Novel biocatalysts based on S-layer self-assembly of Geobacillus stearothermophilus NRS 2004/3a: a nanobiotechnological approach

Two-Dimensional Protein Nanoarray as a Carrier of Sensing Elements for Gold-Based Immunosensing Systems

Homogeneous and high-density immobilization of proteins on gold-based sensing surface without the loss of protein activity is of great significance for high-performance immunosensing but remains challenging. To realize more sensitive immunosensing, an improved method for protein immobilization on the gold surface is urgently required. Here, we propose a biological and mild approach by combining a genetically encoded SpyTag-SpyCatcher interaction system with a redesigned S-layer of bacteria. This method allows proteins of interest to be covalently linked with the S-layer in a biological manner and arranged orderly in a two-dimensional nanoarray on the gold surface. The activity of African swine fever virus proteins was significantly preserved after immobilization. In addition, our S-layer-based immobilization method exhibited an eightfold increase in detection sensitivity compared with the conventional chemical cross-linking for protein immobilization during serological tests. Together, our S-layer-based immobilization method provides an innovative approach for building a quality gold-based biosensing interface and should greatly contribute to the high-sensitivity sensing for a deeper understanding of pathogen infection and host immunity.

Supramolecular protein assembly in cell-free protein synthesis system

Protein-based biomaterials have the characteristics of stability and biocompatibility. Based on these advantages, various bionic materials have been manufactured and used in different fields. However, current protein-based biomaterials generally need to form monomers in cells and be purified before being assembled in vitro. The preparation process takes a long time, and the complex cellular environment is challenging to be optimized for producing the target protein product. Here this study proposed technology for in situ synthesis and assembly of the target protein, namely the cell-free protein synthesis (CFPS), which allowed to shorten the synthesis time and increase the flexibility of adding or removing natural or synthetic components. In this study, successful expression and self-assembly of the dihedral symmetric proteins proved the applicability of the CFPS system for biomaterials production. Furthermore, the fusion of different functional proteins to these six scaffold proteins could form active polymers in the CFPS system. Given the flexibility, CFPS is expected to become a powerful tool as the prototyping and manufacturing technology for protein-based biomaterials in the future.

The S-layer homology domains of Paenibacillus alvei surface protein SpaA bind to cell wall polysaccharide through the terminal monosaccharide residue

Self-assembling (glyco)protein surface layers (S-layers) are ubiquitous prokaryotic cell-surface structures involved in structural maintenance, nutrient diffusion, host adhesion, virulence, and other processes, which makes them appealing targets for therapeutics and biotechnological applications as biosensors or drug delivery systems. However, unlocking this potential requires expanding our understanding of S-layer properties, especially the details of surface-attachment. S-layers of Gram-positive bacteria often are attached through the interaction of S-layer homology (SLH) domain trimers with peptidoglycan-linked secondary cell wall polymers (SCWPs). Cocrystal structures of the SLH domain trimer from the Paenibacillus alvei S-layer protein SpaA (SpaA_SLH) with synthetic, terminal SCWP disaccharide and trisaccharide analogs, together with isothermal titration calorimetry binding analyses, reveal that while SpaA_SLH accommodates longer biologically relevant SCWP ligands within both its primary (G2) and secondary (G1) binding sites, the terminal pyruvylated ManNAc moiety serves as the nearly exclusive SCWP anchoring point. Binding is accompanied by displacement of a flexible loop adjacent to the receptor site that enhances the complementarity between protein and ligand, including electrostatic complementarity with the terminal pyruvate moiety. Remarkably, binding of the pyruvylated monosaccharide SCWP fragment alone is sufficient to cause rearrangement of the receptor-binding sites in a manner necessary to accommodate longer SCWP fragments. The observation of multiple conformations in longer oligosaccharides bound to the protein, together with the demonstrated functionality of two of the three SCWP receptor-binding sites, reveals how the SpaA_SLH-SCWP interaction has evolved to accommodate longer SCWP ligands and alleviate the strain inherent to bacterial S-layer adhesion during growth and division.

