Hydration water mobility is enhanced around tau amyloid fibers

Do Specific Ion Effects on Collective Relaxation Arise from Perturbation of Hydrogen-Bonding Network Structure?

The change in the transport properties (i.e., water diffusivity, shear viscosity, etc.) when adding salts to water has been used to classify ions as either being chaotropic or kosmotropic, a terminology based on the presumption that this phenomenon arises from respective breakdown or enhancement of the hydrogen-bonding network structure. Recent quasi-elastic neutron scattering measurements of the collective structural relaxation time, τC, in aqueous salt solutions were interpreted as confirming this proposed origin of ion effects on the dynamics of water. However, we find similar changes in τC in the same salt solutions based on molecular dynamics (MD) simulations using a coarse-grained water model in which no hydrogen bonding exists, challenging this conventional interpretation of mobility change resulting from the addition of salts to water. A thorough understanding of specific ion effects should be useful in diverse material manufacturing and biomedical applications, where these effects are prevalent, but poorly understood.

Water slowing down drives the occurrence of the low temperature dynamical transition in microgels

The protein dynamical transition marks an increase in atomic mobility and the onset of anharmonic motions at a critical temperature (T d), which is considered relevant for protein functionality. This phenomenon is ubiquitous, regardless of protein composition, structure and biological function and typically occurs at large protein content, to avoid water crystallization. Recently, a dynamical transition has also been reported in non-biological macromolecules, such as poly(N-isopropyl acrylamide) (PNIPAM) microgels, bearing many similarities to proteins. While the generality of this phenomenon is well-established, the role of water in the transition remains a subject of debate. In this study, we use atomistic molecular dynamics (MD) simulations and elastic incoherent neutron scattering (EINS) experiments with selective deuteration to investigate the microscopic origin of the dynamical transition and distinguish water and PNIPAM roles. While a standard analysis of EINS experiments would suggest that the dynamical transition occurs in PNIPAM and water at a similar temperature, simulations reveal a different perspective, also qualitatively supported by experiments. From room temperature down to about 180 K, PNIPAM exhibits only modest changes of dynamics, while water, being mainly hydration water under the probed extreme confinement, significantly slows down and undergoes a mode-coupling transition from diffusive to activated. Our findings therefore challenge the traditional view of the dynamical transition, demonstrating that it occurs in proximity of the water mode-coupling transition, shedding light on the intricate interplay between polymer and water dynamics.

Inelastic neutron scattering and spectroscopy methods to characterize dynamics in colloidal and soft matter systems

Colloidal systems and soft materials are well suited to neutron scattering, and the community has readily adopted elastic scattering techniques to investigate their structure. Due to their unique properties, neutrons may also be used to characterize the dynamics of soft materials over a wide range of length and time scales in situ. Both static structures and an understanding of how molecules move about their equilibrium positions is essential if we are to deliver on the promise of rationally designing soft materials. In this review we introduce the basics of neutron spectroscopy and explore the ways in which inelastic neutron scattering can be used to study colloidal and soft materials. Illustrative examples are chosen that highlight the phenomena suitable for investigation using this suite of techniques.

Molecular Crowding: The History and Development of a Scientific Paradigm

It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.

Molecular Mechanism of Tau Misfolding and Aggregation: Insights from Molecular Dynamics Simulation

Tau dysfunction has a close association with many neurodegenerative diseases, which are collectively referred to as tauopathies. Neurofibrillary tangles (NFTs) formed by misfolding and aggregation of tau are the main pathological process of tauopathy. Therefore, uncovering the misfolding and aggregation mechanism of tau protein will help to reveal the pathogenic mechanism of tauopathies. Molecular dynamics (MD) simulation is well suited for studying the dynamic process of protein structure changes. It provides detailed information on protein structure changes over time at the atomic resolution. At the same time, MD simulation can also simulate various conditions conveniently. Based on these advantages, MD simulations are widely used to study conformational transition problems such as protein misfolding and aggregation. Here, we summarized the structural features of tau, the factors affecting its misfolding and aggregation, and the applications of MD simulations in the study of tau misfolding and aggregation.

Molecular Dynamics Simulation of the Influence of Temperature and Salt on the Dynamic Hydration Layer in a Model Polyzwitterionic Polymer PAEDAPS

We investigate the hydration of poly(3-[2-(acrylamido) ethyldimethylammonio] propanesulfonate) over a range of temperatures in pure water and with the inclusion of 0.1 mol/L NaCl using atomistic molecular dynamics simulation. Drawing on concepts drawn from the field of glass-forming liquids, we use the Debye-Waller parameter () for describing the water mobility gradient around the polybetaine backbone extending to an overall distance ≈18 Å. The water mobility in this layer is defined through the mean-square water molecule displacement at a time on the order of water's β-relaxation time. The brushlike topology of polybetaines leads to two regions in the dynamic hydration layer. The inner region of ≈10.5 Å is explored by pendant group conformational motions, and the outer region of ≈7.5 Å represents an extended layer of reduced water mobility relative to bulk water. The dynamic hydration layer extends far beyond the static hydration layer, adjacent to the polymer.

