Self-catalyzed growth of S layers via an amorphous-to-crystalline transition limited by folding kinetics

A minimal colloid model of solution crystallization nucleates crystals classically

A fundamental assumption of the classical theories of crystal nucleation is that the individual molecules from the "old" phase associate to an emerging nucleus individually and sequentially. Numerous recent studies of crystal nucleation in solution have revealed nonclassical pathways, whereby crystal nuclei are hosted and fed by amorphous clusters pre-formed in the solution. A sizable knowledge gap has persisted, however, in the definition of the molecular-level parameters that direct a solute towards classical or nonclassical nucleation. Here we construct a suspension of colloid particles of hydrodynamic diameter 1.1 μm and monitor their individual motions towards a quasi-two-dimensional crystal by scanning confocal microscopy. We combine electrostatic repulsion and polymer-induced attraction to obtain a simple isotropic pair interaction potential with a single attractive minimum of tunable depth between 1.2kBT and 2.7kBT. We find that even the smallest aggregates that form in this system structure as hexagonal two-dimensional crystals and grow and maturate by the association and exchange of single particles from the solution, signature behaviors during classical nucleation. The particles in the suspension equilibrate with those in the clusters and the volume fractions of suspensions at equilibrium correspond to straightforward thermodynamic predictions based on depth of the interparticle attraction. These results demonstrate that classical nucleation is selected by particles interacting with a minimal potential and present a benchmark for future modifications of the molecular interactions that may induce nonclassical nucleation.

Nonclassical Crystal Growth of Supramolecular Polymers in Aqueous Medium

A mechanistic understanding of the principles governing the hierarchical organization of supramolecular polymers offers a paradigm for tailoring synthetic molecular architectures at the nano to micrometric scales. Herein, the unconventional crystal growth mechanism of a supramolecular polymer of superbenzene(coronene)-diphenylalanine conjugate (Cr-FFOEt ) is demonstrated. 3D electron diffraction (3D ED), a technique underexplored in supramolecular chemistry, is effectively utilized to gain a molecular-level understanding of the gradual growth of the initially formed poorly crystalline hairy, fibril-like supramolecular polymers into the ribbon-like crystallites. The further evolution of these nanosized flat ribbons into microcrystals by oriented attachment and lateral fusion is probed by time-resolved microscopy and electron diffraction. The gradual morphological and structural changes reveal the nonclassical crystal growth pathway, where the balance of strong and weak intermolecular interactions led to a structure beyond the nanoscale. The role of distinct π-stacking and H-bonding interactions that drive the nonclassical crystallization process of Cr-FFOEt supramolecular polymers is analyzed in comparison to analogous molecules, Py-FFOEt and Cr-FF forming helical and twisted fibers, respectively. Furthermore, the Cr-FFOEt crystals formed through nonclassical crystallization are found to improve the functional properties.

Influence of Peptoid Sequence on the Mechanisms and Kinetics of 2D Assembly

Two-dimensional (2D) materials have attracted intense interest due to their potential for applications in fields ranging from chemical sensing to catalysis, energy storage, and biomedicine. Recently, peptoids, a class of biomimetic sequence-defined polymers, have been found to self-assemble into 2D crystalline sheets that exhibit unusual properties, such as high chemical stability and the ability to self-repair. The structure of a peptoid is close to that of a peptide except that the side chains are appended to the amide nitrogen rather than the α carbon. In this study, we investigated the effect of peptoid sequence on the mechanism and kinetics of 2D assembly on mica surfaces using in situ AFM and time-resolved X-ray scattering. We explored three distinct peptoid sequences that are amphiphilic in nature with hydrophobic and hydrophilic blocks and are known to self-assemble into 2D sheets. The results show that their assembly on mica starts with deposition of aggregates that spread to establish 2D islands, which then grow by attachment of peptoids, either monomers or unresolvable small oligomers, following well-known laws of crystal step advancement. Extraction of the solubility and kinetic coefficient from the dependence of the growth rate on peptoid concentration reveals striking differences between the sequences. The sequence with the slowest growth rate in bulk and with the highest solubility shows almost no detachment; i.e., once a growth unit attaches to the island edge, there is almost no probability of detaching. Furthermore, a peptoid sequence with a hydrophobic tail conjugated to the final carboxyl residue in the hydrophilic block has enhanced hydrophobic interactions and exhibits rapid assembly both in the bulk and on mica. These assembly outcomes suggest that, while the π-π interactions between adjacent hydrophobic blocks play a major role in peptoid assembly, sequence details, particularly the location of charged groups, as well as interaction with the underlying substrate can significantly alter the thermodynamic stability and assembly kinetics.

Shape-Anisotropic Assembly of Protein Nanocages with Identical Building Blocks by Designed Intermolecular π-π Interactions

Protein lattices that shift the structure and shape anisotropy in response to environmental cues are closely coupled to potential functionality. However, to design and construct shape-anisotropic protein arrays from the same building blocks in response to different external stimuli remains challenging. Here, by a combination of the multiple, symmetric interaction sites on the outer surface of protein nanocages and the tunable features of phenylalanine-phenylalanine interactions, a protein engineering approach is reported to construct a variety of superstructures with shape anisotropy, including 3D cubic, 2D hexagonal layered, and 1D rod-like crystalline protein nanocage arrays by using one single protein building block. Notably, the assembly of these crystalline protein arrays is reversible, which can be tuned by external stimuli (pH and ionic strength). The anisotropic morphologies of the fabricated macroscopic crystals can be correlated with the Å-to-nm scale protein arrangement details by crystallographic elucidation. These results enhance the understanding of the freedom offered by an object's symmetry and inter-object π-π stacking interactions for protein building blocks to assemble into direction- and shape-anisotropic biomaterials.