New Nanocarrier System for Liposomes Coated with Lactobacillus acidophilus S-Layer Protein to Improve Leu-Gln-Pro-Glu Absorption through the Intestinal Epithelium

The present study describes the development of a novel liposome nanocarrier system. The liposome was coated with Lactobacillus acidophilus CICC 6074 S-layer protein (SLP) to improve the intestinal absorption of the cholesterol-lowering peptide Leu-Gln-Pro-Glu (LQPE). The SLP-coated liposomes were prepared and characterized with morphology, particle size, zeta potential, membrane stability, Fourier transform infrared spectroscopy, and dual-channel surface plasma resonance. The results showed that SLP could successfully self-assemble on liposomes. Then, LQPE liposomes and SLP-coated LQPE liposomes (SLP-L-LQPE) were prepared. SLP-L-LQPE not only showed better sustained release properties and gastrointestinal tolerance in vitro but also increased the retention time in mice intestine. Transepithelial transport experiment indicates that the transshipment of LQPE increased significantly after being embedded by liposomes and coated with SLP. The research provides a theoretical basis for the study of SLP-coated liposomes and a potential drug delivery system for improving the intestinal absorption of peptides.

Design and biosynthesis of functional protein nanostructures

Proteins are one of the major classes of biomolecules that execute biological functions for maintenance of life. Various kinds of nanostructures self-assembled from proteins have been created in nature over millions of years of evolution, including protein nanowires, layers and nanocages. These protein nanostructures can be reconstructed and equipped with desired new functions. Learning from and manipulating the self-assembly of protein nanostructures not only help to deepen our understanding of the nature of life but also offer new routes to fabricate novel nanomaterials for diverse applications. This review summarizes the recent research progress in this field, focusing on the characteristics, functionalization strategies, and applications of protein nanostructures.

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.

Protein Assemblies: Nature-Inspired and Designed Nanostructures

Ordered protein assemblies are attracting interest as next-generation biomaterials with a remarkable range of structural and functional properties, leading to potential applications in biocatalysis, materials templating, drug delivery and vaccine development. This Review covers ordered protein assemblies including protein nanowires/nanofibrils, nanorings, nanotubes, designed two- and three-dimensional ordered protein lattices and protein-like cages including polyhedral virus-like cage structures. The main focus is on designed ordered protein assemblies, in which the spatial organization of the proteins is controlled by tailored noncovalent interactions (including metal ion binding interactions, electrostatic interactions and ligand–receptor interactions among others) or by careful design of modified (mutant) proteins or de novo constructs. The modification of natural protein assemblies including bacterial S-layers and cage-like and rod-like viruses to impart novel function, e.g. enzymatic activity, is also considered. A diversity of structures have been created using distinct approaches, and this Review provides a summary of the state-of-the-art in the development of these systems, which have exceptional potential as advanced bionanomaterials for a diversity of applications.

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.

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.

S-Layer-Based Nanocomposites for Industrial Applications

This chapter covers the fundamental aspects of bacterial S-layers: what are S-layers, what is known about them, and what are their main features that makes them so interesting for the production of nanostructures. After a detailed introduction of the paracrystalline protein lattices formed by S-layer systems in nature the chapter explores the engineering of S-layer-based materials. How can S-layers be used to produce "industry-ready" nanoscale bio-composite materials, and which kinds of nanomaterials are possible (e.g., nanoparticle synthesis, nanoparticle immobilization, and multifunctional coatings)? What are the advantages and disadvantages of S-layer-based composite materials? Finally, the chapter highlights the potential of these innovative bacterial biomolecules for future technologies in the fields of metal filtration, catalysis, and bio-functionalization.

A S-Layer Protein of Bacillus anthracis as a Building Block for Functional Protein Arrays by In Vitro Self-Assembly

S-layer proteins create a cell-surface layer architecture in both bacteria and archaea. Because S-layer proteins self-assemble into a native-like S-layer crystalline structure in vitro, they are attractive building blocks in nanotechnology. Here, the potential use of the S-layer protein EA1 from Bacillus anthracis in constructing a functional nanostructure is investigated, and apply this nanostructure in a proof-of-principle study for serological diagnosis of anthrax. EA1 is genetically fused with methyl parathion hydrolase (MPH), to degrade methyl parathion and provide a label for signal amplification. EA1 not only serves as a nanocarrier, but also as a specific antigen to capture anthrax-specific antibodies. As results, purified EA1-MPH forms a single layer of crystalline nanostructure through self-assembly. Our chimeric nanocatalyst greatly improves enzymatic stability of MPH. When applied to the detection of anthrax-specific antibodies in serum samples, the detection of our EA1-MPH nanostructure is nearly 300 times more sensitive than that of the unassembled complex. Together, it is shown that it is possible to build a functional and highly sensitive nanosensor based on S-layer protein. In conclusion, our present study should serve as a model for the development of other multifunctional nanomaterials using S-layer proteins.

