Dynamics of well-folded and natively disordered proteins in solution: a time-of-flight neutron scattering study

Nanosecond structural dynamics of intrinsically disordered β-casein micelles by neutron spectroscopy

β-casein undergoes a reversible endothermic self-association, forming protein micelles of limited size. In its functional state, a single β-casein monomer is unfolded, which creates a high structural flexibility, which is supposed to play a major role in preventing the precipitation of calcium phosphate particles. We characterize the structural flexibility in terms of nanosecond molecular motions, depending on the temperature by quasielastic neutron scattering. Our major questions are: Does the self-association reduce the chain flexibility? How does the dynamic spectrum of disordered caseins differ from a compactly globular protein? How does the dynamic spectrum of β-casein in solution differ from that of a protein in hydrated powder states? We report on two relaxation processes on a nanosecond and a sub-nanosecond timescale for β-casein in solution. Both processes are analyzed by Brownian oscillator model, by which the spring constant can be defined in the isotropic parabolic potential. The slower process, which is analyzed by neutron spin echo, seems a characteristic feature of the unfolded structure. It requires bulk solvent and is not seen in hydrated protein powders. The faster process, which is analyzed by neutron backscattering, has a smaller amplitude and requires hydration water, which is also observed with folded proteins in the hydrated state. The self-association had no significant influence on internal relaxation, and thus, a β-casein protein monomer flexibility is preserved in the micelle. We derive spring constants of the faster and slower motions of β-caseins in solution and compared them with those of some proteins in various states (folded or hydrated powder).

Pharmaceutical protein solids: Drying technology, solid-state characterization and stability

Despite the boom in biologics over the past decade, the intrinsic instability of these large molecules poses significant challenges to formulation development. Almost half of all pharmaceutical protein products are formulated in the solid form to preserve protein native structure and extend product shelf-life. In this review, both traditional and emerging drying techniques for producing protein solids will be discussed. During the drying process, various stresses can impact the stability of protein solids. However, understanding the impact of stress on protein product quality can be challenging due to the lack of reliable characterization techniques for biological solids. Both conventional and advanced characterization techniques are discussed including differential scanning calorimetry (DSC), solid-state Fourier transform infrared spectrometry (ssFTIR), solid-state fluorescence spectrometry, solid-state hydrogen deuterium exchange (ssHDX), solid-state nuclear magnetic resonance (ssNMR) and solid-state photolytic labeling (ssPL). Advanced characterization tools may offer mechanistic investigations into local structural changes and interactions at higher resolutions. The continuous exploration of new drying techniques, as well as a better understanding of the effects caused by different drying techniques in solid state, would advance the formulation development of biological products with superior quality.

Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation

Understanding and describing the dynamics of proteins is one of the major challenges in biology. Here, we use multifield variable-temperature NMR longitudinal relaxation (R₁) measurements to determine the hierarchical activation energies of motions of four different proteins: two small globular proteins (GB1 and the SH3 domain of α-spectrin), an intrinsically disordered protein (the C-terminus of the nucleoprotein of the Sendai virus, Sendai Ntail), and an outer membrane protein (OmpG). The activation energies map the motions occurring in the side chains, in the backbone, and in the hydration shells of the proteins. We were able to identify similarities and differences in the average motions of the proteins. We find that the NMR relaxation properties of the four proteins do share similar features. The data characterizing average backbone motions are found to be very similar, the same for methyl group rotations, and similar activation energies are measured. The main observed difference occurs for the intrinsically disordered Sendai Ntail, where we observe much lower energy of activation for motions of protons associated with the protein-solvent interface as compared to the others. We also observe variability between the proteins regarding side chain ¹⁵N relaxation of lysine residues, with a higher activation energy observed in OmpG. This hints at strong interactions with negatively charged lipids in the bilayer and provides a possible mechanistic clue for the "positive-inside" rule for helical membrane proteins. Overall, these observations refine the understanding of the similarities and differences between hierarchical dynamics in proteins.

