Polyelectrolyte-protein synergism: pH-responsive polyelectrolyte/insulin complexes as versatile carriers for targeted protein and drug delivery

The co-assembly of polyelectrolytes (PE) with proteins offers a promising approach for designing complex structures with customizable morphologies, charge distribution, and stability for targeted cargo delivery. However, the complexity of protein structure limits our ability to predict the properties of the formed nanoparticles, and our goal is to identify the key triggers of the morphological transition in protein/PE complexes and evaluate their ability to encapsulate multivalent ionic drugs. A positively charged PE can assemble with a protein at pH above isoelectric point due to the electrostatic attraction and disassemble at pH below isoelectric point due to the repulsion. The additional hydrophilic block of the polymer should stabilize the particles in solution and enable them to encapsulate a negatively charged drug in the presence of PE excess. We demonstrated that diblock copolymers, poly(ethylene oxide)-block-poly(N,N-dimethylaminoethyl methacrylate) and poly(ethylene oxide)-block-poly(N,N,N-trimethylammonioethyl methacrylate), consisting of a polycation block and a neutral hydrophilic block, reversibly co-assemble with insulin in pH range between 5 and 8. Using small-angle neutron and X-ray scattering (SANS, SAXS), we showed that insulin arrangement within formed particles is controlled by intermolecular electrostatic forces between protein molecules, and can be tuned by varying ionic strength. For the first time, we observed by fluorescence that formed protein/PE complexes with excess of positive charges exhibited potential for encapsulating and controlled release of negatively charged bivalent drugs, protoporphyrin-IX and zinc(II) protoporphyrin-IX, enabling the development of nanocarriers for combination therapies with adjustable charge, stability, internal structure, and size.

Structure of biomimetic casein micelles: Critical tests of the hydrophobic colloid and multivalent-binding models using recombinant deuterated and phosphorylated β-casein

Milk contains high concentrations of amyloidogenic casein proteins and is supersaturated with respect to crystalline calcium phosphates such as apatite. Nevertheless, the mammary gland normally remains unmineralized and free of amyloid. Unlike κ-casein, β- and αS-caseins are highly effective mineral chaperones that prevent ectopic and pathological calcification of the mammary gland. Milk invariably contains a mixture of two to five different caseins that act on each other as molecular chaperones. Instead of forming amyloid fibrils, several thousand caseins and hundreds of nanoclusters of amorphous calcium phosphate combine to form fuzzy complexes called casein micelles. To understand the biological functions of the casein micelle its structure needs to be understood better than at present. The location in micelles of the highly amyloidogenic κ-casein is disputed. In traditional hydrophobic colloid models, it, alone, forms a stabilizing surface coat that also determines the average size of the micelles. In the recent multivalent-binding model, κ-casein is present throughout the micelle, in intimate contact with the other caseins. To discriminate between these models, a range of biomimetic micelles was prepared using a fixed concentration of the mineral chaperone β-casein and nanoclusters of calcium phosphate, with variable concentrations of κ-casein. A biomimetic micelle was also prepared using a highly deuterated and in vivo phosphorylated recombinant β-casein with calcium phosphate and unlabelled κ-casein. Neutron and X-ray scattering experiments revealed that κ-casein is distributed throughout the micelle, in quantitative agreement with the multivalent-binding model but contrary to the hydrophobic colloid models.

Galactokinase-like protein from Leishmania donovani: Biochemical and structural characterization of a recombinant protein

Leishmaniasis is a spectrum of conditions caused by infection with the protozoan Leishmania spp. parasites. Leishmaniasis is endemic in 98 countries around the world, and resistance to current anti-leishmanial drugs is rising. Our work has identified and characterised a previously unstudied galactokinase-like protein (GalK) in Leishmania donovani, which catalyses the MgATP-dependent phosphorylation of the C-1 hydroxyl group of d-galactose to galactose-1-phosphate. Here, we report the production of the catalytically active recombinant protein in E. coli, determination of its substrate specificity and kinetic constants, as well as analysis of its molecular envelope using in solution X-ray scattering. Our results reveal kinetic parameters in range with other galactokinases with an average apparent Km value of 76 μM for galactose, Vmax and apparent Kcat values with 4.46376 × 10-9 M/s and 0.021 s-1, respectively. Substantial substrate promiscuity was observed, with galactose being the preferred substrate, followed by mannose, fructose and GalNAc. LdGalK has a highly flexible protein structure suggestive of multiple conformational states in solution, which may be the key to its substrate promiscuity. Our data presents novel insights into the galactose salvaging pathway in Leishmania and positions this protein as a potential target for the development of pharmaceuticals seeking to interfere with parasite substrate metabolism.

