Time-resolved neutron scattering provides new insight into protein substrate processing by a AAA+ unfoldase

Small-Angle X-Ray Scattering for Macromolecular Complexes

Small angle X-ray scattering (SAXS) is a versatile technique that can provide unique insights in the solution structure of macromolecules and their complexes, covering the size range from small peptides to complete viral assemblies. Technological and conceptual advances in the last two decades have tremendously improved the accessibility of the technique and transformed it into an indispensable tool for structural biology. In this chapter we introduce and discuss several approaches to collecting SAXS data on macromolecular complexes, including several approaches to online chromatography. We include practical advice on experimental design and point out common pitfalls of the technique.

Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods

Utilized for gaining structural insights, small-angle neutron and X-ray scattering techniques (SANS and SAXS, respectively) enable an examination of biomolecules, including photosynthetic pigment-protein complexes, in solution at physiological temperatures. These methods can be seen as instrumental bridges between the high-resolution structural information achieved by crystallography or cryo-electron microscopy and functional explorations conducted in a solution state. The review starts with a comprehensive overview about the fundamental principles and applications of SANS and SAXS, with a particular focus on the recent advancements permitting to enhance the efficiency of these techniques in photosynthesis research. Among the recent developments discussed are: (i) the advent of novel modeling tools whereby a direct connection between SANS and SAXS data and high-resolution structures is created; (ii) the employment of selective deuteration, which is utilized to enhance spatial selectivity and contrast matching; (iii) the potential symbioses with molecular dynamics simulations; and (iv) the amalgamations with functional studies that are conducted to unearth structure-function relationships. Finally, reference is made to time-resolved SANS/SAXS experiments, which enable the monitoring of large-scale structural transformations of proteins in a real-time framework.

A real-time analysis of GFP unfolding by the AAA+ unfoldase PAN

Protein quality control systems are essential to maintain a healthy proteome. They often consist of an unfoldase unit, typically an AAA+ ATPase, coupled with a protease unit. In all kingdoms of life, they function to eliminate misfolded proteins, and thus prevent that their aggregates do harm to the cell, and to rapidly regulate protein levels in the presence of environmental changes. Despite the huge progress made in the past two decades in understanding the mechanism of function of protein degradation systems, the fate of the substrate during the unfolding and proteolytic processes remains poorly understood. Here we exploit an NMR-based approach to monitor GFP processing by the archaeal PAN unfoldase and the PAN-20S degradation system in real time. We find that PAN-dependent unfolding of GFP does not involve the release of partially-folded GFP molecules resulting from futile unfolding attempts. In contrast, once stably engaged with PAN, GFP molecules are efficiently transferred to the proteolytic chamber of the 20S subunit, despite the only weak affinity of PAN for the 20S subunit in the absence of substrate. This is essential to guarantee that unfolded but not proteolyzed proteins are not released into solution, where they would form toxic aggregates. The results of our studies are in good agreement with previous results derived from real-time small-angle-neutron-scattering experiments and have the advantage of allowing the investigation of substrates and products at amino-acid resolution.

Observing protein degradation in solution by the PAN-20S proteasome complex: Astate-of-the-art example of bio-macromolecular TR-SANS

In the present book chapter we illustrate the state-of-the-art of time-resolved small-angle neutron scattering (TR-SANS) by a concrete example of a dynamic bio-macromolecular system, i.e., regulated protein degradation by the archaeal PAN-20S proteasome complex. We present the specific and unique structural information that can be obtained by this approach, in combination with bio-macromolecular deuteration and online spectrophotometric measurements of a fluorescent substrate (GFP). The complementarity with atomic-resolution structural biology techniques (SAXS, NMR, crystallography and cryo-EM) and with the advent of atomic structure prediction are discussed, as well as the respective limitations and future perspectives.

Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex

The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterised a small orphan protein, Q9UZY3 (Uniprot ID) conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (PAN) as bait. X-ray crystallography and SAXS experiments revealed that the protein is monomeric and adopts a β-barrel core structure with an Oligonucleotide/oligosaccharide-Binding (OB) fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays tRNA binding properties. Pull-downs, co-immunoprecipitation and ITC studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi cellular extracts. The protein was therefore named Pbp11, for Proteasome Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery.

Recent advances in small-angle scattering and its expanding impact in structural biology

Applications of small-angle scattering (SAS) in structural biology have benefited from continuing developments in instrumentation, tools for data analysis, modeling capabilities, standards for data and model presentation, and data archiving. The interplay of these capabilities has enabled SAS to contribute to advances in structural biology as the field pushes the boundaries in studies of biomolecular complexes and assemblies as large as whole cells, membrane proteins in lipid environments, and dynamic systems on time scales ranging from femtoseconds to hours. This review covers some of the important advances in biomolecular SAS capabilities for structural biology focused on over the last 5 years and presents highlights of recent applications that demonstrate how the technique is exploring new territories.

Deuteration Aiming for Neutron Scattering

The distinguished feature of neutron as a scattering probe is an isotope effect, especially the large difference in neutron scattering length between hydrogen and deuterium. The difference renders the different visibility between hydrogenated and deuterated proteins. Therefore, the combination of deuterated protein and neutron scattering enables the selective visualization of a target domain in the complex or a target protein in the multi-component system. Despite of this fascinating character, there exist several problems for the general use of this method: difficulty and high cost for protein deuteration, and control and determination of deuteration ratio of the sample. To resolve them, the protocol of protein deuteration techniques is presented in this report. It is strongly expected that this protocol will offer more opportunity for conducting the neutron scattering studies with deuterated proteins.

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.

Interdomain Flexibility within NADPH Oxidase Suggested by SANS Using LMNG Stealth Carrier

Small angle neutron scattering (SANS) provides a method to obtain important low-resolution information for integral membrane proteins (IMPs), challenging targets for structural determination. Specific deuteration furnishes a "stealth" carrier for the solubilized IMP. We used SANS to determine a structural envelope of SpNOX, the Streptococcus pneumoniae NADPH oxidase (NOX), a prokaryotic model system for exploring structure and function of eukaryotic NOXes. SpNOX was solubilized in the detergent lauryl maltose neopentyl glycol, which provides optimal SpNOX stability and activity. Using deuterated solvent and protein, the lauryl maltose neopentyl glycol was experimentally undetected in SANS. This affords a cost-effective SANS approach for obtaining novel structural information on IMPs. Combining SANS data with molecular modeling provided a first, to our knowledge, structural characterization of an entire NOX enzyme. It revealed a distinctly less compact structure than that predicted from the docking of homologous crystal structures of the separate transmembrane and dehydrogenase domains, consistent with a flexible linker connecting the two domains.

Observing Protein Degradation by the PAN-20S Proteasome by Time-Resolved Neutron Scattering

The proteasome is a key player of regulated protein degradation in all kingdoms of life. Although recent atomic structures have provided snapshots on a number of conformations, data on substrate states and populations during the active degradation process in solution remain scarce. Here, we use time-resolved small-angle neutron scattering of a deuterium-labeled GFPssrA substrate and an unlabeled archaeal PAN-20S system to obtain direct structural information on substrate states during ATP-driven unfolding and subsequent proteolysis in solution. We find that native GFPssrA structures are degraded in a biexponential process, which correlates strongly with ATP hydrolysis, the loss of fluorescence, and the buildup of small oligopeptide products. Our solution structural data support a model in which the substrate is directly translocated from PAN into the 20S proteolytic chamber, after a first, to our knowledge, successful unfolding process that represents a point of no return and thus prevents dissociation of the complex and the release of harmful, aggregation-prone products.

