Local and Global Dynamics in Intrinsically Disordered Synuclein

Sensitivity-enhanced NMR 15N R1 and R1ρ relaxation experiments for the investigation of intrinsically disordered proteins at high magnetic fields

NMR relaxation experiments provide residue-specific insights into the structural dynamics of proteins. Here, we present an optimized set of sensitivity-enhanced 15N R1 and R1ρ relaxation experiments applicable to fully protonated proteins. The NMR pulse sequences are conceptually similar to the set of TROSY-based sequences and their HSQC counterpart (Lakomek et al., J. Biomol. NMR 2012). Instead of the TROSY read-out scheme, a sensitivity-enhanced HSQC read-out scheme is used, with improved and easier optimized water suppression. The presented pulse sequences are applied on the cytoplasmic domain of the SNARE protein Synpatobrevin-2 (Syb-2), which is intrinsically disordered in its monomeric pre-fusion state. A two-fold increase in the obtained signal-to-noise ratio is observed for this intrinsically disordered protein, therefore offering a four-fold reduction of measurement time compared to the TROSY-detected version. The inter-scan recovery delay can be shortened to two seconds. Pulse sequences were tested at 600 MHz and 1200 MHz 1H Larmor frequency, thus applicable over a wide magnetic field range. A comparison between protonated and deuterated protein samples reveals high agreement, indicating that reliable 15N R1 and R1ρ rate constants can be extracted for fully protonated and deuterated samples. The presented pulse sequences will benefit not only for IDPs but also for an entire range of low and medium-sized proteins.

Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations

Peptides or proteins containing small biomolecular aggregates, such as micelles, bicelles, droplets and nanodiscs, are pivotal in many fields ranging from structural biology to pharmaceutics. Monitoring dynamics of such systems has been limited by the lack of experimental methods that could directly detect their fast (picosecond to nanosecond) timescale dynamics. Spin relaxation times from NMR experiments are sensitive to such motions, but their interpretation for biomolecular aggregates is not straightforward. Here we show that the dynamic landscape of peptide-containing molecular assemblies can be determined by a synergistic combination of solution state NMR experiments and molecular dynamics (MD) simulations. Solution state NMR experiments are straightforward to implement without an excessive amount of sample, while direct combination of spin relaxation data to MD simulations enables interpretation of dynamic landscapes of peptides and other aggregated molecules. To demonstrate this, we interpret NMR data from transmembrane, peripheral, and tail anchored peptides embedded in micelles. Our results indicate that peptides and detergent molecules do not rotate together as a rigid body, but peptides rotate in a viscous medium composed of detergent micelle. Spin relaxation times also provide indirect information on peptide conformational ensembles. This work gives new perspectives on peptide dynamics in complex biomolecular assemblies.

Nuclear magnetic resonance/single molecule fluorescence combinations to study dynamic protein systems

Many proteins require different structural states or conformations for function, and intrinsically disordered proteins, i.e. proteins without stable three-dimensional structure, are certainly an extreme. Single molecule fluorescence and nuclear magnetic resonance (NMR) spectroscopy are both exceptionally well suited to decipher and describe these states and their interconversion. Different time scales, from picoseconds to several milliseconds, can be addressed by both techniques. The length scales probed and the sample requirements (e.g. concentration, molecular weight, sample complexity) are, however, vastly different, making NMR and single molecule fluorescence an excellent combination for integrated studies. Here, we review recently undertaken approaches for the combined use of NMR and single molecule fluorescence to study protein dynamics.

Exploring Intra- and Inter-Regional Interactions in the IDP α-Synuclein Using smFRET and MD Simulations

Theoretical concepts from polymer physics are often used to describe intrinsically disordered proteins (IDPs). However, amino acid interactions within and between regions of the protein can lead to deviations from typical polymer scaling behavior and even to short-lived secondary structures. To investigate the key interactions in the dynamic IDP α-synuclein (αS) at the amino acid level, we conducted single-molecule fluorescence resonance energy transfer (smFRET) experiments and coarse-grained molecular dynamics (CG-MD) simulations. We find excellent agreement between experiments and simulations. Our results show that a physiological salt solution is a good solvent for αS and that the protein is highly dynamic throughout its entire chain, with local intra- and inter-regional interactions leading to deviations from global scaling. Specifically, we observe expansion in the C-terminal region, compaction in the NAC region, and a slightly smaller distance between the C- and N-termini than expected. Our simulations indicate that the compaction in the NAC region results from hydrophobic aliphatic contacts, mostly between valine and alanine residues, and cation-π interactions between lysine and tyrosine. In addition, hydrogen bonds also seem to contribute to the compaction of the NAC region. The expansion of the C-terminal region is due to intraregional electrostatic repulsion and increased chain stiffness from several prolines. Overall, our study demonstrates the effectiveness of combining smFRET experiments with CG-MD simulations to investigate the key interactions in highly dynamic IDPs at the amino acid level.