Elucidating the Sluggish Water Dynamics at the Ice-Binding Surface of the Hyperactive Tenebrio molitor Antifreeze Protein

Quasi-ice-like hydration waters on the ice-binding surface (IBS) of an antifreeze protein (AFP) commonly exhibit sluggish dynamics especially at low temperatures. In this work, we have analyzed molecular dynamics (MD) simulation trajectories at two different temperatures for Tenebrio molitor antifreeze protein (TmAFP) to explore whether the unique quasi-ice-like structuring of hydration water has any impact on making their dynamics slower on the IBS of the protein. Our calculation reveals that, as translational dynamics is coupled with the conformational fluctuations, hydration water on the IBS exhibits sluggish translational motion due to reduced flexibility of the IBS compared to that on the non-ice-binding surface (NIBS) of the protein. Interestingly, it is noticed that rotational motion of hydration water is not coupled with the conformational fluctuations of the surfaces. In that case, structural relaxations of the protein-water (PW) and water-water (WW) hydrogen bonds compete with each other to make the rotational dynamics of hydration water around the IBS either faster or slower with respect to those around the NIBS. At low temperature, the slower structural relaxation of water-water hydrogen bonds dominates and imparts sluggish rotational motion of the hydration water on the IBS of the protein. The slower structural relaxation of water-water hydrogen bonds and hence the retarded rotational dynamics, despite the weak short-lived PW hydrogen bonds on the IBS, is clearly a manifestation of the rigid quasi-ice-like structure of the hydration shell on that surface.

Sub-Nanosecond Dynamics of Pathologically Relevant Bio-Macromolecules Observed by Incoherent Neutron Scattering

Incoherent neutron scattering (iNS) is one of the most powerful techniques to study the dynamical behavior of bio-macromolecules such as proteins and lipid molecules or whole cells. This technique has widely been used to elucidate the fundamental aspects of molecular motions that manifest in the bio-macromolecules in relation to their intrinsic molecular properties and biological functions. Furthermore, in the last decade, iNS studies focusing on a possible relationship between molecular dynamics and biological malfunctions, i.e., human diseases and disorders, have gained importance. In this review, we summarize recent iNS studies on pathologically relevant proteins and lipids and discuss how the findings are of importance to elucidate the molecular mechanisms of human diseases and disorders that each study targets. Since some diseases such as amyloidosis have become more relevant in the aging society, research in this field will continue to develop further and be more important in the current increasing trend for longevity worldwide.

Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ42 Peptide Monomer Conformations

Exploring the conformational properties of amyloid β (Aβ) peptides and the role of solvent (water) in guiding the dynamical environment at their interfaces is crucial for microscopic understanding of Aβ misfolding, which is involved in causing the most common neurodegenerative disorder, i.e., Alzheimer's disease. While numerous studies in the past have emphasized examining the conformational states of Aβ peptides, the role of water has not received much attention. Here, we have performed all-atom molecular dynamics simulations of several full-length Aβ₄₂ peptide monomers with different initial configurations. Our efforts are directed toward probing the origin of the heterogeneous dynamics of water around various segments of the Aβ peptide, identified as the two terminal segments (N-term and C-term) and the two hydrophobic segments (hp1 and hp2), along with the central turn region interconnecting hp1 and hp2. Our results revealed that water hydrating hp1, hp2, and turn (nonterminal segments) and C-term segments exhibit nonuniformly restricted translational as well as rotational motions. The degree of such restriction has been found to be correlated with the hydrogen bond relaxation time scales at the interface. Importantly, it is revealed that the water molecules around hp1 and, to some extent, around hp2, form relatively rigid hydration layers, compared to that around the other segments. Such rigid hydration layers arise due to relatively more solid-like caging motions resulting in relatively lesser hydration entropy. As hp1 and hp2 have been demonstrated to play a central role in Aβ aggregation, we believe that distinct water dynamics in the vicinity of these two segments, as outlined in this study, can provide vital information in understanding the early stages of the onset of the aggregation process of such peptides at higher concentration that can further aid toward advances in AD therapeutics.

Dynamic Heterogeneity at the Interface of an Intrinsically Disordered Peptide

It is believed that water around an intrinsically disordered protein or peptide (IDP) in an aqueous environment plays an important role in guiding its conformational properties and aggregation behavior. However, despite its importance, only a handful of studies exploring the correlation between the conformational motions of an IDP and the microscopic properties of water at its surface are reported. Attempts have been made in this work to study the dynamic properties of water present in the vicinity of α-synuclein, an IDP associated with Parkinson's disease (PD). Room temperature molecular dynamics (MD) simulations of eight α-synuclein_1-95 peptides with a wide range of initial conformations have been carried out in aqueous media. The calculations revealed that due to solid-like caging motions, the translational and rotational mobility of water molecules near the surfaces of the peptide repeat unit segments R1 to R7 are significantly restricted. A small degree of dynamic heterogeneity in the hydration environment around the repeat units has been observed with water near the hydrophobic R6 unit exhibiting relatively more restricted diffusivity. The time scales involving the overall structural relaxations of peptide-water and water-water hydrogen bonds near the peptide have been found to be correlated with the time scale of diffusion of the interfacial water molecules. We believe that the relatively more hindered dynamic environment near R6 can help create water-mediated contacts centered around R6 between peptide monomers at a higher concentration, thereby enhancing the early stages of peptide aggregation.

Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics

We use molecular dynamics simulations to investigate the effect of polypeptoid sequence on the structure and dynamics of its hydration waters. Polypeptoids provide an excellent platform to study small-molecule hydration in disordered polymers, as they can be precisely synthesized with a variety of sidechain chemistries. We examine water behavior near a set of peptoid oligomers in which the number and placement of nonpolar versus polar sidechains are systematically varied. To do this, we leverage a new computational workflow enabling accurate sampling of polypeptoid conformations. We find that the hydration waters are less dense, are more tetrahedral, and have slower dynamics compared to bulk water. The magnitude of these shifts increases with the number of nonpolar groups. We also find that shifts in the water structure and dynamics are strongly correlated, suggesting that experimental insight into the dynamics of hydration water obtained by Overhauser dynamic nuclear polarization (ODNP) also contains information about water structural properties. We then demonstrate the ability of ODNP to probe site-specific dynamics of hydration water near these model peptoid systems.

Conformational and Solvation Dynamics of an Amyloidogenic Intrinsically Disordered Domain of a Melanosomal Protein

The conformational plasticity of intrinsically disordered proteins (IDPs) allows them to adopt a range of conformational states that can be important for their biological functions. The driving force for the conformational preference of an IDP emanates from an intricate interplay between chain-chain and chain-solvent interactions. Using ultrafast femtosecond and picosecond time-resolved fluorescence measurements, we characterized the conformational and solvation dynamics around the N- and C-terminal segments of a disordered repeat domain of a melanosomal protein Pmel17 that forms functional amyloid responsible for melanin biosynthesis. Our time-resolved fluorescence anisotropy results revealed slight compaction and slower rotational dynamics around the amyloidogenic C-terminal segment when compared to the proline-rich N-terminal segment of the repeat domain. The compaction of the C-terminal region was also associated with the restrained mobility of hydration water as indicated by our solvation dynamics measurements. Our findings indicate that sequence-dependent chain-solvent interactions govern both the conformational and solvation dynamics that are crucial in directing the conversion of a highly dynamic IDP into an ordered amyloid assembly. Such an interplay of amino acid composition-dependent conformational and solvation dynamics might have important physicochemical consequences in specific water-protein, ion-protein, and protein-protein interactions involved in amyloid formation and phase transitions.

Molecular Dynamics of Lysozyme Amyloid Polymorphs Studied by Incoherent Neutron Scattering

Lysozyme amyloidosis is a hereditary disease, which is characterized by the deposition of lysozyme amyloid fibrils in various internal organs. It is known that lysozyme fibrils show polymorphism and that polymorphs formed at near-neutral pH have the ability to promote more monomer binding than those formed at acidic pH, indicating that only specific polymorphs become dominant species in a given environment. This is likely due to the polymorph-specific configurational diffusion. Understanding the possible differences in dynamical behavior between the polymorphs is thus crucial to deepen our knowledge of amyloid polymorphism and eventually elucidate the molecular mechanism of lysozyme amyloidosis. In this study, molecular dynamics at sub-nanosecond timescale of two kinds of polymorphic fibrils of hen egg white lysozyme, which has long been used as a model of human lysozyme, formed at pH 2.7 (LP27) and pH 6.0 (LP60) was investigated using elastic incoherent neutron scattering (EINS) and quasi-elastic neutron scattering (QENS). Analysis of the EINS data showed that whereas the mean square displacement of atomic motions is similar for both LP27 and LP60, LP60 contains a larger fraction of atoms moving with larger amplitudes than LP27, indicating that the dynamical difference between the two polymorphs lies not in the averaged amplitude, but in the distribution of the amplitudes. Furthermore, analysis of the QENS data showed that the jump diffusion coefficient of atoms is larger for LP60, suggesting that the atoms of LP60 undergo faster diffusive motions than those of LP27. This study thus characterizes the dynamics of the two lysozyme polymorphs and reveals that the molecular dynamics of LP60 is enhanced compared with that of LP27. The higher molecular flexibility of the polymorph would permit to adjust its conformation more quickly than its counterpart, facilitating monomer binding.

Lead(II) ions adsorption onto amyloid particulates: An in depth study

The production of new cost-effective biocompatible sorbent sustainable materials, with natural origins, able to remove heavy metals from water resources is nowadays highly desirable in order to reduce pollution and increase clean water availability. In this context, self-assembled protein materials with amyloid structures seem to have a great potential as natural platform for a broader development of highly-tunable structures. In this work we show how protein particulates, a generic form of protein aggregates, with spherical micro sized shape can be used as adsorbents of Pb²⁺ ions from aqueous solution. The effect of pH, ionic medium, ionic strength and temperature of the metal ion solution on the adsorption ability and affinity has been evaluated revealing the complexity of adsorption mechanisms which are the result of the balance of specific interactions with functional groups in protein structure and not specific ones common to all polypeptide chains, and possibly related to amyloid state and to modification of particulates hydration layer.

Solvent Relaxation NMR: A Tool for Real-Time Monitoring Water Dynamics in Protein Aggregation Landscape

Solvent dynamics strongly induce the fibrillation of an amyloidogenic system. Probing the solvation mechanism is crucial as it enables us to predict different proteins' functionalities, such as the aggregation propensity, structural flexibility, and toxicity. This work shows that a straightforward NMR method in conjunction with phenomenological models gives a global and qualitative picture of water dynamics at different concentrations and temperatures. Here, we study amyloid system Aβ40 and its fragment AV20 (A21-V40) and G37L (mutation at Gly37 → Leu of AV20), having different aggregation and toxic properties. The independent validation of this method is elucidated using all-atom classical MD simulation. These two state-of-the-art techniques are pivotal in linking the effect of solvent environment in the near hydration-shell to their aggregation nature. The time-dependent modulation in solvent dynamics probed with the NMR solvent relaxation method can be further adopted to gain insight into amyloidogenesis and link with their toxicity profiles.