The power of SANS, combined with deuteration and contrast variation, for structural studies of functional and dynamic biomacromolecular systems in solution

Small-angle neutron scattering (SANS), combined with macromolecular deuteration and solvent contrast variation (H2O/D2O exchange) allows focussing selectively on the signal of specific proteins in multi-protein complexes or mixtures of isolated proteins. We illustrate this unique capacity by the example of a functional protein-degradation system in solution, the PAN-20S proteasome complex in the presence of a protein substrate, ssrA-tagged GFP. By comparing experimental SANS data with synthetic SAXS (small-angle X-ray scattering) data, predicted for the same system under identical conditions, we show that SANS, when combined with macromolecular deuteration and solvent contrast variation, can specifically focus on the conformation of the PAN unfoldase, even in the presence of very large GFP aggregates. Likewise, structural information of native GFP states can be visualized in detail, even in the presence of the much larger PAN-20S unfoldase-protease oligomers, which would dominate the overall scattering signal when using X-rays instead of neutrons.

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.

Neutron scattering in the biological sciences: progress and prospects

The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.

Ion Gel Network Formation in an Ionic Liquid Studied by Time-Resolved Small-Angle Neutron Scattering

We report the time-resolved small-angle neutron scattering (SANS) study of tetra-arm poly(ethylene glycol) (TetraPEG) polymer network formation in a typical ionic liquid (IL), 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide ([C₂mim][TFSA]). To observe time-dependent SANS profiles, the reaction rate for the AB-type cross-end coupling reaction of TetraPEG macromers was controlled by adding an analogous protic IL, 1-ethylimidazolium TFSA ([C₂imH][TFSA]). At polymer concentrations higher than the overlap concentration ( c*), the SANS profile remained unchanged during the gelation reaction, indicating that the network structure was independent of macromer connectivity in a semidiluted solution. On the other hand, at low polymer concentrations, an increase in the SANS profile intensity was clearly observed. The correlation length (ξ), estimated by a fitting analysis based on the Ornstein-Zernike function, increased as the reaction proceeded. This result indicated that the sparsely dispersed macromers formed clusters during the cross-linking process and polymer size growth followed thereafter. We found that the network formation process and homogeneity of the network structure were strongly dependent on the polymer concentration in IL solutions.

Biological small-angle neutron scattering: recent results and development

Small-angle neutron scattering (SANS) has increasingly been used by the structural biology community in recent years to obtain low-resolution information on solubilized biomacromolecular complexes in solution. In combination with deuterium labelling and solvent-contrast variation (H2O/D2O exchange), SANS provides unique information on individual components in large heterogeneous complexes that is perfectly complementary to the structural restraints provided by crystallography, nuclear magnetic resonance and electron microscopy. Typical systems studied include multi-protein or protein–DNA/RNA complexes and solubilized membrane proteins. The internal features of these systems are less accessible to the more broadly used small-angle X-ray scattering (SAXS) technique owing to a limited range of intra-complex and solvent electron-density variation. Here, the progress and developments of biological applications of SANS in the past decade are reviewed. The review covers scientific results from selected biological systems, including protein–protein complexes, protein–RNA/DNA complexes and membrane proteins. Moreover, an overview of recent developments in instruments, sample environment, deuterium labelling and software is presented. Finally, the perspectives for biological SANS in the context of integrated structural biology approaches are discussed.

Cotranslocational processing of the protein substrate calmodulin by an AAA+ unfoldase occurs via unfolding and refolding intermediates

Protein remodeling by AAA+ enzymes is central for maintaining proteostasis in a living cell. However, a detailed structural description of how this is accomplished at the level of the substrate molecules that are acted upon is lacking. Here, we combine chemical cross-linking and methyl transverse relaxation-optimized NMR spectroscopy to study, at atomic resolution, the stepwise unfolding and subsequent refolding of the two-domain substrate calmodulin by the VAT AAA+ unfoldase from Thermoplasma acidophilum By engineering intermolecular disulphide bridges between the substrate and VAT we trap the substrate at different stages of translocation, allowing structural studies throughout the translocation process. Our results show that VAT initiates substrate translocation by pulling on intrinsically unstructured N or C termini of substrate molecules without showing specificity for a particular amino acid sequence. Although the B1 domain of protein G is shown to unfold cooperatively, translocation of calmodulin leads to the formation of intermediates, and these differ on an individual domain level in a manner that depends on whether pulling is from the N or C terminus. The approach presented generates an atomic resolution picture of substrate unfolding and subsequent refolding by unfoldases that can be quite different from results obtained via in vitro denaturation experiments.