Fast Motions Dominate Dynamics of Intrinsically Disordered Tau Protein at High Temperatures

Reorientational dynamics of intrinsically disordered proteins (IDPs) contain multiple motions often clustered around three motional modes: ultrafast librational motions of amide groups, fast local backbone conformational fluctuations and slow chain segmental motions. This dynamic picture is mainly based on ¹⁵ N NMR relaxation studies of IDPs at relatively low temperatures where the amide-water proton exchange rates are sufficiently small. Less is known, however, about the dynamics of IDPs at more physiological temperatures. Here, we investigate protein dynamics in a 441-residue long IDP, tau protein, in the temperature range from 0-25 °C, using ¹⁵ N NMR relaxation rates and spectral density analysis. While at these temperatures relaxation rates are still better described in terms of amide group librational motions, local backbone dynamics and chain segmental motions, the temperature-dependent trend of spectral densities suggests that the timescales of fast backbone conformational fluctuations and slower chain segmental motions might become inseparable at higher temperatures. Our data demonstrate the remarkable dynamic plasticity of this prototypical IDP and highlight the need for dynamic studies of IDPs at multiple temperatures.

Concerted enhanced-sampling simulations to elucidate the helix-fibril transition pathway of intrinsically disordered α-Synuclein

Fibril formation of α-synuclein is linked with Parkinson's disease. The intrinsically disordered nature of α-syn provides extensive conformational plasticity and becomes difficult to characterize its transition pathway from native monomeric to disease-associated fibril form. We implemented different simulation methods such as steered dynamics-umbrella sampling, and replica-exchange and conventional MD simulations to access various conformational states of α-syn. Nineteen distinct intermediate structures were identified by free energy landscape and cluster analysis. They were then sorted based on secondary structure and solvent exposure of fibril-core residues to illustrate the fibril dissociation pathway. The analysis showed that following the initial dissociation of the polypeptide chain from the fibril, α-syn might form either compact-conformations by long-range interactions or extended-conformations stabilized by local interactions. This leads α-syn to adapt two different pathways. The secondary structure, solvation, contact distance, interaction energies and backbone dihedrals of thirty-two selected residues were analyzed for all the 19 intermediates. The results suggested that formation of β-turns, reorganization of salt bridges, and dihedral changes in the hydrophobic regions are the major driving forces for helix-fibril transition. Structural features of the intermediates also correlated with the earlier experimental and computational studies. The study provides critical information on the fibrillation pathway of α-syn.

The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy

Intrinsically disordered proteins (IDPs) and regions (IDRs) have emerged as key players across many biological functions and diseases. Differently from structured proteins, disordered proteins lack stable structure and are particularly sensitive to changes in the surrounding environment. Investigation of disordered ensembles requires new approaches and concepts for quantifying conformations, dynamics, and interactions. Here, we provide a short description of the fundamental biophysical properties of disordered proteins as understood through the lens of single-molecule fluorescence observations. Single-molecule Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) provides an extensive and versatile toolbox for quantifying the characteristics of conformational distributions and the dynamics of disordered proteins across many different solution conditions, both in vitro and in living cells.

Polyphenols-Based Nanosheets of Propolis Modulate Cytotoxic Amyloid Fibril Assembly of α-Synuclein

Natural compounds with anti-aggregation capacity are increasingly recognized as viable candidates against neurodegenerative diseases. Recently, the polyphenolic fraction of propolis (PFP), a complex bee product, has been shown to inhibit amyloid aggregation of a model protein especially in the nanosheet form. Here, we examine the aggregation-modulating effects of the PFP nanosheets on α-synuclein (α-syn), an intrinsically disordered protein involved in the pathogenesis of Parkinson's disease. Based on a range of biophysical data including intrinsic and extrinsic fluorescence, circular dichroism (CD) data, and nuclear magnetic resonance spectroscopy, we propose a model for the interaction of α-syn with PFP nanosheets, where the positively charged N-terminal and the middle non-amyloid component regions of α-syn act as the main binding sites with the negatively charged PFP nanosheets. The Thioflavin T (ThT) fluorescence, Congo red absorbance, and CD data reveal a prominent dose-dependent inhibitory effect of PFP nanosheets on α-syn amyloid aggregation, and the microscopy images and MTT assay data suggest that the PFP nanosheets redirect α-syn aggregation toward nontoxic off-pathway oligomers. When preformed α-syn amyloid fibrils are present, fluorescence images show co-localization of PFP nanosheets and ThT, further confirming the binding of PFP nanosheets with α-syn amyloid fibrils. Taken together, our results demonstrate the binding and anti-aggregation activity of PFP nanosheets in a disease-related protein system and propose them as potential nature-based tools for probing and targeting pathological protein aggregates in neurodegenerative diseases.

