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The contrast‐variation method in small‐angle neutron scattering (SANS) is a uniquely powerful technique for determining the structure of individual components in biomolecular systems containing regions of different neutron scattering length density ρ. By altering the ρ of the target solute and the solvent through judicious incorporation of deuterium, the scattering of desired solute features can be highlighted. Most contrast‐variation methods focus on highlighting specific bulk solute elements, but not on how the scattering at specific scattering vectors q, which are associated with specific structural distances, changes with contrast. Indeed, many systems exhibit q‐dependent contrast effects. Here, a method is presented for calculating both bulk contrast‐match points and q‐dependent contrast using 3D models with explicit solute and solvent atoms and SASSENA, an explicit‐atom SANS calculator. The method calculates the bulk contrast‐match points within 2.4% solvent D2O accuracy for test protein–nucleic acid and lipid nanodisc systems. The method incorporates a general model for the incorporation of deuterium at non‐exchangeable sites that was derived by performing mass spectrometry on green fluorescent protein. The method also decomposes the scattering profile into its component parts and identifies structural features that change with contrast. The method is readily applicable to a variety of systems, will expand the understanding of q‐dependent contrast matching and will aid in the optimization of next‐generation neutron scattering experiments. [ABSTRACT FROM AUTHOR]

A particularly promising approach to deconstructing and fractionating lignocellulosic biomass to produce green renewable fuels and high-value chemicals pretreats the biomass with organic solvents in aqueous solution. Here, neutron scattering and moleculardynamics simulations reveal the temperature-dependent morphological changes in poplar wood biomass during tetrahydrofuran (THF):water pretreatment and provide a mechanism by which the solvent components drive efficient biomass breakdown. Whereas lignin dissociates over a wide temperature range (>25 °C) cellulose disruption occurs only above 150 °C. Neutron scattering with contrast variation provides direct evidence for the formation of THF-rich nanoclusters (Rg ~ 0.5 nm) on the nonpolar cellulose surfaces and on hydrophobic lignin, and equivalent waterrich nanoclusters on polar cellulose surfaces. The disassembly of the amphiphilic biomass is thus enabled through the local demixing of highly functional cosolvents, THF and water, which preferentially solvate specific biomass surfaces so as to match the local solute polarity. A multiscale description of the efficiency of THF:water pretreatment is provided: matching polarity at the atomic scale prevents lignin aggregation and disrupts cellulose, leading to improvements in deconstruction at the macroscopic scale. [ABSTRACT FROM AUTHOR]

Dynamic neutron scattering directly probes motions in biological systems on femtosecond to microsecond timescales. When combined with molecular dynamics simulation and normal mode analysis, detailed descriptions of the forms and frequencies of motions can be derived. We examine vibrations in proteins, the temperature dependence of protein motions, and concepts describing the rich variety of motions detectable using neutrons in biological systems at physiological temperatures. New techniques for deriving information on collective motions using coherent scattering are also reviewed. [ABSTRACT FROM AUTHOR]

Understanding of cell membrane organization has evolved significantly from the classic fluid mosaic model. It is now recognized that biological membranes are highly organized structures, with differences in lipid compositions between inner and outer leaflets and in lateral structures within the bilayer plane, known as lipid rafts. These organizing principles are important for protein localization and function as well as cellular signaling. However, the mechanisms and biophysical basis of lipid raft formation, structure, dynamics and function are not clearly understood. One key question, which we focus on in this review, is how lateral organization and leaflet compositional asymmetry are coupled. Detailed information elucidating this question has been sparse because of the small size and transient nature of rafts and the experimental challenges in constructing asymmetric bilayers. Resolving this mystery will require advances in both experimentation and modeling. We discuss here the preparation of model systems along with experimental and computational approaches that have been applied in efforts to address this key question in membrane biology. We seek to place recent and future advances in experimental and computational techniques in context, providing insight into in-plane and transverse organization of biological membranes. [ABSTRACT FROM AUTHOR]

The characterization of the structure and internal dynamics of biomolecules is essential to understanding their biological function. Neutron scattering probes similar time- and length-scales to molecular dynamics simulation. Hence, simulation models of biomolecules have become invaluable in the interpretation of experimental neutron data. Here, we report on advances in the application of simulation in developing neutron scattering to investigate internal protein motions and, as an example of industrial relevance, in the derivation of physical models of use in biofuel renewable energy research. [ABSTRACT FROM AUTHOR]

The article discusses the resiliency of normal-mode analysis (NMA) in its ability to represent functional macromolecular dynamics. It addresses the definition of normal modes by a harmonic potential-energy expansion about a particular configuration. The importance of NMA as a tool for analyzing biomolecular dynamics into functionally relevant motional modes is considered. The relevance of neutron scattering for NMA is also mentioned.