Amyloid-Like Aggregation in Diseases and Biomaterials: Osmosis of Structural Information

The discovery that the polypeptide chain has a remarkable and intrinsic propensity to form amyloid-like aggregates endowed with an extraordinary stability is one of the most relevant breakthroughs of the last decades in both protein/peptide chemistry and structural biology. This observation has fundamental implications, as the formation of these assemblies is systematically associated with the insurgence of severe neurodegenerative diseases. Although the ability of proteins to form aggregates rich in cross-β structure has been highlighted by recent studies of structural biology, the determination of the underlying atomic models has required immense efforts and inventiveness. Interestingly, the progressive molecular and structural characterization of these assemblies has opened new perspectives in apparently unrelated fields. Indeed, the self-assembling through the cross-β structure has been exploited to generate innovative biomaterials endowed with promising mechanical and spectroscopic properties. Therefore, this structural motif has become the fil rouge connecting these diversified research areas. In the present review, we report a chronological recapitulation, also performing a survey of the structural content of the Protein Data Bank, of the milestones achieved over the years in the characterization of cross-β assemblies involved in the insurgence of neurodegenerative diseases. A particular emphasis is given to the very recent successful elucidation of amyloid-like aggregates characterized by remarkable molecular and structural complexities. We also review the state of the art of the structural characterization of cross-β based biomaterials by highlighting the benefits of the osmosis of information between these two research areas. Finally, we underline the new promising perspectives that recent successful characterizations of disease-related amyloid-like assemblies can open in the biomaterial field.

Diffusion Tensor Imaging Detects Acute Pathology-Specific Changes in the P301L Tauopathy Mouse Model Following Traumatic Brain Injury

Traumatic brain injury (TBI) has been linked with tauopathy. However, imaging methods that can non-invasively detect tau-protein abnormalities following TBI need further investigation. This study aimed to investigate the potential of diffusion tensor imaging (DTI) to detect tauopathy following TBI in P301L mutant-tau-transgenic-pR5-mice. A total of 24 9-month-old pR5 mice were randomly assigned to sham and TBI groups. Controlled cortical injuries/craniotomies were performed for TBI/sham groups followed by DTI data acquisition on days 1 and 7 post-injury. DTI data were analyzed by using voxelwise analysis and track-based spatial statistics for gray matter and white matter. Further, immunohistochemistry was performed for total-tau and phosphorylated-tau, astrocytes, and microglia. To detect the association of DTI with these pathological markers, a correlation analysis was performed between DTI and histology findings. At day 1 post-TBI, DTI revealed a widespread reduction in fractional anisotropy (FA) and axial diffusivity (AxD) in the TBI group compared to shams. On day 7, further reduction in FA, AxD, and mean diffusivity and increased radial diffusivity were observed. FA was significantly increased in the amygdala and cortex. Correlation results showed that in the ipsilateral hemisphere FA reduction was associated with increased phosphorylated-tau and glial-immunoreactivity, whereas in the contralateral regions, the FA increase was associated with increased immunostaining for astrocytes. This study is the first to exploit DTI to investigate the effect of TBI in tau-transgenic mice. We show that alterations in the DTI signal were associated with glial activity following TBI and would most likely reflect changes that co-occur with/without phosphorylated-tau. In addition, FA may be a promising measure to identify discrete pathological processes such as increased astroglia activation, tau-hyperphosphorylation or both in the brain following TBI.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

A theoretical study of polymorphism in VQIVYK fibrils

The VQIVYK fragment from the Tau protein, also known as PHF6, is essential for aggregation of Tau into neurofibrillary lesions associated with neurodegenerative diseases. VQIVYK itself forms amyloid fibrils composed of paired β-sheets. Therefore, the full Tau protein and VQIVYK fibrils have been intensively investigated. A central issue in these studies is polymorphism, the ability of a protein to fold into more than one structure. Using all-atom molecular simulations, we generate five stable polymorphs of VQIVYK fibrils, establish their relative free energy with umbrella sampling methods, and identify the side chain interactions that provide stability. The two most stable polymorphs, which have nearly equal free energy, are formed by interdigitation of the mostly hydrophobic VIY "face" sides of the β-sheets. Another stable polymorph is formed by interdigitation of the QVK "back" sides. When we turn to examine structures from cryo-electron microscopy experiments on Tau filaments taken from diseased patients or generated in vitro, we find that the pattern of side chain interactions found in the two most stable face-to-face as well as the back-to-back polymorphs are recapitulated in amyloid structures of the full protein. Thus, our studies suggest that the interactions stabilizing PHF6 fibrils explain the amyloidogenicity of the VQIVYK motif within the full Tau protein and provide justification for the use of VQIVYK fibrils as a test bed for the design of molecules that identify or inhibit amyloid structures.