Effect of red blood cell shape changes on haemoglobin interactions and dynamics: a neutron scattering study

By using a combination of experimental neutron scattering techniques, it is possible to obtain a statistical perspective on red blood cell (RBC) shape in suspensions, and the inter-relationship with protein interactions and dynamics inside the confinement of the cell membrane. In this study, we examined the ultrastructure of RBC and protein-protein interactions of haemoglobin (Hb) in them using ultra-small-angle neutron scattering and small-angle neutron scattering (SANS). In addition, we used the neutron backscattering method to access Hb motion on the ns time scale and Å length scale. Quasi-elastic neutron scattering (QENS) experiments were performed to measure diffusive motion of Hb in RBCs and in an RBC lysate. By using QENS, we probed both internal Hb dynamics and global protein diffusion, on the accessible time scale and length scale by QENS. Shape changes of RBCs and variation of intracellular Hb concentration were induced by addition of the Na⁺-selective ionophore monensin and the K⁺-selective one, valinomycin. The experimental SANS and QENS results are discussed within the framework of crowded protein solutions, where free motion of Hb is obstructed by mutual interactions.

DI-5-Cuffs: Lumbar Intervertebral Disc Proteoglycan and Water Content Changes in Humans after Five Days of Dry Immersion to Simulate Microgravity

Most astronauts experience back pain after spaceflight, primarily located in the lumbar region. Intervertebral disc herniations have been observed after real and simulated microgravity. Spinal deconditioning after exposure to microgravity has been described, but the underlying mechanisms are not well understood. The dry immersion (DI) model of microgravity was used with eighteen male volunteers. Half of the participants wore thigh cuffs as a potential countermeasure. The spinal changes and intervertebral disc (IVD) content changes were investigated using magnetic resonance imaging (MRI) analyses with T1-T2 mapping sequences. IVD water content was estimated by the apparent diffusion coefficient (ADC), with proteoglycan content measured using MRI T1-mapping sequences centered in the nucleus pulposus. The use of thigh cuffs had no effect on any of the spinal variables measured. There was significant spinal lengthening for all of the subjects. The ADC and IVD proteoglycan content both increased significantly with DI (7.34 ± 2.23% and 10.09 ± 1.39%, respectively; mean ± standard deviation), p < 0.05). The ADC changes suggest dynamic and rapid water diffusion inside IVDs, linked to gravitational unloading. Further investigation is needed to determine whether similar changes occur in the cervical IVDs. A better understanding of the mechanisms involved in spinal deconditioning with spaceflight would assist in the development of alternative countermeasures to prevent IVD herniation.

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.

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.

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.

Microscopic diffusion processes measured in living planarians

Living planarian flatworms were probed using quasielastic neutron scattering to measure, on the pico-to-nanosecond time scale and nanometer length scale, microscopic diffusion of water and cell constituents in the planarians. Measurable microscopic diffusivities were surprisingly well defined in such a complex system as living animals. The overall variation in the microscopic diffusivity of cell constituents was found to be far lower than the variation in the microscopic diffusivity of water in planarians in a temperature range of 284.5 to 304.1 K.

Homogeneous and heterogeneous dynamics in native and denatured bovine serum albumin

Quasielastic incoherent neutron spectroscopy experiments reveal that chemical denaturation significantly modifies the internal dynamics of bovine serum albumin.

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.

In Vivo Protein Dynamics on the Nanometer Length Scale and Nanosecond Time Scale

Selectively labeled GroEL protein was produced in living deuterated bacterial cells to enhance its neutron scattering signal above that of the intracellular milieu. Quasi-elastic neutron scattering shows that the in-cell diffusion coefficient of GroEL was (4.7 ± 0.3) × 10^-12 m²/s, a factor of 4 slower than its diffusion coefficient in buffer solution. Internal protein dynamics showed a relaxation time of (65 ± 6) ps, a factor of 2 slower compared to the protein in solution. Comparison to the literature suggests that the effective diffusivity of proteins depends on the length and time scale being probed. Retardation of in-cell diffusion compared to the buffer becomes more significant with the increasing probe length scale, suggesting that intracellular diffusion of biomolecules is nonuniform over the cellular volume. The approach outlined here enables investigation of protein dynamics within living cells to open up new lines of research using "in-cell neutron scattering" to study the dynamics of complex biomolecular systems.