We have applied inelastic neutron scattering (INS) to the understanding of protein dynamics. INS spectrum of staphylococcal nuclease (SNase) at 25 K in the energy range between 100 and 4000 cm [ABSTRACT FROM AUTHOR]

A method is presented to calculate efficiently small-angle neutron and X-ray solution scattering intensities from explicit-atom models of macromolecules and the surrounding solvent. The method is based on a multipole expansion of the scattering amplitude. It is particularly appropriate for extensive configurational averaging, as is required for calculations based on computer-simulation results. In test calculations, excellent agreement with experiment is found between neutron and X-ray scattering profiles calculated from a molecular-dynamics simulation of lysozyme in water. The question of definition of the protein surface is also addressed. For comparison with the continuum model, an analytical envelope around the protein is defined in terms of spherical harmonics and is calculated using a Lebedev grid. The analytical surface thus defined is shown to reproduce well the scattering profile calculated from the explicit-atom model of the protein. [ABSTRACT FROM AUTHOR]

The dynamics of complex molecules can be directly probed by inelastic neutron scattering experiments. However, many of the underlying dynamical processes may exist on similar timescales, which makes it difficult to assign processes seen experimentally to specific structural rearrangements. Here, we show how Markov models can be used to connect structural changes observed in molecular dynamics simulation directly to the relaxation processes probed by scattering experiments. For this, a conformational dynamics theory of dynamical neutron and X-ray scattering is developed, following our previous approach for computing dynamical fingerprints of time-correlation functions [F. Noé, S. Doose, I. Daidone, M. Löllmann, J. Chodera, M. Sauer, and J. Smith, Proc. Natl. Acad. Sci. U.S.A. 108, 4822 (2011)]. Markov modeling is used to approximate the relaxation processes and timescales of the molecule via the eigenvectors and eigenvalues of a transition matrix between conformational substates. This procedure allows the establishment of a complete set of exponential decay functions and a full decomposition into the individual contributions, i.e., the contribution of every atom and dynamical process to each experimental relaxation process. [ABSTRACT FROM AUTHOR]

Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place. [ABSTRACT FROM AUTHOR]

The average mean-square displacement, 〈r²〉, of H atoms in a protein is frequently determined using incoherent neutron-scattering experiments. 〈r²〉 is obtained from the observed elastic incoherent dynamic structure factor, Si(Q,ω = 0), assuming the form Si(Q,ω = 0) = exp(-Q²〈r²〉/3). This is often referred to as the Gaussian approximation (GA) to Si(Q,ω = 0). 〈r²〉 obtained in this way depends on the value of the wave vector, Q considered. Equivalently, the observed Si(Q,ω = 0) deviates from the GA. We investigate the origin of the Q dependence of 〈r²〉 by evaluating the scattering functions in different approximations using molecular dynamics (MD) simulation of the protein lysozyme. We find that keeping only the Gaussian term in a cumulant expansion of S(Q,ω) is an accurate approximation and is not the origin of the Q dependence of 〈r²〉. This is demonstrated by showing that the term beyond the Gaussian is negligible and that the GA is valid for an individual atom in the protein. Rather, the Q dependence (deviation from the GA) arises from the dynamical heterogeneity of the H in the protein. Specifically it arises from representing, in the analysis of data, this diverse dynamics by a single average scattering center that has a single, average 〈r²〉. The observed Q dependence of 〈r²〉 can be used to provide information on the dynamical heterogeneity in proteins. [ABSTRACT FROM AUTHOR]

The relative motion of structural domains is essential for the biological function of many proteins. Here, by analyzing neutron scattering data and performing molecular dynamics simulations, we find that interdomain motion in several proteins obeys the principle of de Gennes narrowing, in which the wave vector dependence of the interdomain diffusion coefficient is inversely proportional to the interdomain structure factor. Thus, the rate of interdomain motion is inversely proportional to the probability distribution of the spatial configurations of domains. [ABSTRACT FROM AUTHOR]