Interface-mediated protein aggregation

The aggregation of proteins at interfaces has significant roles and can also lead to dysfunction of different physiological processes. The interfacial effects on the assembly and aggregation of biopolymers are not only crucial for a comprehensive understanding of protein biological functions, but also hold great potential for advancing the state-of-the-art applications of biopolymer materials. Recently, there has been remarkable progress in a collaborative context, as we strive to gain control over complex interfacial assembly structures of biopolymers. These biopolymer structures range from the nanoscale to mesoscale and even macroscale, and are attained through the rational design of interactions between biological building blocks and surfaces/interfaces. This review spotlights the recent advancements in interface-mediated assembly and properties of biopolymer materials. Initially, we introduce the solid-liquid interface (SIL)-mediated biopolymer assembly that includes the inorganic crystalline template effect and protein self-adoptive deposition through phase transition. Next, we display the advancement of biopolymer assembly instigated by the air-water interface (AWI) that acts as an energy conversion station. Lastly, we discuss succinctly the assembly of biopolymers at the liquid-liquid interface (LLI) along with their applications. It is our hope that this overview will stimulate the integration and progression of the science of interfacial assembled biopolymer materials and surfaces/interfaces.

Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics

Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.

In vitro investigation of protein assembly by combined microscopy and infrared spectroscopy at the nanometer scale

The nanoscale structure and dynamics of proteins on surfaces has been extensively studied using various imaging techniques, such as transmission electron microscopy and atomic force microscopy (AFM) in liquid environments. These powerful imaging techniques, however, can potentially damage or perturb delicate biological material and do not provide chemical information, which prevents a fundamental understanding of the dynamic processes underlying their evolution under physiological conditions. Here, we use a platform developed in our laboratory that enables acquisition of infrared (IR) spectroscopy and AFM images of biological material in physiological liquids with nanometer resolution in a cell closed by atomically thin graphene membranes transparent to IR photons. In this work, we studied the self-assembly process of S-layer proteins at the graphene-aqueous solution interface. The graphene acts also as the membrane separating the solution containing the proteins and Ca²⁺ ions from the AFM tip, thus eliminating sample damage and contamination effects. The formation of S-layer protein lattices and their structural evolution was monitored by AFM and by recording the amide I and II IR absorption bands, which reveal the noncovalent interaction between proteins and their response to the environment, including ionic strength and solvation. Our measurement platform opens unique opportunities to study biological material and soft materials in general.

Molecular Mechanism of Organic Crystal Nucleation: A Perspective of Solution Chemistry and Polymorphism

Crystal nucleation determining the formation and assembly pathway of first organic materials is the central science of various scientific disciplines such as chemical, geochemical, biological, and synthetic materials. However, our current understanding of the molecular mechanisms of nucleation remains limited. Over the past decades, the advancements of new experimental and computational techniques have renewed numerous interests in detailed molecular mechanisms of crystal nucleation, especially structure evolution and solution chemistry. These efforts bifurcate into two categories: (modified) classical nucleation theory (CNT) and non-classical nucleation mechanisms. In this review, we briefly introduce the two nucleation mechanisms and summarize current molecular understandings of crystal nucleation that are specifically applied in polymorphic crystallization systems of small organic molecules. Many important aspects of crystal nucleation including molecular association, solvation, aromatic interactions, and hierarchy in intermolecular interactions were examined and discussed for a series of organic molecular systems. The new understandings relating to molecular self-assembly in nucleating systems have suggested more complex multiple nucleation pathways that are associated with the formation and evolution of molecular aggregates in solution.

Crystal Nucleation and Growth of Inorganic Ionic Materials from Aqueous Solution: Selected Recent Developments, and Implications

In this review article, selected, latest theoretical, and experimental developments in the field of nucleation and crystal growth of inorganic materials from aqueous solution are highlighted, with a focus on literature after 2015 and on non-classical pathways. A key point is to emphasize the so far underappreciated role of water and solvent entropy in crystallization at all stages from solution speciation through to the final crystal. While drawing on examples from current inorganic materials where non-classical behavior has been proposed, the potential of these approaches to be adapted to a wide-range of systems is also discussed, while considering the broader implications of the current re-assessment of pathways for crystallization. Various techniques that are suitable for the exploration of crystallization pathways in aqueous solution, from nucleation to crystal growth are summarized, and a flow chart for the assignment of specific theories based on experimental observations is proposed.

A short helix regulates conversion of dimeric and 24-meric ferritin architectures

The inter-subunit interaction at the protein interfaces plays a key role in protein self-assembly, through which enabling protein self-assembly controllable is of great importance for preparing the novel nanoscale protein materials with unexplored properties. Different from normal 24-meric ferritin, archaeal ferritin, Thermotoga maritima ferritin (TmFtn) naturally occurs as a dimer, which can assemble into a 24-mer nanocage induced by salts. However, the regulation mechanism of protein self-assembly underlying this phenomenon remains unclear. Here, a combination of the computational energy simulation and key interface reconstruction revealed that a short helix involved interactions at the C₄ interface are mainly responsible for the existence of such dimer. Agreeing with this idea, deletion of such short helix of each subunit triggers it to be a stable dimer, which losses the ability to reassemble into 24-meric ferritin in the presence of salts in solution. Further support for this idea comes from the observation that grafting a small helix from human H ferritin onto archaeal subunit resulted in a stable 24-mer protein nanocage even in the absence of salts. Thus, these findings demonstrate that adjusting the interactions at the protein interfaces appears to be a facile, effective approach to control subunit assembly into different protein architectures.

