Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

Tuning Structural Organization via Molecular Design and Hierarchical Assembly to Develop Supramolecular Thermoresponsive Hydrogels

The cellular microenvironment is composed of a dynamic hierarchical fibrillar architecture providing a variety of physical and bioactive signals to the surrounding cells. This dynamicity, although common in biology, is a challenge to control in synthetic matrices. Here, responsive synthetic supramolecular monomers were designed that are able to assemble into hierarchical fibrous structures, combining supramolecular fiber formation via hydrogen bonding interactions, with a temperature-responsive hydrophobic collapse, resulting in cross-linking and hydrogel formation. Therefore, amphiphilic molecules were synthesized, composed of a hydrogen bonding ureido-pyrimidinone (UPy) unit, a hydrophobic alkyl spacer, and a hydrophilic oligo(ethylene glycol) tail. The temperature responsive behavior was introduced by functionalizing these supramolecular amphiphiles with a relatively short poly(N-isopropylacrylamide) (PNIPAM) chain (M n ∼ 2.5 or 5.5 kg/mol). To precisely control the assembly of these monomers, the length of the alkyl spacer between the UPy moiety and PNIPAM was varied in length. A robust sol-gel transition, with the dodecyl UPy-PNIPAM molecule, was obtained, with a network elasticity enhancing over 2000 times upon heating above room temperature. The UPy-PNIPAM compounds with shorter alkyl spacers were already hydrogels at room temperature. The sol-gel transition of the dodecyl UPy-PNIPAM hydrogelator could be tuned by the incorporation of different UPy-functionalized monomers. Furthermore, we demonstrated the suitability of this system for microfluidic cell encapsulation through a convenient temperature sol-gel transition. Our results indicate that this novel thermoresponsive supramolecular system offers a modular platform to study and guide single-cell behavior.

Guanidine Hydrochloride-Induced Hepatitis B Virus Capsid Disassembly Hysteresis

Hepatitis B virus (HBV) displays remarkable self-assembly capabilities that interest the scientific community and biotechnological industries as HBV is leading to an annual mortality of up to 1 million people worldwide (especially in Africa and Southeast Asia). When the ionic strength is increased, hepatitis B virus-like particles (VLPs) can assemble from dimers of the first 149 residues of the HBV capsid protein core assembly domain (Cp149). Using solution small-angle X-ray scattering, we investigated the disassembly of the VLPs by titrating guanidine hydrochloride (GuHCl). Measurements were performed with and without 1 M NaCl, added either before or after titrating GuHCl. Fitting the scattering curves to a linear combination of atomic models of Cp149 dimer (the subunit) and T = 3 and T = 4 icosahedral capsids revealed the mass fraction of the dimer in each structure in all the titration points. Based on the mass fractions, the variation in the dimer-dimer association standard free energy was calculated as a function of added GuHCl, showing a linear relation between the interaction strength and GuHCl concentration. Using the data, we estimated the energy barriers for assembly and disassembly and the critical nucleus size for all of the assembly reactions. Extrapolating the standard free energy to [GuHCl] = 0 showed an evident hysteresis in the assembly process, manifested by differences in the dimer-dimer association standard free energy obtained for the disassembly reactions compared with the equivalent assembly reactions. Similar hysteresis was observed in the energy barriers for assembly and disassembly and the critical nucleus size. The results suggest that above 1.5 M, GuHCl disassembled the capsids by attaching to the protein and adding steric repulsion, thereby weakening the hydrophobic attraction.

INSIGHT: in situ heuristic tool for the efficient reduction of grazing-incidence X-ray scattering data

INSIGHT is a Python-based software tool for processing and reducing 2D grazing-incidence wide- and small-angle X-ray scattering (GIWAXS/GISAXS) data. It offers the geometric transformation of the 2D GIWAXS/GISAXS detector image to reciprocal space, including vectorized and parallelized pixel-wise intensity correction calculations. An explicit focus on efficient data management and batch processing enables full control of large time-resolved synchrotron and laboratory data sets for a detailed analysis of kinetic GIWAXS/GISAXS studies of thin films. It processes data acquired with arbitrarily rotated detectors and performs vertical, horizontal, azimuthal and radial cuts in reciprocal space. It further allows crystallographic indexing and GIWAXS pattern simulation, and provides various plotting and export functionalities. Customized scripting offers a one-step solution to reduce, process, analyze and export findings of large in situ and operando data sets.

Recent progress on polySarcosine as an alternative to PEGylation: Synthesis and biomedical applications

Biotherapeutic PEGylation to prolong action of medications has gained popularity over the last decades. Various hydrophilic natural polymers have been developed to tackle the drawbacks of PEGylation, such as its accelerated blood clearance and non-biodegradability. Polypeptoides, such as polysarcosine (pSar), have been explored as hydrophilic substitutes for PEG. pSar has PEG-like physicochemical characteristics such as water solubility and no reported cytotoxicity and immunogenicity. This review discusses pSar derivatives, synthesis, characterization approaches, biomedical applications, in addition to the challenges and future perspectives of pSar based biomaterials as an alternative to PEG.

Accurate Determination of the Average Rate Constant of Pyrene Excimer Formation for Pyrene-Labeled Macromolecules from the Analysis of Individual Fluorescence Decays with Sums of Exponentials

The average rate constant (⟨k⟩) for pyrene excimer formation (PEF) between an excited and a ground-state pyrenyl label covalently attached to a pyrene-labeled macromolecule (PyLM) has been found to be an ideal parameter to probe macromolecular conformations due to its proportionality to the local concentration ([Py]loc) of pyrenyl labels in PyLM. To date, ⟨k⟩ has only been determined with the model-free analysis (MFA) involving the global analysis of the pyrene monomer and excimer fluorescence decays of PyLM. Unfortunately, the MFA is computationally demanding which prevents its widespread use. To circumvent this complication, a methodology is introduced that involves the analysis of individual fluorescence decays with sums of exponentials (SoE), which are commonly used in the analysis packages of commercial time-resolved fluorometers. The individual fluorescence decays of the pyrene monomer acquired with 286 PyLM were analyzed with a SoE to yield ⟨kSoE-M⟩. The strong correlation between ⟨kSoE-M⟩ and ⟨kMF⟩ obtained from the global MFA indicated that ⟨kSoE-M⟩ was a good representation of ⟨k⟩. Furthermore, the AE-/AE+ ratio, equal to the ratio of the sum of the negative pre-exponential factors over the sum of the positive pre-exponential factors, was determined by fitting the individual pyrene excimer fluorescence decays of the 286 PyLM with a SoE. AE-/AE+ was found to take a value between -1.0 and -0.8, indicating that the pyrenyl labels were not aggregated. This result indicated that [Py]loc was well described by ⟨kSoE-M⟩, so that ⟨kSoE-M⟩ could be used to describe the conformation of macromolecules in the same manner as ⟨kMF⟩. Consequently, the methodology based on the analysis of individual fluorescence decays with sums of exponentials to determine ⟨kSoE-M⟩ and AE-/AE+ provides a robust alternative to the use of the MFA for the study of PyLM to many scientists interested in the characterization of macromolecular conformations.