Rigidity of transmembrane proteins determines their cluster shape

Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as α-helices and β-sheets have different structural rigidities. We use molecular dynamics simulation of a coarse-grained model of protein-embedded lipid membranes to investigate the mechanisms of protein clustering. For a variety of protein concentrations, our simulations under thermal equilibrium conditions reveal that the structural rigidity of transmembrane domains dramatically affects interactions and changes the shape of the cluster. We have observed stable large aggregates even in the absence of hydrophobic mismatch, which has been previously proposed as the mechanism of protein aggregation. According to our results, semiflexible proteins aggregate to form two-dimensional clusters, while rigid proteins, by contrast, form one-dimensional string-like structures. By assuming two probable scenarios for the formation of a two-dimensional triangular structure, we calculate the lipid density around protein clusters and find that the difference in lipid distribution around rigid and semiflexible proteins determines the one- or two-dimensional nature of aggregates. It is found that lipids move faster around semiflexible proteins than rigid ones. The aggregation mechanism suggested in this paper can be tested by current state-of-the-art experimental facilities.

Hierarchical molecular dynamics of bovine serum albumin in concentrated aqueous solution below and above thermal denaturation

The dynamics of proteins in solution is a complex and hierarchical process, affected by the aqueous environment as well as temperature. We present a comprehensive study on nanosecond time and nanometer length scales below, at, and above the denaturation temperature Td. Our experimental data evidence dynamical processes in protein solutions on three distinct time scales. We suggest a consistent physical picture of hierarchical protein dynamics: (i) self-diffusion of the entire protein molecule is confirmed to agree with colloid theory for all temperatures where the protein is in its native conformational state. At higher temperatures T > Td, the self-diffusion is strongly obstructed by cross-linking or entanglement. (ii) The amplitude of backbone fluctuations grows with increasing T, and a transition in its dynamics is observed above Td. (iii) The number of mobile side-chains increases sharply at Td while their average dynamics exhibits only little variations. The combination of quasi-elastic neutron scattering and the presented analytical framework provides a detailed microscopic picture of the protein molecular dynamics in solution, thereby reflecting the changes of macroscopic properties such as cluster formation and gelation.

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

α-synuclein (αSyn) is a protein consisting of 140 amino acid residues and is abundant in the presynaptic nerve terminals in the brain. Although its precise function is unknown, the filamentous aggregates (amyloid fibrils) of αSyn have been shown to be involved in the pathogenesis of Parkinson's disease, which is a progressive neurodegenerative disorder. To understand the pathogenesis mechanism of this disease, the mechanism of the amyloid fibril formation of αSyn must be elucidated. Purified αSyn from bacterial expression is monomeric but intrinsically disordered in solution and forms amyloid fibrils under various conditions. As a first step toward elucidating the mechanism of the fibril formation of αSyn, we investigated dynamical behavior of the purified αSyn in the monomeric state and the fibril state using quasielastic neutron scattering (QENS). We prepared the solution sample of 9.5 mg/ml purified αSyn, and that of 46 mg/ml αSyn in the fibril state, both at pD 7.4 in D2O. The QENS experiments on these samples were performed using the near-backscattering spectrometer, BL02 (DNA), at the Materials and Life Science Facility at the Japan Accelerator Research Complex, Japan. Analysis of the QENS spectra obtained shows that diffusive global motions are observed in the monomeric state but largely suppressed in the fibril state. However, the amplitude of the side chain motion is shown to be larger in the fibril state than in the monomeric state. This implies that significant solvent space exists within the fibrils, which is attributed to the αSyn molecules within the fibrils having a distribution of conformations. The larger amplitude of the side chain motion in the fibril state than in the monomeric state implies that the fibril state is entropically favorable.

Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding

Myoglobin can be trapped in fully folded structures, partially folded molten globules, and unfolded states under stable equilibrium conditions.