Nanoarchitectonics for enhanced antibacterial activity with Lactobacillus buchneri S-layer proteins-coated silver nanoparticles

Various multi-drug-resistant microorganisms have appeared while a single antibacterial agent is increasingly no longer adequate for dealing with these resistant microorganisms. Herein, commercially purchased 50 nm-average-diameter silver nanoparticles (AgNPs) and Lactobacillus buchneri-isolated surface-layer proteins (SLPs) as a capping agent were used to fabricate a hybrid antibacterial agent (SLP-AgNPs) with enhanced antibacterial activity, and the possible synergistic antibacterial mechanism was explored. Characterization results revealed that SLP-AgNPs were uniformly surrounded by protein corona provided from SLP, and the formulations were mainly mediated by the electrostatic interactions and hydrogen bonding, which was evidenced by the results of Fourier transform infrared spectroscopy. According to the antibacterial tests, the minimum inhibitory concentration of SLP-AgNPs against Salmonella enterica (0.010 mg/mL) and Staphylococcus aureus (0.005 mg/mL) was 5-10 times lower than that of bare AgNPs, and while SLP-AgNPs showed a higher antibiofilm activity. Furthermore, bacterial cells exposed to SLP-AgNPs exhibited higher cell membrane permeability and stronger inhibition of respiratory-chain dehydrogenase activity, resulting in more severe cell death compared with bare AgNPs. The synergistic effect of SLP on AgNPs was probably carried out by enhanced function of adhesion to bacteria and antibacterial ability of SLP and SLP's supramolecular lattice structure on the sustained release of silver ion.

Protein Needles Designed to Self-Assemble through Needle Tip Engineering

The dynamic process of formation of protein assemblies is essential to form highly ordered structures in biological systems. Advances in structural and synthetic biology have led to the construction of artificial protein assemblies. However, development of design strategies exploiting the anisotropic shape of building blocks of protein assemblies has not yet been achieved. Here, the 2D assembly pattern of protein needles (PNs) is controlled by regulating their tip-to-tip interactions. The PN is an anisotropic needle-shaped protein composed of β-helix, foldon, and His-tag. Three different types of tip-modified PNs are designed by deleting the His-tag and foldon to change the protein-protein interactions. Observing their assembly by high-speed atomic force microscopy (HS-AFM) reveals that PN, His-tag deleted PN, and His-tag and foldon deleted PN form triangular lattices, the monomeric state with nematic order, and fiber assemblies, respectively, on a mica surface. Their assembly dynamics are observed by HS-AFM and analyzed by the theoretical models. Monte Carlo (MC) simulations indicate that the mica-PN interactions and the flexible and multipoint His-tag interactions cooperatively guide the formation of the triangular lattice. This work is expected to provide a new strategy for constructing supramolecular protein architectures by controlling directional interactions of anisotropic shaped proteins.

Accounting for the Presence of Molecular Clusters in Modeling and Interpreting Nucleation and Growth

The effect of molecular cluster formation on the estimation of kinetic parameters for primary nucleation and growth in different systems has been studied using computationally generated data and three sets of experimental data in the literature. It is shown that the formation of molecular clusters decreases the concentration of monomers and hence the thermodynamic driving force for crystallization, which consequently affects the crystallization kinetics. For a system exhibiting a strong tendency to form molecular clusters, accounting for cluster formation in a kinetic model is critical to interpret kinetic data accurately, for instance, to estimate the specific surface energy γ from a set of primary nucleation rates. On the contrary, for a system with negligible cluster formation, a consideration of cluster formation does not affect parameter estimation outcomes. Moreover, it is demonstrated that using a growth kinetic model that accounts for cluster formation allows the estimation of γ from typical growth kinetic data (i.e., de-supersaturation profiles of seeded batch crystallization), which is a novel method of estimating γ developed in this work. The applicability of the novel method to different systems is proven by showing that the estimated values of γ are closely comparable to the actual values used for generating the kinetic data or the corresponding estimates reported in the literature.

Assembly-based pathways of crystallization

Solution crystallization of materials ranging from simple salts to complex supramolecular assemblies has long been viewed through the lens of classical nucleation and growth theories in which monomeric building blocks...

Reversible structure transformation between protein nanocages and nanorods controlled by small molecules

Constructing different protein nanostructures by using identical building blocks, while realizing their structural transformation in response to external stimuli, remains a challenge. Here, we fabricated protein nanocages and nanorods by using dimeric TmFtn as a building block and reacting with Mg²⁺/(α, L-lysine) with polymerization degrees of 9 (PLL₉) and 15 (PLL₁₅), respectively. Notably, the reversible shape transformation of these two supramolecular protein architectures with different dimensions can be achievable in response to external stimuli.

Encoding hierarchical assembly pathways of proteins with DNA

The structural and functional diversity of materials in nature depends on the controlled assembly of discrete building blocks into complex architectures via specific, multistep, hierarchical assembly pathways. Achieving similar complexity in synthetic materials through hierarchical assembly is challenging due to difficulties with defining multiple recognition areas on synthetic building blocks and controlling the sequence through which those recognition sites direct assembly. Here, we show that we can exploit the chemical anisotropy of proteins and the programmability of DNA ligands to deliberately control the hierarchical assembly of protein-DNA materials. Through DNA sequence design, we introduce orthogonal DNA interactions with disparate interaction strengths ("strong" and "weak") onto specific geometric regions of a model protein, stable protein 1 (Sp1). We show that the spatial encoding of DNA ligands leads to highly directional assembly via strong interactions and that, by design, the first stage of assembly increases the multivalency of weak DNA-DNA interactions that give rise to an emergent second stage of assembly. Furthermore, we demonstrate that judicious DNA design not only directs assembly along a given pathway but can also direct distinct structural outcomes from a single pathway. This combination of protein surface and DNA sequence design allows us to encode the structural and chemical information necessary into building blocks to program their multistep hierarchical assembly. Our findings represent a strategy for controlling the hierarchical assembly of proteins to realize a diverse set of protein-DNA materials by design.

