Surface dependence of protein nanocrystal formation

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.

Measuring interactions of DNA with nanoporous protein crystals by atomic force microscopy

Crosslinked porous protein crystals are a new biomaterial that can be engineered to encapsulate, stabilize, and organize guest molecules, nanoparticles, and biological moieties. In this study, for the first time, the combined interactions of DNA strands with porous protein crystals are quantitatively measured by high-resolution atomic force microscopy (AFM) and chemical force microscopy. The surface structure of protein crystals with unusually large pores was observed in liquid via high-resolution AFM. Force-distance (F-D) curves were also obtained using AFM tips modified to present or capture DNA. The modification of AFM tips allowed the tips to covalently bind DNA that was pre-loaded in the protein crystal nanopores. The modified tips enabled the interactions of DNA molecules with protein crystals to be quantitatively studied while revealing the morphology of the buffer-immersed protein crystal surface in detail, thereby preserving the structure and properties of protein crystals that could be disrupted or destroyed by drying. The hexagonal space group was manifest at the crystal surface, as were the strong interactions between DNA and the porous protein crystals in question. In sum, this study furthered our understanding of how a new protein-based biomaterial can be used to bind guest DNA assemblies.

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.

Silane-based self-assembled monolayer deposited on fluorine doped tin oxide as model system for pharmaceutical and biomedical analysis

Recently, self-assembled monolayers (SAMs) are gaining a lot of interest due to their simplicity of preparation and wide applicability in the development of model systems used in pharmaceutical and biomedical analysis. The most efficient methods used for the investigation of SAM-based structures usually include cyclic voltammetry and electrochemical impedance spectroscopy. Scanning electrochemical microscopy (SECM) could be also used as an alternative method for SAM investigations, because this method enables to map modified surface. In this work, the surface of fluorine doped tin oxide (FTO) was modified with octadeciltrichlorosilane (OTS) based SAM and investigated using SECM. Measurements, which were carried out by SECM, lead to conclusion that highly heterogeneous and distributed monolayer has been formed on FTO surface.

Nanotechnology with S-layer Proteins

Nanosciences are distinguished by the cross-fertilization of biology, chemistry, material sciences, and solid-state physics and, hence, open up a great variety of new opportunities for innovation. The technological utilization of self-assembly systems, wherein molecules spontaneously associate under equilibrium conditions into reproducible supramolecular structures, is one key challenge in nanosciences for life and non-life science applications. The attractiveness of such processes is due to their ability to build uniform, ultra-small functional units with predictable properties down to the nanometer scale. Moreover, newly developed techniques and methods open up the possibility to exploit these structures at meso- and macroscopic scale. An immense significance at innovative approaches for the self-assembly of supramolecular structures and devices with dimensions of a few to tens of nanometers constitutes the utilization of crystalline bacterial cell surface proteins. The latter have proven to be particularly suited as building blocks in a molecular construction kit comprising of all major classes of biological molecules. The controlled immobilization of biomolecules in an ordered fashion on solid substrates and their directed confinement in definite areas of nanometer dimensions are key requirements for many applications including the development of bioanalytical sensors, biochips, molecular electronics, biocompatible surfaces, and signal processing between functional membranes, cells, and integrated circuits.

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.

Life under Continuous Streaming: Recrystallization of Low Concentrations of Bacterial SbpA in Dynamic Flow Conditions

The well-known bacterial S-layer protein SbpA from Lysinibacillus sphaericus CCM2177 induces spontaneous crystal formation via cooperative self-assembly of the protein subunits into an ordered supramolecular structure. Recrystallization occurs in the presence of divalent cations (i.e., Ca2+) and finally leads to producing smooth 2-D crystalline coatings composed of squared (p4) lattice structures. Among the factors interfering in such a process, the rate of protein supply certainly plays an important role since a limited number of accessible proteins might turn detrimental for film completion. Studies so far have mostly focused on high SbpA concentrations provided under stopped-flow or dynamic-flow conditions, thus omitting the possibility of investigating intermediate states, in which dynamic flow is applied for more critical concentrations of SbpA (i.e., 25, 10, and 5 µg/mL). In this work, we have characterized both physico-chemical and topographical aspects of the assembly and recrystallization of SbpA protein in such low concentration conditions by means of in situ Quartz Crystal Microbalance with Dissipation (QCMD) and atomic force microscopy (AFM) measurements, respectively. On the basis of these experiments, we can confirm how the application of a dynamic flow influences the formation of a closed and crystalline protein film from low protein concentrations (i.e., 10 µg/mL), which otherwise would not be formed.