Zinc determines dynamical properties and aggregation kinetics of human insulin

Protein aggregation is a widespread process leading to deleterious consequences in the organism, with amyloid aggregates being important not only in biology but also for drug design and biomaterial production. Insulin is a protein largely used in diabetes treatment, and its amyloid aggregation is at the basis of the so-called insulin-derived amyloidosis. Here, we uncover the major role of zinc in both insulin dynamics and aggregation kinetics at low pH, in which the formation of different amyloid superstructures (fibrils and spherulites) can be thermally induced. Amyloid aggregation is accompanied by zinc release and the suppression of water-sustained insulin dynamics, as shown by particle-induced x-ray emission and x-ray absorption spectroscopy and by neutron spectroscopy, respectively. Our study shows that zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein and suggests that introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity.

Alteration of water absorption in the THz region traces the onset of fibrillation in proteins

Using terahertz spectroscopy, we established the alteration of the collective hydration of water during the fibrillation process (native → intermediate → fibril) of a model protein bovine serum albumin. This label-free study concludes that water dynamics change systematically with protein conformational changes as it experiences a hydrophobic environment during the initial protein unfolding process, followed by the release of bound water during oligomerization and finally the hydrophobic interior of the fibril.

The role of water in the primary nucleation of protein amyloid aggregation

The understanding of the complex conformational landscape of amyloid aggregation and its modulation by relevant physicochemical and cellular factors is a prerequisite for elucidating some of the molecular basis of pathology in amyloid related diseases, and for developing and evaluating effective disease-specific therapeutics to reduce or eliminate the underlying sources of toxicity in these diseases. Interactions of proteins with solvating water have been long considered to be fundamental in mediating their function and folding; however, the relevance of water in the process of protein amyloid aggregation has been largely overlooked. Here, we provide a perspective on the role water plays in triggering primary amyloid nucleation of intrinsically disordered proteins (IDPs) based on recent experimental evidences. The initiation of amyloid aggregation likely results from the synergistic effect between both protein intermolecular interactions and the properties of the water hydration layer of the protein surface. While the self-assembly of both hydrophobic and hydrophilic IDPs would be thermodynamically favoured due to large water entropy contributions, large desolvation energy barriers are expected, particularly for the nucleation of hydrophilic IDPs. Under highly hydrating conditions, primary nucleation is slow, being facilitated by the presence of nucleation-active surfaces (heterogeneous nucleation). Under conditions of poor water activity, such as those found in the interior of protein droplets generated by liquid-liquid phase separation, however, the desolvation energy barrier is significantly reduced, and nucleation can occur very rapidly in the bulk of the solution (homogeneous nucleation), giving rise to structurally distinct amyloid polymorphs. Water, therefore, plays a key role in modulating the transition free energy of amyloid nucleation, thus governing the initiation of the process, and dictating the type of preferred primary nucleation and the type of amyloid polymorph generated, which could vary depending on the particular microenvironment that the protein molecules encounter in the cell.

Tracking Internal and Global Diffusive Dynamics During Protein Aggregation by High-Resolution Neutron Spectroscopy

Proteins can misfold and form either amorphous or organized aggregates with different morphologies and features. Aggregates of amyloid nature are pathological hallmarks in so-called protein conformational diseases, including Alzheimer's and Parkinson's. Evidence prevails that the transient early phases of the reaction determine the aggregate morphology and toxicity. As a consequence, real-time monitoring of protein aggregation is of utmost importance. Here, we employed time-resolved neutron backscattering spectroscopy to follow center-of-mass self-diffusion and nano- to picosecond internal dynamics of lysozyme during aggregation into a specific β-sheet rich superstructure, called particulates, formed at the isoelectric point of the protein. Particulate formation is found to be a one-step process, and protein internal dynamics, to remain unchanged during the entire aggregation process. The time-resolved neutron backscattering spectroscopy approach developed here, in combination with standard kinetics assays, provides a unifying framework in which dynamics and conformational transitions can be related to the different aggregation pathways.

Hydration and Dynamics of Full-Length Tau Amyloid Fibrils Investigated by Solid-State Nuclear Magnetic Resonance

The microtubule-associated protein tau aggregates into distinct neurofibrillary tangles in brains afflicted with multiple neurodegenerative diseases such as Alzheimer's disease and corticobasal degeneration (CBD). The mechanism of tau misfolding and aggregation is poorly understood. Determining the structure, dynamics, and water accessibility of tau filaments may provide insight into the pathway of tau misfolding. Here, we investigate the hydration and dynamics of the β-sheet core of heparin-fibrillized 0N4R tau using solid-state nuclear magnetic resonance spectroscopy. This β-sheet core consists of the second and third microtubule-binding repeats, R2 and R3, respectively, which form a hairpin. Water-edited two-dimensional (2D) 13C-13C and 15N-13C correlation spectra show that most residues in R2 and R3 domains have low water accessibility, indicating that this hairpin is surrounded by other proteinaceous segments. However, a small number of residues, especially S285 and S316, are well hydrated compared to other Ser and Thr residues, suggesting that there is a small water channel in the middle of the hairpin. To probe whether water accessibility correlates with protein dynamics, we measured the backbone N-H dipolar couplings of the β-sheet core. Interestingly, residues in the fourth microtubule-binding repeat, R4, show rigid-limit N-H dipolar couplings, even though this domain exhibits weaker intensities in the 2D 15N-13C correlation spectra. These results suggest that the R4 domain participates in cross-β hydrogen bonding in some of the subunits but exhibits dynamic disorder in other subunits. Taken together, these hydration and dynamics data indicate that the R2-R3 hairpin of 0N4R tau is shielded from water by other proteinaceous segments on the exterior but contains a small water pore in the interior. This structural topology has various similarities with the CBD tau fibril structure but also shows specific differences. The disorder of the R4 domain and the presence of a small water channel in the heparin-fibrillized 4R tau have implications for the structure of tau fibrils in diseased brains.

