Studying the Conformation of a Silaffin-Derived Pentalysine Peptide Embedded in Bioinspired Silica using Solution and Dynamic Nuclear Polarization Magic-Angle Spinning NMR

Molecular insights into complexation between protein and silica: Spectroscopic and simulation investigations

The synergistic effect of protein-silica complexation leads to exacerbated membrane fouling in the membrane desalination process, exceeding the individual impacts of silica scaling or protein fouling. However, the molecular-level dynamics of silica binding to proteins and the resulting structural changes in both proteins and silica remain poorly understood. This study investigates the complexation process between silica and proteins-negatively charged bovine serum albumin (BSA) and positively charged lysozyme (LYZ) at neutral pH-using infrared spectroscopy (IR), in situ attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), and multiple computational simulations. The findings reveal that both protein and silica structures undergo changes during the complexation process, with calcium ions in the solution significantly exacerbating these alterations. In particular, in situ ATR-FTIR combined with two-dimensional correlation spectroscopy analysis shows that BSA experiences more pronounced unfolding, providing additional binding sites for silica adsorption compared to LYZ. The adsorbed proteins promote silica polymerization from lower-polymerized to higher-polymerized species. Furthermore, molecular dynamics simulations demonstrate greater conformational variation in BSA through root-mean-square-deviation analysis and the bridging role of calcium ions via mean square displacement analysis. Molecular docking and density functional theory calculations identify the binding sites and energy of silica on proteins. In summary, this research offers a comprehensive understanding of the protein-silica complexation process, contributing to the knowledge of synergistic behaviors of inorganic scaling and organic fouling on membrane surfaces. The integrated approach used here may also be applicable for exploring other complex complexation processes in various environments.

Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions

Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.

MAS-DNP enables NMR studies of insect wings

NMR is a valuable tool for studying insects. Solid-state NMR has been used to obtain the chemical composition and gain insight into the sclerotization process of exoskeletons. There is typically little difficulty in obtaining sufficient sample quantity for exoskeletons. However, obtaining enough sample of other insect components for solid-state NMR experiments can be problematic while isotopically enriching them is near impossible. This is especially the case for insect wing membranes which is of interest to us. Issues with obtaining sufficient sample are the thickness of wing membranes is on the order of microns, each membrane region is surrounded by veins and occupies a small area, and the membranes are separated from the wing by physical dissection. Accordingly, NMR signal enhancement methods are needed. MAS-DNP has a track record of providing significant signal enhancements for a wide variety of materials. Here we demonstrate that MAS-DNP is useful for providing high quality one-dimensional and two-dimensional solid-state NMR spectra on cicada wing membrane at natural isotopic abundance.

Lysozyme is Sterically Trapped Within the Silica Cage in Bioinspired Silica-Lysozyme Composites: A Multi-Technique Understanding of Elusive Protein-Material Interactions

Lysozyme is widely known to promote the formation of condensed silica networks from solutions containing silicic acid, in a reproducible and cost-effective way. However, little is known about the fate of the protein after the formation of the silica particles. Also, the relative arrangement of the different components in the resulting material is a matter of debate. In this study, we investigate the nature of the protein-silica interactions by means of solid-state nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and electron microscopy. We find that lysozyme and silica are in intimate contact and strongly interacting, but their interaction is neither covalent nor electrostatic: lysozyme is mostly trapped inside the silica by steric effects.

Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement

Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.