A dilute nematic gel produced by intramicellar segregation of two polyoxyethylene alkyl ether carboxylic acids

MOTIVATION

Surfactants like C8E8CH2COOH have such bulky headgroups that they cannot show the common sphere-to-cylinder transition, while surfactants like C18:1E2CH2COOH are mimicking lipids and form only bilayers. Mixing these two types of surfactants allows one to investigate the competition between intramicellar segregation leading to disc-like bicelles and the temperature dependent curvature constraints imposed by the mismatch between heads and tails.

EXPERIMENTS

We establish phase diagrams as a function of temperature, surfactant mole ratio, and active matter content. We locate the isotropic liquid-isotropic liquid phase separation common to all nonionic surfactant systems, as well as nematic and lamellar phases. The stability and rheology of the nematic phase is investigated. Texture determination by polarizing microscopy allows us to distinguish between the different phases. Finally, SANS and SAXS give intermicellar distances as well as micellar sizes and shapes present for different compositions in the phase diagrams.

FINDINGS

In a defined mole ratio between the two components, intramicellar segregation wins and a viscoelastic discotic nematic phase is present at low temperature. Partial intramicellar mixing upon heating leads to disc growth and eventually to a pseudo-lamellar phase. Further heating leads to complete random mixing and an isotropic phase, showing the common liquid-liquid miscibility gap. This uncommon phase sequence, bicelles, lamellar phase, micelles, and water-poor packed micelles, is due to temperature induced mixing combined with dehydration of the headgroups. This general molecular mechanism explains also why a metastable water-poor lamellar phase quenched by cooling can be easily and reproducibly transformed into a nematic phase by gentle hand shaking at room temperature, as well as the entrapment of air bubbles of any size without encapsulation by bilayers or polymers.

BioXTAS RAW 2: new developments for a free open-source program for small angle scattering data reduction and analysis

BioXTAS RAW is a free, open-source program for reduction, analysis and modelling of biological small angle scattering data. Here, the new developments in RAW version 2 are described. These include: improved data reduction using pyFAI; updated automated Guinier fitting and Dmax finding algorithms; automated series (e.g. SEC-SAXS) buffer and sample region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using REGALS; creation of electron density reconstructions via DENSS; a comparison window showing residuals, ratios, and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. In addition, there is now a RAW API, which can be used without the GUI, providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.

Structural characterization of transcription-coupled repair protein UVSSA and its interaction with TFIIH protein

UV-stimulated scaffold protein A (UVSSA) is a key protein in the Transcription-Coupled Nucleotide Excision Repair (TC-NER) pathway. UVSSA, an intrinsically disordered protein, interacts with multiple members of the pathway, tethering them into the complex. Several studies have reported that UVSSA recruits Transcription Factor IIH (TFIIH) via direct interaction, following which CSB is degraded and the lesion recognition TC-NER complex dissociates from the damage site to facilitate the DNA repair. Structural insights into these events remain largely unknown. Herein, we have investigated the interaction of human UVSSA with the Pleckstrin-Homology-domain of p62 subunit of TFIIH (p62-PHD) using biophysical techniques. We observed that UVSSA forms a stable complex with the p62-PHD in vitro. Small-angle scattering measurements using X-rays and neutrons revealed a significant change in pair-distance distribution function for UVSSA662/p62-PHD complex compared to UVSSA alone. Additionally, a significant decrease was observed in the radius of gyration of the complex. Our findings suggest that TFIIH binding to UVSSA causes significant conformational changes in UVSSA. We hypothesize that these conformational changes play an important role in the dissociation of the lesion recognition TC-NER complex.

Small-angle scattering techniques for peptide and peptide hybrid nanostructures and peptide-based biomaterials

The use of small-angle scattering (SAS) in the study of the self-assembly of peptides and peptide conjugates (lipopeptides, polymer-peptide conjugates and others) is reviewed, highlighting selected research that illustrates different methods and analysis techniques. Both small-angle x-ray scattering (SAXS) and small-angle neutron scattering (SANS) are considered along with examples that exploit their unique capabilities. For SAXS, this includes the ability to perform rapid measurements enabling high throughput or fast kinetic studies and measurements under dilute conditions. For SANS, contrast variation using H2O/D2O mixtures enables the study of peptides interacting with lipids and TR-SANS (time-resolved SANS) studies of exchange kinetics and/or peptide-induced structural changes. Examples are provided of studies measuring form factors of different self-assembled structures (micelles, fibrils, nanotapes, nanotubes etc) as well as structure factors from ordered phases (lyotropic mesophases), peptide gels and hybrid materials such as membranes formed by mixing peptides with polysaccharides or peptide/liposome mixtures. SAXS/WAXS (WAXS: wide-angle x-ray scattering) on peptides and peptide hybrids is also discussed, and the review concludes with a perspective on potential future directions for research in the field.