Protein interface redesign facilitates the transformation of nanocage building blocks to 1D and 2D nanomaterials

Although various artificial protein nanoarchitectures have been constructed, controlling the transformation between different protein assemblies has largely been unexplored. Here, we describe an approach to realize the self-assembly transformation of dimeric building blocks by adjusting their geometric arrangement. Thermotoga maritima ferritin (TmFtn) naturally occurs as a dimer; twelve of these dimers interact with each other in a head-to-side manner to generate 24-meric hollow protein nanocage in the presence of Ca²⁺ or PEG. By tuning two contiguous dimeric proteins to interact in a fully or partially side-by-side fashion through protein interface redesign, we can render the self-assembly transformation of such dimeric building blocks from the protein nanocage to filament, nanorod and nanoribbon in response to multiple external stimuli. We show similar dimeric protein building blocks can generate three kinds of protein materials in a manner that highly resembles natural pentamer building blocks from viral capsids that form different protein assemblies.

Patterns in Nature—S-Layer Lattices of Bacterial and Archaeal Cells

Bacterial surface layers (S-layers) have been observed as the outermost cell envelope component in a wide range of bacteria and most archaea. S-layers are monomolecular lattices composed of a single protein or glycoprotein species and have either oblique, square or hexagonal lattice symmetry with unit cell dimensions ranging from 3 to 30 nm. They are generally 5 to 10 nm thick (up to 70 nm in archaea) and represent highly porous protein lattices (30–70% porosity) with pores of uniform size and morphology in the range of 2 to 8 nm. Since S-layers can be considered as one of the simplest protein lattices found in nature and the constituent units are probably the most abundantly expressed proteins on earth, it seems justified to briefly review the different S-layer lattice types, the need for lattice imperfections and the discussion of S-layers from the perspective of an isoporous protein network in the ultrafiltration region. Finally, basic research on S-layers laid the foundation for applications in biotechnology, synthetic biology, and biomimetics.

Nucleation of protein mesocrystals via oriented attachment

Self-assembly of proteins holds great promise for the bottom-up design and production of synthetic biomaterials. In conventional approaches, designer proteins are pre-programmed with specific recognition sites that drive the association process towards a desired organized state. Although proven effective, this approach poses restrictions on the complexity and material properties of the end-state. An alternative, hierarchical approach that has found wide adoption for inorganic systems, relies on the production of crystalline nanoparticles that become the building blocks of a next-level assembly process driven by oriented attachment (OA). As it stands, OA has not yet been observed for protein systems. Here we employ cryo-transmission electron microscopy (cryoEM) in the high nucleation rate limit of protein crystals and map the self-assembly route at molecular resolution. We observe the initial formation of facetted nanocrystals that merge lattices by means of OA alignment well before contact is made, satisfying non-trivial symmetry rules in the process. As these nanocrystalline assemblies grow larger we witness imperfect docking events leading to oriented aggregation into mesocrystalline assemblies. These observations highlight the underappreciated role of the interaction between crystalline nuclei, and the impact of OA on the crystallization process of proteins.

A New Method for Dispersing Pristine Carbon Nanotubes Using Regularly Arranged S-Layer Proteins

Homogeneous and stable dispersions of functionalized carbon nanotubes (CNTs) in aqueous solutions are imperative for a wide range of applications, especially in life and medical sciences. Various covalent and non-covalent approaches were published to separate the bundles into individual tubes. In this context, this work demonstrates the non-covalent modification and dispersion of pristine multi-walled carbon nanotubes (MWNTs) using two S-layer proteins, namely, SbpA from Lysinibacillus sphaericus CCM2177 and SbsB from Geobacillus stearothermophilus PV72/p2. Both the S-layer proteins coated the MWNTs completely. Furthermore, it was shown that SbpA can form caps at the ends of MWNTs. Reassembly experiments involving a mixture of both S-layer proteins in the same solution showed that the MWNTs were primarily coated with SbsB, whereas SbpA formed self-assembled layers. The dispersibility of the pristine nanotubes coated with SbpA was determined by zeta potential measurements (−24.4 +/− 0.6 mV, pH = 7). Finally, the SbpA-coated MWNTs were silicified with tetramethoxysilane (TMOS) using a mild biogenic approach. As expected, the thickness of the silica layer could be controlled by the reaction time and was 6.3 +/− 1.25 nm after 5 min and 25.0 +/− 5.9 nm after 15 min. Since S-layer proteins have already demonstrated their capability to bind (bio)molecules in dense packing or to act as catalytic sites in biomineralization processes, the successful coating of pristine MWNTs has great potential in the development of new materials, such as biosensor architectures.

S-Layer Ultrafiltration Membranes

Monomolecular arrays of protein subunits forming surface layers (S-layers) are the most common outermost cell envelope components of prokaryotic organisms (bacteria and archaea). Since S-layers are periodic structures, they exhibit identical physicochemical properties for each constituent molecular unit down to the sub-nanometer level. Pores passing through S-layers show identical size and morphology and are in the range of ultrafiltration membranes. The functional groups on the surface and in the pores of the S-layer protein lattice are accessible for chemical modifications and for binding functional molecules in very precise fashion. S-layer ultrafiltration membranes (SUMs) can be produced by depositing S-layer fragments as a coherent (multi)layer on microfiltration membranes. After inter- and intramolecular crosslinking of the composite structure, the chemical and thermal resistance of these membranes was shown to be comparable to polyamide membranes. Chemical modification and/or specific binding of differently sized molecules allow the tuning of the surface properties and molecular sieving characteristics of SUMs. SUMs can be utilized as matrices for the controlled immobilization of functional biomolecules (e.g., ligands, enzymes, antibodies, and antigens) as required for many applications (e.g., biosensors, diagnostics, enzyme- and affinity-membranes). Finally, SUM represent unique supporting structures for stabilizing functional lipid membranes at meso- and macroscopic scale.