We propose a method for obtaining the intrinsic, long-time mean square displacement (MSD) of atoms and molecules in proteins from finite-time molecular dynamics (MD) simulations. Typical data from simulations are limited to times of 1 to 10 ns, and over this time period the calculated MSD continues to increase without a clear limiting value. The proposed method consists of fitting a model to MD simulation-derived values of the incoherent intermediate neutron scattering function, Iinc(Q,t), for finite times. The infinite-time MSD, (r²), appears as a parameter in the model and is determined by fits of the model to the finite-time Iinc(Q,t). Specifically, the (r²) is defined in the usual way in terms of the Debye-Waller factor as I(Q,t=∞)=exp(-Q²(r²)/3). The method is illustrated by obtaining the intrinsic MSD (r²) of hydrated lysozyme powder (h=0.4 g water/g protein) over a wide temperature range. The intrinsic (r²) obtained from data out to 1 and to 10 ns is found to be the same. The intrinsic (r²) is approximately twice the value of the MSD that is reached in simulations after times of 1 ns which correspond to those observed using neutron instruments that have an energy resolution width of 1 µeV. [ABSTRACT FROM AUTHOR]

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Finally, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains. This article is part of a Special Issue entitled “Science for Life” Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo. [ABSTRACT FROM AUTHOR]

The mechanical and dynamical propertiesof cellulose, the mostabundant biomolecule on earth, are essential for its function in plantcell walls and advanced biomaterials. Cellulose is almost always foundin a hydrated state, and it is therefore important to understand howhydration influences its dynamics and mechanics. Here, the nanosecond-timescale dynamics of cellulose is characterized using dynamic neutronscattering experiments and molecular dynamics (MD) simulation. Theexperiments reveal that hydrated samples exhibit a higher averagemean-square displacement above ∼240 K. The MD simulation revealsthat the fluctuations of the surface hydroxymethyl atoms determinethe experimental temperature and hydration dependence. The increasein the conformational disorder of the surface hydroxymethyl groupswith temperature follows the cellulose persistence length, suggestinga coupling between structural and mechanical properties of the biopolymer.In the MD simulation, 20% hydrated cellulose is more rigid than thedry form, due to more closely packed cellulose chains and water moleculesbridging cellulose monomers with hydrogen bonds. This finding mayhave implications for understanding the origin of strength and rigidityof secondary plant cell walls. The detailed characterization obtainedhere describes how hydration-dependent increased fluctuations andhydroxymethyl disorder at the cellulose surface lead to enhancementof the rigidity of this important biomolecule. [ABSTRACT FROM AUTHOR]

Flexibility, or softness, is crucial for protein function and consists of a conformational component, involving jumps between potential wells, and an elastic component, involving fluctuations within the wells. Combining molecular dynamics simulation with incoherent neutron scattering and light scattering measurements on green fluorescent protein, we reveal a relationship between the intrawell fluctuations and elastic moduli of the protein. This finding leads to a simple means of experimentally separating the conformational from the elastic atomic displacements. [ABSTRACT FROM AUTHOR]

The derivation of mean-square displacements from elasticincoherentneutron scattering (EINS) of proteins is examined, with the aid ofexperiments on camphor-bound cytochrome P450cam and complementarymolecular dynamics simulations. It is shown that a q4correction to the elastic incoherent structure factor(where qis the scattering vector) can be simplyused to reliably estimate from the experiment both the average mean-squareatomic displacement, ⟨Δr2⟩ of the nonexchanged hydrogen atoms in the protein and itsvariance, σ2. The molecular dynamics simulation resultsare in broad agreement with the experimentally derived ⟨Δr2⟩ and σ2derived fromEINS on instruments at two different energy resolutions, correspondingto dynamics on the ∼100 ps and ∼1 ns time scales. Significantdynamical heterogeneity is found to arise from methyl-group rotations.The easy-to-apply q4correction extendsthe information extracted from elastic incoherent neutron scatteringexperiments and should be of wide applicability. [ABSTRACT FROM AUTHOR]

A simplified description of the 295 K dynamics of a globular protein over a wide frequency range (1-1000 GHz) is obtained by combining neutron scattering of lysozyme with molecular dynamics simulation. The molecular dynamics simulation agrees quantitatively with experiment for both the protein and the hydration water and shows that, whereas the hydration water molecules subdiffuse, the protein atoms undergo confined motion decomposable into three distinct classes: localized diffusion, methyl group rotations, and jumps. Each of the three classes gives rise to a characteristic neutron susceptibility signal. [ABSTRACT FROM AUTHOR]

Water is widely assumed to be essential for protein dynamics and function. In particular, the well-documented "dynamical" transition at ~200 K, at which the protein changes from a rigid, nonfunctional form to a flexible, functional state, as detected in hydrogenated protein by incoherent neutron scattering, requires hydration. Here, we report on coherent neutron scattering experiments on perdeuterated proteins and reveal that a transition occurs in dry proteins at the same temperature resulting primarily from the collective heavy-atom motions. The dynamical transition discovered is intrinsic to the energy landscape of dry proteins. [ABSTRACT FROM AUTHOR]