Slow internal protein dynamics in solution

Metastable States in the Hinge-Bending Landscape of an Enzyme in an Atomistic Cytoplasm Simulation

Many enzymes undergo major conformational changes to function in cells, particularly when they bind to more than one substrate. We quantify the large-amplitude hinge-bending landscape of human phosphoglycerate kinase (PGK) in a human cytoplasm. Approximately 70 μs of all-atom simulations, upon coarse graining, reveal three metastable states of PGK with different hinge angle distributions and additional substates. The "open" state was more populated than the "semi-open" or "closed" states. In addition to free energies and barriers within the landscape, we characterized the average transition state passage time of ≈0.3 μs and reversible substrate and product binding. Human PGK in a dilute solution simulation shows a transition directly from the open to closed states, in agreement with previous SAXS experiments, suggesting that the cell-like model environment promotes stability of the human PGK semi-open state. Yeast PGK also sampled three metastable states within the cytoplasm model, with the closed state favored in our simulation.

The Onset of Molecule-Spanning Dynamics in Heat Shock Protein Hsp90

Protein dynamics have been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is largely unknown how fast (local) fluctuations can lead to slow global (allosteric) changes. Here, fast molecule-spanning dynamics on the 100 to 200 ns time scale in the heat shock protein 90 (Hsp90) are shown. Global real-space movements are assigned to dynamic modes on this time scale, which is possible by a combination of single-molecule fluorescence, quasi-elastic neutron scattering and all-atom molecular dynamics (MD) simulations. The time scale of these dynamic modes depends on the conformational state of the Hsp90 dimer. In addition, the dynamic modes are affected to various degrees by Sba1, a co-chaperone of Hsp90, depending on the location within Hsp90, which is in very good agreement with MD simulations. Altogether, this data is best described by fast molecule-spanning dynamics, which precede larger conformational changes in Hsp90 and might be the molecular basis for allostery. This integrative approach provides comprehensive insights into molecule-spanning dynamics on the nanosecond time scale for a multi-domain protein.

Interchain Hydrodynamic Interaction and Internal Friction of Polyelectrolytes

Polyelectrolytes (PE) are polymeric macromolecules in aqueous solutions characterized by their chain topology and intrinsic charge in a neutralizing fluid. Structure and dynamics are related to several characteristic screening length scales determined by electrostatic, excluded volume, and hydrodynamic interactions. We examine PE dynamics in dilute to semidilute conditions using dynamic light scattering, neutron spinecho spectroscopy, and pulse field gradient NMR spectroscopy. We connect macroscopic diffusion to segmental chain dynamics, revealing a decoupling of local chain dynamics from interchain interactions. Collective diffusion is described within a colloidal picture, including electrostatic and hydrodynamic interactions. Chain dynamics is characterized by the classical Zimm model of a neutral chain retarded by internal friction. We observe that hydrodynamic interactions are not fully screened between chains and that the internal friction within the chain increases with an increase in ion condensation on the chain.

How neutron scattering techniques benefit investigating structures and dynamics of monoclonal antibody

Over the past several decades, great progresses have been made for the pharmaceutical industry of monoclonal antibody (mAb). More and more mAb products were approved for human therapeutics. This review describes the state of art of utilizing neutron scattering to investigate mAbs, in the aspects of structures, dynamics, physicochemical stability, functionality, etc. Firstly, brief histories of mAbs and neutron scattering, as well as some basic knowledges and principles of neutron scattering were introduced. Then specific examples were demonstrated. For the structure and structural evolution investigation of in dilute and concentrated mAbs solution, in situ small angle neutron scattering (SANS) was frequently utilized. Neutron reflectometry (NR) is powerful to probe the absorption behaviors of mAbs on various surfaces and interfaces. While for dynamic investigation, quasi-elastic scattering techniques such as neutron spin echo (NSE) demonstrate the capabilities. With this review, how to utilize and take advantages of neutron scattering on investigating structures and dynamics of mAbs were demonstrated and discussed.

Variation of Structural and Dynamical Flexibility of Myelin Basic Protein in Response to Guanidinium Chloride

Myelin basic protein (MBP) is intrinsically disordered in solution and is considered as a conformationally flexible biomacromolecule. Here, we present a study on perturbation of MBP structure and dynamics by the denaturant guanidinium chloride (GndCl) using small-angle scattering and neutron spin–echo spectroscopy (NSE). A concentration of 0.2 M GndCl causes charge screening in MBP resulting in a compact, but still disordered protein conformation, while GndCl concentrations above 1 M lead to structural expansion and swelling of MBP. NSE data of MBP were analyzed using the Zimm model with internal friction (ZIF) and normal mode (NM) analysis. A significant contribution of internal friction was found in compact states of MBP that approaches a non-vanishing internal friction relaxation time of approximately 40 ns at high GndCl concentrations. NM analysis demonstrates that the relaxation rates of internal modes of MBP remain unaffected by GndCl, while structural expansion due to GndCl results in increased amplitudes of internal motions. Within the model of the Brownian oscillator our observations can be rationalized by a loss of friction within the protein due to structural expansion. Our study highlights the intimate coupling of structural and dynamical plasticity of MBP, and its fundamental difference to the behavior of ideal polymers in solution.