Dynamic nuclear polarization-enhanced, double-quantum filtered 13C-13C dipolar correlation spectroscopy of natural 13C abundant bone-tissue biomaterial

Here, we describe a method for obtaining a dynamic nuclear polarization (DNP)-enhanced double-quantum filtered (DQF) two-dimensional (2D) dipolar ¹³C-¹³C correlation spectra of bone-tissue material at natural ¹³C abundance. DNP-enhanced DQF 2D dipolar ¹³C-¹³C spectra were obtained using a few different mixing times of the dipolar-assisted rotational resonance (DARR) scheme and these spectra were compared to a conventional 2D through-space double-quantum (DQ)-single-quantum (SQ) correlation spectrum. While this scheme can only be used for an assignment purpose to reveal the carbon-carbon connectivity within a residue, the DQF ¹³C-¹³C dipolar correlation scheme introduced here can be used to obtain longer distance carbon-carbon constraints. A DQF pulse block is placed before the DARR mixing scheme for removing dominant ¹³C single-quantum (SQ) signals because these SQ ¹³C signals are overwhelmingly large compared to those ¹³C-¹³C dipolar cross-peaks generated and therefore saturate the dynamic range of the NMR detection. This approach exhibits strong enough 2D cross-peaks in a dipolar ¹³C-¹³C correlation spectrum and potentially provides pairwise ¹³C-¹³C dipolar constraints because the dipolar truncation effect as well as multi-step signal propagations involving a spin cluster that contains more than two spins can be ignored probabilistically. To obtain fast signal averaging, AsymPolPOK was used to provide a short ¹H DNP signal build-up time (1.3 s) and to expedite our MAS DNP NMR acquisitions while still maintaining a satisfactory DNP enhancement factor (ε = 50). Under long DARR mixing, a t₁-noise-like artifact was observed at a site that possesses a large chemical shift anisotropy (CSA) and a few different strategies to address this problem were discussed.

Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR

Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.

Mimicking Biosintering: The Identification of Highly Condensed Surfaces in Bioinspired Silica Materials

Interfacial interactions between inorganic surfaces and organic additives are vital to develop new complex nanomaterials. Learning from biosilica materials, composite nanostructures have been developed, which exploit the strength and directionality of specific polyamine additive-silica surface interactions. Previous interpretations of these interactions are almost universally based on interfacial charge matching and/or hydrogen bonding. In this study, we analyzed the surface chemistry of bioinspired silica (BIS) materials using solid-state nuclear magnetic resonance (NMR) spectroscopy as a function of the organic additive concentration. We found significant additional association between the additives and fully condensed (Q⁴) silicon species compared to industrial silica materials, leading to more overall Q⁴ concentration and higher hydrothermal stability, despite BIS having a shorter synthesis time. We posit that the polyfunctionality and catalytic activity of additives in the BIS synthesis lead to both of these surface phenomena, contrasting previous studies on monofunctional surfactants used in most other artificial templated silica syntheses. From this, we propose that additive polyfunctionality can be used to generate tailored artificial surfaces in situ and provide insights into the process of biosintering in biosilica systems, highlighting the need for more in-depth simulations on interfacial interactions at silica surfaces.

On the Mechanism of Bioinspired Formation of Inorganic Oxides: Structural Evidence of the Electrostatic Nature of the Interaction between a Mononuclear Inorganic Precursor and Lysozyme

Nature has evolved several molecular machineries to promote the formation at physiological conditions of inorganic materials, which would otherwise be formed in extreme conditions. The molecular determinants of this process have been established over the last decade, identifying a strong role of electrostatics in the first steps of the precipitation. However, no conclusive, structure-based evidence has been provided so far. In this manuscript, we test the binding of lysozyme with silica and titania potential precursors. In contrast with the absence of structural information about the interaction with the silica precursor, we observe the interaction with a mononuclear titanium(IV) species, which is found to occur in a region rich of positive charges.

Siliplant1 protein precipitates silica in sorghum silica cells

Silicon is absorbed by plant roots as silicic acid. The acid moves with the transpiration stream to the shoot, and mineralizes as silica. In grasses, leaf epidermal cells called silica cells deposit silica in most of their volume using an unknown biological factor. Using bioinformatics tools, we identified a previously uncharacterized protein in Sorghum bicolor, which we named Siliplant1 (Slp1). Slp1 is a basic protein with seven repeat units rich in proline, lysine, and glutamic acid. We found Slp1 RNA in sorghum immature leaf and immature inflorescence. In leaves, transcription was highest just before the active silicification zone (ASZ). There, Slp1 was localized specifically to developing silica cells, packed inside vesicles and scattered throughout the cytoplasm or near the cell boundary. These vesicles fused with the membrane, releasing their content in the apoplastic space. A short peptide that is repeated five times in Slp1 precipitated silica in vitro at a biologically relevant silicic acid concentration. Transient overexpression of Slp1 in sorghum resulted in ectopic silica deposition in all leaf epidermal cell types. Our results show that Slp1 precipitates silica in sorghum silica cells.