Controlled and Stable Patterning of Diverse Inorganic Nanocrystals on Crystalline Two-Dimensional Protein Arrays

Controlled patterning of nanoparticles on bioassemblies enables synthesis of complex materials for applications in optics, nanoelectronics, and sensing. Biomolecular self-assembly offers molecular control for engineering patterned nanomaterials, but current approaches have been limited in their ability to combine high nanoparticle coverage with generality that enables incorporation of multiple nanoparticle types. Here, we synthesize photonic materials on crystalline two-dimensional (2D) protein sheets using orthogonal bioconjugation reactions, organizing quantum dots (QDs), gold nanoparticles (AuNPs), and upconverting nanoparticles along the surface-layer (S-layer) protein SbsB from the extremophile Geobacillus stearothermophilus. We use electron and optical microscopy to show that isopeptide bond-forming SpyCatcher and SnoopCatcher systems enable the simultaneous and controlled conjugation of multiple types of nanoparticles (NPs) at high densities along the SbsB sheets. These NP conjugation reactions are orthogonal to each other and to Au-thiol bond formation, allowing tailorable nanoparticle combinations at sufficient labeling efficiencies to permit optical interactions between nanoparticles. Fluorescence lifetime imaging of SbsB sheets conjugated to QDs and AuNPs at distinct attachment sites shows spatially heterogeneous QD emission, with shorter radiative decays and brighter fluorescence arising from plasmonic enhancement at short interparticle distances. This specific, stable, and efficient conjugation of NPs to 2D protein sheets enables the exploration of interactions between pairs of nanoparticles at defined distances for the engineering of protein-based photonic nanomaterials.

LytR-CpsA-Psr Glycopolymer Transferases: Essential Bricks in Gram-Positive Bacterial Cell Wall Assembly

The cell walls of Gram-positive bacteria contain a variety of glycopolymers (CWGPs), a significant proportion of which are covalently linked to the peptidoglycan (PGN) scaffolding structure. Prominent CWGPs include wall teichoic acids of Staphylococcus aureus, streptococcal capsules, mycobacterial arabinogalactan, and rhamnose-containing polysaccharides of lactic acid bacteria. CWGPs serve important roles in bacterial cellular functions, morphology, and virulence. Despite evident differences in composition, structure and underlaying biosynthesis pathways, the final ligation step of CWGPs to the PGN backbone involves a conserved class of enzymes-the LytR-CpsA-Psr (LCP) transferases. Typically, the enzymes are present in multiple copies displaying partly functional redundancy and/or preference for a distinct CWGP type. LCP enzymes require a lipid-phosphate-linked glycan precursor substrate and catalyse, with a certain degree of promiscuity, CWGP transfer to PGN of different maturation stages, according to in vitro evidence. The prototype attachment mode is that to the C6-OH of N-acetylmuramic acid residues via installation of a phosphodiester bond. In some cases, attachment proceeds to N-acetylglucosamine residues of PGN-in the case of the Streptococcus agalactiae capsule, even without involvement of a phosphate bond. A novel aspect of LCP enzymes concerns a predicted role in protein glycosylation in Actinomyces oris. Available crystal structures provide further insight into the catalytic mechanism of this biologically important class of enzymes, which are gaining attention as new targets for antibacterial drug discovery to counteract the emergence of multidrug resistant bacteria.

Hierarchical supramolecular assembly of a single peptoid polymer into a planar nanobrush with two distinct molecular packing motifs

Hierarchical nanomaterials have received increasing interest for many applications. Here, we report a facile programmable strategy based on an embedded segmental crystallinity design to prepare unprecedented supramolecular planar nanobrush-like structures composed of two distinct molecular packing motifs, by the self-assembly of one particular diblock copolymer poly(ethylene glycol)-block-poly(N-octylglycine) in a one-pot preparation. We demonstrate that the superstructures result from the temperature-controlled hierarchical self-assembly of preformed spherical micelles by optimizing the crystallization-solvophobicity balance. Particularly remarkable is that these micelles first assemble into linear arrays at elevated temperatures, which, upon cooling, subsequently template further lateral, crystallization-driven assembly in a living manner. Addition of the diblock copolymer chains to the growing nanostructure occurs via a loosely organized micellar intermediate state, which undergoes an unfolding transition to the final crystalline state in the nanobrush. This assembly mechanism is distinct from previous crystallization-driven approaches which occur via unimer addition, and is more akin to protein crystallization. Interestingly, nanobrush formation is conserved over a variety of preparation pathways. The precise control ability over the superstructure, combined with the excellent biocompatibility of polypeptoids, offers great potential for nanomaterials inaccessible previously for a broad range of advanced applications.

Rationally Designed Protein Building Blocks for Programmable Hierarchical Architectures

Diverse natural/artificial proteins have been used as building blocks to construct a variety of well-ordered nanoscale structures over the past couple of decades. Sophisticated protein self-assemblies have attracted great scientific interests due to their potential applications in disease diagnosis, illness treatment, biomechanics, bio-optics and bio-electronics, etc. This review outlines recent efforts directed to the creation of structurally defined protein assemblies including one-dimensional (1D) strings/rings/tubules, two-dimensional (2D) planar sheets and three-dimensional (3D) polyhedral scaffolds. We elucidate various innovative strategies for manipulating proteins to self-assemble into desired architectures. The emergent applications of protein assemblies as versatile platforms in medicine and material science with improved performances have also been discussed.

Molecular Logic of Prokaryotic Surface Layer Structures

Most prokaryotic cells are encased in a surface layer (S-layer) consisting of a paracrystalline array of repeating lattice-forming proteins. S-layer proteins populate a vast and diverse sequence space, performing disparate functions in prokaryotic cells, including cellular defense, cell-shape maintenance, and regulation of import and export of materials. This article highlights recent advances in the understanding of S-layer structure and assembly, made possible by rapidly evolving structural and cell biology methods. We underscore shared assembly principles revealed by recent work and discuss a common molecular framework that may be used to understand the structural organization of S-layer proteins across bacteria and archaea.

Despite enormous sequence diversity in surface (S)-layer proteins, structural diversity is much lower than previously thought.

S-layer proteins have a bipartite arrangement with a lattice-forming and an anchoring segment.

Novel structural biology methods are revealing the architectures of S-layers in situ.

S-layer assembly across prokaryotes is tightly coupled to the cell cycle, including the cell division machinery.