Study on the Effects of Wettability and Pressure in Shale Matrix Nanopore Imbibition during Shut-in Process by Molecular Dynamics Simulations

Shut-in after fracturing is generally adopted for wells in shale oil reservoirs, and imbibition occurring in matrix nanopores has been proven as an effective way to improve recovery. In this research, a molecular dynamics (MD) simulation was used to investigate the effects of wettability and pressure on nanopore imbibition during shut-in for a typical shale reservoir, Jimsar. The results indicate that the microscopic advancement mechanism of the imbibition front is the competitive adsorption between "interfacial water molecules" at the imbibition front and "adsorbed oil molecules" on the pore wall. The essence of spontaneous imbibition involves the adsorption and aggregation of water molecules onto the hydroxyl groups on the pore wall. The flow characteristics of shale oil suggest that the overall push of the injected water to the oil phase is the main reason for the displacement of adsorbed oil molecules. Thus, shale oil, especially the heavy hydrocarbon component in the adsorbed layer, tends to slip on the walls. However, the weak slip ability of heavy components on the wall surface is an important reason that restricts the displacement efficiency of shale oil during spontaneous imbibition. The effectiveness of spontaneous imbibition is strongly dependent on the hydrophilicity of the matrix pore's wall. The better hydrophilicity of the matrix pore wall facilitates higher levels of adsorption and accumulation of water molecules on the pore wall and requires less time for "interfacial water molecules" to compete with adsorbed oil molecules. During the forced imbibition process, the pressure difference acts on both the bulk oil and the boundary adsorption oil, but mainly on the bulk oil, which leads to the occurrence of wetting hysteresis. Meanwhile, shale oil still existing in the pore always maintains a good, stratified adsorption structure. Because of the wetting hysteresis phenomenon, as the pressure difference increases, the imbibition effect gradually increases, but the actual capillary pressure gradually decreases and there is a loss in the imbibition velocity relative to the theoretical value. Simultaneously, the decline in hydrophilicity further weakens the synergistic effect on the imbibition of the pressure difference because of the more pronounced wetting hysteresis. Thus, selecting an appropriate well pressure enables cost savings and maximizes the utilization of the formation's natural power for enhanced oil recovery (EOR).

Automated selection of nanoparticle models for small-angle X-ray scattering data analysis using machine learning

Small-angle X-ray scattering (SAXS) is widely used to analyze the shape and size of nanoparticles in solution. A multitude of models, describing the SAXS intensity resulting from nanoparticles of various shapes, have been developed by the scientific community and are used for data analysis. Choosing the optimal model is a crucial step in data analysis, which can be difficult and time-consuming, especially for non-expert users. An algorithm is proposed, based on machine learning, representation learning and SAXS-specific preprocessing methods, which instantly selects the nanoparticle model best suited to describe SAXS data. The different algorithms compared are trained and evaluated on a simulated database. This database includes 75 000 scattering spectra from nine nanoparticle models, and realistically simulates two distinct device configurations. It will be made freely available to serve as a basis of comparison for future work. Deploying a universal solution for automatic nanoparticle model selection is a challenge made more difficult by the diversity of SAXS instruments and their flexible settings. The poor transferability of classification rules learned on one device configuration to another is highlighted. It is shown that training on several device configurations enables the algorithm to be generalized, without degrading performance compared with configuration-specific training. Finally, the classification algorithm is evaluated on a real data set obtained by performing SAXS experiments on nanoparticles for each of the instrumental configurations, which have been characterized by transmission electron microscopy. This data set, although very limited, allows estimation of the transferability of the classification rules learned on simulated data to real data.

Effect of ligand and shell densities on the surface structure of core-shell nanoparticles self-assembled from function-spacer-lipid constructs

Biomolecular corona is the major obstacle to the clinical translation of nanomedicines. Since corona formation is governed by molecular interactions at the nano-bio interface, nanoparticle surface properties such as topography, charge and surface chemistry can be tuned to manipulate biomolecular corona formation. To this end, as the first step towards a deep understanding of the processes of corona formation, it is necessary to develop nanoparticles employing various biocompatible materials and characterize their surface structure and dynamics at the molecular level. In this work, we applied molecular dynamics simulation to study the surface structure of organic core-shell nanoparticles formed by the self-assembly of synthetic molecules composed of a DOPE lipid, a carboxymethylglycine spacer and biotin. Lipid moieties form the hydrophobic core, spacer motifs serve as a hydrophilic shell and biotin residues function as a targeting ligand. By mixing such function-spacer-lipid, spacer-lipid and lipid-only constructs at various molar ratios, densities of the ligand and spacer on the nanoparticle surface were modified. For convenient analysis of the structure and dynamics of all regions of the nanoparticle surface, we compiled topography maps based on atomic coordinates. It was shown that an increase in the density of the shell does not reduce exposure of the core, but increases shell average thickness. Biotin, due to its alkyl valeric acid chain and spacer flexibility, is localized primarily near the hydrophobic core and its partial presentation on the surface occurs only in nanoparticles with higher ligand densities. However, an increase in biotin density leads to its clustering. In turn, ligand clustering diminishes the stealth properties of the shell and targeting efficiency. Based on nanoparticle surface structures, we determined the optimal density of biotin. Experimental studies reported in the literature confirm these conclusions. We also suggest design tips to achieve the preferred biotin presentation. Simulation results are consistent with the synchrotron SAXS profile. We believe that such studies will contribute to a better understanding of nano-bio interactions towards the rational design of efficient drug delivery systems.

Computational approaches for modeling and structural design of biological systems: A comprehensive review

The convergence of biology and computational science has ushered in a revolutionary era, revolutionizing our understanding of biological systems and providing novel solutions to global problems. The field of genetic engineering has facilitated the manipulation of genetic codes, thus providing opportunities for the advancement of innovative disease therapies and environmental enhancements. The emergence of bio-molecular simulation represents a significant advancement in this particular field, as it offers the ability to gain microscopic insights into molecular-level biological processes over extended periods. Biomolecular simulation plays a crucial role in advancing our comprehension of organismal mechanisms by establishing connections between molecular structures, interactions, and biological functions. The field of computational biology has demonstrated its significance in deciphering intricate biological enigmas through the utilization of mathematical models and algorithms. The process of decoding the human genome has resulted in the advancement of therapies for a wide range of genetic disorders, while the simulation of biological systems contributes to the identification of novel pharmaceutical compounds. The potential of biomolecular simulation and computational biology is vast and limitless. As the exploration of the underlying principles that govern living organisms progresses, the potential impact of this understanding on cancer treatment, environmental restoration, and other domains is anticipated to be transformative. This review examines the notable advancements achieved in the field of computational biology, emphasizing its potential to revolutionize the comprehension and enhancement of biological systems.