Structure and Transition Dynamics of Intrinsically Disordered Proteins Probed by Single-Molecule Spectroscopy

Intrinsically disordered proteins (IDPs) are a class of proteins that do not follow the unanimated perspective of the structure-function paradigm. IDPs enunciate the dynamics of motions which are often difficult to characterize by a particular experimental or theoretical approach. The chameleon nature of the IDPs is a result of an alteration or transition in their conformation upon binding with ligands. Experimental investigations via ensemble-average approaches to probe this randomness are often difficult to synchronize. Thus, to sense the substates of different conformational ensembles of IDPs, researchers have often targeted approaches based on single-molecule measurements. In this Perspective, we will discuss various single-molecule approaches to explore the conformational transitions of IDPs in different scenarios, the outcome, challenges, and future prospects.

Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins

For intrinsically disordered proteins (IDPs), a pressing question is how sequence codes for function. Dynamics serves as a crucial link, reminiscent of the role of structure in sequence-function relations of structured proteins. To define general rules governing sequence-dependent backbone dynamics, we carried out long molecular dynamics simulations of eight IDPs. Blocks of residues exhibiting large amplitudes in slow dynamics are rigidified by local inter-residue interactions or secondary structures. A long region or an entire IDP can be slowed down by long-range contacts or secondary-structure packing. On the other hand, glycines promote fast dynamics and either demarcate rigid blocks or facilitate multiple modes of local and long-range inter-residue interactions. The sequence-dependent backbone dynamics endows IDPs with versatile response to binding partners, with some blocks recalcitrant while others readily adapting to intermolecular interactions.

Identification and quantification of within-burst dynamics in singly labeled single-molecule fluorescence lifetime experiments

Single-molecule spectroscopy has revolutionized molecular biophysics and provided means to probe how structural moieties within biomolecules spatially reorganize at different timescales. There are several single-molecule methodologies that probe local structural dynamics in the vicinity of a single dye-labeled residue, which rely on fluorescence lifetimes as readout. Nevertheless, an analytical framework to quantify dynamics in such single-molecule single dye fluorescence bursts, at timescales of microseconds to milliseconds, has not yet been demonstrated. Here, we suggest an analytical framework for identifying and quantifying within-burst lifetime-based dynamics, such as conformational dynamics recorded in single-molecule photo-isomerization-related fluorescence enhancement. After testing the capabilities of the analysis on simulations, we proceed to exhibit within-burst millisecond local structural dynamics in the unbound α-synuclein monomer. The analytical framework provided in this work paves the way for extracting a full picture of the energy landscape for the coordinate probed by fluorescence lifetime-based single-molecule measurements.

Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) are highly dynamic systems that play an important role in cell signaling processes and their misfunction often causes human disease. Proper understanding of IDP function not only requires the realistic characterization of their three-dimensional conformational ensembles at atomic-level resolution but also of the time scales of interconversion between their conformational substates. Large sets of experimental data are often used in combination with molecular modeling to restrain or bias models to improve agreement with experiment. It is shown here for the N-terminal transactivation domain of p53 (p53TAD) and Pup, which are two IDPs that fold upon binding to their targets, how the latest advancements in molecular dynamics (MD) simulations methodology produces native conformational ensembles by combining replica exchange with series of microsecond MD simulations. They closely reproduce experimental data at the global conformational ensemble level, in terms of the distribution properties of the radius of gyration tensor, and at the local level, in terms of NMR properties including 15N spin relaxation, without the need for reweighting. Further inspection revealed that 10-20% of the individual MD trajectories display the formation of secondary structures not observed in the experimental NMR data. The IDP ensembles were analyzed by graph theory to identify dominant inter-residue contact clusters and characteristic amino-acid contact propensities. These findings indicate that modern MD force fields with residue-specific backbone potentials can produce highly realistic IDP ensembles sampling a hierarchy of nano- and picosecond time scales providing new insights into their biological function.

Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins

The most commonly occurring intrinsically disordered proteins (IDPs) are polyampholytes, which are defined by the duality of low net charge per residue and high fractions of charged residues. Recent experiments have uncovered nuances regarding sequence–ensemble relationships of model polyampholytic IDPs. These include differences in conformational preferences for sequences with lysine vs. arginine and the suggestion that well-mixed sequences form a range of conformations, including globules, conformations with ensemble averages that are reminiscent of ideal chains, or self-avoiding walks. Here, we explain these observations by analyzing results from atomistic simulations. We find that polyampholytic IDPs generally sample two distinct stable states, namely, globules and self-avoiding walks. Globules are favored by electrostatic attractions between oppositely charged residues, whereas self-avoiding walks are favored by favorable free energies of hydration of charged residues. We find sequence-specific temperatures of bistability at which globules and self-avoiding walks can coexist. At these temperatures, ensemble averages over coexisting states give rise to statistics that resemble ideal chains without there being an actual counterbalancing of intrachain and chain-solvent interactions. At equivalent temperatures, arginine-rich sequences tilt the preference toward globular conformations whereas lysine-rich sequences tilt the preference toward self-avoiding walks. We also identify differences between aspartate- and glutamate-containing sequences, whereby the shorter aspartate side chain engenders preferences for metastable, necklace-like conformations. Finally, although segregation of oppositely charged residues within the linear sequence maintains the overall two-state behavior, compact states are highly favored by such systems.

Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure

The paradigmatic disordered protein tau plays an important role in neuronal function and neurodegenerative diseases. To disentangle the factors controlling the balance between functional and disease-associated conformational states, we build a structural ensemble of the tau K18 fragment containing the four pseudorepeat domains involved in both microtubule binding and amyloid fibril formation. We assemble 129-residue-long tau K18 chains with atomic detail from an extensive fragment library constructed with molecular dynamics simulations. We introduce a reweighted hierarchical chain growth (RHCG) algorithm that integrates experimental data reporting on the local structure into the assembly process in a systematic manner. By combining Bayesian ensemble refinement with importance sampling, we obtain well-defined ensembles and overcome the problem of exponentially varying weights in the integrative modeling of long-chain polymeric molecules. The resulting tau K18 ensembles capture nuclear magnetic resonance (NMR) chemical shift and J-coupling measurements. Without further fitting, we achieve very good agreement with measurements of NMR residual dipolar couplings. The good agreement with experimental measures of global structure such as single-molecule Förster resonance energy transfer (FRET) efficiencies is improved further by ensemble refinement. By comparing wild-type and mutant ensembles, we show that pathogenic single-point P301L, P301S, and P301T mutations shift the population from the turn-like conformations of the functional microtubule-bound state to the extended conformations of disease-associated tau fibrils. RHCG thus provides us with an atomically detailed view of the population equilibrium between functional and aggregation-prone states of tau K18, and demonstrates that global structural characteristics of this intrinsically disordered protein emerge from its local structure.

Single-molecule Detection of Ultrafast Biomolecular Dynamics with Nanophotonics

Single-molecule Förster resonance energy transfer (FRET) is a versatile technique for probing the structure and dynamics of biomolecules even in heterogeneous ensembles. However, because of the limited fluorescence brightness per molecule and the relatively long fluorescence lifetimes, probing ultrafast structural dynamics in the nanosecond time scale has thus far been very challenging. Here, we demonstrate that nanophotonic fluorescence enhancement in zero-mode waveguides enables measurements of previously inaccessible low-nanosecond dynamics by dramatically improving time resolution and reduces data acquisition times by more than an order of magnitude. As a prototypical example, we use this approach to probe the dynamics of a short intrinsically disordered peptide that were previously inaccessible with single-molecule FRET measurements. We show that we are now able to detect the low-nanosecond correlations in this peptide, and we obtain a detailed interpretation of the underlying distance distributions and dynamics in conjunction with all-atom molecular dynamics simulations, which agree remarkably well with the experiments. We expect this combined approach to be widely applicable to the investigation of very rapid biomolecular dynamics.

Synergies of Single Molecule Fluorescence and NMR for the Study of Intrinsically Disordered Proteins

Single molecule fluorescence and nuclear magnetic resonance spectroscopy (NMR) are two very powerful techniques for the analysis of intrinsically disordered proteins (IDPs). Both techniques have individually made major contributions to deciphering the complex properties of IDPs and their interactions, and it has become evident that they can provide very complementary views on the distance-dynamics relationships of IDP systems. We now review the first approaches using both NMR and single molecule fluorescence to decipher the molecular properties of IDPs and their interactions. We shed light on how these two techniques were employed synergistically for multidomain proteins harboring intrinsically disordered linkers, for veritable IDPs, but also for liquid–liquid phase separated systems. Additionally, we provide insights into the first approaches to use single molecule Förster resonance energy transfer (FRET) and NMR for the description of multiconformational models of IDPs.

When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes

The degree of proteins structural organization ranges from highly structured, compact folding to intrinsic disorder, where each degree of self-organization corresponds to specific functions: well-organized structural motifs in enzymes offer a proper environment for precisely positioned functional groups to participate in catalytic reactions; at the other end of the self-organization spectrum, intrinsically disordered proteins act as binding hubs via the formation of multiple, transient and often non-specific interactions. This review focusses on cases where structurally organized proteins or domains associate with highly disordered protein chains, leading to the formation of interfaces with varying degrees of fuzziness. We present a review of the computational methods developed to provide us with information on such fuzzy interfaces, and how they integrate experimental information. The discussion focusses on two specific cases, microtubules and homologous recombination nucleoprotein filaments, where a network of intrinsically disordered tails exerts regulatory function in recruiting partner macromolecules, proteins or DNA and tuning the atomic level association. Notably, we show how computational approaches such as molecular dynamics simulations can bring new knowledge to help bridging the gap between experimental analysis, that mostly concerns ensemble properties, and the behavior of individual disordered protein chains that contribute to regulation functions.

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.

Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins

Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have emerged from a niche corner of biophysics to be recognized as essential drivers of cellular function. Various techniques have provided fundamental insight into the function and dysfunction of IDRs. Among these techniques, single-molecule fluorescence spectroscopy and molecular simulations have played a major role in shaping our modern understanding of the sequence-encoded conformational behavior of disordered proteins. While both techniques are frequently used in isolation, when combined they offer synergistic and complementary information that can help uncover complex molecular details. Here we offer an overview of single-molecule fluorescence spectroscopy and molecular simulations in the context of studying disordered proteins. We discuss the various means in which simulations and single-molecule spectroscopy can be integrated, and consider a number of studies in which this integration has uncovered biological and biophysical mechanisms.

Advanced fluorescence correlation spectroscopy for studying biomolecular conformation

We present the recent developments and advances in fluorescence correlation spectroscopy (FCS) and their application to the investigation of biomolecular conformations. In particular, we present and discuss three techniques: multichannel nanosecond FCS, photo-induced electron transfer FCS, and fluorescence lifetime correlation spectroscopy. We briefly describe each method and discuss recent applications to diverse biophysical studies of biomolecular conformation.

Transient Tertiary Structures of Disordered Dynein Intermediate Chain Regulate its Interactions with Multiple Partners

The N-terminal domain of dynein intermediate chain (N-IC) is central to the cytoplasmic dynein 'cargo attachment subcomplex' and regulation of motor activity. It is a prototypical intrinsically disordered protein (IDP), serving as a primarily disordered polybivalent molecular scaffold for numerous binding partners, including three dimeric dynein light chains and coiled coil domains of dynein partners dynactin p150^Glued and NudE. At the very N-terminus, a 40 amino acid single alpha helix (SAH) forms the major binding site for both p150^Glued and NudE, while a shorter nascent helix (H2) separated from SAH by a disordered linker, is necessary for tight binding to dynactin p150^Glued but not to NudE. Here we demonstrate that transient tertiary interactions in this highly dynamic protein underlie the differences in its interactions with p150^Glued and NudE. NMR paramagnetic relaxation enhancement experiments and restrained molecular dynamics simulations identify interactions between the two non-contiguous SAH and H2 helical regions, the extent of which correlates with the length and stability of H2, showing clearly that tertiary and secondary structure formation are coupled in IDPs. These interactions are significantly attenuated when N-IC is bound to NudE, suggesting that NudE binding shifts the conformational ensemble to one that is more extended and with less structure in H2. While the intrinsic disorder and flexibility in N-IC modulate its ability to serve as a binding platform for numerous partners, deviations of this protein from random-coil behavior provide a process for regulating these binding interactions and potentially the dynein motor.

Unveiling protein dynamics in solution with field-cycling NMR relaxometry

Field-cycling NMR relaxometry is a well-established technique that can give information on molecular structure and dynamics of biological systems. It provides the nuclear relaxation rates as a function of the applied magnetic field, starting from fields as low as ~ 10^-4 T up to about 1-3 T. The profiles so collected, called nuclear magnetic relaxation dispersion (NMRD) profiles, can be extended to include the relaxation rates at the largest fields achievable with high resolution NMR spectrometers. By exploiting this wide range of frequencies, the NMRD profiles can provide information on motions occurring on time scales from 10^-6 to 10^-9 s. ¹H NMRD measurements have proved very useful also for the characterization of paramagnetic proteins, because they can help characterise a number of parameters including the number, distance and residence time of water molecules coordinated to the paramagnetic center, the reorientation correlation times and the electron spin relaxation time, and the electronic structure at the metal site.

NMR illuminates intrinsic disorder

Nuclear magnetic resonance (NMR) has long been instrumental in the characterization of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs). This method continues to offer rich insights into the nature of IDPs in solution, especially in combination with other biophysical methods such as small-angle scattering, single-molecule fluorescence, electron paramagnetic resonance (EPR), and mass spectrometry. Substantial advances have been made in recent years in studies of proteins containing both ordered and disordered domains and in the characterization of problematic sequences containing repeated tracts of a single or a few amino acids. These sequences are relevant to disease states such as Alzheimer's, Parkinson's, and Huntington's diseases, where disordered proteins misfold into harmful amyloid. Innovative applications of NMR are providing novel insights into mechanisms of protein aggregation and the complexity of IDP interactions with their targets. As a basis for understanding the solution structural ensembles, dynamic behavior, and functional mechanisms of IDPs and IDRs, NMR continues to prove invaluable.

Insights into the molecular mechanism of amyloid filament formation: Segmental folding of α-synuclein on lipid membranes

Recent advances in the structural biology of disease-relevant α-synuclein fibrils have revealed a variety of structures, yet little is known about the process of fibril aggregate formation. Characterization of intermediate species that form during aggregation is crucial; however, this has proven very challenging because of their transient nature, heterogeneity, and low population. Here, we investigate the aggregation of α-synuclein bound to negatively charged phospholipid small unilamellar vesicles. Through a combination of kinetic and structural studies, we identify key time points in the aggregation process that enable targeted isolation of prefibrillar and early fibrillar intermediates. By using solid-state nuclear magnetic resonance, we show the gradual buildup of structural features in an α-synuclein fibril filament, revealing a segmental folding process. We identify distinct membrane-binding domains in α-synuclein aggregates, and the combined data are used to present a comprehensive mechanism of the folding of α-synuclein on lipid membranes.