Emulsomes meet S-layer proteins: an emerging targeted drug delivery system

Here, the use of emulsomes as a drug delivery system is reviewed and compared with other similar lipidic nanoformulations. In particular, we look at surface modification of emulsomes using S-layer proteins, which are self-assembling proteins that cover the surface of many prokaryotic organisms. It has been shown that covering emulsomes with a crystalline S-layer lattice can protect cells from oxidative stress and membrane damage. In the future, the capability to recrystallize S-layer fusion proteins on lipidic nanoformulations may allow the presentation of binding functions or homing protein domains to achieve highly specific targeted delivery of drug-loaded emulsomes. Besides the discussion on several designs and advantages of composite emulsomes, the success of emulsomes for the delivery of drugs to fight against viral and fungal infections, dermal therapy, cancer, and autoimmunity is summarized. Further research might lead to smart, biocompatible emulsomes, which are able to protect and reduce the side effects caused by the drug, but at the same time are equipped with specific targeting molecules to find the desired site of action.

Relevance of glycosylation of S-layer proteins for cell surface properties

Elucidating the building principles and intrinsic features modulating certain water-associated processes (e.g., surface roughness in the nanometer scale, surface hydration and accompanied antifouling property, etc.) of surface structures from (micro)organisms is nowadays a highly challenging task in fields like microbiology, biomimetic engineering and (bio)material sciences. Here, we show for the first time the recrystallization of the wild-type S-layer glycoprotein wtSgsE from Geobacillus stearothermophilus NRS 2004/3a and its recombinantly produced non-glycosylated form, rSgsE, on gold sensor surfaces. Whereas the proteinaceous lattice of the S-layer proteins is forming a rigid layer on the sensor surface, the glycan chains are developing an overall soft, highly dissipative film. Interestingly, to the wtSgsE lattice almost twice the amount of water is bound and/or coupled in comparison with the non-glycosylated rSgsE with the preferred region being the extending glycan residues. The present results are discussed in terms of the effect of the glycan residues on the recrystallization, the adjoining hydration layer, and the nanoscale roughness and fluidic behavior. The latter features may turn out to be one of the most general ones among bacterial and archaeal S-layer lattices.

The genus Geobacillus and their biotechnological potential

The genus Geobacillus comprises a group of Gram-positive thermophilic bacteria, including obligate aerobes, denitrifiers, and facultative anaerobes that can grow over a range of 45-75°C. Originally classified as group five Bacillus spp., strains of Bacillus stearothermophilus came to prominence as contaminants of canned food and soon became the organism of choice for comparative studies of metabolism and enzymology between mesophiles and thermophiles. More recently, their catabolic versatility, particularly in the degradation of hemicellulose and starch, and rapid growth rates have raised their profile as organisms with potential for second-generation (lignocellulosic) biorefineries for biofuel or chemical production. The continued development of genetic tools to facilitate both fundamental investigation and metabolic engineering is now helping to realize this potential, for both metabolite production and optimized catabolism. In addition, this catabolic versatility provides a range of useful thermostable enzymes for industrial application. A number of genome-sequencing projects have been completed or are underway allowing comparative studies. These reveal a significant amount of genome rearrangement within the genus, the presence of large genomic islands encompassing all the hemicellulose utilization genes and a genomic island incorporating a set of long chain alkane monooxygenase genes. With G+C contents of 45-55%, thermostability appears to derive in part from the ability to synthesize protamine and spermine, which can condense DNA and raise its Tm.

S-layers: principles and applications

Monomolecular arrays of protein or glycoprotein subunits forming surface layers (S-layers) are one of the most commonly observed prokaryotic cell envelope components. S-layers are generally the most abundantly expressed proteins, have been observed in species of nearly every taxonomical group of walled bacteria, and represent an almost universal feature of archaeal envelopes. The isoporous lattices completely covering the cell surface provide organisms with various selection advantages including functioning as protective coats, molecular sieves and ion traps, as structures involved in surface recognition and cell adhesion, and as antifouling layers. S-layers are also identified to contribute to virulence when present as a structural component of pathogens. In Archaea, most of which possess S-layers as exclusive wall component, they are involved in determining cell shape and cell division. Studies on structure, chemistry, genetics, assembly, function, and evolutionary relationship of S-layers revealed considerable application potential in (nano)biotechnology, biomimetics, biomedicine, and synthetic biology.