Interaction between tau and water during the induced aggregation revealed by near-infrared spectroscopy

Near-infrared (NIR) spectra are sensitive to the variation of water structure. In this work, NIR spectroscopy was used to investigate the variation of hydration water during the aggregation of R2/wt induced by heparin. The osmolytes, urea and trehalose, were used to slow down and speed up the aggregation. The spectra of R2/wt aqueous solution obtained by NIR spectroscopy at 37 °C were adopted to analyze the structure of water during the aggregation. The spectral features of different water species were observed by principal component analysis (PCA) from the resolution enhanced NIR spectra. The existence of the water molecules with one and two hydrogen bonds around the NH and CH groups of R2/wt, respectively, was suggested, and the variation of the hydrogen-bonded water was found to be an indicator to monitor the process of aggregation. Then, the variation of the water species during the aggregation was analyzed by two-dimensional correlation spectroscopy. The water hydrogen bonded with NH group was found to change earlier than the water around the hydrophobic groups. The results suggest that β-sheet forms though the hydrogen bonds of amide groups in the early stage of the aggregation, and the destruction of the hydrogen bond network of the water around the side chains maybe the main reason for the formation of the ordered amyloid fibers.

Ultrafast Dynamics of Water-Protein Coupled Motions around the Surface of Eye Crystallin

Water dynamics on the protein surface mediate both protein structure and function. However, many questions remain about the role of the protein hydration layers in protein fluctuations and how the dynamics of these layers relate to specific protein properties. The fish eye lens protein γM7-crystallin (γM7) is found in vivo at extremely high concentrations nearing the packing limit, corresponding to only a few water layers between adjacent proteins. In this study, we conducted a site-specific probing of hydration water motions and side-chain dynamics at nine selected sites around the surface of γM7 using a tryptophan scan with femtosecond spectroscopy and NMR nuclear spin relaxation (NSR). We observed correlated fluctuations between hydration water and protein side chains on the time scales of a few picoseconds and hundreds of picoseconds, corresponding to local reorientations and network restructuring, respectively. These motions are heterogeneous over the protein surface and relate to the various steric and chemical properties of the local protein environment. Overall, we found that γM7 has relatively slower water dynamics within the hydration shell than a similar β-sheet protein, which may contribute to the high packing limit of this unique protein.

Probing the dynamics of biological matter by elastic, quasi-elastic, and inelastic neutron scattering

The so-called function-structure-dynamics paradigm established that a close relationship links the way biological molecules work (function), their 3-dimensional organization (structure) and the changes of this organization in time (dynamics), which characterize biomolecules as highly dynamic objects. A typical example of protein dynamics is provided by protein reactions with substrates: equilibrium thermal fluctuations of protein structure are necessary to allow the access of substrates to the active site, where the functional reaction occurs. Neutron scattering is a powerful technique to study equilibrium protein structural dynamics. The incoherent structure factor, which is dominant in neutron scattering from biological matter, is related to the time-position self correlation function of protein/solvent nuclei. Here the basic theory of neutron scattering and the principles of the technologies used to measure it are described. Some selected applications of neutron scattering for investigating the structural dynamics of biological molecules are also reviewed.

Role of hydration water in the onset of protein structural dynamics

Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.

A computational approach to get insights into multiple faces of additives in modulation of protein aggregation pathways

An enormous population worldwide is presently confronted with debilitating neurodegenerative diseases. The etiology of the disease is connected to protein aggregation and the events involved therein. Thus, a complete understanding of an inhibitor at different stages in the process is imperative for the formulation of a drug molecule. This review presents a detailed summary of the current status of different cosolvents. It further develops how the complex aggregation pathway can be simplified into three steps common to all proteins and the way computer simulations can be exploited to gain insights into the ways by which known inhibitors can affect all these stages. Computation of theoretical parameters in this regard and their correlation with experimental techniques is accentuated. In addition to providing an outline of the scope of different additives, this review showcases the way by which the problem of analyzing an effect of an additive can be addressed effectively via MD simulations.

The role of water in amyloid aggregation kinetics

The role of water in protein function and aggregation is highly important and may hold some answers to understanding initiation of misfolding diseases such as Parkinson's, Alzheimer's and Huntington's where soluble intrinsically disordered proteins (IDPs) aggregate into fibrillar structures. IDPs are highly dynamic and have larger solvent exposed areas compared to globular proteins, meaning they make and break hydrogen bonds with the surrounding water more frequently. The mobility of water can be altered by presence of ions, sugars, osmolytes, proteins and membranes which differ in different cell types, cell compartments and also as cells age. A reduction in water mobility and thus protein mobility enhances the probability that IDPs can associate to form intermolecular bonds and propagate into aggregates. This poses an interesting question as to whether localised water mobility inside cells can influence the propensity of an IDP to aggregate and furthermore whether it can influence fibril polymorphism and disease outcome.