Wound healing activity of aqueous dispersion of fullerene C60 produced by "green technology"

In addition to exhibited antioxidant and anti-inflammatory activity, fullerene C60 is a promising wound healing agent. An important stage in the production of fullerene-based ointments is the stability of the aqueous fullerene dispersion (AFD) with minimum size of colloidal fullerene aggregates and sufficiently high concentration. To achieve these parameters tangential flow filtration of fullerene C60 was used ("green technology"). As estimated by small-angle neutron scattering and dynamic light scattering purified AFDs with narrow-size distribution nanoclusters have a size of 6 nm and are assembled into agglomerates which reach a size of 150 nm. The ability of the AFD to exhibit regenerative activity was studied using the animal wound model. This study shows for the first time that the fullerene-based composition stimulates the healing of wounds of various origins. We assume that the mechanism of the AFD wound-healing activity is associated with the aryl hydrocarbon receptor and macrophages activity.

Data quality assurance, model validation, and data sharing for biomolecular structures from small-angle scattering

Key to small-angle scattering (SAS) maturing and becoming a mainstream structural biology technique was the work done by the SAS community to establish standards for data quality, model validation and data sharing. Through a consultative process spanning more than a decade and a half, guidelines for publication have been established that include criteria for evaluating data quality and for model validation. In this process gaps were identified that stimulated innovation and development of new tools, for example new measures of model ambiguity and of the goodness-of-fit of a model to SAS data that complement the traditional global fit parameter χ². The need for a global repository for biomolecular SAS data and models was identified and the SASBDB was established as a searchable, curated, freely accessible, downloadable database of experimental data, experimental conditions, sample details, derived models, and their fit to the data. Importantly, the SASBDB uses a common dictionary format that supports archiving of structures solved using integrative methods to support seamless data exchange with a federated system of public databanks that includes the world-wide Protein Data Bank (wwPDB) as the major repository for structural biology. Thus, biomolecular SAS is now well-positioned to achieve its full potential as a mainstream structural biology technique contributing at the frontier of integrative structural biology and meeting "best practice" standards for data quality assurance and data sharing.

Structure and ensemble refinement against SAXS data: Combining MD simulations with Bayesian inference or with the maximum entropy principle

Small-angle X-ray scattering (SAXS) is a powerful method for tracking conformational transitions of proteins or soft-matter complexes in solution. However, the interpretation of the experimental data is challenged by the low spatial resolution and the low information content of the data, which lead to a high risk of overinterpreting the data. Here, we illustrate how SAXS data can be integrated into all-atom molecular dynamics (MD) simulation to derive atomic structures or heterogeneous ensembles that are compatible with the data. Besides providing atomistic insight, the MD simulation adds physicochemical information, as encoded in the MD force fields, which greatly reduces the risk of overinterpretation. We present an introduction into the theory of SAXS-driven MD simulations as implemented in GROMACS-SWAXS, a modified version of the GROMACS simulation software. We discuss SAXS-driven parallel-replica ensemble refinement with commitment to the maximum entropy principle as well as a Bayesian formulation of SAXS-driven structure refinement. Practical considerations for running and interpreting the simulations are presented. The methods are freely available via GitLab at https://gitlab.com/cbjh/gromacs-swaxs.

Computational methods for the analysis of solution small-angle X-ray scattering of biomolecules: ATSAS

The ATSAS software suite provides a comprehensive set of programs for the processing, analysis and modeling of small-angle scattering data, tailored for but not limited to data acquired on biological macromolecules. In this review the major components and developments in the ATSAS package are described, with a focus on user driven application. Data reduction, analysis and modeling approaches and strategies will be introduced and discussed. At the time of writing the latest package, ATSAS 3.1, is freely available for academic users at: https://www.embl-hamburg.de/biosaxs/software.html.

