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

Dynamic Observation of the Membrane Interaction Processes of β-Lactoglobulin by Time-Resolved Vacuum-Ultraviolet Circular Dichroism

The elucidation of protein-membrane interactions is pivotal for comprehending the mechanisms underlying diverse biological phenomena and membrane-related diseases. In this investigation, vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy, utilizing synchrotron radiation (SR), was employed to dynamically observe membrane interaction processes involving water-soluble proteins at the secondary-structure level. The study utilized a time-resolved (TR) T-shaped microfluidic cell, facilitating the rapid and efficient mixing of protein and membrane solutions. This system was instrumental in acquiring measurements of the time-resolved circular dichroism (TRCD) spectra of β-lactoglobulin (bLG) during its interaction with lysoDMPG micelles. The results indicate that bLG undergoes a β-α conformation change, leading to the formation of the membrane-interacting state (M-state), with structural alterations occurring in more than two steps. Global fitting analysis, employing biexponential functions with all of the TRCD spectral data sets, yielded two distinct rate constants (0.18 ± 0.01 and 0.06 ± 0.003/s) and revealed a unique spectrum corresponding to an intermediate state (I-state). Secondary-structure analysis of bLG in its native (N-, I-, and M-states) highlighted that structural changes from the N- to I-states predominantly occurred in the N- and C-terminal regions, which were prominently exposed to the membrane. Meanwhile, transitions from the I- to M-states extended into the inner barrel regions of bLG. Further examination of the physical properties of α-helical segments, such as effective charge and hydrophobicity, revealed that the N- to I- and I- to M-state transitions, which are ascribed to first- and second-rate constants, respectively, are primarily driven by electrostatic and hydrophobic interactions, respectively. These findings underscore the capability of the TR-VUVCD system as a robust tool for characterizing protein-membrane interactions at the molecular level.

Excitation energy migration to study protein oligomerization and amyloid formation

Excitation energy migration via homo-FRET (Förster resonance energy transfer) is a unique variant of traditional FRET that involves a non-radiative energy transfer between the dipoles of two or more chemical identical fluorophores in close proximity and with an overlap between its excitation and emission spectra. Such energy migrations between chemically identical fluorophores within the Förster distance having their dipoles oriented over a wide angular spread results in the depolarization of fluorescence anisotropy depending on the local density of the fluorophores. Therefore, this methodology can be employed to study protein oligomerization and amyloid fibril formation. The conceptual framework involves extracting structural information by identifying proximal and distal locations in supramolecular assemblies by monitoring the efficiency of homo-FRET between fluorophore-conjugated protein molecules within these supramolecular assemblies. This review highlights two such cases in which excitation energy migration via homo-FRET was used to characterize the formation of membrane-mediated β-sheet rich oligomers of the prion protein as well as to construct a site-specific 2D-proximity correlation map to probe inter-residue proximities within the highly organized amyloid fibrils of α-synuclein. Energy migration studies will find applications in studying a wide range of biomolecular assemblies such as lipid-protein complexes, oligomers, amyloids, and phase-separated condensates.

New strategies for fluorescently labeling proteins in the study of amyloids

Amyloid proteins are widely studied, both for their unusual biophysical properties and their association with disorders such as Alzheimer's and Parkinson's disease. Fluorescence-based methods using site-specifically labeled proteins can provide information on the details of their structural dynamics and their roles in specific biological processes. Here, we describe the application of different labeling methods and novel fluorescent probe strategies to the study of amyloid proteins, both for in vitro biophysical experiments and for in vivo imaging. These labeling tools can be elegantly used to answer important questions on the function and pathology of amyloid proteins.

Fluorescence Depolarization Kinetics Captures Short-Range Backbone Dihedral Rotations and Long-Range Correlated Dynamics of an Intrinsically Disordered Protein

Intrinsically disordered proteins (IDPs) do not autonomously fold into well-defined three-dimensional structures and are best described as a heterogeneous ensemble of rapidly interconverting conformers. It is challenging to elucidate their complex dynamic signatures using a single technique. In this study, we employed sensitive fluorescence depolarization kinetics by following picosecond time-resolved fluorescence anisotropy decays to directly capture the essential dynamical features of intrinsically disordered α-synuclein (α-syn) site-specifically labeled with thiol-active fluorophores. By utilizing a long-lifetime (≥10 ns) anisotropic label, we were able to discern three distinct rotational components of α-syn. The subnanosecond component represents the local wobbling-in-cone motion of the fluorophore, whereas the slower (∼1.4 ns) component corresponds to the short-range backbone dynamics governed by collective torsional fluctuations in the Ramachandran Φ-Ψ dihedral space. This backbone dihedral rotational time scale is sensitive to the local chain stiffness and slows down in the presence of an adjacent proline residue. We also observed a small-amplitude (≤10%) slower rotational correlation time (6-10 ns) that represents the long-range correlated dynamics involving a much longer segment of the polypeptide chain. These intrinsic dynamic signatures of IDPs will provide critical mechanistic underpinnings in a mosaic of biophysical phenomena involving internal friction, allosteric interactions, and phase separation.