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.

Cation-chelation and pH induced controlled switching of the non-fouling properties of bacterial crystalline films

We report the controlled loss of the anti-fouling activity of the S-layer protein SbpA from Lysinibacillus sphaericus (CCM2177). This protein forms crystal-like films with square lattice (p4) via self-assembly on almost any type of surfaces. Such engineered bioinspired nanometric membranes are known by their excellent preventive performance under biological conditions. However, their exposure to certain treatments can lead to gradual degradation of the S-protein layer. In this work, two distinctive approaches are studied for understanding either specific or non-specific degradation of the film, by treatment with a chelating agent (EDTA), which interacts with inner Ca²⁺ ions, or Citrate buffer (with pH<pI), respectively. Subsequently, the degraded protein films have been tested upon binding of polyelectrolytes of different charge and endothelial HUVEC cells, and their performance compared to that of intact S-layers. The SbpA protein layer degradation process as well as its impact on the loss of anti-fouling properties have been characterized, in terms of mass and structural changes, by means of real time quartz crystal microbalance with dissipation (QCM-D) monitoring, atomic force microscopy (AFM) experiments, and fluorescence microscopy. The results show that overall structure degradation (citrate buffer) has a higher impact on the loss of antifouling properties than selective removal of divalent cations. Thus, crystal structure integrity is a necessary condition for bacterial antifouling properties.

In Vitro Characterization of the Two-Stage Non-Classical Reassembly Pathway of S-Layers

The recombinant bacterial surface layer (S-layer) protein rSbpA of Lysinibacillus sphaericus CCM 2177 is an ideal model system to study non-classical nucleation and growth of protein crystals at surfaces since the recrystallization process may be separated into two distinct steps: (i) adsorption of S-layer protein monomers on silicon surfaces is completed within 5 min and the amount of bound S-layer protein sufficient for the subsequent formation of a closed crystalline monolayer; (ii) the recrystallization process is triggered—after washing away the unbound S-layer protein—by the addition of a CaCl₂ containing buffer solution, and completed after approximately 2 h. The entire self-assembly process including the formation of amorphous clusters, the subsequent transformation into crystalline monomolecular arrays, and finally crystal growth into extended lattices was investigated by quartz crystal microbalance with dissipation (QCM-D) and atomic force microscopy (AFM). Moreover, contact angle measurements showed that the surface properties of S-layers change from hydrophilic to hydrophobic as the crystallization proceeds. This two-step approach is new in basic and application driven S-layer research and, most likely, will have advantages for functionalizing surfaces (e.g., by spray-coating) with tailor-made biological sensing layers.

Impact of surface wettability on S-layer recrystallization: a real-time characterization by QCM-D

Quartz crystal microbalance with dissipation monitoring (QCM-D) has been employed to study the assembly and recrystallization kinetics of isolated SbpA bacterial surface proteins onto silicon dioxide substrates of different surface wettability. Surface modification by UV/ozone oxidation or by vapor deposition of 1H,1H,2H,2H-perfluorododecyltrichlorosilane yielded hydrophilic or hydrophobic samples, respectively. Time evolution of frequency and dissipation factors, either individually or combined as the so-called Df plots, showed a much faster formation of crystalline coatings for hydrophobic samples, characterized by a phase-transition peak at around the 70% of the total mass adsorbed. This behavior has been proven to mimic, both in terms of kinetics and film assembly steps, the recrystallization taking place on an underlying secondary cell-wall polymer (SCWP) as found in bacteria. Complementary atomic force microscopy (AFM) experiments corroborate these findings and reveal the impact on the final structure achieved.