Human myelin proteolipid protein structure and lipid bilayer stacking

The myelin sheath is an essential, multilayered membrane structure that insulates axons, enabling the rapid transmission of nerve impulses. The tetraspan myelin proteolipid protein (PLP) is the most abundant protein of compact myelin in the central nervous system (CNS). The integral membrane protein PLP adheres myelin membranes together and enhances the compaction of myelin, having a fundamental role in myelin stability and axonal support. PLP is linked to severe CNS neuropathies, including inherited Pelizaeus-Merzbacher disease and spastic paraplegia type 2, as well as multiple sclerosis. Nevertheless, the structure, lipid interaction properties, and membrane organization mechanisms of PLP have remained unidentified. We expressed, purified, and structurally characterized human PLP and its shorter isoform DM20. Synchrotron radiation circular dichroism spectroscopy and small-angle X-ray and neutron scattering revealed a dimeric, α-helical conformation for both PLP and DM20 in detergent complexes, and pinpoint structural variations between the isoforms and their influence on protein function. In phosphatidylcholine membranes, reconstituted PLP and DM20 spontaneously induced formation of multilamellar myelin-like membrane assemblies. Cholesterol and sphingomyelin enhanced the membrane organization but were not crucial for membrane stacking. Electron cryomicroscopy, atomic force microscopy, and X-ray diffraction experiments for membrane-embedded PLP/DM20 illustrated effective membrane stacking and ordered organization of membrane assemblies with a repeat distance in line with CNS myelin. Our results shed light on the 3D structure of myelin PLP and DM20, their structure-function differences, as well as fundamental protein-lipid interplay in CNS compact myelin.

Membrane stiffening in Chitosan mediated multilamellar vesicles of alkyl ether carboxylates

HYPOTHESIS

Membrane undulations are known to strongly affect the stability of uni- and multilamellar vesicles formed by surfactants or phospholipids. Herein, based on the same arguments, we hypothesise that the properties of polyelectrolyte mediated surfactant multilamellar vesicles, in particular the multiplicity - i.e. the number of layers forming the vesicle - depend on the dynamics of the membrane.

EXPERIMENTS

Small-angle neutron scattering (SANS) and neutron spin-echo (NSE) were used to probe the structure and the dynamics of the multilayered vesicles formed in mixtures of the biopolymer chitosan and oppositely charged alkyl ether carboxylates. The neutron scattering data are complemented by static and dynamic light scattering experiments. Experiments were performed in polyelectrolyte excess conditions, and at a pH close to the pKa of the surfactant.

FINDINGS

The structural investigation shows very clearly that multilayered surfactant/polyelectrolyte vesicles are formed in the investigated mixtures. Only 3 to 5 layers form, on average, one vesicle, as similarly found in mixtures of chitosan and phospholipid vesicles. NSE shows that the surfactant membrane becomes stiffer upon complexation with chitosan, and that the fluctuation of the layers is strongly coupled in time and space. Such strong coupling and the increase in overall stiffness is associated with a high entropic cost. Accordingly, the combined SANS and NSE study points out that the low multiplicity found in multilayered vesicles involving the rigid polysaccharide chitosan arises from the strongly coupled dynamics of the membrane layers.

Non-ionic detergent assists formation of supercharged nanodiscs and insertion of membrane proteins

Nanodiscs are used to stabilize membrane proteins in a lipid environment and enable investigations of the function and structure of these. Membrane proteins are often only available in small amounts, and thus the stability and ease of use of the nanodiscs are essential. We have recently explored circularizing and supercharging membrane scaffolding proteins (MSPs) for nanodisc formation and found increased temporal stability at elevated temperatures. In the present study, we investigate six different supercharged MSPs and their ability to form nanodiscs: three covalently circularized and the three non-circularized, linear versions. Using standard reconstitution protocols using cholate as the reconstitution detergent, we found that two of the linear constructs formed multiple lipid-protein species, whereas adding n-Dodecyl-B-D-maltoside (DDM) with the cholate in the reconstitution gave rise to single-species nanodisc formation for these MSPs. For all MSPs, the formed nanodiscs were analyzed by small-angle X-ray scattering (SAXS), which showed similar structures for each MSP, respectively, suggesting that the structures of the formed nanodiscs are independent of the initial DDM content, as long as cholate is present. Lastly, we incorporated the membrane protein proteorhodopsin into the supercharged nanodiscs and observed a considerable increase in incorporation yield with the addition of DDM. For the three circularized MSPs, a single major species appeared in the size exclusion chromatography (SEC) chromatogram, suggesting monodisperse nanodiscs with proteorhodopsin incorporated, which is in strong contrast to the samples without DDM showing almost no incorporation and high polydispersity.