Interactions of Long-Chain Polyamines with Silica Studied by Molecular Dynamics Simulations and Solid-State NMR Spectroscopy

The investigation of molecular interactions between silica phases and organic components is crucial for elucidating the main steps involved in the biosilica mineralization process. In this respect, the structural characterization of the organic/inorganic interface is particularly useful for a deeper understanding of the dominant mechanisms of biomineralization. In this work, we have investigated the interaction of selectively ¹³C- and ¹⁵N-labeled atoms of organic long-chain polyamines (LCPAs) with ²⁹Si-labeled atoms of a silica layer at the molecular level. In particular, silica/LCPA nanocomposites were analyzed by solid-state NMR spectroscopy in combination with all-atom molecular dynamics simulations. Solid-state NMR experiments allow the determination of ²⁹Si-¹⁵N and ²⁹Si-¹³C internuclear distances, providing the parameters for direct verification of atomistic simulations. Our results elucidate the relevant molecular conformations as well as the nature of the interaction between the LCPA and a silica substrate. Specifically, distances and second moments suggest a picture compatible with (i) LCPA completely embedded in the silica phase and (ii) the charged amino groups located in close vicinity of silanol groups.

Peptides from diatoms and grasses harness phosphate ion binding to silica to help regulate biomaterial structure

Many life forms generate intricate submicron biosilica structures with various important biological functions. The formation of such structures, from the silicic acid in the waters and in the soil, is thought to be regulated by unique proteins with high repeats of specific amino acids and unusual sidechain modifications. Some silicifying proteins are characterized by high prevalence of basic amino acids in their primary structures. Lysine-rich domains are found, for instance, in diatom silaffin proteins and in the sorghum grass siliplant1 protein. These domains exhibit catalytic activity in silica chain condensation, owing to molecular interactions of the lysine amine groups with the forming mineral. The use of amine chemistry by two very remote organisms has motivated us to seek other molecular biosilicification processes that may be common to the two life forms. In diatom silaffins, domains rich in phosphoserine residues are thought to assist the assembly of silaffin molecules into an organic supra-structure which serves as a template for the silica to precipitate on. This mold, held by salt bridges between serine phosphates and lysine amines, dictates the shape of the silica particles formed. Yet, silica synthesized with the dephosphorylated silaffin in phosphate buffer showed similar morphology to the one prepared with the native protein, suggesting that a defined spatial arrangement of serine phosphates is not required to generate silica with the desired shape. Concurrently, free phosphates enhanced the activity of siliplant1 in silica formation. It is therefore beneficial to characterize the involvement of these anions as co-factors in regulated silicification by functional peptides from the two proteins and to understand whether they play similar molecular role in the mechanism of mineralization. Here we analyze the molecular interactions of free phosphate ions with silica and the silaffin peptide PL12 and separately with silica and siliplant1 peptide SLP1 in the two biomimetic silica products generated by the two peptides. MAS NMR measurements show that the phosphate ions interact with the peptides and at the same time may be forming bonds with the silica mineral. This bridging capability may add another avenue by which the structure of the silica material is influenced. A model for the molecular/ionic interactions at the bio-inorganic interface is described, which may have bearings for the role of phosphorylated residues beyond the function as intermolecular cross linkers or free phosphate ions as co-factors in regulation of silicification. STATEMENT OF SIGNIFICANCE: The manuscript addresses the question how proteins in diatoms and plants regulate the biosilica materials that are produced for various purposes in organisms. It uses preparation of silica in vitro with functional peptide derivatives from a sorghum grass protein and from a diatom silaffin protein separately to show that phosphate ions are important for the control that is achieved by these proteins on the final shape of the silica material produced. It portrays via magnetic resonance spectroscopic measurements, in atomic detail, the interface between atoms in the peptide, atoms on the surface of the silica formed and the phosphate ions that form chemical bonds with atoms on the silica as part of the mechanism of action of these peptides.