Hyperphosphorylation of Human Osteopontin and Its Impact on Structural Dynamics and Molecular Recognition

Protein phosphorylation is an abundant post-translational modification (PTM) and an essential modulator of protein functionality in living cells. Intrinsically disordered proteins (IDPs) are particular targets of PTM protein kinases due to their involvement in fundamental protein interaction networks. Despite their dynamic nature, IDPs are far from having random-coil conformations but exhibit significant structural heterogeneity. Changes in the molecular environment, most prominently in the form of PTM via phosphorylation, can modulate these structural features. Therefore, how phosphorylation events can alter conformational ensembles of IDPs and their interactions with binding partners is of great interest. Here we study the effects of hyperphosphorylation on the IDP osteopontin (OPN), an extracellular target of the Fam20C kinase. We report a full characterization of the phosphorylation sites of OPN using a combined nuclear magnetic resonance/mass spectrometry approach and provide evidence for an increase in the local flexibility of highly phosphorylated regions and the ensuing overall structural elongation. Our study emphasizes the simultaneous importance of electrostatic and hydrophobic interactions in the formation of compact substates in IDPs and their relevance for molecular recognition events.

Atomic Resolution Map of Hierarchical Self-Assembly for an Amyloidogenic Protein Probed through Thermal 15N-R2 Correlation Matrices

Soluble oligomers formed by amyloidogenic intrinsically disordered proteins are some of the most cytotoxic species linked to neurodegeneration. Due to the transient and heterogeneous nature of such oligomeric intermediates, the underlying self-association events often remain elusive. NMR relaxation measurements sensitive to zero-frequency spectral densities (J(0)), such as the ¹⁵N - R₂ rates, are ideally suited to map sites of self-association at atomic resolution without the need of exogenous labels. Such experiments exploit the dynamic exchange between NMR visible monomers and slowly tumbling oligomers. However,¹⁵N - R₂ rates are also sensitive to intrinsic monomer dynamics, and it is often difficult to discern these contributions from those arising from exchange with oligomers. Another challenge pertains to defining a hierarchy of self-association. Here, using the archetypical amyloidogenic protein alpha synuclein (αS), we show that the temperature-dependence of ¹⁵N - R₂ effectively identifies self-association sites with reduced bias from internal dynamics. The key signature of the residues involved in self-association is a nonlinear temperature-dependence of ¹⁵N - R₂ with a positive ΔR₂/ΔT slope. These two hallmarks are systematically probed through a thermal R₂ correlation matrix, from which the network of residues involved in self-association as well as the hierarchy of αS self-association sites is extracted through agglomerative clustering. We find that aggregation is initiated by residues within the NAC region that is solvent inaccessible in αS fibrils and eventually extends to the N-terminal segment harboring familial PD mutations. These hierarchical self-association maps help dissect the essential drivers of oligomerization and reveal how amyloid inhibitors affect oligomer formation.

Heterogeneous dynamics in partially disordered proteins

Importance of disordered protein regions is increasingly recognized in biology, but their characterization remains challenging due to the lack of suitable experimental and theoretical methods. NMR experiments can detect multiple timescale dynamics and structural details of disordered protein regions, but their detailed interpretation is often difficult. Here we combine protein backbone 15N spin relaxation data with molecular dynamics (MD) simulations to detect not only heterogeneous dynamics of large partially disordered proteins but also their conformational ensembles. We observed that the rotational dynamics of folded regions in partially disordered proteins is dominated by similar rigid body rotation as in globular proteins, thereby being largely independent of flexible disordered linkers. Disordered regions, on the other hand, exhibit complex rotational motions with multiple timescales below ∼30 ns which are difficult to detect from experimental data alone, but can be captured by MD simulations. Combining MD simulations and backbone 15N spin relaxation data, measured applying segmental isotopic labeling with salt-inducible split intein, we resolved the conformational ensemble and dynamics of partially disordered periplasmic domain of TonB protein from Helicobacter pylori containing 250 residues. To demonstrate the universality of our approach, it was applied also to the partially disordered region of chicken Engrailed 2. Our results pave the way in understanding how TonB transfers energy from inner membrane to the outer membrane receptors in Gram-negative bacteria, as well as the function of other proteins with disordered domains.

