Dynamical Behavior of Human α-Synuclein Studied by Quasielastic Neutron Scattering

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.

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.

Data Collection for Dilute Protein Solutions via a Neutron Backscattering Spectrometer

Understanding protein functions requires not only static but also dynamic structural information. Incoherent quasi-elastic neutron scattering (QENS), which utilizes the highly incoherent scattering ability of hydrogen, is a powerful technique for revealing the dynamics of proteins in deuterium oxide (D2O) buffer solutions. The background scattering of sample cells suitable for aqueous protein solution samples, conducted with a neutron backscattering spectrometer, was evaluated. It was found that the scattering intensity of an aluminum sample cell coated with boehmite using D2O was lower than that of a sample cell coated with regular water (H2O). The D2O-Boehmite coated cell was used for the QENS measurement of a 0.8 wt.% aqueous solution of an intrinsically disordered protein in an intrinsically disordered region of a helicase-associated endonuclease for a fork-structured type of DNA. The cell was inert against aqueous samples at 283–363 K. In addition, meticulous attention to cells with small individual weight differences and the positional reproducibility of the sample cell relative to the spectrometer neutron beam position enabled the accurate subtraction of the scattering profiles of the D2O buffer and the sample container. Consequently, high-quality information on protein dynamics could be extracted from dilute protein solutions.

Self-Diffusive Properties of the Intrinsically Disordered Protein Histatin 5 and the Impact of Crowding Thereon: A Combined Neutron Spectroscopy and Molecular Dynamics Simulation Study

Intrinsically disordered proteins (IDPs) are proteins that, in comparison with globular/structured proteins, lack a distinct tertiary structure. Here, we use the model IDP, Histatin 5, for studying its dynamical properties under self-crowding conditions with quasi-elastic neutron scattering in combination with full atomistic molecular dynamics (MD) simulations. The aim is to determine the effects of crowding on the center-of-mass diffusion as well as the internal diffusive behavior. The diffusion was found to decrease significantly, which we hypothesize can be attributed to some degree of aggregation at higher protein concentrations, (≥100 mg/mL), as indicated by recent small-angle X-ray scattering studies. Temperature effects are also considered and found to, largely, follow Stokes–Einstein behavior. Simple geometric considerations fail to accurately predict the rates of diffusion, while simulations show semiquantitative agreement with experiments, dependent on assumptions of the ratio between translational and rotational diffusion. A scaling law that previously was found to successfully describe the behavior of globular proteins was found to be inadequate for the IDP, Histatin 5. Analysis of the MD simulations show that the width of the distribution with respect to diffusion is not a simplistic mirroring of the distribution of radius of gyration, hence, displaying the particular features of IDPs that need to be accounted for.

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.

Universal dynamical onset in water at distinct material interfaces

Interfacial water remains liquid and mobile much below 0 °C, imparting flexibility to the encapsulated materials to ensure their diverse functions at subzero temperatures. However, a united picture that can describe the dynamical differences of interfacial water on different materials and its role in imparting system-specific flexibility to distinct materials is lacking. By combining neutron spectroscopy and isotope labeling, we explored the dynamics of water and the underlying substrates independently below 0 °C across a broad range of materials. Surprisingly, while the function-related anharmonic dynamical onset in the materials exhibits diverse activation temperatures, the surface water presents a universal onset at a common temperature. Further analysis of the neutron experiment and simulation results revealed that the universal onset of water results from an intrinsic surface-independent relaxation: switching of hydrogen bonds between neighboring water molecules with a common energy barrier of ∼35 kJ mol⁻¹.

We demonstrated that the dynamical onset of interfacial water is an intrinsic property of water itself, resulting from a surface independent relaxation process in water with an approximately universal energy barrier of ∼35 kJ mol⁻¹.

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.