Phase Transitions by an Abundant Protein in the Anammox Extracellular Matrix Mediate Cell-to-Cell Aggregation and Biofilm Formation

By employing biophysical and liquid-liquid phase separation concepts, this study revealed how a highly abundant extracellular protein enhances the key environmental and industrial bioprocess of anaerobic ammonium oxidation (anammox). Extracellular proteins of environmental biofilms are understudied and poorly annotated in public databases. Understanding the function of extracellular proteins is also increasingly important for improving bioprocesses and resource recovery. Here, protein functions were assessed based on theoretical predictions of intrinsically disordered domains, known to promote adhesion and liquid-liquid phase separation, and available surface layer protein properties. A model is thus proposed to explain how the protein promotes aggregation and biofilm formation by extracellular matrix remodeling and phase transitions. This work provides a strong foundation for functional investigations of extracellular proteins involved in biofilm development.

This study describes the first direct functional assignment of a highly abundant extracellular protein from a key environmental and biotechnological biofilm performing an anaerobic ammonium oxidation (anammox) process. Expression levels of Brosi_A1236, belonging to a class of proteins previously suggested to be cell surface associated, were in the top one percentile of all genes in the “Candidatus Brocadia sinica”-enriched biofilm. The Brosi_A1236 structure was computationally predicted to consist of immunoglobulin-like anti-parallel β-strands, and circular dichroism conducted on the isolated surface protein indicated that β-strands are the dominant higher-order structure. The isolated protein was stained positively by the β-sheet-specific stain thioflavin T, along with cell surface- and matrix-associated regions of the biofilm. The surface protein has a large unstructured content, including two highly disordered domains at its C terminus. The disordered domains bound to the substratum and thereby facilitated the adhesion of negatively charged latex microspheres, which were used as a proxy for cells. The disordered domains and isolated whole surface protein also underwent liquid-liquid phase separation to form liquid droplets in suspension. Liquid droplets of disordered protein wet the surfaces of microspheres and bacterial cells and facilitated their coalescence. Furthermore, the surface layer protein formed gels as well as ordered crystalline structures. These observations suggest that biophysical remodeling through phase transitions promotes aggregation and biofilm formation.

In Situ Monitoring of the Seeding and Growth of Silver Metal-Organic Nanotubes by Liquid-Cell Transmission Electron Microscopy

Metal-organic nanotubes (MONTs) are highly ordered one-dimensional crystalline porous frameworks. Despite being nanomaterials, virtually all studies of MONTs rely on characterization of the bulk crystalline material (micron-sized) by single-crystal X-ray diffraction. For MONTs to achieve their raison d'être as tunable one-dimensional nanomaterials, individual tubes or small finite bundles of tubes must be synthesized and characterized. Therefore, to directly observe their formation under a variety of reaction conditions in solution, we employ liquid-cell transmission electron microscopy (LCTEM), which allows the early stages of MONT assembly to be monitored in real time. Notably, changing the metal-to-ligand ratio alters the local concentrations of reactant monomers, resulting in multiple nucleation and growth pathways and diverse morphologies at the nanoscale. These various initial seeds grow to form the same nanocrystalline needle phase. This approach of employing LCTEM to study these nanomaterials is analogous to monitoring typical homogeneous solution phase reactions by NMR for controlled nanomaterial formation.

Molecular insights on NaCl crystal formation approaching PVDF membranes functionalized with graphene

Atomistic simulations of graphene–PVDF membranes speeding up NaCl crystal nucleation and growth in comparison to the pristine PVDF membranes.

Recent experimental explorations of non-classical nucleation

This work provides a clearer picture for non-classical nucleation by revealing the presence of various intermediates using advanced characterization techniques.

A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly

Many microbes assemble a crystalline protein layer on their outer surface as an additional barrier and communication platform between the cell and its environment. Surface layer proteins efficiently crystallize to continuously coat the cell, and this trait has been utilized to design functional macromolecular nanomaterials. Here, we report that rapid crystallization of a bacterial surface layer protein occurs through a multistep pathway involving a crystalline intermediate. Upon calcium binding, sequential changes occur in the structure and arrangement of the protein, which are captured by time-resolved small angle X-ray scattering and transmission electron cryo-microscopy. We demonstrate that a specific domain is responsible for enhancing the rate of self-assembly, unveiling possible evolutionary mechanisms to enhance the kinetics of 2D protein crystallization.

Surface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular self-assembly by crystallizing when exposed to an environmental trigger. However, molecular mechanisms governing rapid protein crystallization in vivo or in vitro are largely unknown. Here, we demonstrate that the Caulobacter crescentus SLP readily crystallizes into sheets in vitro via a calcium-triggered multistep assembly pathway. This pathway involves 2 domains serving distinct functions in assembly. The C-terminal crystallization domain forms the physiological 2-dimensional (2D) crystal lattice, but full-length protein crystallizes multiple orders of magnitude faster due to the N-terminal nucleation domain. Observing crystallization using a time course of electron cryo-microscopy (Cryo-EM) imaging reveals a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Dynamic flexibility between the 2 domains rationalizes efficient S-layer crystal nucleation on the curved cellular surface. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials.

Pyruvate Substitutions on Glycoconjugates

Glycoconjugates are the most diverse biomolecules of life. Mostly located at the cell surface, they translate into cell-specific "barcodes" and offer a vast repertoire of functions, including support of cellular physiology, lifestyle, and pathogenicity. Functions can be fine-tuned by non-carbohydrate modifications on the constituting monosaccharides. Among these modifications is pyruvylation, which is present either in enol or ketal form. The most commonly best-understood example of pyruvylation is enol-pyruvylation of N-acetylglucosamine, which occurs at an early stage in the biosynthesis of the bacterial cell wall component peptidoglycan. Ketal-pyruvylation, in contrast, is present in diverse classes of glycoconjugates, from bacteria to algae to yeast-but not in humans. Mild purification strategies preventing the loss of the acid-labile ketal-pyruvyl group have led to a collection of elucidated pyruvylated glycan structures. However, knowledge of involved pyruvyltransferases creating a ring structure on various monosaccharides is scarce, mainly due to the lack of knowledge of fingerprint motifs of these enzymes and the unavailability of genome sequences of the organisms undergoing pyruvylation. This review compiles the current information on the widespread but under-investigated ketal-pyruvylation of monosaccharides, starting with different classes of pyruvylated glycoconjugates and associated functions, leading to pyruvyltransferases, their specificity and sequence space, and insight into pyruvate analytics.