Sequence-Dependent Correlated Segments in the Intrinsically Disordered Region of ChiZ

How sequences of intrinsically disordered proteins (IDPs) code for their conformational dynamics is poorly understood. Here, we combined NMR spectroscopy, small-angle X-ray scattering (SAXS), and molecular dynamics (MD) simulations to characterize the conformations and dynamics of ChiZ1-64. MD simulations, first validated by SAXS and secondary chemical shift data, found scant α-helices or β-strands but a considerable propensity for polyproline II (PPII) torsion angles. Importantly, several blocks of residues (e.g., 11–29) emerge as “correlated segments”, identified by their frequent formation of PPII stretches, salt bridges, cation-π interactions, and sidechain-backbone hydrogen bonds. NMR relaxation experiments showed non-uniform transverse relaxation rates (R₂s) and nuclear Overhauser enhancements (NOEs) along the sequence (e.g., high R₂s and NOEs for residues 11–14 and 23–28). MD simulations further revealed that the extent of segmental correlation is sequence-dependent; segments where internal interactions are more prevalent manifest elevated “collective” motions on the 5–10 ns timescale and suppressed local motions on the sub-ns timescale. Amide proton exchange rates provides corroboration, with residues in the most correlated segment exhibiting the highest protection factors. We propose the correlated segment as a defining feature for the conformations and dynamics of IDPs.

Advances in studying protein disorder with solid-state NMR

Solution NMR is a key tool to study intrinsically disordered proteins (IDPs), whose importance for biological function is widely accepted. However, disordered proteins are not limited to solution and are also found in non-soluble systems such as fibrils and membrane proteins. In this Trends article, I will discuss how solid-state NMR can be used to study disorder in non-soluble proteins. Techniques based on dipolar couplings can study static protein disorder which either occurs naturally as e.g. in spider silk or can be induced by freeze trapping IDPs or unfolded proteins. In this case, structural ensembles are directly reflected by a static distribution of dihedral angels that can be determined by the distribution of chemical shifts or other methods. Techniques based on J-couplings can detect dynamic protein disorder under MAS. In this case, only average chemical shifts are measured but disorder can be characterized with a variety of data including secondary chemical shifts, relaxation rates, paramagnetic relaxation enhancements, or residual dipolar couplings. I describe both technical aspects and examples of solid-state NMR on protein disorder and end the article with a discussion of challenges and opportunities of this emerging field.

Salient Features of Monomeric Alpha-Synuclein Revealed by NMR Spectroscopy

Elucidating the structural details of proteins is highly valuable and important for the proper understanding of protein function. In the case of intrinsically disordered proteins (IDPs), however, obtaining the structural details is quite challenging, as the traditional structural biology tools have only limited use. Nuclear magnetic resonance (NMR) is a unique experimental tool that provides ensemble conformations of IDPs at atomic resolution, and when studying IDPs, a slightly different experimental strategy needs to be employed than the one used for globular proteins. We address this point by reviewing many NMR investigations carried out on the α-synuclein protein, the aggregation of which is strongly correlated with Parkinson’s disease.

Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations

Intrinsically disordered proteins (IDPs) constitute a large fraction of the human proteome and are critical in the regulation of cellular processes. A detailed understanding of the conformational dynamics of IDPs could help to elucidate their roles in health and disease. However, the inherent flexibility of IDPs makes structural studies and their interpretation challenging. Molecular dynamics (MD) simulations could address this challenge in principle, but inaccuracies in the simulation models and the need for long simulations have stymied progress. To overcome these limitations, we adopt a hierarchical approach that builds on the "flexible-meccano" model reported by Bernadó et al. (J. Am. Chem. Soc. 2005, 127, 17968-17969). First, we exhaustively sample small IDP fragments in all-atom simulations to capture their local structures. Then, we assemble the fragments into full-length IDPs to explore the stereochemically possible global structures of IDPs. The resulting ensembles of three-dimensional structures of full-length IDPs are highly diverse, much more so than in standard MD simulation. For the paradigmatic IDP α-synuclein, our ensemble captures both the local structure, as probed by nuclear magnetic resonance spectroscopy, and its overall dimension, as obtained from small-angle X-ray scattering in solution. By generating representative and meaningful starting ensembles, we can begin to exploit the massive parallelism afforded by current and future high-performance computing resources for atomic-resolution characterization of IDPs.

The Ambivalent Role of Proline Residues in an Intrinsically Disordered Protein: From Disorder Promoters to Compaction Facilitators

Intrinsically disordered proteins (IDPs) carry out many biological functions. They lack a stable three-dimensional structure, but rather adopt many different conformations in dynamic equilibrium. The interplay between local dynamics and global rearrangements is key for their function. In IDPs, proline residues are significantly enriched. Given their unique physicochemical and structural properties, a more detailed understanding of their potential role in stabilizing partially folded states in IDPs is highly desirable. Nuclear magnetic resonance (NMR) spectroscopy, and in particular ¹³C-detected NMR, is especially suitable to address these questions. We applied a ¹³C-detected strategy to study Osteopontin, a largely disordered IDP with a central compact region. By using the exquisite sensitivity and spectral resolution of these novel techniques, we gained unprecedented insight into cis-Pro populations, their local structural dynamics, and their role in mediating long-range contacts. Our findings clearly call for a reassessment of the structural and functional role of proline residues in IDPs. The emerging picture shows that proline residues have ambivalent structural roles. They are not simply disorder promoters but rather can, depending on the primary sequence context, act as nucleation sites for structural compaction in IDPs. These unexpected features provide a versatile mechanistic toolbox to enrich the conformational ensembles of IDPs with specific features for adapting to changing molecular and cellular environments.