Neutron Scattering Techniques and Complementary Methods for Structural and Functional Studies of Biological Macromolecules and Large Macromolecular Complexes

Abstract

The review describes the application of small-angle scattering (SAS) of neutrons and complementary methods to study the structures of biomacromolecules. Here we cover SAS techniques, such as the contrast variation, the neutron spin-echo, and the solution of direct and inverse problems of three-dimensional reconstruction of the structures of macromolecules from SAS spectra by means of molecular modeling. A special section is devoted to specific objects of research, such as supramolecular complexes, influenza virus nucleoprotein, and chromatin.

Intermediate scattering functions of a rigid body monoclonal antibody protein in solution studied by dissipative particle dynamic simulation

In the past decade, there was increased research interest in studying internal motions of flexible proteins in solution using Neutron Spin Echo (NSE) as NSE can simultaneously probe the dynamics at the length and time scales comparable to protein domain motions. However, the collective intermediate scattering function (ISF) measured by NSE has the contributions from translational, rotational, and internal motions, which are rather complicated to be separated. Widely used NSE theories to interpret experimental data usually assume that the translational and rotational motions of a rigid particle are decoupled and independent to each other. To evaluate the accuracy of this approximation for monoclonal antibody (mAb) proteins in solution, dissipative particle dynamic computer simulation is used here to simulate a rigid-body mAb for up to about 200 ns. The total ISF together with the ISFs due to only the translational and rotational motions as well as their corresponding effective diffusion coefficients is calculated. The aforementioned approximation introduces appreciable errors to the calculated effective diffusion coefficients and the ISFs. For the effective diffusion coefficient, the error introduced by this approximation can be as large as about 10% even though the overall agreement is considered reasonable. Thus, we need to be cautious when interpreting the data with a small signal change. In addition, the accuracy of the calculated ISFs due to the finite computer simulation time is also discussed.

Dynamics studied by Quasielastic Neutron Scattering (QENS)

Quasielastic neutron scattering (QENS) allows measurement of the molecular displacements in time and space, from pico- to tens of nanoseconds and from Ångstroms to nanometers, respectively. The method probes dynamics from fast vibrational modes down to slow diffusive motion. Every scattering experiment leads to a dynamic structure factor $$S\left( {\vec Q,\omega } \right)$$ S Q → , ω or its spatial and temporal Fourier transform (van Hove correlation function $$G\left( {\vec r,t} \right)$$ G r → , t ). This shows exactly where the atoms are and how they move. In this manuscript the basics of the QENS method are presented and a few examples highlighting the potentials of QENS are given: (i) diffusion of liquids and gases in nano- and mesoporous materials; (ii) hydrogen dynamics in a high temperature polymer electrolyte fuel cell (HT-PEFC) and (iii) influence of the surface interactions on polymer dynamics in nanopores.

Structure and Dynamics of Ribonuclease A during Thermal Unfolding: The Failure of the Zimm Model

Disordered regions as found in intrinsically disordered proteins (IDP) or during protein folding define response time to stimuli and protein folding times. Neutron spin-echo spectroscopy is a powerful tool to directly access the collective motions of the unfolded chain to enlighten the physical origin of basic conformational relaxation. During the thermal unfolding of native ribonuclease A, we examine the structure and dynamics of the disordered state within a two-state transition model using polymer models, including internal friction, to describe the chain dynamics. The presence of four disulfide bonds alters the disordered configuration to a more compact configuration compared to a Gaussian chain that is defined by the additional links, as demonstrated by coarse-grained simulation. The dynamics of the disordered chain is described by Zimm dynamics with internal friction (ZIF) between neighboring amino acids. Relaxation times are dominated by mode-independent internal friction. Internal friction relaxation times show an Arrhenius-like behavior with an activation energy of 33 kJ/mol. The Zimm dynamics is dominated by internal friction and suggest that the characteristic motions correspond to overdamped elastic modes similar to the motions observed for folded proteins but within a pool of disordered configurations spanning the configurational space. For IDP, internal friction dominates while solvent friction and hydrodynamic interactions are smaller corrections.