Femtosecond Hydration Map of Intrinsically Disordered α-Synuclein

Protein hydration water plays a fundamentally important role in protein folding, binding, assembly, and function. Little is known about the hydration water in intrinsically disordered proteins that challenge the conventional sequence-structure-function paradigm. Here, by combining experiments and simulations, we show the existence of dynamical heterogeneity of hydration water in an intrinsically disordered presynaptic protein, namely α-synuclein, implicated in Parkinson's disease. We took advantage of nonoccurrence of cysteine in the sequence and incorporated a number of cysteine residues at the N-terminal segment, the central amyloidogenic nonamyloid-β component (NAC) domain, and the C-terminal end of α-synuclein. We then labeled these cysteine variants using environment-sensitive thiol-active fluorophore and monitored the solvation dynamics using femtosecond time-resolved fluorescence. The site-specific femtosecond time-resolved experiments allowed us to construct the hydration map of α-synuclein. Our results show the presence of three dynamically distinct types of water: bulk, hydration, and confined water. The amyloidogenic NAC domain contains dynamically restrained water molecules that are strikingly different from the water molecules present in the other two domains. Atomistic molecular dynamics simulations revealed longer residence times for water molecules near the NAC domain and supported our experimental observations. Additionally, our simulations allowed us to decipher the molecular origin of the dynamical heterogeneity of water in α-synuclein. These simulations captured the quasi-bound water molecules within the NAC domain originating from a complex interplay between the local chain compaction and the sequence composition. Our findings from this synergistic experimental simulation approach suggest longer trapping of interfacial water molecules near the amyloidogenic hotspot that triggers the pathological conversion into amyloids via chain sequestration, chain desolvation, and entropic liberation of ordered water molecules.

Cosolvent Impurities in SWCNT Nanochannel Confinement: Length Dependence of Water Dynamics Investigated with Atomistic Simulations

The advent of nanotechnology has seen a growing interest in the nature of fluid flow and transport under nanoconfinement. The present study leverages fully atomistic molecular dynamics (MD) simulations to study the effect of nanochannel length and intrusion of molecules of the organic solvent, hexafluoro-2-propanol (HFIP), on the dynamical characteristics of water within it. Favorable interactions of HFIP with the nanochannels comprised of single-walled carbon nanotubes traps them over time scales greater than 100 ns, and confinement confers small but distinguishable spatial redistribution between neighboring HFIP pairs. Water molecules within the nanochannels show clear signatures of dynamical slowdown relative to bulk water even for pure systems. The presence of HFIP causes further rotational and translational slowdown in waters when the nanochannel dimension falls below a critical length of 30 Å. The enhanced slowdown in the presence of HFIP is quantified from characteristic relaxation parameters and diffusion coefficients in the absence and presence of HFIP. It is finally seen that the net flow of water between the ends of the nanochannel shows a decreasing dependence with nanochannel length only when the number of HFIP molecules is small. These results lend insights into devising ways of modulating solvent properties within nanochannels with cosolvent impurities.

Length-Dependent Manifestation of Vibration Modes Regulates a Specific Intermediate Morphology of Aβ17-42 in Different Environments

Various cytotoxic mechanisms for neurodegenerative disease are induced by specific conformations of Aβ intermediates. The efforts to understand the diverse intermediate forms of amyloid oligomers have been focused on understanding the aggregation mechanism of specific morphologies for Aβ intermediates. However, these are still not easy tasks to be accomplished because the diverse conformations of Aβ intermediates can be altered during the aggregation process, even though the same Aβ monomers are present. Thus, efforts to reveal the conformational change mechanism could be a fundamental process to understand the formation of diverse Aβ intermediate conformations. Here, we evaluate the conformational characteristics of Aβ_17-42 fibrillar oligomers in different environments according to the length. We observed that Aβ fibrillar oligomers optimize their inherent hydrogen bonds and configurational entropy to stabilize their structure according to the simulation time and their length increase. In addition, we revealed the role of the expressed vibration mode shape in the fibrillar oligomers' elongation and deformation processes. Our results suggest that limitations in amyloid oligomer growth and transformations of their morphologies can be regulated and controlled by modifying the vibration features.

Distribution of tightly and loosely bound water in biological macromolecules and age-related diseases

This mini-review article is focused on publications devoted to the changes in water binding energy and content of bound water in biological tissues during aging processes, when bound water lost from the hydration layer becomes free water. Bound water is released during cataractogenesis. In skin, water bound to proteins and other biomacromolecules becomes more mobile with increasing skin age. Extracellular to intracellular water ratio increases with age and was associated with muscle cell atrophy. Bound water concentration decreases with age in hydrated human bone and can be correlated with the strength and toughness of the bone. Higher fraction of free water in malignant tissues compared to normal tissues was observed. Hydration water mobility is enhanced around tau amyloid fibers. Water plays a decisive role in amyloid formation as entropic driving force. In the natural aging processes dehydration and glycation may be considered as subsequent steps.

Paradoxical Effect of Trehalose on the Aggregation of α-Synuclein: Expedites Onset of Aggregation yet Reduces Fibril Load

Aggregation of α-synuclein is closely connected to the pathology of Parkinson's disease. The phenomenon involves multiple steps, commenced by partial misfolding and eventually leading to mature amyloid fibril formation. Trehalose, a widely accepted osmolyte, has been shown previously to inhibit aggregation of various globular proteins owing to its ability to prevent the initial unfolding of protein. In this study, we have examined if it behaves in a similar fashion with intrinsically disordered protein α-synuclein and possesses the potential to act as therapeutic agent against Parkinson's disease. It was observed experimentally that samples coincubated with trehalose fibrillate faster compared to the case in its absence. Molecular dynamics simulations suggested that this initial acceleration is manifestation of trehalose's tendency to perturb the conformational transitions between different conformers of monomeric protein. It stabilizes the aggregation prone "extended" conformer of α-synuclein, by binding to its exposed acidic residues of the C terminus. It also favors the β-rich oligomers once formed. Interestingly, the total fibrils formed are still promisingly less since it accelerates the competing pathway toward formation of amorphous aggregates.