Synthesis of monodisperse rod-shaped silica particles through biotemplating of surface-functionalized bacteria

Mesoporous silica particles of controlled size and shape are potentially beneficial for many applications, but their usage may be limited by the complex procedure of fabrication. Biotemplating provides a facile approach to synthesize materials with desired shapes. Herein, a bioinspired design principle is adopted through displaying silaffin-derived 5R5 proteins on the surface of Escherichia coli by genetic manipulations. The genetically modified Escherichia coli provides a three-dimensional template to regulate the synthesis of rod-shaped silica. The silicification is initiated on the cell surface under the functionality of 5R5 proteins and subsequentially the inner space is gradually filled. Density functional theory simulation reveals the interfacial interactions between silica precursors and R5 peptides at the atomic scale. There is a large conformation change of this protein during biosilicification. Electrostatic interactions contribute to the high affinity between positively charged residues (Lys4, Arg16, Arg17) and negatively charged tetraethyl orthosilicate. Hydrogen bonds develop between Arg16 (OH), Arg17 (OH and NH), Leu19 (OH) residues and the forming silica agglomerates. In addition, the resulting rod-shaped silica copy of the bacteria can transform into mesoporous SiOx nanorods composed of carbon-coated nanoparticles after carbonization, which is shown to allow superior lithium storage performance.

Phosphate-Silica Interactions in Diatom Biosilica and Synthetic Composites Studied by Rotational Echo Double Resonance (REDOR) NMR Spectroscopy

Biosilica is a biogenic composite material produced by organisms like diatoms. Various biomolecules are tightly attached or incorporated into biosilica. Examples are special proteins termed silaffins and long-chain polyamines (LCPAs). Presumably, these biomolecules are involved in the biosilica formation process. Silaffins are highly phosphorylated zwitterions with LCPAs post-translationally attached to lysine residues. In the present work, we use distance-dependent solid-state NMR experiments, especially the ³¹P{²⁹Si} Rotational Echo Double Resonance (REDOR) technique, to study the environment of phosphate moieties in biosilica and in vitro synthesized SiO₂-based composites. In contrast to the heterogeneous mixtures of biomolecules found in native biosilica, the described in vitro silicification experiments make use of a single synthetic phosphopeptide and an LCPA of well-defined and uniform structure. The heteronuclear correlations measured from these silica composites provide reliable ³¹P-²⁹Si dipolar second moments and information about the distribution of the phosphopeptide within the silica material. The calculated second moment indicates close contact between phosphopeptides and silica. The phosphopeptides are incorporated into the silica composite in a disperse manner. Moreover, the REDOR data acquired for diatom biosilica also imply that phosphate groups are part of the silica-organic interface in this material.

Heteronuclear cross-relaxation effect modulated by the dynamics of N-functional groups in the solid state under 15N DP-MAS DNP

In a typical magic-angle spinning (MAS) dynamic nuclear polarization (DNP) nuclear magnetic resonance (NMR) experiment, several mechanisms are simultaneously involved when transferring much larger polarization of electron spins to NMR active nuclei of interest. Recently, specific cross-relaxation enhancement by active motions under DNP (SCREAM-DNP) [Daube et al. JACS 2016] has been reported as one of these mechanisms. Thereby ¹³C enhancement with inverted sign was observed in a direct polarization (DP) MAS DNP experiment, caused by reorientation dynamics of methyl that was not frozen out at 100 K. Here, we report on the spontaneous polarization transfer from hyperpolarized ¹H to both primary amine and ammonium nitrogens, resulting in an additional positive signal enhancement in the ¹⁵N NMR spectra during ¹⁵N DP-MAS DNP. The cross-relaxation induced signal enhancement (CRE) for ¹⁵N is of opposite sign compared to that observed for ¹³C due to the negative sign of the gyromagnetic ratio of ¹⁵N. The influence on CRE efficiency caused by variation of the radical solution composition and by temperature was also investigated.