SARS-CoV-2 proteins structural studies using synchrotron radiation

In the process of the development of structural biology, both the size and the complexity of the determined macromolecular structures have grown significantly. As a result, the range of application areas for the results of structural studies of biological macromolecules has expanded. Significant progress in the development of structural biology methods has been largely achieved through the use of synchrotron radiation. Modern sources of synchrotron radiation allow to conduct high-performance structural studies with high temporal and spatial resolution. Thus, modern techniques make it possible to obtain not only static structures, but also to study dynamic processes, which play a key role in understanding biological mechanisms. One of the key directions in the development of structural research is the drug design based on the structures of biomolecules. Synchrotron radiation offers insights into the three-dimensional time-resolved structure of individual viral proteins and their complexes at atomic resolution. The rapid and accurate determination of protein structures is crucial for understanding viral pathogenicity and designing targeted therapeutics. Through the application of experimental techniques, including X-ray crystallography and small-angle X-ray scattering (SAXS), it is possible to elucidate the structural details of SARS-CoV-2 virion containing 4 structural, 16 nonstructural proteins (nsp), and several accessory proteins. The most studied potential targets for vaccines and drugs are the structural spike (S) protein, which is responsible for entering the host cell, as well as nonstructural proteins essential for replication and transcription, such as main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp). This article provides a brief overview of structural analysis techniques, with focus on synchrotron radiation-based methods applied to the analysis of SARS-CoV-2 proteins.

Can BioSAXS detect ultrastructural changes of antifungal compounds in Candida albicans?-an exploratory study

The opportunistic yeast Candida albicans is the most common cause of candidiasis. With only four classes of antifungal drugs on the market, resistance is becoming a problem in the treatment of fungal infections, especially in immunocompromised patients. The development of novel antifungal drugs with different modes of action is urgent. In 2016, we developed a groundbreaking new medium-throughput method to distinguish the effects of antibacterial agents. Using small-angle X-ray scattering for biological samples (BioSAXS), it is now possible to screen hundreds of new antibacterial compounds and select those with the highest probability for a novel mode of action. However, yeast (eukaryotic) cells are highly structured compared to bacteria. The fundamental question to answer was if the ultrastructural changes induced by the action of an antifungal drug can be detected even when most structures in the cell stay unchanged. In this exploratory work, BioSAXS was used to measure the ultrastructural changes of C. albicans that were directly or indirectly induced by antifungal compounds. For this, the well-characterized antifungal drug Flucytosine was used. BioSAXS measurements were performed on the synchrotron P12 BioSAXS beamline, EMBL (DESY, Hamburg) on treated and untreated yeast C. albicans. BioSAXS curves were analysed using principal component analysis (PCA). The PCA showed that Flucytosine-treated and untreated yeast were separated. Based on that success further measurements were performed on five antifungal peptides {1. Cecropin A-melittin hybrid [CA (1-7) M (2-9)], KWKLFKKIGAVLKVL; 2. Lasioglossin LL-III, VNWKKILGKIIKVVK; 3. Mastoparan M, INLKAIAALAKKLL; 4. Bmkn2, FIGAIARLLSKIFGKR; and 5. optP7, KRRVRWIIW}. The ultrastructural changes of C. albicans indicate that the peptides may have different modes of action compared to Flucytosine as well as to each other, except for the Cecropin A-melittin hybrid [CA (1-7) M (2-9)] and optP7, showing very similar effects on C. albicans. This very first study demonstrates that BioSAXS shows promise to be used for antifungal drug development. However, this first study has limitations and further experiments are necessary to establish this application.

Exploring the inhibitory potential of novel piperidine-derivatives against main protease (Mpro) of SARS-CoV-2: A hybrid approach consisting of molecular docking, MD simulations and MMPBSA analysis

In the current study, a hybrid computational approach consisting of different computational methods to explore the molecular electronic structures, bioactivity and therapeutic potential of piperidine compounds against SARS-CoV-2. The quantum chemical methods are used to study electronic structures of designed derivatives, molecular docking methods are used to see the most potential docking interactions for main protease (M^Pro) of SARS-CoV-2 while molecular dynamic and MMPBSA analyses are performed in bulk water solvation process to mimic real protein like aqueous environment and effectiveness of docked complexes. We designed and optimized piperidine derivatives from experimentally known precursor using quantum chemical methods. The UV-Visible, IR, molecular orbitals, molecular electrostatic plots, and global chemical reactivity descriptors are carried out which illustrate that the designed compounds are kinetically stable and reactive. The results of MD simulations and binding free energy revealed that all the complex systems possess adequate dynamic stability, and flexibility based on their RMSD, RMSF, radius of gyration, and hydrogen bond analysis. The computed net binding free energy ( Δ G b i n d ) as calculated by MMPBSA method for the complexes showed the values of -4.29 kcal.mol^-1 for P1, -5.52 kcal.mol^-1 for P2, -6.12 kcal.mol^-1 for P3, -6.35 kcal.mol^-1 for P4, -5.19 kcal.mol^-1 for P5, 3.09 kcal.mol^-1 for P6, -6.78 kcal.mol^-1 for P7, and -6.29 kcal.mol^-1 for P8.The ADMET analysis further confirmed that none of among the designed ligands violates the Lipinski rule of five (RO5). The current comprehensive investigation predicts that all our designed compounds are recommended as prospective therapeutic drugs against M^pro of SARS-CoV-2 and it provokes the scientific community to further perform their in-vitro analysis.

Cholesterol-Containing Liposomes Decorated With Au Nanoparticles as Minimal Tunable Fusion Machinery

Membrane fusion is essential for the basal functionality of eukaryotic cells. In physiological conditions, fusion events are regulated by a wide range of specialized proteins, operating with finely tuned local lipid composition and ionic environment. Fusogenic proteins, assisted by membrane cholesterol and calcium ions, provide the mechanical energy necessary to achieve vesicle fusion in neuromediator release. Similar cooperative effects must be explored when considering synthetic approaches for controlled membrane fusion. We show that liposomes decorated with amphiphilic Au nanoparticles (AuLips) can act as minimal tunable fusion machinery. AuLips fusion is triggered by divalent ions, while the number of fusion events dramatically changes with, and can be finely tuned by, the liposome cholesterol content. We combine quartz-crystal-microbalance with dissipation monitoring (QCM-D), fluorescence assays, and small-angle X-ray scattering (SAXS) with molecular dynamics (MD) at coarse-grained (CG) resolution, revealing new mechanistic details on the fusogenic activity of amphiphilic Au nanoparticles (AuNPs) and demonstrating the ability of these synthetic nanomaterials to induce fusion regardless of the divalent ion used (Ca²⁺ or Mg²⁺ ). The results provide a novel contribution to developing new artificial fusogenic agents for next-generation biomedical applications that require tight control of the rate of fusion events (e.g., targeted drug delivery).