Conformation-specific perturbation of membrane dynamics by structurally distinct oligomers of Alzheimer's amyloid-β peptide

The accumulation of toxic soluble oligomers of the amyloid-β peptide (Aβ) is a key step in the pathogenesis of Alzheimer's disease. There are mainly two conformationally distinct oligomers, namely, prefibrillar and fibrillar oligomers, that are recognized by conformation-specific antibodies, anti-amyloid oligomer antibody (A11) and anti-amyloid fibrillar antibody (OC), respectively. Previous studies have shown that the interaction of Aβ oligomers with the lipid membrane is one of the key mechanisms of toxicity produced by Aβ oligomers. However, the mechanism by which structurally distinct Aβ oligomers interact with the lipid membrane remains elusive. In this work, we dissect the molecular mechanism underlying the interaction of structurally distinct Aβ42 oligomers with the lipid membrane derived from the brain total lipid extract. Using picosecond time-resolved fluorescence spectroscopy, we show that the A11-positive Aβ42 oligomers undergo a membrane-induced conformational change that promotes the deeper immersion of these oligomers into the lipid hydrocarbon region and results in an increase in the membrane micro-viscosity. In sharp contrast, OC-positive Aβ42 oligomers interact with the lipid membrane via electrostatic interactions between the negatively-charged lipid headgroup and positively-charged residues of Aβ42 without perturbing the membrane dynamics. We show that the two structurally distinct Aβ42 oligomers demonstrating different interaction mechanisms with the lipid membrane eventually lead to the formation of typical amyloid fibrils. Our findings provide the mechanistic underpinning of the perturbation of lipid membranes by two conformationally distinct Aβ42 oligomers and can be of prime importance in designing anti-Alzheimer's therapeutic agents targeting Aβ-membrane interactions.

Interaction of α-Synuclein with Phospholipids and the Associated Restructuring of Interfacial Lipid Water: An Interface-Selective Vibrational Spectroscopic Study

Interaction of α-Synuclein (αS) with biological lipids is crucial for the onset of its fibrillation at the cell membrane/water interface. Probed herein is the interaction of αS with membrane-mimicking lipid monolayer/water interfaces. The results depict that αS interacts negligibly with zwitterionic lipids, but strongly affects the pristine air/water and charged lipid/water interfaces by perturbing the structure and orientation of the interfacial water. The net negative αS (-9 in bulk water; pH 7.4) reorients the water as hydrogen-up (H-up) at the air/water interface, and electrostatically interacts with positively charged lipids, making the interface nearly net neutral. αS also interacts with negatively charged lipids: the net H-up orientation of the interfacial water decreases at the anionic lipid/water interface, revealing a domain-specific interaction of net negative αS with the negatively charged lipids at the membrane surface.

The Dynamism of Intrinsically Disordered Proteins: Binding-Induced Folding, Amyloid Formation, and Phase Separation

Intrinsically disordered proteins (IDPs) or natively unfolded proteins do not undergo autonomous folding into a well-defined 3-D structure and challenge the conventional structure-function paradigm. They are involved in a multitude of critical physiological functions by adopting various structural states via order-to-disorder transitions or by maintaining their disordered characteristics in functional complexes. In recent times, there has been a burgeoning interest in the investigation of intriguing behavior of IDPs using highly multidisciplinary and complementary approaches due to the pivotal role of this unique class of protein chameleons in physiology and disease. Over the past decade or so, our laboratory has been actively investigating the unique physicochemical properties of this class of highly dynamic, flexible, rapidly interconverting proteins. We have utilized a diverse array of existing and emerging tools involving steady-state and time-resolved fluorescence, Raman spectroscopy, circular dichroism, light scattering, fluorescence microscopy, and atomic force microscopy coupled with site-directed mutagenesis and other biochemical and biophysical tools to study a variety of interesting and important aspects of IDPs. In this Feature Article, I describe our work on the conformational characteristics, solvation dynamics, binding-induced folding, amyloid formation, and liquid-liquid phase separation of a number of amyloidogenic IDPs. A series of these studies described here captures the role of conformational plasticity and dynamics in directing binding, folding, assembly, aggregation, and phase transitions implicated in physiology and pathology.