Perdeuteration of cholesterol for neutron scattering applications using recombinant Pichia pastoris

Deuteration of biomolecules has a major impact on both quality and scope of neutron scattering experiments. Cholesterol is a major component of mammalian cells, where it plays a critical role in membrane permeability, rigidity and dynamics, and contributes to specific membrane structures such as lipid rafts. Cholesterol is the main cargo in low and high-density lipoprotein complexes (i.e. LDL, HDL) and is directly implicated in several pathogenic conditions such as coronary artery disease which leads to 17 million deaths annually. Neutron scattering studies on membranes or lipid-protein complexes exploiting contrast variation have been limited by the lack of availability of fully deuterated biomolecules and especially perdeuterated cholesterol. The availability of perdeuterated cholesterol provides a unique way of probing the structural and dynamical properties of the lipoprotein complexes that underly many of these disease conditions. Here we describe a procedure for in vivo production of perdeuterated recombinant cholesterol in lipid-engineered Pichia pastoris using flask and fed-batch fermenter cultures in deuterated minimal medium. Perdeuteration of the purified cholesterol was verified by mass spectrometry and its use in a neutron scattering study was demonstrated by neutron reflectometry measurements using the FIGARO instrument at the ILL.

Solution scattering approaches to dynamical ordering in biomolecular systems

Clarification of solution structure and its modulation in proteins and protein complexes is crucially important to understand dynamical ordering in macromolecular systems. Small-angle x-ray scattering (SAXS) and small-angle neutron scattering (SANS) are among the most powerful techniques to derive structural information. Recent progress in sample preparation, instruments and software analysis is opening up a new era for small-angle scattering. In this review, recent progress and trends of SAXS and SANS are introduced from the point of view of instrumentation and analysis, touching on general features and standard methods of small-angle scattering. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.

Characterization of conformational deformation-coupled interaction between immunoglobulin G1 Fc glycoprotein and a low-affinity Fcγ receptor by deuteration-assisted small-angle neutron scattering

A recently developed integrative approach combining varied types of experimental data has been successfully applied to three-dimensional modelling of larger biomacromolecular complexes. Deuteration-assisted small-angle neutron scattering (SANS) plays a unique role in this approach by making it possible to observe selected components in the complex. It enables integrative modelling of biomolecular complexes based on building-block structures typically provided by X-ray crystallography. In this integrative approach, it is important to be aware of the flexible properties of the individual building blocks. Here we examine the ability of SANS to detect a subtle conformational change of a multidomain protein using the Fc portion of human immunoglobulin G (IgG) interacting with a soluble form of the low-affinity Fcγ receptor IIIb (sFcγRIIIb) as a model system. The IgG-Fc glycoprotein was subjected to SANS in the absence and presence of 75%-deuterated sFcγRIIIb, which was matched out in D₂O solution. This inverse contrast-matching technique enabled selective observation of SANS from IgG-Fc, thereby detecting its subtle structural deformation induced by the receptor binding. The SANS data were successfully interpreted by considering previously reported crystallographic data and an equilibrium between free and sFcγRIIIb-bound forms. Our SANS data thus demonstrate the applicability of SANS in the integrative approach dealing with biomacromolecular complexes composed of weakly associated building blocks with conformational plasticity.

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IgG-Fc glycoprotein was structurally characterized by small-angle neutron scattering.

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Fc was selectively observed under equilibrium between free and receptor-bound forms.

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Receptor-induced conformational change of Fc was successfully detected.