Experiment-guided molecular simulations define a heterogeneous structural ensemble for the PTPN11 tandem SH2 domains

SHP2 plays an important role in regulating cellular processes, and its pathogenic mutations cause developmental disorders and are linked to cancer. SHP2 is a multidomain protein, comprising two SH2 domains arranged in tandem, a catalytic PTP domain, and a disordered C-terminal tail. SHP2 is activated upon binding two linked phosphopeptides to its SH2 domains, and the peptide orientation and spacing between binding sites are critical for enzymatic activation. For decades, the tandem SH2 has been extensively studied to identify the relative orientation of the two SH2 domains that most effectively binds effectors. So far, neither crystallography nor experiments in solution have provided conclusive results. Using experiment-guided molecular simulations, we determine the heterogeneous structural ensemble of the tandem SH2 in solution in agreement with experimental data from small-angle X-ray scattering and NMR residual dipolar couplings. In the solution ensemble, N-SH2 adopts different orientations and positions relative to C-SH2. We suggest that the intrinsic structural plasticity of the tandem SH2 allows SHP2 to respond to external stimuli and is essential for its functional activity.

Stretchable Clay Nanocomposite Barrier Film for Flexible Packaging

The goal of reconciling all packaging requirements, e.g., mechanical resistance, transparency, flexibility, and gas barrier properties, is immensely challenging for packaging materials. Particularly, the combination of flexibility and good gas barrier properties poses a serious problem, especially when barrier requirements can only be met by lamination with a metal foil, metalization, or vapor-deposited ceramic layers, as all of these tend to be nonstretchable. In this work, we produced a stretchable nanocomposite barrier composed of one-dimensional (1D) crystalline (Bragg stack) barrier films composed of alternating layers of poly(ethylene glycol) (PEG) and synthetic sodium fluorohectorite (Hec) nanosheets. By sandwiching the Bragg stack type film between two plasticized poly(vinyl alcohol) (PVOH) layers, a waterborne laminate was obtained that outperforms commercial polymer materials in terms of water vapor permeability (WVP = 2.8 g mm m^-2 day^-1 bar^-1 at 23 °C and 85% relative humidity), which is remarkable for an entirely water-soluble film. Moreover, no deterioration of barrier performance up to 10% elongation was observed, rendering the transparent self-standing laminate promising for thermoformed blister packaging, shrink wrap, or vacuum packaging. Besides the low WVP, the scalable and green processing method makes this technology auspicious for real-world applications.

Fabrication of Bragg stack films of clay nanosheets and polycations via co-polymerization of intercalated monomers and functional interlayer cations

The fabrication of one-dimensional (1D) crystalline, monodomain nanocomposite films (hybrid Bragg stacks) is still limited to a few combinations of polymers and clay. The main reason is the segregation of clay and polymers driven by the entropic loss faced by the polymer confined in a narrow slit between the nanosheets. By exchanging synthetic sodium-fluorohectorite with vinylbenzyltrimethylammonium chloride, we succeeded in delaminating clay via 1D dissolution in N-methylformamide to obtain a liquid crystalline suspension. By combining this with bisphenol A glycerolate diacrylate, 1D crystalline nanocomposites could be obtained via photopolymerization of doctor bladed wet coatings. Infrared spectroscopy confirmed the co-polymerization of monomers and the organic modifier between the hectorite platelets. This single-phase hybrid material shows very low oxygen and water vapor transmission rates. The incorporation of the modified clay into the polymer leads to an oxygen transmission rate of 0.21 cm³ m^-2 day^-1 atm^-1 at 50% r.h. and 23 °C and a water vapor transmission rate of 0.05 g m^-2 day^-1 for a coating of 3.7 μm, making this material appropriate for challenging packaging applications.

Investigation of Dielectric and Mechanical Properties of Pretreated Natural Sunn Hemp Fiber-Reinforced Composite in Correlation with Macromolecular Structure of the Fiber

The present study attempts to establish a correlation between the macromolecular parameters obtained from small angle X-ray scattering (SAXS) analysis of pretreated sunn hemp (Crotalaria juncea) fibers with the dielectric and mechanical properties of their composites. Sunn hemp fiber is pretreated chemically by dewaxing and alkalization methods and physically by microwave irradiation. The treatment effect is structurally investigated using a correlation function from SAXS data and correlated with the mechanical as well as electrical properties of composites. The macromolecular parameters are observed to be influenced by pretreatment methods. Macromolecular structural modifications are seen in dewaxed fiber (DSHC), fiber treated with 10% of alkali soaked for 6 h (10K6C), and fiber microwave irradiated with 800 watts for 6 min (800W6M), improving the mechanical as well as electric properties of the reinforced composites.

Ultrasonically controlled synthesis of UO2+x colloidal nanoparticles

Actinide colloids and nanoparticles (NPs) currently constitute a topic of strong interest due to their potential role in advanced nuclear energetics and the environmental migration of radioactivity. A better understanding of the physico-chemical properties of nanoscale actinide oxides requires robust synthesis approaches. In this work, UO_2+x NPs were successfully prepared by sonochemistry from U(IV) solutions previously stabilised in a hydrochloric medium (20 kHz, 65 °C, Ar/(10%)CO). Colloidal suspensions were found to be composed of crystalline and spherical NPs showing a UO₂-like structure and measuring 18.0 ± 0.1 nm (SAXS, HR-TEM and PXRD techniques). In comparison with the controlled hydrolysis approach used as a reference, sonochemistry appears to be a simple and original synthesis route providing larger, better defined and more crystalline UO_2+x NPs with a narrower size distribution. These well-defined NPs offer new opportunities for the preparation of reference actinide materials devoted to fundamental, technological and environmental studies.

Using Small-angle X-ray Scattering to Characterize Biological Systems: A General Overview and Practical Tips

Small-angle X-ray Scattering (SAXS) is a versatile and powerful technique with applications in a wide range of fields. The continuous improvements in hardware, data analysis software, and standards for validation significantly contributed to increase its popularity and, nowadays, SAXS is a well-established method. SAXS allows to study flexible and dynamic systems (e.g., proteins and other biomolecules) in solution, providing information about their size and shape. Contrary to other structural characterization methods, SAXS has no limitations on the size of the particle under study and can be used in integrated approaches to reveal important insights otherwise difficult to obtain regarding folding-unfolding, conformational changes, movement of flexible regions, and the formation of complexes.This chapter, in addition to a concise overview on the methodology, intends to systematically enumerate the main steps involved in sample preparation and data collection, processing and analysis including useful practical notes to identify and overcome common bottlenecks. This way, a less experienced user can use the content of the chapter as a starting point to properly design and perform a successful SAXS experiment.