NMR of Immobilized Enzymes

Solid-state NMR has become the method of choice for the assessment of protein structure for insoluble objects lacking long-range order. In this context, it is apparent that solid-state NMR is also perfectly poised toward the characterization of immobilized proteins. For these systems, it is possible to understand at the atomic level which perturbations, if any, are occurring as a result of the functionalization. Here we describe how it is possible to accomplish the NMR characterization of enzymes that have been immobilized through different approaches, and we introduce the reader to the choice of the experimental strategy that can be useful in different cases. An outlook on the level of information that can be attained is also given, in view of recent methodological advancements.

Brute-force solvent suppression for DNP studies of powders at natural isotopic abundance

A method based on highly concentrated radical solutions is investigated for the suppression of the NMR signals arising from solvents that are usually used for dynamic nuclear polarization experiments. The presented method is suitable in the case of powders, which are impregnated with a radical-containing solution. It is also demonstrated that the intensity and the resolution of the signals due to the sample of interest is not affected by the high concentration of radicals. The method proposed here is therefore valuable when sensitivity is of the utmost importance, namely samples at natural isotopic abundance.

Atom Probe Tomography for 3D Structural and Chemical Analysis of Individual Proteins

Determination of the 3D structure of proteins and other biomolecules is a major goal in structural biology, to provide insights to their biological function. Such structures are historically unveiled experimentally by X-ray crystallography or NMR spectroscopy, and in recent years using cryo-electron microscopy. Here, a method for structural analysis of individual proteins on the sub-nanometer scale using atom probe tomography is described. This technique offers a combination of high-resolution analysis of biomolecules in 3D, and the chemical sensitivity of mass spectrometry. As a model protein, the well-characterized antibody IgG is used. IgG is encapsulated in an amorphous solid silica matrix via a sol-gel process to provide the requisite support for atom probe analysis. The silica synthesis is tuned to resemble physiological conditions. The 3D reconstructions show good agreement with the protein databank IgG crystal structure. This suggests that the silica-embedding strategy can open the field of atom probe tomography to the analysis of biological molecules. In addition to high-resolution structural information, the technique may potentially provide chemical information on the atomic scale using isotopic labeling. It is envisaged that this method may constitute a useful complement to existing tools in structural biology, particularly for the examination of proteins with low propensity for crystallization.

Reducing the computational cost of NMR crystallography of organic powders at natural isotopic abundance with the help of 13 C-13 C dipolar couplings

Structure determination of functional organic compounds remains a formidable challenge when the sample exists as a powder. Nuclear magnetic resonance crystallography approaches based on the comparison of experimental and Density Functional Theory (DFT)-computed ¹ H chemical shifts have already demonstrated great potential for structure determination of organic powders, but limitations still persist. In this study, we discuss the possibility of using ¹³ C-¹³ C dipolar couplings quantified on powdered theophylline at natural isotopic abundance with the help of dynamic nuclear polarization, to realize a DFT-free, rapid screening of a pool of structures predicted by ab initio random structure search. We show that although ¹³ C-¹³ C dipolar couplings can identify structures possessing long range structural motifs and unit cell parameters close to those of the true structure, it must be complemented with other data to recover information about the presence and the chemical nature of the supramolecular interactions.