WT and A53T α-Synuclein Systems: Melting Diagram and Its New Interpretation

The potential barriers governing the motions of α-synuclein (αS) variants' hydration water, especially energetics of them, is in the focus of the work. The thermodynamical approach yielded essential information about distributions and heights of the potential barriers. The proteins' structural disorder was measured by ratios of heterogeneous water-binding interfaces. They showed the αS monomers, oligomers and amyloids to possess secondary structural elements, although monomers are intrinsically disordered. Despite their disordered nature, monomers have 33% secondary structure, and therefore they are more compact than a random coil. At the lowest potential barriers with mobile hydration water, monomers are already functional, a monolayer of mobile hydration water is surrounding them. Monomers realize all possible hydrogen bonds with the solvent water. αS oligomers and amyloids have half of the mobile hydration water amount than monomers because aggregation involves less mobile hydration. The solvent-accessible surface of the oligomers is ordered or homogenous in its interactions with water to 66%. As a contrast, αS amyloids are disordered or heterogeneous to 75% of their solvent accessible surface and both wild type and A53T amyloids show identical, low-level hydration. Mobile water molecules in the first hydration shell of amyloids are the weakest bound compared to other forms.

A New Look into the Mode of Action of Metal-Based Anticancer Drugs

The mode of action of Pt- and Pd-based anticancer agents (cisplatin and Pd₂Spm) was studied by characterising their impact on DNA. Changes in conformation and mobility at the molecular level in hydrated DNA were analysed by quasi-elastic and inelastic neutron scattering techniques (QENS and INS), coupled to Fourier transform infrared (FTIR) and microRaman spectroscopies. Although INS, FTIR and Raman revealed drug-triggered changes in the phosphate groups and the double helix base pairing, QENS allowed access to the nanosecond motions of the biomolecule’s backbone and confined hydration water within the minor groove. Distinct effects were observed for cisplatin and Pd₂Spm, the former having a predominant effect on DNA’s spine of hydration, whereas the latter had a higher influence on the backbone dynamics. This is an innovative way of tackling a drug’s mode of action, mediated by the hydration waters within its pharmacological target (DNA).

Solution Structure and Conformational Flexibility in the Active State of the Orange Carotenoid Protein. Part II: Quasielastic Neutron Scattering

Orange carotenoid proteins (OCPs), which are protecting cyanobacterial light-harvesting antennae from photodamage, undergo a pronounced structural change upon light absorption. In addition, the active state is anticipated to boost a significantly higher molecular flexibility similar to a "molten globule" state. Here, we used quasielastic neutron scattering to directly characterize the vibrational and conformational molecular dynamics of OCP in its ground and active states, respectively, on the picosecond time scale. At a temperature of 100 K, we observe mainly (vibronic) inelastic features with peak energies at 5 and 6 meV (40 and 48 cm^-1, respectively). At physiological temperatures, however, two (Lorentzian) quasielastic components represent localized protein motions, that is, stochastic structural fluctuations of protein side chains between various conformational substates of the protein. Global diffusion of OCP is not observed on the given time scale. The slower Lorentzian component is affected by illumination and can be well-characterized by a jump-diffusion model. While the jump diffusion constant D is (2.82 ± 0.01) × 10^-5 cm²/s at 300 K in the ground state, it is increased by ∼20% to (3.48 ± 0.01) × 10^-5 cm²/s in the active state, revealing a strong enhancement of molecular mobility. The increased mobility is also reflected in the average atomic mean square displacement ⟨u²⟩; we determine a ⟨u²⟩ of 1.47 ± 0.05 Å in the ground state, but 1.86 ± 0.05 Å in the active state (at 300 K). This effect is assigned to two factors: (i) the elongated structure of the active state with two widely separated protein domains is characterized by a larger number of surface residues with a concomitantly higher degree of motional freedom and (ii) a larger number of hydration water molecules bound at the surface of the protein. We thus conclude that the active state of the orange carotenoid protein displays an enhanced conformational dynamics. The higher degree of flexibility may provide additional channels for nonradiative decay so that harmful excess energy can be more efficiently converted to heat.