Integrative ensemble modeling of proteins and their complexes with distance distribution restraints

Many proteins and protein complexes exhibit regions that are intrinsically disordered. Whereas an arsenal of techniques exists to characterize structured proteins or protein regions, characterization of the vast conformational space occupied by intrinsically disordered regions remains a challenging task due the ensemble-averaging nature of many techniques that provide mean value restraints. More representative information can be gained in the form of distribution restraints, such as EPR-derived distance distributions. Previously we developed the ensemble modeling tool MMM, where we partition the macromolecule into structured and unstructured domains and utilize an integrative structural approach with a focus on EPR-derived distance restraints. Here we present the successor program of MMM: MMMx. All the modeling functionality was ported to MMMx and is now accessed by a uniform script format, allowing to combine the different modules at will to modeling pipelines. During the conception of MMMx many of the tools were improved or updated. We discuss the general functionality of MMMx and its modules, and illustrate some of the modeling tools by application examples.

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.

Small-Angle Neutron Scattering of Liposomes: Sample Preparation to Simple Modeling

Small-angle scattering (SAS) is a technique commonly used in the soft matter sciences to characterize the structure of molecules self-assembling in solution. As such, it is suitable to study preparations of homogeneous liposomes to extract simple structural parameters such as radius and lipid bilayer thickness in solution. Here, we describe the preparation of liposomes for small-angle neutron scattering via extrusion and present the simplest way the resulting data can be modeled.

Methods for Small-Angle Scattering Measurements on Peptiplexes of DNA with Cell-Penetrating Peptides

Peptiplexes are soft biomaterials formed through the noncovalent association between cell-penetrating peptides and nucleic acids. Although internalization often involves electrostatic anchoring followed by endocytosis, the mode of action of these transporters remains elusive in many cases, and proper understanding of mechanisms behind their penetrating capabilities necessarily entails structural data at the nanoscopic scale. In this chapter, we examine the structural landscape of peptiplexes, emphasizing the complex behavior of these polyelectrolyte self-assemblies and how supramolecular order impacts their translocation efficiency. We discuss experimental tools commonly used to investigate the structure of peptiplexes and pay special attention to small-angle X-ray scattering (SAXS) as a suitable method for unveiling their nanoscale organization. A roadmap for standard SAXS measurements in CPP/DNA samples is presented alongside a selection of observations from our own experience dealing with SAXS applied to the investigation of CPPs.

Reversible multilayered vesicle-like structures with fluid hydrophobic and interpolyelectrolyte layers

Hydrophobic blocks of amphiphilic block copolymers often form glassy micellar cores at room temperature with a rigid structure that limits their applications as nanocapsules for targeted delivery. Nevertheless, we prepared and analyzed core/shell micelles with a soft core, formed by a self-assembled block copolymer consisting of a hydrophobic block and a polycation block, poly(lauryl acrylate)-block-poly(trimethyl-aminoethyl acrylate) (PLA-QPDMAEA), in aqueous solution. By light and small-angle neutron scattering, by transmission electron microscopy and by fluorescence spectroscopy, we showed that these core/shell micelles are spherical and cylindrical with a fluid-like PLA core and a positively charged outer shell and that they can encapsulate and release hydrophobic solutes. Moreover, after mixing these PLA-QPDMAEA core/shell micelles with another diblock copolymer, consisting of a hydrophilic block and a polyanion block, namely poly(ethylene oxide)-block-poly(methacrylic acid) (PEO-PMAA), we observed the formation of novel vesicle-like multicompartment structures containing both soft hydrophobic and interpolyelectrolyte (IPEC) layers. By combining small-angle neutron scattering with self-consistent field modeling, we confirmed the formation of these complex vesicle-like structures with a swollen PEO core, an IPEC inner layer, a PLA soft layer, an IPEC outer layer and a loose PEO corona. Thus, these multicompartment micelles with fluid and IPEC layers and a hydrophilic corona may be used as nanocapsules with several tunable properties, including the ability to control the thickness of each layer, the charge of the IPEC layers and the stability of the micelles, to deliver both hydrophobic and multivalent solutes.