Hyperpolarized MAS NMR of unfolded and misfolded proteins

In this article we give an overview over the use of DNP-enhanced solid-state NMR spectroscopy for the investigation of unfolded, disordered and misfolded proteins. We first provide an overview over studies in which DNP spectroscopy has successfully been applied for the structural investigation of well-folded amyloid fibrils formed by short peptides as well as full-length proteins. Sample cooling to cryogenic temperatures often leads to severe line broadening of resonance signals and thus a loss in resolution. However, inhomogeneous line broadening at low temperatures provides valuable information about residual dynamics and flexibility in proteins, and, in combination with appropriate selective isotope labeling techniques, inhomogeneous linewidths in disordered proteins or protein regions may be exploited for evaluation of conformational ensembles. In the last paragraph we highlight some recent studies where DNP-enhanced MAS-NMR-spectroscopy was applied to the study of disordered proteins/protein regions and inhomogeneous sample preparations.

Biofunctionalization of Nano Channels by Direct In-Pore Solid-Phase Peptide Synthesis

Diatom biosilica are highly complex inorganic/organic hybrid materials. To get deeper insights on their structure at a molecular level, model systems that mimic the complex natural compounds were synthesized and characterized. A simple and efficient peptide immobilization strategy was developed, which uses a well-ordered porous silica material as a support and commercially available Fmoc-amino acids, similar to the known solid-phase peptide synthesis. As an example, Fmoc-glycine and Fmoc-phenylalanine are immobilized on the silica support. The success of functionalization was investigated by ¹³ C CP MAS and ²⁹ Si CP MAS solid-state NMR. Thermogravimetric analysis (TGA) and elemental analysis (EA) were performed to quantify the functionalization. Changes of the specific surface area, pore volume, and pore diameters in all modification steps were studied by Brunauer-Emmett-Teller based nitrogen adsorption-desorption measurements (BET). The combination of the analytical methods provided high grafting densities of 2.1±0.2 molecules/nm² on the surface. Furthermore, they allowed for monitoring chemical changes on the pore surface and changes of the pore properties of the material during the different functionalization steps. This universal approach is suitable for the selective synthesis of pores with tunable surface-peptide functionalization, with applications to the synthesis of a big variety of silica-peptide model systems, which in the future may lead to a deeper understanding of complex biological systems.

Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications

Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO₂, SiO₂, and GeO₂ has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.

DNP NMR of biomolecular assemblies

Dynamic Nuclear Polarization (DNP) is an effective approach to alleviate the inherently low sensitivity of solid-state NMR (ssNMR) under magic angle spinning (MAS) towards large-sized multi-domain complexes and assemblies. DNP relies on a polarization transfer at cryogenic temperatures from unpaired electrons to adjacent nuclei upon continuous microwave irradiation. This is usually made possible via the addition in the sample of a polarizing agent. The first pioneering experiments on biomolecular assemblies were reported in the early 2000s on bacteriophages and membrane proteins. Since then, DNP has experienced tremendous advances, with the development of extremely efficient polarizing agents or with the introduction of new microwaves sources, suitable for NMR experiments at very high magnetic fields (currently up to 900 MHz). After a brief introduction, several experimental aspects of DNP enhanced NMR spectroscopy applied to biomolecular assemblies are discussed. Recent demonstration experiments of the method on viral capsids, the type III and IV bacterial secretion systems, ribosome and membrane proteins are then described.

Engineering l-asparaginase for spontaneous formation of calcium phosphate bioinspired microreactors

Active bioinspired materials are appealing biotechnological targets, and their study is gaining momentum. These materials, which comprise of an inorganic matrix and one or more biomolecules, are extremely variable and therefore may result difficult to characterize in their intimate structure. In this work we have prepared a hydroxyapatite-l-asparaginase composite, with the perspective of using it in acute leukemia treatment. We demonstrate that the use of electron microscopy and powder X-ray diffraction, combined with the atomic-resolution information coming from solid-state NMR, allows us to understand the topology of the material and how the different components interplay to obtain an active composite.