Molecular Dynamics Simulations of a Powder Model of the Intrinsically Disordered Protein Tau

The tau protein, whose aggregates are involved in Alzheimer's disease, is an intrinsically disordered protein (IDP) that regulates microtubule activity in neurons. An IDP lacks a single, well-defined structure and, rather, constantly exchanges among multiple conformations. In order to study IDP dynamics, the combination of experimental techniques, such as neutron scattering, and computational techniques, such as molecular dynamics (MD) simulations, is a powerful approach. Amorphous hydrated powder samples have been very useful for studying protein internal dynamics experimentally, e.g., using neutron scattering. Thus, there is demand for realistic in silico models of hydrated protein powders. Here we present an MD simulation analysis of a powder hydrated at 0.4 g water/g protein of the IDP tau in the temperature range 20-300 K. By comparing with neutron scattering data, we identify the protein-water interface as the predominant feature determining IDP dynamics. The so-called protein dynamical transition is shown to be attenuated, but not suppressed, in the parts of the protein that are not exposed to the solvent. In addition, we find similarities in the mean-squared displacements of the core of a globular protein and "dry" clusters formed by the IDP in hydrated powders. Thus, the ps to ns dynamics of proteins in hydrated powders originate mainly from those residues in contact with solvent. We propose that by measuring the dynamics of protein assemblies, such as aggregates, one might assess qualitatively their state of hydration.

Dynamic footprint of sequestration in the molecular fluctuations of osteopontin

The sequestration of calcium phosphate by unfolded proteins is fundamental to the stabilization of biofluids supersaturated with respect to hydroxyapatite, such as milk, blood or urine. The unfolded state of osteopontin (OPN) is thought to be a prerequisite for this activity, which leads to the formation of core-shell calcium phosphate nanoclusters. We report on the structures and dynamics of a native OPN peptide from bovine milk, studied by neutron spectroscopy and small-angle X-ray and neutron scattering. The effects of sequestration are quantified on the nanosecond- ångström resolution by elastic incoherent neutron scattering. The molecular fluctuations of the free phosphopeptide are in agreement with a highly flexible protein. An increased resilience to diffusive motions of OPN is corroborated by molecular fluctuations similar to those observed for globular proteins, yet retaining conformational flexibilities. The results bring insight into the modulation of the activity of OPN and phosphopeptides with a role in the control of biomineralization. The quantification of such effects provides an important handle for the future design of new peptides based on the dynamics-activity relationship.

Protein dynamics: from rattling in a cage to structural relaxation

We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss the coupling of these processes to solvent dynamics. Our analysis suggests that the microsecond backbone relaxation process might be the main structural relaxation of the protein that defines its glass transition temperature, while faster processes present some localized secondary relaxations. Based on the overview, we formulate a general picture of protein dynamics and discuss the challenges in this field.

Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

Hydration water plasticizes protein structures and is essential for their biological functions, such as enzymatic catalysis. Here, the authors use neutron scattering and molecular dynamics simulations to study hydration water at the dynamical transition of folded and disordered proteins.

Temperature-dependent dynamics of dry and hydrated β-casein studied by quasielastic neutron scattering

β-Casein is a component of casein micelle with amphillic nature and is recognized as a "natively disordered" protein that lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of β-casein are explored by quasielastic neutron scattering (QENS). An upturn in the mean square displacement (MSD) of hydrated β-casein indicates an increase of protein flexibility at a temperature of ~225 K. Another increase in MSD at ~100 K, observed in both dry and hydrated β-casein, is ascribed to the methyl group rotations, which are not sensitive to hydration. QENS analysis in the energy domain reveals that the fraction of hydrogen atoms participating in motion in a sphere of diffusion is highly hydration dependent and increases with temperature. In the time domain analysis, a logarithmic-like decay is observed in the range of picosecond to nanosecond (β-relaxation time) in the dynamics of hydrated β-casein. This dynamical behavior has been observed in hydrated globular and oligomeric proteins. Our temperature-dependent QENS experiments provide evidence that lack of a secondary structure in β-casein results in higher flexibility in its dynamics and easier reversible thermal unfolding compared to other rigid biomolecules.

Dynamics and rigidity in an intrinsically disordered protein, β-casein

The emergence of intrinsically disordered proteins (IDPs) as a recognized structural class has forced the community to confront a new paradigm of structure, dynamics, and mechanical properties for proteins. We present novel data on the similarities and differences in the dynamics and nanomechanical properties of IDPs and other biomacromolecules on the picosecond time scale. An IDP, β-casein (CAS), has been studied in a calcium bound and unbound state using neutron and light scattering techniques. We show that CAS partially folds and stiffens upon calcium binding, but in the unfolded state, it is softer than folded proteins such as green fluorescence protein (GFP). We also see that some localized diffusive motions in CAS have a larger amplitude than in GFP at this time scale but are still smaller than those observed in tRNA. In spite of these differences, CAS dynamics are consistent with the classes of motions seen in folded protein on this time scale.