Extracting structural insights from soft X-ray scattering of biological assemblies

Resonant soft X-ray scattering (RSoXS), a technique that combines X-ray absorption spectroscopy and X-ray scattering, can probe the nano- and meso-scale structure of biological assemblies with chemical specificity. RSoXS experiments yield scattering data collected at several photon energies, for example across an elemental absorption edge of interest. Collecting a near-edge X-ray absorption fine structure (NEXAFS) spectrum complements RSoXS experiments and determines X-ray energies that are best suited for RSoXS measurements. The analysis of RSoXS data is similar in many ways to analysis of small angle X-ray scattering using hard X-rays, with an added dimension that includes an X-ray energy dependence. This chapter discusses procedures for predicting scattering contrast and thereby identifying energies suitable for RSoXS measurements using NEXAFS spectra, analyses of 2D RSoXS images through integration into 1D profiles, and strategies for elucidating the origin of RSoXS scattering features. It also discusses existing and potential methods for interpretation of RSoXS data to gain detailed structural insights into biological systems.

Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation

The phosphatase and tensin homologue deleted on chromosome 10 (PTEN) tumor suppressor gene encodes a tightly regulated dual-specificity phosphatase that serves as the master regulator of PI3K/AKT/mTOR signaling. The carboxy-terminal tail (CTT) is key to regulation and harbors multiple phosphorylation sites (Ser/Thr residues 380-385). CTT phosphorylation suppresses the phosphatase activity by inducing a stable, closed conformation. However, little is known about the mechanisms of phosphorylation-induced CTT-deactivation dynamics. Using explicit solvent microsecond molecular dynamics simulations, we show that CTT phosphorylation leads to a partially collapsed conformation, which alters the secondary structure of PTEN and induces long-range conformational rearrangements that encompass the active site. The active site rearrangements prevent localization of PTEN to the membrane, precluding lipid phosphatase activity. Notably, we have identified phosphorylation-induced allosteric coupling between the interdomain region and a hydrophobic site neighboring the active site in the phosphatase domain. Collectively, the results provide a mechanistic understanding of CTT phosphorylation dynamics and reveal potential druggable allosteric sites in a previously believed clinically undruggable protein.

Recent Advances in Understanding the Structures of Translesion Synthesis DNA Polymerases

DNA damage in the template strand causes replication forks to stall because replicative DNA polymerases are unable to efficiently incorporate nucleotides opposite template DNA lesions. To overcome these replication blocks, cells are equipped with multiple translesion synthesis polymerases that have evolved specifically to incorporate nucleotides opposite DNA lesions. Over the past two decades, X-ray crystallography has provided a wealth of information about the structures and mechanisms of translesion synthesis polymerases. This approach, however, has been limited to ground state structures of these polymerases bound to DNA and nucleotide substrates. Three recent methodological developments have extended our understanding of the structures and mechanisms of these polymerases. These include time-lapse X-ray crystallography, which allows one to identify novel reaction intermediates; full-ensemble hybrid methods, which allow one to examine the conformational flexibility of the intrinsically disordered regions of proteins; and cryo-electron microscopy, which allows one to determine the high-resolution structures of larger protein complexes. In this article, we will discuss how these three methodological developments have added to our understanding of the structures and mechanisms of translesion synthesis polymerases.

Using small-angle scattering to guide functional magnetic nanoparticle design

Magnetic nanoparticles offer unique potential for various technological, biomedical, or environmental applications thanks to the size-, shape- and material-dependent tunability of their magnetic properties. To optimize particles for a specific application, it is crucial to interrelate their performance with their structural and magnetic properties. This review presents the advantages of small-angle X-ray and neutron scattering techniques for achieving a detailed multiscale characterization of magnetic nanoparticles and their ensembles in a mesoscopic size range from 1 to a few hundred nanometers with nanometer resolution. Both X-rays and neutrons allow the ensemble-averaged determination of structural properties, such as particle morphology or particle arrangement in multilayers and 3D assemblies. Additionally, the magnetic scattering contributions enable retrieving the internal magnetization profile of the nanoparticles as well as the inter-particle moment correlations caused by interactions within dense assemblies. Most measurements are used to determine the time-averaged ensemble properties, in addition advanced small-angle scattering techniques exist that allow accessing particle and spin dynamics on various timescales. In this review, we focus on conventional small-angle X-ray and neutron scattering (SAXS and SANS), X-ray and neutron reflectometry, gracing-incidence SAXS and SANS, X-ray resonant magnetic scattering, and neutron spin-echo spectroscopy techniques. For each technique, we provide a general overview, present the latest scientific results, and discuss its strengths as well as sample requirements. Finally, we give our perspectives on how future small-angle scattering experiments, especially in combination with micromagnetic simulations, could help to optimize the performance of magnetic nanoparticles for specific applications.

Pyrophosphate-stabilised amorphous calcium carbonate for bone substitution: toward a doping-dependent cluster-based model

Multiscale and multitool advanced characterisation of pyrophosphate-stabilised amorphous calcium carbonates allowed building a cluster-based model paving the way for tunable biomaterials.

On the Stiffness of Gold at the Nanoscale

The density and compressibility of nanoscale gold (both nanospheres and nanorods) and microscale gold (bulk) were simultaneously studied by X-ray diffraction with synchrotron radiation up to 30 GPa. Colloidal stability (aggregation state and nanoparticle shape and size) in both hydrostatic and nonhydrostatic regions was monitored by small-angle X-ray scattering. We demonstrate that nonhydrostatic effects due to solvent solidification had a negligible influence on the stability of the nanoparticles. Conversely, nonhydrostatic effects produced axial stresses on the nanoparticle up to a factor 10× higher than those on the bulk metal. Working under hydrostatic conditions (liquid solution), we determined the equation of state of individual nanoparticles. From the values of the lattice parameter and bulk modulus, we found that gold nanoparticles are slightly denser (0.3%) and stiffer (2%) than bulk gold: V0 = 67.65(3) Å3, K0 = 170(3)GPa, at zero pressure.

MOFs in the time domain

Many of the proposed applications of metal-organic framework (MOF) materials may fail to materialize if the community does not fully address the difficult fundamental work needed to map out the 'time gap' in the literature - that is, the lack of investigation into the time-dependent behaviours of MOFs as opposed to equilibrium or steady-state properties. Although there are a range of excellent investigations into MOF dynamics and time-dependent phenomena, these works represent only a tiny fraction of the vast number of MOF studies. This Review provides an overview of current research into the temporal evolution of MOF structures and properties by analysing the time-resolved experimental techniques that can be used to monitor such behaviours. We focus on innovative techniques, while also discussing older methods often used in other chemical systems. Four areas are examined: MOF formation, guest motion, electron motion and framework motion. In each area, we highlight the disparity between the relatively small amount of (published) research on key time-dependent phenomena and the enormous scope for acquiring the wider and deeper understanding that is essential for the future of the field.