Bacterial cell-envelope glycoconjugates

Prokaryotic glycosylation fulfills an important role in maintaining and protecting the structural integrity and function of the bacterial cell wall, as well as serving as a flexible adaption mechanism to evade environmental and host-induced pressure. The scope of bacterial and archaeal protein glycosylation has considerably expanded over the past decade(s), with numerous examples covering the glycosylation of flagella, pili, glycosylated enzymes, as well as surface-layer proteins. This article addresses structure, analysis, function, genetic basis, biosynthesis, and biomedical and biotechnological applications of cell-envelope glycoconjugates, S-layer glycoprotein glycans, and "nonclassical" secondary-cell wall polysaccharides. The latter group of polymers mediates the important attachment and regular orientation of the S-layer to the cell wall. The structures of these glycopolymers reveal an enormous diversity, resembling the structural variability of bacterial lipopolysaccharides and capsular polysaccharides. While most examples are presented for Gram-positive bacteria, the S-layer glycan of the Gram-negative pathogen Tannerella forsythia is also discussed. In addition, archaeal S-layer glycoproteins are briefly summarized.

Fluorescent sensors based on bacterial fusion proteins

Fluorescence proteins are widely used as markers for biomedical and technological purposes. Therefore, the aim of this project was to create a fluorescent sensor, based in the green and cyan fluorescent protein, using bacterial S-layers proteins as scaffold for the fluorescent tag. We report the cloning, expression and purification of three S-layer fluorescent proteins: SgsE-EGFP, SgsE-ECFP and SgsE-13aa-ECFP, this last containing a 13-amino acid rigid linker. The pH dependence of the fluorescence intensity of the S-layer fusion proteins, monitored by fluorescence spectroscopy, showed that the ECFP tag was more stable than EGFP. Furthermore, the fluorescent fusion proteins were reassembled on silica particles modified with cationic and anionic polyelectrolytes. Zeta potential measurements confirmed the particle coatings and indicated their colloidal stability. Flow cytometry and fluorescence microscopy showed that the fluorescence of the fusion proteins was pH dependent and sensitive to the underlying polyelectrolyte coating. This might suggest that the fluorescent tag is not completely exposed to the bulk media as an independent moiety. Finally, it was found out that viscosity enhanced the fluorescence intensity of the three fluorescent S-layer proteins.

Protein bodies in nature and biotechnology

Protein bodies are natural structures containing protein aggregates that exist in many organisms ranging from bacteria to mammals and plants. In bacteria they are often a phenomenon associated to over-expression of heterologous proteins. In mammals the so called Russell bodies indicate an accumulation of mutated immune globulins. In plants the protein bodies play a major role as protein storage organelle in seeds. Besides these natural cases, protein bodies can also be artificially induced primarily using self-assembling peptides. Frequently plant derived proteins such as prolamins or their derivatives are used. In some cases the help of an endoplasmatic retention signal is needed to create artificial protein bodies. The biotechnological application of protein bodies offers novel solutions such as the simplification of downstream processing in protein manufacture, the utilisation as particle for immunisation as vaccines or as carrier free self immobilised enzyme particle for many industrial catalytic processes.

Surface-layer lattices as patterning element for multimeric extremozymes

A promising new approach for the production of biocatalysts comprises the use of surface-layer (S-layer) lattices that present functional multimeric enzymes on their surface, thereby guaranteeing most accurate spatial distribution and orientation, as well as maximal effectiveness and stability of these enzymes. For proof of concept, a tetrameric and a trimeric extremozyme are chosen for the construction of S-layer/extremozyme fusion proteins. By using a flexible peptide linker, either one monomer of the tetrameric xylose isomerase XylA from the thermophilic Thermoanaerobacterium strain JW/SL-YS 489 or, in another approach, one monomer of the trimeric carbonic anhydrase from the methanogenic archaeon Methanosarcina thermophila are genetically linked to one monomer of the S-layer protein SbpA of Lysinibacillus sphaericus CCM 2177. After isolation and purification, the self-assembly properties of both S-layer fusion proteins as well as the specific activity of the fused enzymes are confirmed, thus indicating that the S-layer protein moiety does not influence the nature of the multimeric enzymes and vice versa. By recrystallization of the S-layer/extremozyme fusion proteins on solid supports, the active enzyme multimers are exposed on the surface of the square S-layer lattice with 13.1 nm spacing.

