diseases, including Alzheimer's, Parkinson's, and Huntington's. While it is unknown how these disorders are initiated, in vitro and cellular experiments confirm the importance of membranes. Ubiquitous in vivo, membranes induce conformational changes in amyloidogenic proteins and in some cases, facilitate aggregation. Reciprocally, perturbations in the bilayer structure can be induced by amyloid formation. Here, we review studies in the last 10 years describing α-synuclein (α-syn) and its interactions with membranes, detailing the roles of anionic and zwitterionic lipids in aggregation, and their contribution to Parkinson's disease. We summarize the impact of α-syn - comparing monomeric, oligomeric, and fibrillar forms - on membrane structure, and the effect of membrane remodeling on amyloid formation. Finally, perspective on future studies investigating the interplay between α-syn aggregation and membranes is discussed. This article is part of a Special Issue entitled: Amyloids.

Multiconfigurational Coarse-Grained Molecular Dynamics

Standard low resolution coarse-grained modeling techniques have difficulty capturing multiple configurations of protein systems. Here, we present a method for creating accurate coarse-grained (CG) models with multiple configurations using a linear combination of functions or “states”. Individual CG models are created to capture the individual states, and the approximate coupling between the two states is determined from an all-atom potential of mean force. We show that the resulting multiconfiguration coarse-graining (MCCG) method accurately captures the transition state as well as the free energy between the two states. We have tested this method on the folding of dodecaalanine, as well as the amphipathic helix of endophilin.

Cooperation of Helix Insertion and Lateral Pressure to Remodel Membranes

Nature has developed different protein mediated mechanisms to remodel cellular membranes. One of the proteins that is implicated in these processes is α-synuclein (αS). Here we investigate if besides αS’s membrane bound amphipathic helix the disordered, solvent exposed tail of the protein contributes to membrane reshaping. We produced αS variants with elongated or truncated disordered solvent exposed domains. We observe a transformation of opaque multi lamellar vesicle solutions into nonscattering solutions containing smaller structures upon addition of all αS variants. Experimental data combined with model calculations show that the cooperation of helix insertion and lateral pressure exerted by the disordered domain makes the full length protein decidedly more efficient in membrane remodeling than the truncated version. Using disordered domains may not only be cost-efficient, it may also add a new level of control over vesicle fusion/fission by expansion or compaction of the domain.

α-Synuclein: A Multifunctional Player in Exocytosis, Endocytosis, and Vesicle Recycling

α-synuclein (α-Syn) is a presynaptic enriched protein involved in the pathogenesis of Parkinson’s disease. However, the physiological roles of α-Syn remain poorly understood. Recent studies have indicated a critical role of α-Syn in the sensing and generation of membrane curvature during vesicular exocytosis and endocytosis. It has been known to modulate the assembly of SNARE complex during exocytosis including vesicle docking, priming and fusion steps. Growing evidence suggests that α-Syn also plays critical roles in the endocytosis of synaptic vesicles. It also modulates the availability of releasable vesicles by promoting synaptic vesicles clustering. Here, we provide an overview of recent progresses in understanding the function of α-Syn in the regulation of exocytosis, endocytosis, and vesicle recycling under physiological and pathological conditions.

Curvature sensing by cardiolipin in simulated buckled membranes

Cardiolipin is a non-bilayer phospholipid with a unique dimeric structure. It localizes to negative curvature regions in bacteria and is believed to stabilize respiratory chain complexes in the highly curved mitochondrial membrane. Cardiolipin's localization mechanism remains unresolved, because important aspects such as the structural basis and strength for lipid curvature preferences are difficult to determine, partly due to the lack of efficient simulation methods. Here, we report a computational approach to study curvature preferences of cardiolipin by simulated membrane buckling and quantitative modeling. We combine coarse-grained molecular dynamics with simulated buckling to determine the curvature preferences in three-component bilayer membranes with varying concentrations of cardiolipin, and extract curvature-dependent concentrations and lipid acyl chain order parameter profiles. Cardiolipin shows a strong preference for negative curvatures, with a highly asymmetric chain order parameter profile. The concentration profiles are consistent with an elastic model for lipid curvature sensing that relates lipid segregation to local curvature via the material constants of the bilayers. These computations constitute new steps to unravel the molecular mechanism by which cardiolipin senses curvature in lipid membranes, and the method can be generalized to other lipids and membrane components as well.