Novel biodegradable and non-fouling systems for controlled-release based on poly(ε-caprolactone)/Quercetin blends and biomimetic bacterial S-layer coatings

Quercetin is a strong antioxidant with low bioavailability due to its high crystallinity. A further drawback is that Quercetin has potentially toxic effects at high concentrations. To improve this low water solubility, as well as control the concentration of the flavonoid in the body, Quercetin is incorporated into a polymeric matrix to form an amorphous solid dispersion (ASD) stable enough to resist the recrystallization of the drug. For this purpose, miscible poly(ε-caprolactone) (PCL) and Quercetin (Q) blends are prepared, provided that they have complementary interacting groups. For compositions in which the flavonoid remains in an amorphous state thanks to the interactions with polymer chains, various PCL/Q drug release platforms are fabricated: micrometric films by solvent casting, nanometric films by spin coating, and nanofibers by electrospinning. Then, the potential use of bacterial S-layer proteins as release-preventive membranes is tested on PCL-Quercetin blends, due to their ability to construct a biomimetic coating including nanometric pores. For all the platforms, the SbpA coating can maintain a stable release under the toxicity level of Quercetin. Accordingly, a PCL/Q system with an S-layer coating allows the design of versatile bioavailable Quercetin eluting devices that prevent toxicity and biofouling issues.

Topologically-guided continuous protein crystallization controls bacterial surface layer self-assembly

Many bacteria and most archaea possess a crystalline protein surface layer (S-layer), which surrounds their growing and topologically complicated outer surface. Constructing a macromolecular structure of this scale generally requires localized enzymatic machinery, but a regulatory framework for S-layer assembly has not been identified. By labeling, superresolution imaging, and tracking the S-layer protein (SLP) from C. crescentus, we show that 2D protein self-assembly is sufficient to build and maintain the S-layer in living cells by efficient protein crystal nucleation and growth. We propose a model supported by single-molecule tracking whereby randomly secreted SLP monomers diffuse on the lipopolysaccharide (LPS) outer membrane until incorporated at the edges of growing 2D S-layer crystals. Surface topology creates crystal defects and boundaries, thereby guiding S-layer assembly. Unsupervised assembly poses challenges for therapeutics targeting S-layers. However, protein crystallization as an evolutionary driver rationalizes S-layer diversity and raises the potential for biologically inspired self-assembling macromolecular nanomaterials.

Bacteria assemble the surface layer (S-layer), a crystalline protein coat surrounding the curved surface, using protein self-assembly. Here authors image native and purified RsaA, the S-layer protein from C. crescentus, and show that protein crystallization alone is sufficient to assemble and maintain the S-layer in vivo.

Contrasting Chemistry of Block Copolymer Films Controls the Dynamics of Protein Self-Assembly at the Nanoscale

Biological systems are able to control the assembly and positioning of proteins with nanoscale precision, as exemplified by the intricate molecular structures within cell membranes, virus capsids, and collagen matrices. Controlling the assembly of biomolecules is critical for the use of biomaterials in artificial systems such as antibacterial coatings, engineered tissue samples, and implanted medical devices. Furthermore, understanding the dynamics of protein assembly on heterogeneous templates will ultimately enable the control of protein crystallization in general. Here, we show a biomimetic, hierarchical bottom-up approach to direct the self-assembly of crystalline S-layers through nonspecific interactions with nanostructured block copolymer (BCP) thin-film templates. A comparison between physically and chemically patterned BCP substrates shows that chemical heterogeneity is required to confine the adhesion and self-assembly of S-layers to specific BCP domains. Furthermore, we show that this mechanism can be extended to direct the formation of collagen fibers along the principal direction of the underlying BCP substrate. The dynamics of protein self-assembly at the solid-liquid interface are followed using in situ high-resolution atomic force microscopy under continuous flow conditions, allowing the determination of the rate constants of the self-assembly. A pattern of alternating, chemically distinct nanoscale domains drastically increases the rate of self-assembly compared to non-patterned chemically homogeneous substrates.

Slp-coated liposomes for drug delivery and biomedical applications: potential and challenges

Slp forms a crystalline array of proteins on the outermost envelope of bacteria and archaea with a molecular weight of 40-200 kDa. Slp can self-assemble on the surface of liposomes in a proper environment via electrostatic interactions, which could be employed to functionalize liposomes by forming Slp-coated liposomes for various applications. Among the molecular characteristics, the stability, adhesion, and immobilization of biomacromolecules are regarded as the most meaningful. Compared to plain liposomes, Slp-coated liposomes show excellent physicochemical and biological stabilities. Recently, Slp-coated liposomes were shown to specifically adhere to the gastrointestinal tract, which was attributed to the "ligand-receptor interaction" effect. Furthermore, Slp as a "bridge" can immobilize functional biomacromol-ecules on the surface of liposomes via protein fusion technology or intermolecular forces, endowing liposomes with beneficial functions. In view of these favorable features, Slp-coated liposomes are highly likely to be an ideal platform for drug delivery and biomedical uses. This review aims to provide a general framework for the structure and characteristics of Slp and the interactions between Slp and liposomes, to highlight the unique properties and drug delivery as well as the biomedical applications of the Slp-coated liposomes, and to discuss the ongoing challenges and perspectives.