Two-dimensional nanoarchitectonics: organic and hybrid materials

Programmed molecular assemblies with molecular-level precision have always intrigued mankind in the quest to master the art of molecular engineering. In this regard, our review seeks to highlight the state of the art in supramolecular engineering. Herein we describe two-dimensional (2D) nanoarchitectonics of organic and organic-inorganic based hybrid materials. Molecular systems ranging from simpler hydrogen bonding driven bis-acylurea and cyclic dipeptide derivatives to complex peptoids, arylenes, cucurbiturils, biphenyls, organosilicons and organometallics, which involve a delicate interplay of multiple noncovalent interactions are discussed. These specifically chosen examples illustrate the molecular design principles and synthetic protocols to realize 2D nanosheets. The description also emphasizes the wide variety of functional properties and technological implications of these 2D nanomaterials besides an outlook for future progress.

S-layer fusion proteins--construction principles and applications

Crystalline bacterial cell surface layers (S-layers) are the outermost cell envelope component of many bacteria and archaea. S-layers are monomolecular arrays composed of a single protein or glycoprotein species and represent the simplest biological membrane developed during evolution. The wealth of information available on the structure, chemistry, genetics and assembly of S-layers revealed a broad spectrum of applications in nanobiotechnology and biomimetics. By genetic engineering techniques, specific functional domains can be incorporated in S-layer proteins while maintaining the self-assembly capability. These techniques have led to new types of affinity structures, microcarriers, enzyme membranes, diagnostic devices, biosensors, vaccines, as well as targeting, delivery and encapsulation systems.

Multitechnique study on a recombinantly produced Bacillus halodurans laccase and an S-layer/laccase fusion protein

Methods for organizing functional materials at the nanometer scale are essential for the development of novel fabrication techniques. One of the most relevant areas of research in nanobiotechnology concerns technological utilization of self-assembly systems, wherein molecules spontaneously associate into reproducible supramolecular structures. For this purpose, the laccase of Bacillus halodurans C-125 was immobilized on the S-layer lattice formed by SbpA of Lysinibacillus sphaericus CCM 2177 either by (i) covalent linkage of the enzyme to the natural protein self-assembly system or (ii) by construction of a fusion protein comprising the S-layer protein and the laccase. The laccase and the S-layer fusion protein were produced heterologously in Escherichia coli. After isolation and purification, the properties of the proteins, as well as the specific activity of the enzyme moiety, were investigated. Interestingly, the S-layer part confers a much higher solubility on the laccase as observed for the sole enzyme. Comparative spectrophotometric measurements of the enzyme activity revealed similar but significantly higher values for rLac and rSbpA/Lac in solution compared to the immobilized state. However, rLac covalently linked to the SbpA monolayer yielded a four to five time higher enzymatic activity than rSbpA/Lac immobilized on a solid support. Combined quartz crystal microbalance with dissipation monitoring (QCM-D) and electrochemical measurements (performed in an electrochemical QCM-D cell) revealed that rLac immobilized on the SbpA lattice had an approximately twofold higher enzymatic activity compared to that obtained with the fusion protein.

Rationally engineering natural protein assemblies in nanobiotechnology

Multimeric protein assemblies are essential components in viruses, bacteria, eukaryotic cells, and organisms where they act as cytoskeletal scaffold, storage containers, or for directional transport. The bottom-up structures can be exploited in nanobiotechnology by harnessing their built-in properties and combining them with new functional modules. This review summarizes the design principles of natural protein assemblies, highlights recent progress in their structural elucidation, and shows how rational engineering can create new biomaterials for applications in vaccine development, biocatalysis, materials science, and synthetic biology.

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: from protein structure to nanodisk assemblies

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

Nanobiotechnology with S-layer proteins as building blocks

One of the key challenges in nanobiotechnology is the utilization of self- assembly systems, wherein molecules spontaneously associate into reproducible aggregates and supramolecular structures. In this contribution, we describe the basic principles of crystalline bacterial surface layers (S-layers) and their use as patterning elements. The broad application potential of S-layers in nanobiotechnology is based on the specific intrinsic features of the monomolecular arrays composed of identical protein or glycoprotein subunits. Most important, physicochemical properties and functional groups on the protein lattice are arranged in well-defined positions and orientations. Many applications of S-layers depend on the capability of isolated subunits to recrystallize into monomolecular arrays in suspension or on suitable surfaces (e.g., polymers, metals, silicon wafers) or interfaces (e.g., lipid films, liposomes, emulsomes). S-layers also represent a unique structural basis and patterning element for generating more complex supramolecular structures involving all major classes of biological molecules (e.g., proteins, lipids, glycans, nucleic acids, or combinations of these). Thus, S-layers fulfill key requirements as building blocks for the production of new supramolecular materials and nanoscale devices as required in molecular nanotechnology, nanobiotechnology, biomimetics, and synthetic biology.