Strategies for a direct characterization of phosphoproteins on hydroxyapatite surfaces

We show in this work how systems formed by phosphoproteins on calcium phosphate surfaces can be directly characterized, in real time, in liquid medium, without the need for elution or labeling. Specifically, we show how this is possible by applying three different techniques: ellipsometry, quartz crystal microbalance with dissipation, and atomic force microscopy-based friction force spectroscopy. We apply these techniques to study two different model systems, i.e. those formed upon the adsorption of two model phosphoproteins (κ- and β-casein) on hydroxyapatite (HA) surfaces. Information on the kinetics of adsorption, surface excess, viscoelasticity, water content, thickness of the layers, and protein-surface interaction is provided. Results indicate that both phosphoproteins form homogeneous elastic highly hydrated monolayers on the HA surfaces, the strength of β-casein layers being higher by approximately a factor of 4. Based on the experimental results, models for the conformation of κ- and β-casein molecules adsorbed on HA surfaces are proposed.

Secondary structure and rigidity in model proteins

There is tremendous interest in understanding the role that secondary structure plays in the rigidity and dynamics of proteins. In this work we analyze nanomechanical properties of proteins chosen to represent different secondary structures: α-helices (myoglobin and bovine serum albumin), β-barrels (green fluorescent protein), and α + β + loop structures (lysozyme). Our experimental results show that in these model proteins, the β motif is a stiffer structural unit than the α-helix in both dry and hydrated states. This difference appears not only in the rigidity of the protein, but also in the amplitude of fast picosecond fluctuations. Moreover, we show that for these examples the secondary structure correlates with the temperature- and hydration-induced changes in the protein dynamics and rigidity. Analysis also suggests a connection between the length of the secondary structure (α-helices) and the low-frequency vibrational mode, the so-called boson peak. The presented results suggest an intimate connection of dynamics and rigidity with the protein secondary structure.

Dynamical coupling of intrinsically disordered proteins and their hydration water: comparison with folded soluble and membrane proteins

Hydration water is vital for various macromolecular biological activities, such as specific ligand recognition, enzyme activity, response to receptor binding, and energy transduction. Without hydration water, proteins would not fold correctly and would lack the conformational flexibility that animates their three-dimensional structures. Motions in globular, soluble proteins are thought to be governed to a certain extent by hydration-water dynamics, yet it is not known whether this relationship holds true for other protein classes in general and whether, in turn, the structural nature of a protein also influences water motions. Here, we provide insight into the coupling between hydration-water dynamics and atomic motions in intrinsically disordered proteins (IDP), a largely unexplored class of proteins that, in contrast to folded proteins, lack a well-defined three-dimensional structure. We investigated the human IDP tau, which is involved in the pathogenic processes accompanying Alzheimer disease. Combining neutron scattering and protein perdeuteration, we found similar atomic mean-square displacements over a large temperature range for the tau protein and its hydration water, indicating intimate coupling between them. This is in contrast to the behavior of folded proteins of similar molecular weight, such as the globular, soluble maltose-binding protein and the membrane protein bacteriorhodopsin, which display moderate to weak coupling, respectively. The extracted mean square displacements also reveal a greater motional flexibility of IDP compared with globular, folded proteins and more restricted water motions on the IDP surface. The results provide evidence that protein and hydration-water motions mutually affect and shape each other, and that there is a gradient of coupling across different protein classes that may play a functional role in macromolecular activity in a cellular context.

Effect of gallic acid on peptides released by trypsin digestion of bovine α-casein

In this study, the effects of gallic acid (GA) on trypsin digestion of commercial α-casein (α-CN), which contains α(s1)-CN and α(s2)-CN, and the peptides released during digestion were investigated. Gallic acid showed no effect on the initial rate of digestion. However, the apparent degree of hydrolysis achieved its maximum value after 1 h, then decreased in the presence of GA, suggesting the cross-linking between peptides once released from α-CN during digestion. In the presence of GA, three peaks derived from α(s1)-CN disappeared and three new peaks appeared in high-performance liquid chromatography (HPLC) analysis. In these peptides, two Met residues corresponding to the Met(135) and Met(196) in α(s1)-CN were oxidized to Met sulfoxide residues. The oxidation of Met(196) was quicker than that of Met(135). The inhibitory activity of TTMPLW (α(s1)-CN 193-199) against angiotensin I-converting enzyme was reduced slightly by the oxidation of its Met residue.