Dynamics of proteins in solution

The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

Anticancer drug impact on DNA – a study by neutron spectroscopy coupled with synchrotron-based FTIR and EXAFS

Complementary information on drug–DNA interplay has been achieved for Pt/Pd anticancer agents, by a combined QENS, SR-FTIR-ATR and EXAFS approach.

Quasielastic neutron scattering study of microscopic dynamics in polybutadiene reinforced with an unsaturated carboxylate

We studied the dynamics of zinc diacrylate (ZDA) reinforced polybutadiene rubber (BR) (ZDA/BR) using the quasielastic neutron scattering technique to determine the effect of concentration of ZDA on polymer dynamics. First, we evaluated the temperature dependence of mean square displacements (〈u²〉) for ZDA/BR with different ZDA volume fractions. 〈u²〉 increased with temperature below 170 K, and we observed no significant ZDA volume fraction dependence. However, it increased more steeply above 170 K, and the value of 〈u²〉 was smaller for the samples with increasing ZDA fraction. To elucidate the origin of the decrease in 〈u²〉 with increasing ZDA content, dynamic scattering laws (S(Q,ω)) were analyzed. An increase in the elastic component, an increase in the mean relaxation time, and a broadening of distribution of relaxation time were observed with the increasing volume fraction of ZDA. In addition, the ZDA volume fraction dependence of the elastic component roughly corresponded to that of elastic modulus, indicating that the elastic component is related to its mechanical strength. Referring to the previously reported static structure of the present ZDA/BR system, a model for the heterogeneous BR dynamics was proposed. This model assumes the coexistence of immobile, mobile, and interfacial constrained mobile regions. It was found to be appropriate for the explanation of the observed dynamics. We proposed that a network-like structure of the BR having a high crosslinking density around ZDA aggregates is mainly responsible for the high elastic modulus of ZDA/BR.

Modulation of the picosecond dynamics of troponin by the cardiomyopathy-causing mutation K247R of troponin T observed by quasielastic neutron scattering

Troponin (Tn), consisting of three subunits (TnC, TnI, and TnT), regulates cardiac muscle contraction in a Ca²⁺-dependent manner. Various point mutations of human cardiac Tn are known to cause familial hypertrophic cardiomyopathy due to aberration of the regulatory function. In this study, we investigated the effects of one of these mutations, K247R of TnT, on the picosecond dynamics of the Tn core domain (Tn-CD), consisting of TnC, TnI and TnT2 (183-288 residues of TnT), by carrying out the quasielastic neutron scattering measurements on the reconstituted Tn-CD containing either the wild-type TnT2 (wtTn-CD) or the mutant TnT2 (K247R-Tn-CD) in the absence and presence of Ca²⁺. It was found that Ca²⁺-binding to the wtTn-CD decreases the residence time of atomic motions in the Tn-CD with slight changes in amplitudes, suggesting that the regulatory function mainly requires modulation of frequency of atomic motions. On the other hand, the K247R-Tn-CD shows different dynamic behavior from that of the wtTn-CD both in the absence and presence of Ca²⁺. In particular, the K247R-Tn-CD exhibits a larger amplitude than the wtTn-CD in the presence of Ca²⁺, suggesting that the mutant can explore larger conformational space than the wild-type. This increased flexibility should be relevant to the functional aberration of this mutant.

Inelastic and quasi-elastic neutron scattering spectrometers in J-PARC

J-PARC, Japan Proton Accelerator Research Complex provides short pulse proton beam at a repetition rate 25Hz and the maximum power is expected to be 1MW. Materials and Life Science Experimental Facility (MLF) has 23 neutron beam ports and 21 instruments have already been operated or under construction/commissioning. There are 6 inelastic/quasi-elastic neutron scattering spectrometers and the complementary use of these spectrometers will open new insight for life science. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.