Fluorescence energy transfer in the bi-fluorescent S-layer tandem fusion protein ECFP-SgsE-YFP

This work reports for the first time on the fabrication of a bi-functional S-layer tandem fusion protein which is able to self-assemble on solid supports without losing its functionality. Two variants of the green fluorescent protein (GFP) were genetically combined with a self-assembly system having the remarkable opportunity to interact with each other and act as functional nanopatterning biocoating. The S-layer protein SgsE of Geobacillus stearothermophilus NRS 2004/3a was fused with the cyan ECFP donor protein at the SgsE N-terminus and with the yellow YFP acceptor protein at the C-terminus. The fluorescence energy transfer was studied with spectrofluorimetry, confocal microscopy and flow cytometry, whilst protein self-assembly (on silicon dioxide particles) and structural investigations were carried out with atomic force microscopy (AFM). The fluorescence resonance energy transfer efficiency of reassembled SgsE tandem protein was 20.0 ± 6.1% which is almost the same transfer efficiency shown in solution (19.6 ± 0.1%). This work shows that bi-fluorescent S-layer fusion proteins self-assemble on silica particles retaining their fluorescent properties.

Absorption, steady-state fluorescence, fluorescence lifetime, and 2D self-assembly properties of engineered fluorescent S-layer fusion proteins of Geobacillus stearothermophilus NRS 2004/3a

S-layer fusion protein technology was used to design four different fluorescent fusion proteins with three different GFP mutants and the red fluorescent protein mRFP1. Their absorption spectra, steady-state fluorescence, and fluorescence lifetime were investigated as a function of pH. It was found that fluorescence intensities and lifetime of the GFP mutant S-layer fusion proteins decreased about 50% between pH 6 and pH 5. The spectral properties of the red S-layer fusion protein were minimally affected by pH variations. These results were compared with His-tagged reference fluorescent proteins, demonstrating that the S-layer protein did not change the general spectral properties of the whole fusion protein. In addition, the pK(a) values of the fluorescent S-layer fusion proteins were calculated. Finally, it was shown that the S-layer fusion proteins were able to self-assemble forming 2D nanostructures of oblique p2 symmetry with lattice parameters of about a = 11 nm, b = 14 nm, and gamma = 80 degrees . The fluorescence tag did not hinder the natural self-assembly process of the S-layer protein. The combination of the fluorescence properties and the self-assembly ability of the engineered fusion proteins make them a promising tool to generate biomimetic surfaces for future applications in nanobiotechnology at a wide range of pH.

Carrier-free immobilized enzymes for biocatalysis

Methods for the preparation of carrier-free insoluble enzymes are reviewed. The technology of cross-linked enzyme aggregates has now been applied to a range of synthetically useful activities. Fusion proteins are also gaining momentum because they allow a relatively selective aggregation or even a specific self-assembly of the desired enzyme activity into insoluble particles in the absence of potentially denaturing chemicals required for precipitation and cross-linking. Recycling of insoluble protein particles for multiple rounds of batchwise reaction has been demonstrated in selected biotransformations. However, for application in a fully continuous biocatalytic process, low resistance to mechanical stress and high compressibility are issues for consideration on carrier-free enzyme particles.

Membrane proteins in nanotechnology

Integral membrane proteins are important biological macromolecules with structural features and functionalities that make them attractive targets for nanotechnology. I provide here a broad review of current activity in nanotechnology related to membrane proteins, including their application as nanoscale sensors, switches, components of optical devices and as templates for self-assembled arrays.