Morphology of bile salts micelles and mixed micelles with lipolysis products, from scattering techniques and atomistic simulations

HYPOTHESES

Bile salts (BS) are biosurfactants released into the small intestine, which play key and contrasting roles in lipid digestion: they adsorb at interfaces and promote the adsorption of digestive enzymes onto fat droplets, while they also remove lipolysis products from that interface, solubilising them into mixed micelles. Small architectural variations on their chemical structure, specifically their bile acid moiety, are hypothesised to underlie these conflicting functionalities, which should be reflected in different aggregation and solubilisation behaviour.

EXPERIMENTS

The micellisation of two BS, sodium taurocholate (NaTC) and sodium taurodeoxycholate (NaTDC), which differ by one hydroxyl group on the bile acid moiety, was assessed by pyrene fluorescence spectroscopy, and the morphology of aggregates formed in the absence and presence of fatty acids (FA) and monoacylglycerols (MAG) - typical lipolysis products - was resolved by small-angle X-ray/neutron scattering (SAXS, SANS) and molecular dynamics simulations. The solubilisation by BS of triacylglycerol-incorporating liposomes - mimicking ingested lipids - was studied by neutron reflectometry and SANS.

FINDINGS

Our results demonstrate that BS micelles exhibit an ellipsoidal shape. NaTDC displays a lower critical micellar concentration and forms larger and more spherical aggregates than NaTC. Similar observations were made for BS micelles mixed with FA and MAG. Structural studies with liposomes show that the addition of BS induces their solubilisation into mixed micelles, with NaTDC displaying a higher solubilising capacity.

Synthesis and characterization of nanoemulsion-mediated core crosslinked nanoparticles, and in vivo pharmacokinetics depending on the structural characteristics

For designing nanoparticles as drug carriers, a covalently crosslinked structure is necessary for the structural stability in vivo. In this study, we prepared core crosslinked nanoparticles through the formation of nanoemulsions stabilized by poly(ethylene glycol) (PEG)-bearing surfactants. The structural characteristics of these particles were carefully evaluated using small-angle scattering techniques including dynamic, static, X-ray, and neutron scattering. The particles demonstrated high stability even in vivo, with the suppression of premature drug release owing to the crosslinked structure. Interestingly, the ability to retain encapsulated molecules was dependent on the molecular weight of PEG in vivo, presumably due to the difference in the crowding density of PEG chains at the outermost surface. This suggests that conferring structural stability via a core crosslinked structure is surely important, but we also need to consider controlling the crowding density of the hydrophilic polymer chains in the particle shell when designing drug carriers.

How the central domain of dystrophin acts to bridge F-actin to sarcolemmal lipids

Dystrophin is a large intracellular protein that prevents sarcolemmal ruptures by providing a mechanical link between the intracellular actin cytoskeleton and the transmembrane dystroglycan complex. Dystrophin deficiency leads to the severe muscle wasting disease Duchenne Muscular Dystrophy and the milder allelic variant, Becker Muscular Dystrophy (DMD and BMD). Previous work has shown that concomitant interaction of the actin binding domain 2 (ABD2) comprising spectrin like repeats 11 to 15 (R11-15) of the central domain of dystrophin, with both actin and membrane lipids, can greatly increase membrane stiffness. Based on a combination of SAXS and SANS measurements, mass spectrometry analysis of cross-linked complexes and interactive low-resolution simulations, we explored in vitro the molecular properties of dystrophin that allow the formation of ABD2-F-actin and ABD2-membrane model complexes. In dystrophin we identified two subdomains interacting with F-actin, one located in R11 and a neighbouring region in R12 and another one in R15, while a single lipid binding domain was identified at the C-terminal end of R12. Relative orientations of the dystrophin central domain with F-actin and a membrane model were obtained from docking simulation under experimental constraints. SAXS-based models were then built for an extended central subdomain from R4 to R19, including ABD2. Overall results are compatible with a potential F-actin/dystrophin/membrane lipids ternary complex. Our description of this selected part of the dystrophin associated complex bridging muscle cell membrane and cytoskeleton opens the way to a better understanding of how cell muscle scaffolding is maintained through this essential protein.