Reduced Internal Friction by Osmolyte Interaction in Intrinsically Disordered Myelin Basic Protein

Urea is a strong denaturing osmolyte that disrupts noncovalent bonds in proteins. Here, we present a small-angle neutron scattering (SANS) and neutron spin-echo spectroscopy (NSE) study on the structure and dynamics of the intrinsically disordered myelin basic protein (MBP) denatured by urea. SANS results show that urea-denatured MBP is more compact than ideal polymers, while its secondary structure content is entirely lost. NSE experiments reveal concomitantly an increase of the relaxation time and of the amplitude of internal motions in urea-denatured MBP as compared to native MBP. If interpreted in terms of the Zimm model including internal friction (ZIF), the internal friction parameter decreased by a factor of 6.5. Urea seems to not only smooth local energy barriers, reducing internal friction on a local scale, but also significantly reduces the overall depth of the global energy landscape. This leads to a nearly complete loss of restoring forces beyond entropic forces and in turn allows for larger motional amplitudes. Obviously, the noncovalent H-bonds are largely eliminated, driving the unfolded protein to be more similar to a synthetic polymer.

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.

Jscatter, a program for evaluation and analysis of experimental data

The aim of Jscatter is the processing of experimental data and physical models with the focus to enable the user to develop/modify their own models and use them within experimental data evaluation. The basic structures dataArray and dataList contain matrix-like data of different size including attributes to store corresponding metadata. The attributes are used in fit routines as parameters allowing multidimensional attribute dependent fitting. Several modules provide models mainly applied in neutron and X- ray scattering for small angle scattering (form factors and structure factors) and inelastic neutron scattering. The intention is to provide an environment with fit routines, data handling routines (based on NumPy arrays) and a model library to allow the user to focus onto user-written models for data analysis with the benefit of convenient documentation of scientific data evaluation in a scripting environment.

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.

Perspective: Chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single-molecule FRET

The dynamics of unfolded proteins are important both for the process of protein folding and for the behavior of intrinsically disordered proteins. However, methods for investigating the global chain dynamics of these structurally diverse systems have been limited. A versatile experimental approach is single-molecule spectroscopy in combination with Förster resonance energy transfer and nanosecond fluorescence correlation spectroscopy. The concepts of polymer physics offer a powerful framework both for interpreting the results and for understanding and classifying the properties of unfolded and intrinsically disordered proteins. This information on long-range chain dynamics can be complemented with spectroscopic techniques that probe different length scales and time scales, and integration of these results greatly benefits from recent advances in molecular simulations. This increasing convergence between the experiment, theory, and simulation is thus starting to enable an increasingly detailed view of the dynamics of disordered proteins.

Relevance of Internal Friction and Structural Constraints for the Dynamics of Denatured Bovine Serum Albumin

A general property of disordered proteins is their structural expansion that results in a high molecular flexibility. The structure and dynamics of bovine serum albumin (BSA) denatured by guanidinium hydrochloride (GndCl) were investigated using small-angle neutron scattering (SANS) and neutron spin-echo spectroscopy (NSE). SANS experiments demonstrated the relevance of intrachain interactions for structural expansion. Using NSE experiments, we observed a high internal flexibility of denatured BSA in addition to center-of-mass diffusion detected by dynamic light scattering. Internal motions measured by NSE were described using concepts based on polymer theory. The contribution of residue-solvent friction was accounted for using the Zimm model including internal friction (ZIF). Disulfide bonds forming loops of amino acids of the peptide backbone have a major impact on internal dynamics that can be interpreted with a reduced set of Zimm modes.

Intermediate scattering function for macromolecules in solutions probed by neutron spin echo

The neutron-spin-echo method (NSE) is a powerful technique for studying internal dynamics of macromolecules in solutions because it can simultaneously probe length and time scales comparable to intramolecular density fluctuations of macromolecules. Recently, there has been increased, strong interest in studying protein internal motions using NSE. The coherent intermediate scattering function (ISF) measured by NSE depends on internal, rotational, and translational motions of macromolecules in solutions. It is thus critical, but highly nontrivial, to separate the internal motion from other motions in order to properly understand protein internal dynamics. Even though many experiments are performed at relatively high concentrations, current theories of calculating the ISF of concentrated protein solutions are either inaccurate or flawed by incorrect assumptions for realistic protein systems with anisotropic shapes. Here, a theoretical framework is developed to establish the quantitative relationship of different motions included in the ISF. This theory based on the dynamic decoupling approximation is applicable to a wide range of protein concentrations, including dilute cases. It is also, in general, useful for studying many other types of macromolecule systems studied by NSE.

Structure and domain dynamics of human lactoferrin in solution and the influence of Fe(III)-ion ligand binding

Background

Human lactoferrin is an iron-binding protein of the innate immune system consisting of two connected lobes, each with a binding site located in a cleft. The clefts in each lobe undergo a hinge movement from open to close when Fe³⁺ is present in the solution and can be bound. The binding mechanism was assumed to relate on thermal domain fluctuations of the cleft domains prior to binding. We used Small Angle Neutron Scattering and Neutron Spin Echo Spectroscopy to determine the lactoferrin structure and domain dynamics in solution.