Enzymatically active fibrils generated by the self-assembly of the ApoA-I fibrillogenic domain functionalized with a catalytic moiety

Enzymatically active fibrils were produced by self-assembly of a bifunctional chimeric protein, made up of a fibrillogenic and a catalytic moiety. For this purpose, the fibrillogenic domain of Apolipoprotein A-I (ApoA-I), a 93-residue polypeptide named [1-93]ApoA-I, was functionalized with the enzyme glutathione S-transferase (GST). The fusion protein GST-[1-93]ApoA-I was expressed, isolated to homogeneity and characterized. In the soluble form, GST-[1-93]ApoA-I was found to be fully active as a GST enzyme, and to have high propensity to self-aggregate. Upon incubation for 3 weeks at pH 6.4, insoluble aggregates were generated. Analyzed by AFM, they were found to contain fibrillar structures often organized into large fiber networks. Fibrils were loaded on the membrane of a microfiltration unit and tested for enzymatic activity by filtering the substrate through the fibrillar network. Fibrils were shown to be catalytically active, stable over time and reusable, as no loss of activity was detected when fibrils were repeatedly tested. Our findings suggest that catalytically active fibrils may be of interest for biocatalytic applications in nanobiotechnology.

Recombinant glycans on an S-layer self-assembly protein: a new dimension for nanopatterned biomaterials

Crucial biological phenomena are mediated through carbohydrates that are displayed in a defined manner and interact with molecular scale precision. We lay the groundwork for the integration of recombinant carbohydrates into a "biomolecular construction kit" for the design of new biomaterials, by utilizing the self-assembly system of the crystalline cell surface (S)-layer protein SgsE of Geobacillus stearothermophilus NRS 2004/3a. SgsE is a naturally O-glycosylated protein, with intrinsic properties that allow it to function as a nanopatterned matrix for the periodic display of glycans. By using a combined carbohydrate/protein engineering approach, two types of S-layer neoglycoproteins are produced in Escherichia coli. Based on the identification of a suitable periplasmic targeting system for the SgsE self-assembly protein as a cellular prerequisite for protein glycosylation, and on engineering of one of the natural protein O-glycosylation sites into a target for N-glycosylation, the heptasaccharide from the AcrA protein of Campylobacter jejuni and the O7 polysaccharide of E. coli are co- or post-translationally transferred to the S-layer protein by the action of the oligosaccharyltransferase PglB. The degree of glycosylation of the S-layer neoglycoproteins after purification from the periplasmic fraction reaches completeness. Electron microscopy reveals that recombinant glycosylation is fully compatible with the S-layer protein self-assembly system. Tailor-made ("functional") nanopatterned, self-assembling neoglycoproteins may open up new strategies for influencing and controlling complex biological systems with potential applications in the areas of biomimetics, drug targeting, vaccine design, or diagnostics.

Molecular basis of S-layer glycoprotein glycan biosynthesis in Geobacillus stearothermophilus

The Gram-positive bacterium Geobacillus stearothermophilus NRS 2004/3a possesses a cell wall containing an oblique surface layer (S-layer) composed of glycoprotein subunits. O-Glycans with the structure [-->2)-alpha-L-Rhap-(1-->3)-beta-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->](n) (= 13-18), a2-O-methyl group capping the terminal repeating unit at the nonreducing end and a -->2)-alpha-L-Rhap-[(1-->3)-alpha-L-Rhap](n) (= 1-2)(1-->3)- adaptor are linked via a beta-D-Galp residue to distinct sites of the S-layer protein SgsE. S-layer glycan biosynthesis is encoded by a polycistronic slg (surface layer glycosylation) gene cluster. Four assigned glycosyltransferases named WsaC-WsaF, were investigated by a combined biochemical and NMR approach, starting from synthetic octyl-linked saccharide precursors. We demonstrate that three of the enzymes are rhamnosyltransferases that are responsible for the transfer of L-rhamnose from a dTDP-beta-L-Rha precursor to the nascent S-layer glycan, catalyzing the formation of the alpha1,3- (WsaC and WsaD) and beta1,2-linkages (WsaF) present in the adaptor saccharide and in the repeating units of the mature S-layer glycan, respectively. These enzymes work in concert with a multifunctional methylrhamnosyltransferase (WsaE). The N-terminal portion of WsaE is responsible for the S-adenosylmethionine-dependent methylation reaction of the terminal alpha1,3-linked L-rhamnose residue, and the central and C-terminal portions are involved in the transfer of L-rhamnose from dTDP-beta-L-rhamnose to the adaptor saccharide to form the alpha1,2- and alpha1,3-linkages during S-layer glycan chain elongation, with the methylation and the glycosylation reactions occurring independently. Characterization of these enzymes thus reveals the complete molecular basis for S-layer glycan biosynthesis.