Serine-Lysine Peptides as Mediators for the Production of Titanium Dioxide: Investigating the Effects of Primary and Secondary Structures Using Solid-State NMR Spectroscopy and DFT Calculations

A biomimetic approach to the formation of titania (TiO₂) nanostructures is desirable because of the mild conditions required in this form of production. We have identified a series of serine-lysine peptides as candidates for the biomimetic production of TiO₂ nanostructures. We have assayed these peptides for TiO₂-precipitating activity upon exposure to titanium bis(ammonium lactato)dihydroxide and have characterized the resulting coprecipitates using scanning electron microscopy. A subset of these assayed peptides efficiently facilitates the production of TiO₂ nanospheres. Here, we investigate the process of TiO₂ nanosphere formation mediated by the S-K peptides KSSKK- and SKSK₃SKS using one-dimensional and two-dimensional solid-state NMR (ssNMR) on peptide samples with uniformly ¹³C-enriched residues. ssNMR is used to assign ¹³C chemical shifts (CSs) site-specifically in each free peptide and TiO₂-embedded peptide, which are used to derive secondary structures in the neat and TiO₂ coprecipitated states. The backbone ¹³C CSs are used to assess secondary structural changes undergone during the coprecipitation process. Side-chain ¹³C CS changes are analyzed with density functional theory calculations and used to determine side-chain conformational changes that occur upon coprecipitation with TiO₂ and to determine surface orientation of lysine side chains in TiO₂-peptide composites.

Dynamic nuclear polarization for sensitivity enhancement in modern solid-state NMR

The field of dynamic nuclear polarization has undergone tremendous developments and diversification since its inception more than 6 decades ago. In this review we provide an in-depth overview of the relevant topics involved in DNP-enhanced MAS NMR spectroscopy. This includes the theoretical description of DNP mechanisms as well as of the polarization transfer pathways that can lead to a uniform or selective spreading of polarization between nuclear spins. Furthermore, we cover historical and state-of-the art aspects of dedicated instrumentation, polarizing agents, and optimization techniques for efficient MAS DNP. Finally, we present an extensive overview on applications in the fields of structural biology and materials science, which underlines that MAS DNP has moved far beyond the proof-of-concept stage and has become an important tool for research in these fields.

Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P5 S3 during silicic acid condensation and silica decondensation

The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5 S3 , a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains 5 protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5 S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2 ) at globally undersaturated concentrations. The secondary structure of P5 S3 during these 2 processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in the absence of silicate. The NMR studies of dual-labeled (13 C, 15 N) P5 S3 revealed a disordered structure at pH 2.8 and 4.5. Within the pH range of 4.5-9.5 in the absence of silicic acid, the CD data showed a disordered structure with the suggestion of some polyproline II character. Upon silicic acid polymerization and during dissolution of preformed silica, the CD spectrum of P5 S3 indicated partial transition into an α-helical conformation which was transient during silica-dissolution. The secondary structural changes observed for P5 S3 correlate with the presence of oligomeric/polymeric silicic acid, presumably due to P5 S3 -silica interactions. These P5 S3 -silica interactions appear, at least in part, ionic in nature since negatively charged dodecylsulfate caused similar perturbations to the P5 S3 CD spectrum as observed with silica, while uncharged ß-d-dodecyl maltoside did not affect the CD spectrum of P5 S3 . Thus, with an associated increase in α-helical character, P5 S3 influences both the condensation of silicic acid into silica and its decondensation back to silicic acid.

Comparative Study of Secondary Structure and Interactions of the R5 Peptide in Silicon Oxide and Titanium Oxide Coprecipitates Using Solid-State NMR Spectroscopy

A biomimetic, peptide-mediated approach to inorganic nanostructure formation is of great interest as an alternative to industrial production methods. To investigate the role of peptide structure on silica (SiO₂) and titania (TiO₂) morphologies, we use the R5 peptide domain derived from the silaffin protein to produce uniform SiO₂ and TiO₂ nanostructures from the precursor silicic acid and titanium bis(ammonium lactato)dihydroxide, respectively. The resulting biosilica and biotitania nanostructures are characterized using scanning electron microscopy. To investigate the process of R5-mediated SiO₂ and TiO₂ formation, we carry out 1D and 2D solid-state NMR (ssNMR) studies on R5 samples with uniformly ¹³C- and ¹⁵N-labeled residues to determine the backbone and side-chain chemical shifts. ¹³C chemical shift data are in turn used to determine peptide backbone torsion angles and secondary structure for the R5 peptide neat, in silica, and in titania. We are thus able to assess the impact of the different mineral environments on peptide structure, and we can further elucidate from ¹³C chemical shifts change the degree to which various side chains are in close proximity to the mineral phases. These comparisons add to the understanding of the role of R5 and its structure in both SiO₂ and TiO₂ formation.