Results

When Fe³⁺ is present in solution interparticle interactions change from repulsive to attractive in conjunction with emerging metas aggregates, which are not observed without Fe³⁺. The protein form factor shows the expected change due to lobe closing if Fe³⁺ is present. The dominating motions of internal domain dynamics with relaxation times in the 30–50 ns range show strong bending and stretching modes with a steric suppressed torsion, but are almost independent of the cleft conformation. Thermally driven cleft closing motions of relevant amplitude are not observed if the cleft is open.

Conclusion

The Fe³⁺ binding mechanism is not related to thermal equilibrium fluctuations closing the cleft. A likely explanation may be that upon entering the cleft the iron ion first binds weakly which destabilizes and softens the hinge region and enables large fluctuations that then close the cleft resulting in the final formation of the stable iron binding site and, at the same time, stable closed conformation.

Electronic supplementary material

The online version of this article (doi:10.1186/s13628-016-0032-3) contains supplementary material, which is available to authorized users.

Fast antibody fragment motion: flexible linkers act as entropic spring

A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unbound state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. The Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function.

Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling

Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins (IDPs) and regions (IDRs), which represent ∼30% of the proteome and enable unique regulatory mechanisms. In this review, we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of conformational ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as "ultrasensitivity" and "regulated folding and unfolding". We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information.

Monomeric Amyloid Beta Peptide in Hexafluoroisopropanol Detected by Small Angle Neutron Scattering

Small proteins like amyloid beta (Aβ) monomers are related to neurodegenerative disorders by aggregation to insoluble fibrils. Small angle neutron scattering (SANS) is a nondestructive method to observe the aggregation process in solution. We show that SANS is able to resolve monomers of small molecular weight like Aβ for aggregation studies. We examine Aβ monomers after prolonged storing in d-hexafluoroisopropanol (dHFIP) by using SANS and dynamic light scattering (DLS). We determined the radius of gyration from SANS as 1.0±0.1 nm for Aβ_1–40 and 1.6±0.1 nm for Aβ_1–42 in agreement with 3D NMR structures in similar solvents suggesting a solvent surface layer with 5% increased density. After initial dissolution in dHFIP Aβ aggregates sediment with a major component of pure monomers showing a hydrodynamic radius of 1.8±0.3 nm for Aβ_1–40 and 3.2±0.4 nm for Aβ_1–42 including a surface layer of dHFIP solvent molecules.

Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells

Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement of the thylakoid membranes in response to environmental conditions have been widely investigated. However, there is limited knowledge about the internal dynamics of these membranes in terms of their flexibility and motion during the photosynthetic process. We present a direct observation of thylakoid membrane undulatory motion in vivo and show a connection between membrane mobility and photosynthetic activity. High-resolution inelastic neutron scattering experiments on the cyanobacterium Synechocystis sp. PCC 6803 assessed the flexibility of cyanobacterial thylakoid membrane sheets and the dependence of the membranes on illumination conditions. We observed softer thylakoid membranes in the dark that have three-to four fold excess mobility compared to membranes under high light conditions. Our analysis indicates that electron transfer between photosynthetic reaction centers and the associated electrochemical proton gradient across the thylakoid membrane result in a significant driving force for excess membrane dynamics. These observations provide a deeper understanding of the relationship between photosynthesis and cellular architecture.

Nanoscale protein domain motion and long-range allostery in signaling proteins- a view from neutron spin echo sprectroscopy

Many cellular proteins are multi-domain proteins. Coupled domain-domain interactions in these multidomain proteins are important for the allosteric relay of signals in the cellular signaling networks. We have initiated the application of neutron spin echo spectroscopy to the study of nanoscale protein domain motions on submicrosecond time scales and on nanometer length scale. Our NSE experiments reveal the activation of protein domain motions over a long distance of over more than 100 Å in a multidomain scaffolding protein NHERF1 upon binding to another protein Ezrin. Such activation of nanoscale protein domains motions is correlated with the allosteric assembly of multi-protein complexes by NHERF1 and Ezrin. Here, we summarize the theoretical framework that we have developed, which uses simple concepts from nonequilibrium statistical mechanics to interpret the NSE data, and employs a mobility tensor to describe nanoscale protein domain motion. Extracting nanoscale protein domain motion from the NSE does not require elaborate molecular dynamics simulations, or complex fits to rotational motion, or elastic network models. The approach is thus more robust than multiparameter techniques that require untestable assumptions. We also demonstrate that an experimental scheme of selective deuteration of a protein subunit in a complex can highlight and amplify specific domain dynamics from the abundant global translational and rotational motions in a protein. We expect NSE to provide a unique tool to determine nanoscale protein dynamics for the understanding of protein functions, such as how signals are propagated in a protein over a long distance to a distal domain.