In-Situ Synchrotron SAXS and WAXS Investigation on the Deformation of Single and Coaxial Electrospun P(VDF-TrFE)-Based Nanofibers

Coaxial core/shell electrospun nanofibers consisting of ferroelectric P(VDF-TrFE) and relaxor ferroelectric P(VDF-TrFE-CTFE) are tailor-made with hierarchical structures to modulate their mechanical properties with respect to their constituents. Compared with two single and the other coaxial membranes prepared in the research, the core/shell-TrFE/CTFE membrane shows a more prominent mechanical anisotropy between revolving direction (RD) and cross direction (CD) associated with improved resistance to tensile stress for the crystallite phase stability and good strength-ductility balance. This is due to the better degree of core/shell-TrFE-CTFE nanofiber alignment and the crystalline/amorphous ratio. The coupling between terpolymer P(VDF-TrFE-CTFE) and copolymer P(VDF-TrFE) is responsible for phase stabilization, comparing the core/shell-TrFE/CTFE with the pristine terpolymer. Moreover, an impressive collective deformation mechanism of a two-length scale in the core/shell composite structure is found. We apply in-situ synchrotron X-ray to resolve the two-length scale simultaneously by using the small-angle X-ray scattering to characterize the nanofibers and the wide-angle X-ray diffraction to identify the phase transformations. Our findings may serve as guidelines for the fabrication of the electrospun nanofibers used as membranes-based electroactive polymers.

Disorder-Order Transition-Improving the Moisture Sensitivity of Waterborne Nanocomposite Barriers

Systematic studies on the influence of crystalline vs disordered nanocomposite structures on barrier properties and water vapor sensitivity are scarce as it is difficult to switch between the two morphologies without changing other critical parameters. By combining water-soluble poly(vinyl alcohol) (PVOH) and ultrahigh aspect ratio synthetic sodium fluorohectorite (Hec) as filler, we were able to fabricate nanocomposites from a single nematic aqueous suspension by slot die coating that, depending on the drying temperature, forms different desired morphologies. Increasing the drying temperature from 20 to 50 °C for the same formulation triggers phase segregation and disordered nanocomposites are obtained, while at room temperature, one-dimensional (1D) crystalline, intercalated hybrid Bragg Stacks form. The onset of swelling of the crystalline morphology is pushed to significantly higher relative humidity (RH). This disorder-order transition renders PVOH/Hec a promising barrier material at RH of up to 65%, which is relevant for food packaging. The oxygen permeability (OP) of the 1D crystalline PVOH/Hec is an order of magnitude lower compared to the OP of the disordered nanocomposite at this elevated RH (OP = 0.007 cm³ μm m^-2 day^-1 bar^-1 cf. OP = 0.047 cm³ μm m^-2 day^-1 bar^-1 at 23 °C and 65% RH).

Ultrasonically assisted conversion of uranium trioxide into uranium(vi) intrinsic colloids

Under oxidizing conditions, the corrosion of spent nuclear fuel may lead to the leaching of radionuclides including soluble uranyl-based species. The speciation of the generated chemical forms is complex and the related potential formation of colloidal species appears surprisingly poorly reported in the literature. Their formation could however contribute significantly to the mobility of radionuclides in the environment. A better knowledge in the speciation and reactivity of these species appears particularly relevant. This study describes the preparation and characterization of intrinsic uranium(vi) colloids from amorphous and crystalline UO₃ in pure water assisted by 20 kHz ultrasound. In the presence of carbon monoxide preventing the sonochemical formation of hydrogen peroxide, ultrasonic treatment boosts the conversion of UO₃ powder into (meta-)schoepite precipitates and yields very stable and notably concentrated uranium(vi) nanoparticles in the liquid phase. Using HR-TEM, SAXS and XAS techniques, we confirmed that the colloidal suspension is composed of quasi-spherical nanoparticles measuring ca. 3.8 ± 0.3 nm and exhibiting a schoepite-like crystallographic structure. The proposed method demonstrates the possible formation of environmentally relevant U(vi) colloidal nanoparticles appearing particularly interesting for the preparation of reference systems in the absence of added ions and capping agents.

Small-angle X-ray scattering for the proteomics community: current overview and future potential

Introduction: Proteins are biological nanoparticles. For structural proteomics and hybrid structural biology, complementary methods are required that allow both high throughput and accurate automated data analysis. Small-angle X-ray scattering (SAXS) is a method for observing the size and shape of particles, such as proteins and complexes, in solution. SAXS data can be used to model both the structure, oligomeric state, conformational changes, and flexibility of biomolecular samples.Areas covered: The key principles of SAXS, its sample requirements, and its current and future applications for structural proteomics are briefly reviewed. Recent technical developments in SAXS experiments are discussed, and future potential of the method in structural proteomics is evaluated.Expert opinion: SAXS is a method suitable for several aspects of integrative structural proteomics, with current technical developments allowing for higher throughput and time-resolved studies, as well as the analysis of complex samples, such as membrane proteins. Increasing automation and streamlined data analysis are expected to equip SAXS for structure-based screening workflows. Originally, structural genomics had a heavy focus on folded, crystallizable proteins and complexes - SAXS is a method allowing an expansion of this focus to flexible and disordered systems.

Effect of mesoscale phase contrast on fatigue-delaying behavior of self-healing hydrogels

We investigate the fatigue resistance of chemically cross-linked polyampholyte hydrogels with a hierarchical structure due to phase separation and find that the details of the structure, as characterized by SAXS, control the mechanisms of crack propagation. When gels exhibit a strong phase contrast and a low cross-linking level, the stress singularity around the crack tip is gradually eliminated with increasing fatigue cycles and this suppresses crack growth, beneficial for high fatigue resistance. On the contrary, the stress concentration persists in weakly phase-separated gels, resulting in low fatigue resistance. A material parameter, λtran, is identified, correlated to the onset of non-affine deformation of the mesophase structure in a hydrogel without crack, which governs the slow-to-fast transition in fatigue crack growth. The detailed role played by the mesoscale structure on fatigue resistance provides design principles for developing self-healing, tough, and fatigue-resistant soft materials.

X-ray-Based Techniques to Study the Nano-Bio Interface

X-ray-based analytics are routinely applied in many fields, including physics, chemistry, materials science, and engineering. The full potential of such techniques in the life sciences and medicine, however, has not yet been fully exploited. We highlight current and upcoming advances in this direction. We describe different X-ray-based methodologies (including those performed at synchrotron light sources and X-ray free-electron lasers) and their potentials for application to investigate the nano-bio interface. The discussion is predominantly guided by asking how such methods could better help to understand and to improve nanoparticle-based drug delivery, though the concepts also apply to nano-bio interactions in general. We discuss current limitations and how they might be overcome, particularly for future use in vivo.