High-Resolution Solid-State NMR Characterization of Ligand Binding to a Protein Immobilized in a Silica Matrix

Solid-state NMR is becoming a powerful tool to detect atomic-level structural features of biomolecules even when they are bound to (or trapped in) solid systems that lack long-range three-dimensional order. We here demonstrate that it is possible to probe protein-ligand interactions from a protein-based perspective also when the protein is entrapped in silica, thus translating into biomolecular solid-state NMR all of the considerations that are usually made to understand the chemical nature of the interaction of a protein with its ligands. This work provides a proof of concept that also immobilized enzymes can be used for protein-based NMR protein-ligand interactions for drug discovery.

Ubiquitin immobilized on mesoporous MCM41 silica surfaces - Analysis by solid-state NMR with biophysical and surface characterization

Deriving the conformation of adsorbed proteins is important in the assessment of their functional activity when immobilized. This has particularly important bearings on the design of contemporary and new encapsulated enzyme-based drugs, biosensors, and other bioanalytical devices. Solid-state nuclear magnetic resonance (NMR) measurements can expand our molecular view of proteins in this state and of the molecular interactions governing protein immobilization on popular biocompatible surfaces such as silica. Here, the authors study the immobilization of ubiquitin on the mesoporous silica MCM41 by NMR and other techniques. Protein molecules are shown to bind efficiently at pH 5 through electrostatic interactions to individual MCM41 particles, causing their agglutination. The strong attraction of ubiquitin to MCM41 surface is given molecular context through evidence of proximity of basic, carbonyl and polar groups on the protein to groups on the silica surface using NMR measurements. The immobilized protein exhibits broad peaks in two-dimensional 13C dipolar-assisted rotational resonance spectra, an indication of structural multiplicity. At the same time, cross-peaks related to Tyr and Phe sidechains are missing due to motional averaging. Overall, the favorable adsorption of ubiquitin to MCM41 is accompanied by conformational heterogeneity and by a major loss of motional degrees of freedom as inferred from the marked entropy decrease. Nevertheless, local motions of the aromatic rings are retained in the immobilized state.

Dendritic polarizing agents for DNP SENS

Dendrimer-shielded polarizing agents for the application of DNP SENS to reactive surfaces.

Dynamic Nuclear Polarization Surface Enhanced NMR Spectroscopy (DNP SENS) is an effective method to significantly improve solid-state NMR investigation of solid surfaces. The presence of unpaired electrons (polarizing agents) is crucial for DNP, but it has drawbacks such as leading to faster nuclear spin relaxation, or even reaction with the substrate under investigation. The latter can be a particular problem for heterogeneous catalysts. Here, we present a series of carbosilane-based dendritic polarizing agents, in which the bulky dendrimer can reduce the interaction between the solid surface and the free radical. We thereby preserve long nuclear T′₂ of the surface species, and even successfully enhance a reactive heterogeneous metathesis catalyst.

(1)H-detected solid-state NMR of proteins entrapped in bioinspired silica: a new tool for biomaterials characterization

Proton-detection in solid-state NMR, enabled by high magnetic fields (>18 T) and fast magic angle spinning (>50 kHz), allows for the acquisition of traditional (1)H-(15)N experiments on systems that are too big to be observed in solution. Among those, proteins entrapped in a bioinspired silica matrix are an attractive target that is receiving a large share of attention. We demonstrate that (1)H-detected SSNMR provides a novel approach to the rapid assessment of structural integrity in proteins entrapped in bioinspired silica.