Order out of disorder: working cycle of an intrinsically unfolded chaperone

The redox-regulated chaperone Hsp33 protects organisms against oxidative stress that leads to protein unfolding. Activation of Hsp33 is triggered by the oxidative unfolding of its own redox-sensor domain, making Hsp33 a member of a recently discovered class of chaperones that require partial unfolding for full chaperone activity. Here we address the long-standing question of how chaperones recognize client proteins. We show that Hsp33 uses its own intrinsically disordered regions to discriminate between unfolded and partially structured folding intermediates. Binding to secondary structure elements in client proteins stabilizes Hsp33's intrinsically disordered regions, and this stabilization appears to mediate Hsp33's high affinity for structured folding intermediates. Return to nonstress conditions reduces Hsp33's disulfide bonds, which then significantly destabilizes the bound client proteins and in doing so converts them into less-structured, folding-competent client proteins of ATP-dependent foldases. We propose a model in which energy-independent chaperones use internal order-to-disorder transitions to control substrate binding and release.

Expanding the proteome: disordered and alternatively folded proteins

Proteins provide much of the scaffolding for life, as well as undertaking a variety of essential catalytic reactions. These characteristic functions have led us to presuppose that proteins are in general functional only when well structured and correctly folded. As we begin to explore the repertoire of possible protein sequences inherent in the human and other genomes, two stark facts that belie this supposition become clear: firstly, the number of apparent open reading frames in the human genome is significantly smaller than appears to be necessary to code for all of the diverse proteins in higher organisms, and secondly that a significant proportion of the protein sequences that would be coded by the genome would not be expected to form stable three-dimensional (3D) structures. Clearly the genome must include coding for a multitude of alternative forms of proteins, some of which may be partly or fully disordered or incompletely structured in their functional states. At the same time as this likelihood was recognized, experimental studies also began to uncover examples of important protein molecules and domains that were incompletely structured or completely disordered in solution, yet remained perfectly functional. In the ensuing years, we have seen an explosion of experimental and genome-annotation studies that have mapped the extent of the intrinsic disorder phenomenon and explored the possible biological rationales for its widespread occurrence. Answers to the question 'why would a particular domain need to be unstructured?' are as varied as the systems where such domains are found. This review provides a survey of recent new directions in this field, and includes an evaluation of the role not only of intrinsically disordered proteins but also of partially structured and highly dynamic members of the disorder-order continuum.

Broadband depolarized light scattering study of diluted protein aqueous solutions

A broadband depolarized light scattering (DLS) study is performed on diluted lysozyme aqueous solutions as a function of temperature and concentration. The dynamical susceptibility, obtained in a wide spectral range (0.6-36000 GHz) through the coupled use of interferometric and dispersive devices, is interpreted and compared with neutron scattering and Raman-induced optical Kerr-effect literature data, thus giving a general picture of relaxation phenomena. We show that the proposed approach represents a suitable tool for investigating the hydration dynamics of protein-water solutions. A detailed analysis of the quasi-elastic scattering region evidences the existence of two distinct relaxational processes at picosecond time scales. The fast process (fractions of picosecond) is attributed to bulk water dynamics, while the slow one (few picoseconds) is attributed to dynamical rearrangements of water molecules strongly influenced by the protein (hydration water). The retardation effect here estimated of about 6-7 can be regarded as a direct measure of the increased protein-water and water-water hydrogen bond stability of the water molecules within the protein hydration shell. Interestingly, a similar effect was previously observed on small hydrophilic sugar molecules. Moreover, backbone and side chains torsional motions of the protein in the 600-5300 GHz frequency range are found to be insensitive to thermal variations and to eventual changes occurring in the premelting zone.