Novel Detection Scheme for X-ray Small-Angle Scattering

X-ray imaging techniques, including x-ray radiography and computed tomography, have been in use for decades and proven effective and indispensable in diagnosis and therapy due to their fine resolution and fast acquisition speed. However, the innate disadvantage of x-ray is the poor soft tissue contrast. Small-angle scattering signals were shown to provide unique information about the abnormality of soft tissues that is complementary to the traditional attenuation image. Currently, there is no effective small-angle scattering detection system. In this paper, we propose a new "collimation" design dedicated to capture a small-angle scattering radiographic image directly, which carries critical pathological information for differentiation between normal and abnormal tissues. Our design consists of two interlaced gratings so that both the primary flux and Compton scattering photons are effectively blocked to leave the apertures mainly open to small-angle scattering photons. Theoretical analysis and Monte Carlo simulations demonstrate that small-angle scattering radiography is feasible with our proposed technology.

The role of small-angle scattering in structure-based screening applications

In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.

A method for efficient Bayesian optimization of self-assembly systems from scattering data

BACKGROUND

The ability of collections of molecules to spontaneously assemble into large functional complexes is central to all cellular processes. Using the viral capsid as a model system for complicated macro-molecular assembly, we develop methods for probing fine details of the process by learning kinetic rate parameters consistent with experimental measures of assembly. We have previously shown that local rule based stochastic simulation methods in conjunction with bulk indirect experimental data can meaningfully constrain the space of possible assembly trajectories and allow inference of experimentally unobservable features of the real system.

RESULTS

In the present work, we introduce a new Bayesian optimization framework using multi-Gaussian process model regression. We also extend our prior work to encompass small-angle X-ray/neutron scattering (SAXS/SANS) as a possibly richer experimental data source than the previously used static light scattering (SLS). Method validation is based on synthetic experiments generated using protein data bank (PDB) structures of cowpea chlorotic mottle virus. We also apply the same approach to computationally cheaper differential equation based simulation models.

CONCLUSIONS

We present a flexible approach for the global optimization of computationally costly objective functions associated with dynamic, multidimensional models. When applied to the stochastic viral capsid system, our method outperforms a current state of the art black box solver tailored for use with noisy objectives. Our approach also has wide applicability to general stochastic optimization problems.

Small Angle Scattering and Structural Biology: Data Quality and Model Validation

This chapter provides a brief review of the current state-of-the-art in small-angle scattering (SAS) from biomolecules in solution in regard to: (1) sample preparation and instrumentation, (2) data reduction and analysis, and (3) three-dimensional structural modelling and validation. In this context, areas of ongoing research in regard to the interpretation of SAS data will be discussed with a particular focus on structural modelling using computational methods and data from different experimental techniques, including SAS (hybrid methods). Finally, progress made in establishing community accepted publication guidelines and a standard reporting framework that includes SAS data deposition in a public data bank will be described. Importantly, SAS data with associated meta-data can now be held in a format that supports exchange between data archives and seamless interoperability with the world-wide Protein Data Bank (wwPDB). Biomolecular SAS is thus well positioned to contribute to an envisioned federation of data archives in support of hybrid structural biology.

Excitation energy transfer in phycobiliproteins of the cyanobacterium Acaryochloris marina investigated by spectral hole burning

The cyanobacterium Acaryochloris marina developed two types of antenna complexes, which contain chlorophyll-d (Chl d) and phycocyanobilin (PCB) as light-harvesting pigment molecules, respectively. The latter membrane-extrinsic complexes are denoted as phycobiliproteins (PBPs). Spectral hole burning was employed to study excitation energy transfer and electron-phonon coupling in PBPs. The data reveal a rich spectral substructure with a total of four low-energy electronic states whose absorption bands peak at 633, 644, 654, and at about 673 nm. The electronic states at ~633 and 644 nm can be tentatively attributed to phycocyanin (PC) and allophycocyanin (APC), respectively. The remaining low-energy electronic states including the terminal emitter at 673 nm may be associated with different isoforms of PC, APC, or the linker protein. Furthermore, the hole burning data reveal a large number of excited state vibrational frequencies, which are characteristic for the chromophore PCB. In summary, the results are in good agreement with the low-energy level structure of PBPs and electron-phonon coupling parameters reported by Gryliuk et al. (BBA 1837:1490-1499, 2014) based on difference fluorescence line-narrowing experiments.

Fibrillar assembly of bacterial cellulose in the presence of wood-based hemicelluloses

Composite materials mimicking the plant cell wall structure were made by culturing cellulose-producing bacteria together with secondary-wall hemicelluloses from wood. The effects of spruce galactoglucomannan (GGM) and beech xylan on the nanoscale morphology of bacterial cellulose were studied in the original, hydrated state with small-angle X-ray scattering (SAXS). The SAXS intensities were fitted with a model covering multiple levels of the hierarchical structure. Additional information on the structure of dried samples was obtained using scanning and transmission electron microscopy and infra-red spectroscopy. Both hemicelluloses induced a partial conversion of the cellulose crystal structure from I_α to I_β and a reduction of the cross-sectional dimensions of the cellulose microfibrils, thereby affecting also their packing into bundles. The differences were more pronounced in samples with xylan instead of GGM, and they became more significant with higher hemicellulose concentrations.