Distinctive Weak Interactions Underlie Diverse Nucleation and Small-Angle Scattering Behavior of Aqueous Cholesterol, Cholesteryl Hemisuccinate, and Glycocholic Acid

Increased total cholesterol is a major cause of serious heart ailments leading to an estimated 3 million deaths annually throughout the world. Understanding the flocculation behavior of small lipids is thus quintessential. Nucleation, small-angle scattering, and dynamical behavior of lipids and analogues like cholesterol (CHL), cholesteryl hemisuccinate (CHM), and glycocholic acid (GHL) are studied in water by molecular dynamics simulation. The study shows a distinct aggregation behavior of these physiologically relevant molecules owing to a systematic gradation in their non-bonding interactions with solvents and near neighbors. Spontaneous self-assemblies formed during simulation are observed to have different stability, aggregation patterns, and dynamics depending crucially on the nature of the hydrophobic/hydrophilic tails. With increasing hydrophilicity, in the order CHL < CHM < GHL, the aggregates become breakable and less compact, often interposed by water molecules in the interstitial spaces between the lipids. Small-angle scattering data obtained from our simulations provide insights toward the structural integrity and shape of the aggregates formed. Unique features are noticed while following the time evolution of the packing of the nucleated assemblies from the solution phase in terms of local density and molecular orientation. As hydrophilicity increases from CHL to GHL, the packing becomes progressively erratic with diverse angles between the molecular vectors. Surface electrostatic potential calculation indicates drastic increase in positive surface charge from CHL to CHM, which has strong implication in water and ion transport through membranes. These observations can be further correlated to comprehend the flocculation of cholesterol and bile acids in the human body.

Osmotic Delamination: A Forceless Alternative for the Production of Nanosheets Now in Highly Polar and Aprotic Solvents

Repulsive osmotic delamination is thermodynamically allowed "dissolution" of two-dimensional (2D) materials and therefore represents an attractive alternative to liquid-phase exfoliation to obtain strictly monolayered nanosheets with an appreciable aspect ratio with quantitative yield. However, osmotic delamination was so far restricted to aqueous media, severely limiting the range of accessible 2D materials. Alkali-metal intercalation compounds of MoS₂ or graphite are excluded because they cannot tolerate even traces of water. We now succeeded in extending osmotic delamination to polar and aprotic organic solvents. Upon complexation of interlayer cations of synthetic hectorite clay by crown ethers, either 15-crown-5 or 18-crown-6, steric pressure is exerted, which helps in reaching the threshold separation required to trigger osmotic delamination based on translational entropy. This way, complete delamination in water-free solvents like aprotic ethylene and propylene carbonate, N-methylformamide, N-methylacetamide, and glycerol carbonate was achieved.

Assessment of AMBER Force Fields for Simulations of ssDNA

Single-stranded DNA (ssDNA) plays an important role in biological processes and is used in DNA nanotechnology and other novel applications. Many important research questions can be addressed with molecular simulations of ssDNA molecules; however, no dedicated force field for ssDNA has been developed, and there is limited experimental information about ssDNA structures. This study assesses the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, such as ff99, bsc0, bsc1, and OL15, in implicit and explicit solvents via comparison to available experimental data, such as Forster resonance energy transfer and small angle X-ray scattering. We observed that some force fields agree better with experiments than others mainly due to the difference in parameterization of the propensity for hydrogen bonding and base stacking. Overall, the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experiment.

Porous hollow TiO2 microparticles for photocatalysis: exploiting novel ABC triblock terpolymer templates synthesised in supercritical CO2

We report the synthesis of phase separated PMMA-b-PS-b-P4VP microparticles via RAFT-mediated dispersion polymerisation in scCO₂ and their use as a structure-directing agent for the fabrication of TiO₂ microparticles for photocatalysis.

pH dependent aggregation and conformation changes of rituximab using SAXS and its comparison with the standard regulatory approach of biophysical characterization

Development of biologics and biosimilars involves extensive physical and structural characterization, which underlines the further course of its implementation. These characterization techniques require considerable standardization and are labor intensive. It is therefore, important to have an immediate, independent and affordable characterization strategy that may meet the regulatory guidelines. In this study, we have compared the standard biophysical characterization of an anti-CD 20 antibody with characterization by small angle x ray scattering (SAXS). Aggregation of this mAb was analyzed using standard techniques like size exclusion HPLC, dynamic light scattering and sedimentation velocity - analytical ultracentrifugation, whereas structure analysis was conducted using mass spectrometry, circular dichroism spectroscopy and fluorescence spectroscopy. Our results demonstrated that the inferences about the state of mAb aggregation and its structure deduced using the standard approaches were comparable to the data interpreted using SAXS. The radius of gyration and the P(r) distribution plot obtained using the SAXS scattering data allowed analysis of aggregation and conformation of mAb via a single experiment. Thus, SAXS can be used as an independent technique to complement orthogonal analysis for determining the aggregation profile and structure of mAbs.

Structural insights into the membrane receptor ShuA in DDM micelles and in a model of gram-negative bacteria outer membrane as seen by SAXS and MD simulations

Successful crystallization of membrane proteins in detergent micelles depends on key factors such as conformational stability of the protein in micellar assemblies, the protein-detergent complex (PDC) monodispersity and favorable protein crystal contacts by suitable shielding of the protein hydrophobic surface by the detergent belt. With the aim of studying the influence of amphiphilic environment on membrane protein structure, stability and crystallizability, we combine molecular dynamics (MD) simulations with SEC-MALLS and SEC-SAXS (Size Exclusion Chromatography in line with Multi Angle Laser Light Scattering or Small Angle X-ray Scattering) experiments to describe the protein-detergent interactions that could help to rationalize PDC crystallization. In this context, we compare the protein-detergent interactions of ShuA from Shigella dysenteriae in n-Dodecyl-β-D-Maltopyranoside (DDM) with ShuA inserted in a realistic model of gram-negative bacteria outer membrane (OM) containing a mixture of bacterial lipopolysaccharide and phospholipids. To evaluate the quality of the PDC models, we compute the corresponding SAXS curves from the MD trajectories and compare with the experimental ones. We show that computed SAXS curves obtained from the MD trajectories reproduce better the SAXS obtained from the SEC-SAXS experiments for ShuA surrounded by 268 DDM molecules. The MD results show that the DDM molecules form around ShuA a closed belt whose the hydrophobic thickness appears slightly smaller (~22 Å) than the hydrophobic transmembrane domain of the protein (24.6 Å) suggested by Orientations of Proteins in Membranes (OPM) database. The simulations also show that ShuA transmembrane domain is remarkably stable in all the systems except for the extracellular and periplasmic loops that exhibit larger movements due to specific molecular interactions with lipopolysaccharides (LPS). We finally point out that this detergent behavior may lead to the occlusion of the periplasmic hydrophilic surface and poor crystal contacts leading to difficulties in crystallization of ShuA in DDM.