Biochemical studies of membrane fusion at the single-particle level

To study membrane fusion mediated by synaptic proteins, proteoliposomes have been widely used for in vitro ensemble measurements with limited insights into the fusion mechanism. Single-particle techniques have proven to be powerful in overcoming the limitations of traditional ensemble methods. Here, we summarize current single-particle methods in biophysical and biochemical studies of fusion mediated by soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and other synaptic proteins, together with their advantages and limitations.

Computational insights into lipid assisted peptide misfolding and aggregation in neurodegeneration

An overview of recent advances in computational investigation of peptide–lipid interactions in neurodegeneration – Alzheimer's, Parkinson's and Huntington's disease.

Directed Supramolecular Organization of N-BAR Proteins through Regulation of H0 Membrane Immersion Depth

Many membrane remodeling events rely on the ability of curvature-generating N-BAR membrane proteins to organize into distinctive supramolecular configurations. Experiments have revealed a conformational switch in N-BAR proteins resulting in vesicular or tubular membrane shapes, with shallow membrane immersion of the H0 amphipathic helices of N-BAR proteins on vesicles but deep H0 immersion on tubes. We develop here a minimal elastic model of the local thinning of the lipid bilayer resulting from H0 immersion. Our model predicts that the observed conformational switch in N-BAR proteins produces a corresponding switch in the bilayer-mediated N-BAR interactions due to the H0 helices. In agreement with experiments, we find that bilayer-mediated H0 interactions oppose N-BAR multimerization for the shallow H0 membrane immersion depths measured on vesicles, but promote self-assembly of supramolecular N-BAR chains for the increased H0 membrane immersion depths measured on tubes. Finally, we consider the possibility that bilayer-mediated H0 interactions might contribute to the concerted structural reorganization of N-BAR proteins suggested by experiments. Our results indicate that the membrane immersion depth of amphipathic protein helices may provide a general molecular control parameter for membrane organization.

Disruptive membrane interactions of alpha-synuclein aggregates

Alpha synuclein (αS) is a ~14 kDa intrinsically disordered protein. Decades of research have increased our knowledge on αS yet its physiological function remains largely elusive. The conversion of monomeric αS into oligomers and amyloid fibrils is believed to play a central role of the pathology of Parkinson's disease (PD). It is becoming increasingly clear that the interactions of αS with cellular membranes are important for both αS's functional and pathogenic actions. Therefore, understanding interactions of αS with membranes seems critical to uncover functional or pathological mechanisms. This review summarizes our current knowledge of how physicochemical properties of phospholipid membranes affect the binding and aggregation of αS species and gives an overview of how post-translational modifications and point mutations in αS affect phospholipid membrane binding and protein aggregation. We discuss the disruptive effects resulting from the interaction of αS aggregate species with membranes and highlight current approaches and hypotheses that seek to understand the pathogenic and/or protective role of αS in PD.

Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales

At the micron scale, where cell organelles display an amazing complexity in their shape and organization, the physical properties of a biological membrane can be better-understood using continuum models subject to thermal (stochastic) undulations. Yet, the chief orchestrators of these complex and intriguing shapes are a specialized class of membrane associating often peripheral proteins called curvature remodeling proteins (CRPs) that operate at the molecular level through specific protein-lipid interactions. We review multiscale methodologies to model these systems at the molecular as well as at the mesoscopic and cellular scales, and also present a free energy perspective of membrane remodeling through the organization and assembly of CRPs. We discuss the morphological space of nearly planar to highly curved membranes, methods to include thermal fluctuations, and review studies that model such proteins as curvature fields to describe the emergent curved morphologies. We also discuss several mesoscale models applied to a variety of cellular processes, where the phenomenological parameters (such as curvature field strength) are often mapped to models of real systems based on molecular simulations. Much insight can be gained from the calculation of free energies of membranes states with protein fields, which enable accurate mapping of the state and parameter values at which the membrane undergoes morphological transformations such as vesiculation or tubulation. By tuning the strength, anisotropy, and spatial organization of the curvature-field, one can generate a rich array of membrane morphologies that are highly relevant to shapes of several cellular organelles. We review applications of these models to budding of vesicles commonly seen in cellular signaling and trafficking processes such as clathrin mediated endocytosis, sorting by the ESCRT protein complexes, and cellular exocytosis regulated by the exocyst complex. We discuss future prospects where such models can be combined with other models for cytoskeletal assembly, and discuss their role in understanding the effects of cell membrane tension and the mechanics of the extracellular microenvironment on cellular processes.

Mitochondrial dynamics in Parkinson's disease: a role for α-synuclein?

The distinctive pathological hallmarks of Parkinson's disease are the progressive death of dopaminergic neurons and the intracellular accumulation of Lewy bodies enriched in α-synuclein protein. Several lines of evidence from the study of sporadic, familial and pharmacologically induced forms of human Parkinson's disease also suggest that mitochondrial dysfunction plays an important role in disease progression. Although many functions have been proposed for α-synuclein, emerging data from human and animal models of Parkinson's disease highlight a role for α-synuclein in the control of neuronal mitochondrial dynamics. Here, we review the α-synuclein structural, biophysical and biochemical properties that influence relevant mitochondrial dynamic processes such as fusion-fission, transport and clearance. Drawing on current evidence, we propose that α-synuclein contributes to the mitochondrial defects that are associated with the pathology of this common and progressive neurodegenerative disease.

Summary: The authors review the α-synuclein structural, biophysical and biochemical properties that influence relevant mitochondrial physiological processes such as fusion-fission, transport and clearance, and propose that α-synuclein contributes to the mitochondrial defects that are associated with Parkinson's disease.

Physics of HIV

This review summarizes over a decade of investigations into how membrane-binding proteins from the HIV-1 virus interact with lipid membrane mimics various HIV and host T-cell membranes. The goal of the work was to characterize at the molecular level both the elastic and structural changes that occur due to HIV protein/membrane interactions, which could lead to new drugs to thwart the HIV virus. The main technique used to study these interactions is diffuse X-ray scattering, which yields the bending modulus, K_C, as well as structural parameters such as membrane thickness, area/lipid and position of HIV peptides (parts of HIV proteins) in the membrane. Our methods also yield information about lipid chain order or disorder caused by the peptides. This review focuses on three stages of the HIV-1 life cycle: 1) infection, 2) Tat membrane transport, and 3) budding. In the infection stage, our lab studied three different parts of HIV-1 gp41 (glycoprotein 41 fusion protein): 1) FP23, the N-terminal 23 amino acids that interact non-specifically with the T-cell host membrane to cause fusion of two membranes, and its trimer version, 2) CRAC (cholesterol recognition amino acid consensus sequence), on the MPER (membrane proximal external region) near the membrane-spanning domain, and 3) LLP2 (lentiviral lytic peptide 2) on the CTT (cytoplasmic C-terminal tail). For Tat transport, we used membrane mimics of the T-cell nuclear membrane as well as simpler models that varied charge and negative curvature. For membrane budding, we varied the myristoylation of the MA₃₁ peptide as well as the negatively charged lipid. These studies show that HIV peptides with different roles in the HIV life cycle affect differently the relevant membrane mimics. In addition, the membrane lipid composition plays an important role in the peptides' effects.