Depicting Conformational Ensembles of α-Synuclein by Single Molecule Force Spectroscopy and Native Mass Spectroscopy

Description of heterogeneous molecular ensembles, such as intrinsically disordered proteins, represents a challenge in structural biology and an urgent question posed by biochemistry to interpret many physiologically important, regulatory mechanisms. Single-molecule techniques can provide a unique contribution to this field. This work applies single molecule force spectroscopy to probe conformational properties of α-synuclein in solution and its conformational changes induced by ligand binding. The goal is to compare data from such an approach with those obtained by native mass spectrometry. These two orthogonal, biophysical methods are found to deliver a complex picture, in which monomeric α-synuclein in solution spontaneously populates compact and partially compacted states, which are differently stabilized by binding to aggregation inhibitors, such as dopamine and epigallocatechin-3-gallate. Analyses by circular dichroism and Fourier-transform infrared spectroscopy show that these transitions do not involve formation of secondary structure. This comparative analysis provides support to structural interpretation of charge-state distributions obtained by native mass spectrometry and helps, in turn, defining the conformational components detected by single molecule force spectroscopy.

A facile oxygen-17 NMR method to determine effective viscosity in dilute, molecularly crowded and confined aqueous media

We present an NMR method based on natural abundance 17O relaxation of water to determine effective viscosity in biological aqueous samples. The method accurately captures viscosity of dilute and crowded protein solutions and offers a fairly simple way to quantify the internal fluidity of biological condensates formed through phase separation.

NMR characterization of solvent accessibility and transient structure in intrinsically disordered proteins

In order to understand the conformational behavior of intrinsically disordered proteins (IDPs) and their biological interaction networks, the detection of residual structure and long-range interactions is required. However, the large number of degrees of conformational freedom of disordered proteins require the integration of extensive sets of experimental data, which are difficult to obtain. Here, we provide a straightforward approach for the detection of residual structure and long-range interactions in IDPs under near-native conditions using solvent paramagnetic relaxation enhancement (sPRE). Our data indicate that for the general case of an unfolded chain, with a local flexibility described by the overwhelming majority of available combinations, sPREs of non-exchangeable protons can be accurately predicted through an ensemble-based fragment approach. We show for the disordered protein α-synuclein and disordered regions of the proteins FOXO4 and p53 that deviation from random coil behavior can be interpreted in terms of intrinsic propensity to populate local structure in interaction sites of these proteins and to adopt transient long-range structure. The presented modification-free approach promises to be applicable to study conformational dynamics of IDPs and other dynamic biomolecules in an integrative approach.

Reorientational Dynamics of Amyloid-β from NMR Spin Relaxation and Molecular Simulation

Amyloid-β (Aβ) aggregation is a hallmark of Alzheimer's disease. As an intrinsically disordered protein, Aβ undergoes extensive dynamics on multiple length and time scales. Access to a comprehensive picture of the reorientational dynamics in Aβ requires therefore the combination of complementary techniques. Here, we integrate ¹⁵N spin relaxation rates at three magnetic fields with microseconds-long molecular dynamics simulation, ensemble-based hydrodynamic calculations, and previously published nanosecond fluorescence correlation spectroscopy to investigate the reorientational dynamics of Aβ1-40 (Aβ40) at single-residue resolution. The integrative analysis shows that librational and dihedral angle fluctuations occurring at fast and intermediate time scales are not sufficient to decorrelate orientational memory in Aβ40. Instead, slow segmental motions occurring at ∼5 ns are detected throughout the Aβ40 sequence and reach up to ∼10 ns for selected residues. We propose that the modulation of time scales of reorientational dynamics with respect to intra- and intermolecular diffusion plays an important role in disease-related Aβ aggregation.

Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDP) are abundant in the human genome and have recently emerged as major therapeutic targets for various diseases. Unlike traditional proteins that adopt a definitive structure, IDPs in free solution are disordered and exist as an ensemble of conformations. This enables the IDPs to signal through multiple signaling pathways and serve as scaffolds for multi-protein complexes. The challenge in studying IDPs experimentally stems from their disordered nature. Nuclear magnetic resonance (NMR), circular dichroism, small angle X-ray scattering, and single molecule Förster resonance energy transfer (FRET) can give the local structural information and overall dimension of IDPs, but seldom provide a unified picture of the whole protein. To understand the conformational dynamics of IDPs and how their structural ensembles recognize multiple binding partners and small molecule inhibitors, knowledge-based and physics-based sampling techniques are utilized in-silico, guided by experimental structural data. However, efficient sampling of the IDP conformational ensemble requires traversing the numerous degrees of freedom in the IDP energy landscape, as well as force-fields that accurately model the protein and solvent interactions. In this review, we have provided an overview of the current state of computational methods for studying IDP structure and dynamics and discussed the major challenges faced in this field.