How Detergents Dissolve Polymeric Micelles: Kinetic Pathways of Hybrid Micelle Formation in SDS and Block Copolymer Mixtures

Mixtures of amphiphilic polymers and surfactants are used in a wide range of applications, e.g., pharmaceuticals, detergents, cosmetics, and drug delivery systems. Still, many questions remain on how the structure and, in particular, the kinetics of block copolymer micelles are affected in the presence of surfactants and what controls the solubilization kinetics. In this work, we have studied the stability and solubilization kinetics of block copolymer micelles upon the addition of the surfactant sodium dodecyl sulfate (SDS) using small-angle X-ray/neutron scattering. The ability of the surfactant to dissolve polymer micelles or form mixed micelles has been investigated using two types of amphiphilic polymers, poly(ethylene-alt-propylene)-poly(ethylene oxide) (PEP1-PEO20) and n-alkyl-functionalized PEO (C28-PEO5). The exchange kinetics of C28-PEO5 micelles are in the order of hours, while PEP1-PEO20 micelles are known to be frozen on a practical timescale. In this work, we show that the addition of SDS to PEP1-PEO20 provides virtually no solubilization, even after an extended period of time. However, upon adding SDS to C28-PEO5 micelles, we observe micellar dissolution and formation of mixed micelles occurring on the timescale of hours. Using a coexistence model of mixed and neat micelles, the SAXS data were analyzed to provide detailed structural parameters over time. First, we observe a fast fragmentation/fission step followed by a slow reorganization process. The latter process is essentially independent of concentration at low volume fraction but is greatly accelerated at larger concentrations. This might indicate a crossover from a predominance of molecular exchange to fusion/fission processes.

Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods

The self-assembly of proteins is an essential process for a variety of cellular functions including cell respiration, mobility and division. On the other hand, protein or peptide misfolding and aggregation is related to the development of Parkinson's disease and Alzheimer's disease, among other aggregopathies. As a consequence, significant research efforts are directed towards the understanding of this process. In this review, we are focused on the use of UV-Visible Absorption Spectroscopy, Fluorescence Spectroscopy and Circular Dichroism to evaluate the self-organization of proteins and peptides in solution. These spectroscopic techniques are commonly available in most chemistry and biochemistry research laboratories, and together they are a powerful approach for initial as well as routine evaluation of protein and peptide self-assembly and aggregation under different environmental stimulus. Furthermore, these spectroscopic techniques are even suitable for studying complex systems like those in the food industry or pharmaceutical formulations, providing an overall idea of the folding, self-assembly, and aggregation processes, which is challenging to obtain with high-resolution methods. Here, we compiled and discussed selected examples, together with our results and those that helped us better to understand the process of protein and peptide aggregation. We put particular emphasis on the basic description of the methods as well as on the experimental considerations needed to obtain meaningful information, to help those who are just getting into this exciting area of research. Moreover, this review is particularly useful to those out of the field who would like to improve reproducibility in their cellular and biomedical experiments, especially while working with peptide and protein systems as an external stimulus. Our final aim is to show the power of these low-resolution techniques to improve our understanding of the self-assembly of peptides and proteins and translate this fundamental knowledge in biomedical research or food applications.

Combining Experimental Data and Computational Methods for the Non-Computer Specialist

Experimental methods are indispensable for the study of the function of biological macromolecules, not just as static structures, but as dynamic systems that change conformation, bind partners, perform reactions, and respond to different stimulus. However, providing a detailed structural interpretation of the results is often a very challenging task. While experimental and computational methods are often considered as two different and separate approaches, the power and utility of combining both is undeniable. The integration of the experimental data with computational techniques can assist and enrich the interpretation, providing new detailed molecular understanding of the systems. Here, we briefly describe the basic principles of how experimental data can be combined with computational methods to obtain insights into the molecular mechanism and expand the interpretation through the generation of detailed models.

The dynamics of linear polyubiquitin

Polyubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable them to regulate multiple biological pathways. Their dynamic is determined by the linkage between ubiquitins and by the number of ubiquitin units. Characterizing polyubiquitin behavior as a function of their length is hampered because of increasing system size and conformational variability. Here, we introduce a new approach to efficiently integrating small-angle x-ray scattering with simulations allowing us to accurately characterize the dynamics of linear di-, tri-, and tetraubiquitin in the free state as well as of diubiquitin in complex with NEMO, a central regulator in the NF-κB pathway. Our results show that the behavior of the diubiquitin subunits is independent of the presence of additional ubiquitin modules and that the dynamics of polyubiquitins with different lengths follow a simple model. Together with experimental data from multiple biophysical techniques, we then rationalize the 2:1 NEMO:polyubiquitin binding.

On the X-ray Scattering Pre-peak of Linear Mono-ols and the Related Microstructure from Computer Simulations

The X-ray scattering intensities (I(k)) of linear alkanols OH(CH₂)_n-1CH₃ obtained from experiments (methanol to 1-undecanol) and computer simulations (methanol to 1-nonanol) of different force field models are comparatively studied particularly in order to explain the origin and the properties of the scattering pre-peak in the k-vector range 0.3-1 Å^-1. The experimental I(k) values show two apparent features: the pre-peak position k_P decreases with increasing n, and more intriguingly, the amplitude A_P goes through a maximum at 1-butanol (n = 4). The first feature is well reproduced by all force-field models, while the second shows strong model dependence. The simulations reveal various shapes of clusters of the hydroxyl head-group from n>2. k_P is directly related to the size of the meta-objects corresponding to such clusters surrounded by their alkyl tails. The explanation of the A_P turnover at n = 4 is more involved in terms of cancellations of atom-atom structure factor S(k) contributions related to domain ordering. The flexibility of the alkyl tails tends to reduce the cross contributions, thus revealing the crucial importance of this parameter in the models. Force fields with all-atom representation are less successful in reproducing the pre-peak features for smaller alkanols, n<6, possibly because they blur the charge ordering process since all atoms bear partial charges. The analysis clearly shows that it is not possible to obtain a model-free explanation of the features of I(k).

New Light on the Mechanism of Phototransduction in Phototropin

Phototropins are photoreceptor proteins that regulate blue light-dependent biological processes for efficient photosynthesis in plants and algae. The proteins consist of a photosensory domain that responds to the ambient light and an output module that triggers cellular responses. The photosensory domain of phototropin from Chlamydomonas reinhardtii contains two conserved LOV (light-oxygen-voltage) domains with flavin chromophores. Blue light triggers the formation of a covalent cysteine-flavin adduct and upregulates the phototropin kinase activity. Little is known about the structural mechanism that leads to kinase activation and how the two LOV domains contribute to this. Here, we investigate the role of the LOV1 domain from C. reinhardtii phototropin by characterizing the structural changes occurring after blue light illumination with nano- to millisecond time-resolved X-ray solution scattering. By structurally fitting the data with atomic models generated by molecular dynamics simulations, we find that adduct formation induces a rearrangement of the hydrogen bond network from the buried chromophore to the protein surface. In particular, the change in conformation and the associated hydrogen bonding of the conserved glutamine 120 induce a global movement of the β-sheet, ultimately driving a change in the electrostatic potential on the protein surface. On the basis of the change in the electrostatics, we propose a structural model of how LOV1 and LOV2 domains interact and regulate the full-length phototropin from C. reinhardtii. This provides a rationale for how LOV photosensor proteins function and contributes to the optimal design of optogenetic tools based on LOV domains.