A Probabilistic Model for Crystal Growth Applied toProtein Deposition at the Microscale

A probabilistic discrete model for 2D protein crystal growth is presented. This model takes into account the available space and can describe growing processes of a different nature due to the versatility of its parameters, which gives the model great flexibility. The accuracy of the simulation is tested against a real recrystallization experiment, carried out with the bacterial protein SbpA from Lysinibacillus sphaericus CCM2177, showing high agreement between the proposed model and the actual images of the crystal growth. Finally, it is also discussed how the regularity of the interface (i.e., the curve that separates the crystal from the substrate) affects the evolution of the simulation.

Developing Biopolymer Mesocrystals by Crystallization of Secondary Structures

Particle-based mesocrystals have been known for over 10 years; however, examples of biopolymer mesocrystals are rather scarce. The synthesis of particle precursors of biopolymers, the identification of particle-mediated crystallization processes, and thus the synthesis of mesocrystals of biopolymers are challenging. Here, we summarize the existing examples of biopolymer crystallization based on self-assembly of the secondary structures, which could induce the formation of biopolymer mesocrystals. As basic building units, simple secondary structures such as β-sheets or α-helixes could provide a useful tool for the design of biopolymer mesocrystals.

In-situ 2D bacterial crystal growth as a function of protein concentration: An atomic force microscopy study

The interplay between protein concentration and (observation) time has been investigated for the adsorption and crystal growth of the bacterial SbpA proteins on hydrophobic fluoride-functionalized SiO2 surfaces. For this purpose, atomic force microscopy (AFM) has been performed in real-time for monitoring protein crystal growth at different protein concentrations. Results reveal that (1) crystal formation occurs at concentrations above 0.08 µM and (2) the compliance of the formed crystal decreases by increasing protein concentration. All the crystal domains observed presented similar lattice parameters (being the mean value for the unit cell: a = 14.8 ± 0.5 nm, b = 14.7 ± 0.5 nm, γ = 90 ° ± 2). Protein film formation is shown to take place from initial nucleation points which originate a gradual and fast extension of the crystalline domains. The Avrami equation describes well the experimental results. Overall, the results suggest that protein-substrate interactions prevail over protein-protein interactions. RESEARCH HIGHLIGHTS: AFM enables to monitor protein crystallization in real-time. AFM high-resolution determines lattice parameters and viscoelastic properties. S-layer crystal growth rate increases with protein concentration. Avrami equation models protein crystal growth.

Dynamically resolved self-assembly of S-layer proteins on solid surfaces

By using high-speed and high-resolution Atomic Force Microscopy (AFM), it was possible to resolve within a single experiment the kinetic pathway in S-layer self-assembly at the solid-liquid interface, obtaining a model that accounts for the nucleation, growth and structural rearrangements in 2D protein self assembly across time (second to hours) and spatial scales (nm to microns).

Structural basis of cell wall anchoring by SLH domains in Paenibacillus alvei

Self-assembling protein surface (S-) layers are common cell envelope structures of prokaryotes and have critical roles from structural maintenance to virulence. S-layers of Gram-positive bacteria are often attached through the interaction of S-layer homology (SLH) domain trimers with peptidoglycan-linked secondary cell wall polymers (SCWPs). Here we present an in-depth characterization of this interaction, with co-crystal structures of the three consecutive SLH domains from the Paenibacillus alvei S-layer protein SpaA with defined SCWP ligands. The most highly conserved SLH domain residue SLH-Gly29 is shown to enable a peptide backbone flip essential for SCWP binding in both biophysical and cellular experiments. Furthermore, we find that a significant domain movement mediates binding by two different sites in the SLH domain trimer, which may allow anchoring readjustment to relieve S-layer strain caused by cell growth and division.

Gram-positive bacterial envelopes comprise proteinaceous surface layers (S-layers) important for survival and virulence that are often anchored to the cell wall through secondary cell wall polymers. Here the authors use a structural and biophysical approach to define the molecular mechanism of this important interaction.

In vitro single-cell dissection revealing the interior structure of cable bacteria

Filamentous Desulfobulbaceae bacteria were recently discovered as long-range transporters of electrons from sulfide to oxygen in marine sediments. The long-range electron transfer through these cable bacteria has created considerable interests, but it has also raised many questions, such as what structural basis will be required to enable micrometer-sized cells to build into centimeter-long continuous filaments? Here we dissected cable bacteria cells in vitro by atomic force microscopy and further explored the interior, which is normally hidden behind the outer membrane. Using nanoscale topographical and mechanical maps, different types of bacterial cell-cell junctions and strings along the cable length were identified. More important, these strings were found to be continuous along the bacterial cells passing through the cell-cell junctions. This indicates that the strings serve an important function in maintaining integrity of individual cable bacteria cells as a united filament. Furthermore, ridges in the outer membrane are found to envelop the individual strings at cell-cell junctions, and they are proposed to strengthen the junctions. Finally, we propose a model for the division and growth of the cable bacteria, which illustrate the possible structural requirements for the formation of centimeter-length filaments in the recently discovered cable bacteria.

Nucleation of protein crystals - a nanoscopic perspective

Macromolecular phase transitions bear great medical, scientific and industrial relevance, yet the molecular picture of their earliest beginnings is still far from complete. For decades, progress has been hampered by the challenges associated with studying stochastic nucleation phenomena occurring on nanoscopic length scales. In the last 5 years, however, the field has advanced with great strides due to the recent buildout of experimental techniques that allow us to observe details of the nucleation process on the nanoscale. In this review, we present a historical overview and state-of-the-art analysis of protein crystal nucleation from an experimentalist's perspective. After a short introduction of key concepts from classical nucleation theory, we discuss the advancements that have led to the development of alternative models of protein nucleation. We summarize the experimental proof in favour of these various models, but we also focus on some of their shortcomings and experimental blind spots. In our penultimate section we highlight recent works that have provided direct nanoscopic insight into the nucleation of protein crystals. We end with concluding paragraphs discussing outstanding questions and possible strategies to advance the field further in the future.