Macromolecular dynamics in red blood cells investigated using neutron spectroscopy

We present neutron scattering measurements on the dynamics of haemoglobin (Hb) in human red blood cells (RBCs) in vivo. Global and internal Hb dynamics were measured in the ps to ns time and Å length scales using quasi-elastic neutron backscattering spectroscopy. We observed the cross over from global Hb short-time to long-time self-diffusion. Both short- and long-time diffusion coefficients agree quantitatively with predicted values from the hydrodynamic theory of non-charged hard-sphere suspensions when a bound water fraction of around 0.23 gram H(2)O per gram Hb is taken into account. The higher amount of water in the cells facilitates internal protein fluctuations in the ps time scale when compared with fully hydrated Hb powder. Slower internal dynamics of Hb in RBCs in the ns time range were found to be rather similar to results obtained with fully hydrated protein powders, solutions and Escherichia coli cells.

Susceptibility of different proteins to flow-induced conformational changes monitored with Raman spectroscopy

By directly monitoring stirred protein solutions with Raman spectroscopy, the reversible unfolding of proteins caused by fluid shear is examined for several natural proteins with varying structural properties and molecular weight. While complete denaturation is not observed, a wide range of spectral variances occur for the different proteins, indicating subtle conformational changes that appear to be protein-specific. A number of significant overall trends are apparent from the study. For globular proteins, the overall extent of spectral variance increases with protein size and the proportion of beta-structure. For two less structured proteins, fetuin and alpha-casein, the observed changes are of relatively low magnitude, despite the greater molecular structural mobility of these proteins. This implies that other protein-specific factors, such as posttranslational modifications, may also be significant. Individual band changes occurring in the spectral profiles of each individual protein are also discussed in detail.

Introduction to Quasielastic Neutron Scattering

This tutorial introduction has been written for people who are not specialized in neutron scattering or in other scattering methods but who are interested and would like to get an impression and learn about the method of Quasielastic Neutron Scattering (QENS). The theoretical (scattering process) as well as the experimental basics (neutron sources, neutron scattering instruments, experimental periphery) are explained in a generally understandable way, with only the most essential formulas. QENS addresses the stochastic dynamics in condensed matter, and it is pointed out for which problems and for which systems in condensed matter research QENS is a powerful method. Thus sufficient information is provided to enable non-experts to think about their own QENS experiment and to understand related literature in this area of research.

From powder to solution: hydration dependence of human hemoglobin dynamics correlated to body temperature

A transition in hemoglobin (Hb), involving partial unfolding and aggregation, has been shown previously by various biophysical methods. The correlation between the transition temperature and body temperature for Hb from different species, suggested that it might be significant for biological function. To focus on such biologically relevant human Hb dynamics, we studied the protein internal picosecond motions as a response to hydration, by elastic and quasielastic neutron scattering. Rates of fast diffusive motions were found to be significantly enhanced with increasing hydration from fully hydrated powder to concentrated Hb solution. In concentrated protein solution, the data showed that amino acid side chains can explore larger volumes above body temperature than expected from normal temperature dependence. The body temperature transition in protein dynamics was absent in fully hydrated powder, indicating that picosecond protein dynamics responsible for the transition is activated only at a sufficient level of hydration. A collateral result from the study is that fully hydrated protein powder samples do not accurately describe all aspects of protein picosecond dynamics that might be necessary for biological function.

Protein diffusion in crowded electrolyte solutions

We report on a combined cold neutron backscattering and spin-echo study of the short-range and long-range nanosecond diffusion of the model globular protein bovine serum albumin (BSA) in aqueous solution as a function of protein concentration and NaCl salt concentration. Complementary small angle X-ray scattering data are used to obtain information on the correlations of the proteins in solution. Particular emphasis is put on the effect of crowding, i.e. conditions under which the proteins cannot be considered as objects independent of each other. We thus address the question at which concentration this crowding starts to influence the static and in particular also the dynamical behaviour. We also briefly discuss qualitatively which charge effects, i.e. effects due to the interplay of charged molecules in an electrolyte solution, may be anticipated. Both the issue of crowding as well as that of charge effects are particularly relevant for proteins and their function under physiological conditions, where the protein volume fraction can be up to approximately 40% and salt ions are ubiquitous. The interpretation of the data is put in the context of existing studies on related systems and of existing theoretical models.