Accounting for thermodynamic non-ideality in the Guinier region of small-angle scattering data of proteins

Hydrodynamic studies of the solution properties of proteins and other biological macromolecules are often hard to interpret when the sample is present at a reasonably concentrated solution. The reason for this is that solutions exhibit deviations from ideal behaviour which is manifested as thermodynamic non-ideality. The range of concentrations at which this behaviour typically is exhibited is as low as 1–2 mg/ml, well within the range of concentrations used for their analysis by techniques such as small-angle scattering. Here we discuss thermodynamic non-ideality used previously used in the context of light scattering and sedimentation equilibrium analytical ultracentrifugation and apply it to the Guinier region of small-angle scattering data. The results show that there is a complementarity between the radially averaged structure factor derived from small-angle X-ray scattering/small-angle neutron scattering studies and the second virial coefficient derived from sedimentation equilibrium analytical ultracentrifugation experiments.

Identifying and Visualizing Macromolecular Flexibility in Structural Biology

Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates) continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes.

Small-angle neutron scattering reveals the assembly of alpha-synuclein in lipid membranes

The aggregation of α-synuclein (asyn), an intrinsically disordered protein (IDP), is a hallmark in Parkinson's disease (PD). We investigated the conformational changes that asyn undergoes in the presence of membrane and membrane mimetics using small-angle neutron scattering (SANS). In solution, asyn is monomeric and unfolded assuming an ensemble of conformers spanning extended and compact conformations. Using the contrast variation technique and SANS, the protein scattering signal in the membrane-protein complexes is selectively highlighted in order to monitor its conformational changes in this environment. We showed that in the presence of phospholipid membranes asyn transitions from a monodisperse state to aggregated structures with sizes ranging from 200 to 900Å coexisting with the monomeric species. Detailed SANS data analysis revealed that asyn aggregates have a hierarchical organization in which clusters of smaller asyn aggregates assemble to form the larger structures. This study provides new insight into the mechanism of asyn aggregation. We propose an aggregation mechanism in which stable asyn aggregates seed the aggregation process and hence the hierarchical assembly of structures. Our findings demonstrate that membrane-induced conformational changes in asyn lead to its heterogeneous aggregation which could be physiologically relevant in its function or in the diseased state.

X-ray microdiffraction of biominerals

Biominerals have complex and heterogeneous architectures, hence diffraction experiments with spatial resolutions between 500 nm and 10 μm are extremely useful to characterize them. X-ray beams in this size range are now routinely produced at many synchrotrons. This chapter provides a review of the different hard X-ray diffraction and scattering techniques, used in conjunction with efficient, state-of-the-art X-ray focusing optics. These include monochromatic X-ray microdiffraction, polychromatic (Laue) X-ray microdiffraction, and microbeam small-angle X-ray scattering. We present some of the most relevant discoveries made in the field of biomineralization using these approaches.

Small-angle scattering gives direct structural information about a membrane protein inside a lipid environment

Monomeric bacteriorhodopsin (bR) reconstituted into POPC/POPG-containing nanodiscs was investigated by combined small-angle neutron and X-ray scattering. A novel hybrid approach to small-angle scattering data analysis was developed. In combination, these provided direct structural insight into membrane-protein localization in the nanodisc and into the protein-lipid interactions. It was found that bR is laterally decentred in the plane of the disc and is slightly tilted in the phospholipid bilayer. The thickness of the bilayer is reduced in response to the incorporation of bR. The observed tilt of bR is in good accordance with previously performed theoretical predictions and computer simulations based on the bR crystal structure. The result is a significant and essential step on the way to developing a general small-angle scattering-based method for determining the low-resolution structures of membrane proteins in physiologically relevant environments.

A novel application of small-angle scattering techniques: Quality assurance testing of virus quantification technology

Small-angle scattering (SAS) techniques, like small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS), were used to measure and thus to validate the accuracy of a novel technology for virus sizing and concentration determination. These studies demonstrate the utility of SAS techniques for use in quality assurance measurements and as novel technology for the physical characterization of viruses.