Looking at the Disordered Proteins through the Computational Microscope

Intrinsically disordered proteins (IDPs) have attracted wide interest over the past decade due to their surprising prevalence in the proteome and versatile roles in cell physiology and pathology. A large selection of IDPs has been identified as potential targets for therapeutic intervention. Characterizing the structure-function relationship of disordered proteins is therefore an essential but daunting task, as these proteins can adapt transient structure, necessitating a new paradigm for connecting structural disorder to function. Molecular simulation has emerged as a natural complement to experiments for atomic-level characterizations and mechanistic investigations of this intriguing class of proteins. The diverse range of length and time scales involved in IDP function requires performing simulations at multiple levels of resolution. In this Outlook, we focus on summarizing available simulation methods, along with a few interesting example applications. We also provide an outlook on how these simulation methods can be further improved in order to provide a more accurate description of IDP structure, binding, and assembly.

In Vivo Detection of Gray Matter Neuropathology in the 3xTg Mouse Model of Alzheimer's Disease with Diffusion Tensor Imaging

A diagnosis of Alzheimer's disease (AD), a neurodegenerative disorder accompanied by severe functional and cognitive decline, is based on clinical findings, with final confirmation of the disease at autopsy by the presence of amyloid-β (Aβ) plaques and neurofibrillary tangles. Given that microstructural brain alterations occur years prior to clinical symptoms, efforts to detect brain changes early could significantly enhance our ability to diagnose AD sooner. Diffusion tensor imaging (DTI), a type of MRI that characterizes the magnitude, orientation, and anisotropy of the diffusion of water in tissues, has been used to infer neuropathological changes in vivo. Its utility in AD, however, is still under investigation. The current study used DTI to examine brain regions susceptible to AD-related pathology; the cerebral cortex, entorhinal cortex, and hippocampus, in 12-14-month-old 3xTg AD mice that possess both Aβ plaques and neurofibrillary tangles. Mean diffusivity did not differ between 3xTg and control mice in any region. Decreased fractional anisotropy (p < 0.01) and axial diffusivity (p < 0.05) were detected only in the hippocampus, in which both congophilic Aβ plaques and hyperphosphorylated tau accumulation, consistent with neurofibrillary tangle formation, were detected. Pathological tau accumulation was seen in the cortex. The entorhinal cortex was largely spared from AD-related neuropathology. This is the first study to demonstrate DTI abnormalities in gray matter in a mouse model of AD in which both pathological hallmarks are present, suggesting the feasibility of DTI as a non-invasive means of detecting brain pathology in vivo in early-stage AD.

Inhibition of GNNQQNY prion peptide aggregation by trehalose: a mechanistic view

Deposition of amyloid fibrils is the seminal event in the pathogenesis of numerous neurodegenerative diseases. The formation of this amyloid assembly is the manifestation of a cascade of structural transitions including toxic oligomer formation in the early stages of aggregation. Thus a viable therapeutic strategy involves the use of small molecular ligands to interfere with this assembly. In this perspective, we have explored the kinetics of aggregate formation of the fibril forming GNNQQNY peptide fragment from the yeast prion protein SUP35 using multiple all atom MD simulations with explicit solvent and provided mechanistic insights into the way trehalose, an experimentally known aggregation inhibitor, modulates the aggregation pathway. The results suggest that the assimilation process is impeded by different barriers at smaller and larger oligomeric sizes: the initial one being easily surpassed at higher temperatures and peptide concentrations. The kinetic profile demonstrates that trehalose delays the aggregation process by increasing both these activation barriers, specifically the latter one. It increases the sampling of small-sized aggregates that lack the beta sheet conformation. Analysis reveals that the barrier in the growth of larger stable oligomers causes the formation of multiple stable small oligomers which then fuse together bimolecularly. The PCA of 26 properties was carried out to deconvolute the events within the temporary lag phases, which suggested dynamism in lags involving an increase in interchain contacts and burial of SASA. The predominant growth route is monomer addition, which changes to condensation on account of a large number of depolymerisation events in the presence of trehalose. The favourable interaction of trehalose specifically with the sidechain of the peptide promotes crowding of trehalose molecules in its vicinity - the combination of both these factors imparts the observed behaviour. Furthermore, increasing trehalose concentration leads to faster expulsion of water molecules than interpeptide interactions. These expelled water molecules have larger translational movement, suggesting an entropy factor to favor the assembly process. Different conformations observed under this condition suggest the role of water molecules in guiding the morphology of the aggregates as well. A similar scenario exists on increasing peptide concentration.

The fold preference and thermodynamic stability of α-synuclein fibrils is encoded in the non-amyloid-β component region

The strain-dependent synucleinopathies may be partially imprinted in the fold-dependent thermodynamic properties of non-amyloid-β component (NAC) fibrils.