S-layer nanoglycobiology of bacteria

Cell surface layers (S-layers) are common structures of the bacterial cell envelope with a lattice-like appearance that are formed by a self-assembly process. Frequently, the constituting S-layer proteins are modified with covalently linked glycan chains facing the extracellular environment. S-layer glycoproteins from organisms of the Bacillaceae family possess long, O-glycosidically linked glycans that are composed of a great variety of sugar constituents. The observed variations already exceed the display found in eukaryotic glycoproteins. Recent investigations of the S-layer protein glycosylation process at the molecular level, which has lagged behind the structural studies due to the lack of suitable molecular tools, indicated that the S-layer glycoprotein glycan biosynthesis pathway utilizes different modules of the well-known biosynthesis routes of lipopolysaccharide O-antigens. The genetic information for S-layer glycan biosynthesis is usually present in S-layer glycosylation (slg) gene clusters acting in concert with housekeeping genes. To account for the nanometer-scale cell surface display feature of bacterial S-layer glycosylation, we have coined the neologism 'nanoglycobiology'. It includes structural and biochemical aspects of S-layer glycans as well as molecular data on the machinery underlying the glycosylation event. A key aspect for the full potency of S-layer nanoglycobiology is the unique self-assembly feature of the S-layer protein matrix. Being aware that in many cases the glycan structures associated with a protein are the key to protein function, S-layer protein glycosylation will add a new and valuable component to an 'S-layer based molecular construction kit'. In our long-term research strategy, S-layer nanoglycobiology shall converge with other functional glycosylation systems to produce 'functional' S-layer neoglycoproteins for diverse applications in the fields of nanobiotechnology and vaccine technology. Recent advances in the field of S-layer nanoglycobiology have made our overall strategy a tangible aim of the near future.

The surface location of individual residues in a bacterial S-layer protein

Bacterial surface layer (S-layer) proteins self-assemble into large two-dimensional crystalline lattices that form the outermost cell-wall component of all archaea and many eubacteria. Despite being a large class of self-assembling proteins, little is known about their molecular architecture. We investigated the S-layer protein SbsB from Geobacillus stearothermophilus PV72/p2 to identify residues located at the subunit-subunit interface and to determine the S-layer's topology. Twenty-three single cysteine mutants, which were previously mapped to the surface of the SbsB monomer, were subjected to a cross-linking screen using the photoactivatable, sulfhydryl-reactive reagent N-[4-(p-azidosalicylamido)butyl]-3'-(2'-pyridyldithio)propionamide. Gel electrophoretic analysis on the formation of cross-linked dimers indicated that 8 out of the 23 residues were located at the interface. In combination with surface accessibility data for the assembled protein, 10 residues were assigned to positions at the inner, cell-wall-facing lattice surface, while 5 residues were mapped to the outer, ambient-exposed lattice surface. In addition, the cross-linking screen identified six positions of intramolecular cross-linking within the assembled protein but not in the monomeric S-layer protein. Most likely, these intramolecular cross-links result from conformational changes upon self-assembly. The results are an important step toward the further structural elucidation of the S-layer protein via, for example, X-ray crystallography and cryo-electron microscopy. Our approach of identifying the surface location of residues is relevant to other planar supramolecular protein assemblies.

Exploitation of the S-layer self-assembly system for site directed immobilization of enzymes demonstrated for an extremophilic laminarinase from Pyrococcus furiosus

A fusion protein based on the S-layer protein SbpA from Bacillus sphaericus CCM 2177 and the enzyme laminarinase (LamA) from Pyrococcus furiosus was designed and overexpressed in Escherichia coli. Due to the construction principle, the S-layer fusion protein fully retained the self-assembly capability of the S-layer moiety, while the catalytic domain of LamA remained exposed at the outer surface of the formed protein lattice. The enzyme activity of the S-layer fusion protein monolayer obtained upon recrystallization on silicon wafers, glass slides and different types of polymer membranes was determined colorimetrically and related to the activity of sole LamA that has been immobilized with conventional techniques. LamA aligned within the S-layer fusion protein lattice in a periodic and orientated fashion catalyzed twice the glucose release from the laminarin polysaccharide substrate in comparison to the randomly immobilized enzyme. In combination with the good shelf-life and the high resistance towards temperature and diverse chemicals, these novel composites are regarded a promising approach for site-directed enzyme immobilization.