Truncation Derivatives of the S-Layer Protein of Sporosarcina ureae ATCC 13881 (SslA): Towards Elucidation of the Protein Domain Responsible for Self-Assembly

The cell surface of Sporosarcina ureae ATCC 13881 is covered by an S-layer (SslA) consisting of identical protein subunits that assemble into lattices exhibiting square symmetry. In this work the self-assembly properties of the recombinant SslA were characterised with an emphasis on the identification of protein regions responsible for self-assembly. To this end, recombinant mature SslA (aa 31-1097) and three SslA truncation derivatives (one N-terminal, one C-terminal and one CN-terminal) were produced in a heterologous expression system, isolated, purified and their properties analysed by in vitro recrystallisation experiments on a functionalised silicon wafer. As a result, recombinant mature SslA self-assembled into crystalline monolayers with lattices resembling the one of the wild-type SslA. The study identifies the central protein domain consisting of amino acids 341-925 self-sufficient for self-assembly. Neither the first 341 amino acids nor the last 172 amino acids of the protein sequence are required to self-assemble into lattices.

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.

The dynamics and energetics of matrix assembly and mineralization

Formation of biominerals commonly occurs within the context of an organic matrix composed of proteins, polysaccharides, and other macromolecules. Much has been learned about the structure of matrices and the spatial and molecular relationships between matrix and mineral. Only recently has quantitative study of matrix organization and subsequent mineralization been pursued. Here, we review findings from physical studies of matrix assembly in the system of microbial S-layer proteins and of calcium carbonate nucleation on organic templates composed of organothiol self-assembled monolayers on noble metals. Studies on S-layers reveal the importance of multistage assembly pathways and kinetic traps associated with the conformational transformations required to build the basic oligomeric building blocks of the matrix. Experimental investigations of calcium carbonate nucleation on carboxyl-terminated self-assembled monolayers combined with theoretical analyses demonstrate the applicability of classical concepts of nucleation, even when cluster-aggregation pathways are considered, and reveal the underlying energetic and structural source of matrix control over the process. Taken together, these studies highlight the ways in which matrix assembly and mineralization deviate from our classical concepts of crystallization but clearly demonstrate that the concepts of physical chemistry that date back to the days of Gibbs and Ostwald still serve us well in understanding the nucleation and growth of organic matrices and mineral phases.

S-layer protein self-assembly

Crystalline S(urface)-layers are the most commonly observed cell surface structures in prokaryotic organisms (bacteria and archaea). S-layers are highly porous protein meshworks with unit cell sizes in the range of 3 to 30 nm, and thicknesses of ~10 nm. One of the key features of S-layer proteins is their intrinsic capability to form self-assembled mono- or double layers in solution, and at interfaces. Basic research on S-layer proteins laid foundation to make use of the unique self-assembly properties of native and, in particular, genetically functionalized S-layer protein lattices, in a broad range of applications in the life and non-life sciences. This contribution briefly summarizes the knowledge about structure, genetics, chemistry, morphogenesis, and function of S-layer proteins and pays particular attention to the self-assembly in solution, and at differently functionalized solid supports.

Nanotechnology with s-layer proteins

Nanosciences are distinguished by the cross-fertilization of biology, chemistry, material sciences, and solid-state physics and hence open up a great variety of new opportunities for innovation. The technological utilization of self-assembly systems, wherein molecules spontaneously associate under equilibrium conditions into reproducible supramolecular aggregates, is one key challenge in nanosciences for life and nonlife science applications. The attractiveness of such processes is due to their ability to build uniform, ultrasmall functional units and the possibility to exploit such structures at meso- and macroscopic scale very frequently by newly developed techniques and methods. By the utilization of crystalline bacterial cell-surface proteins (S-layer proteins) innovative approaches for the assembly of supramolecular structures and devices with dimensions of a few to tens of nanometers have been developed. S-layers have proven to be particularly suited as building blocks in a molecular construction kit involving all major classes of biological molecules. The controlled immobilization of biomolecules in an ordered fashion on solid substrates and their controlled confinement in definite areas of nanometer dimensions are key requirements for many applications including the development of bioanalytical sensors, biochips, molecular electronics, biocompatible surfaces, and signal processing between functional membranes, cells, and integrated circuits.

Layer thickness of hydrophobin films leads to oscillation in wettability

In nanobiotechnology, the properties of surfaces are often key to sensor applications. If analytes possess a low tolerance or affinity regarding the sensory substrate (surface), then the setup of mediators may be indicated. Hydrophobins enable biocompatible surface functionalization without significant restrictions of the physicochemical substrate properties. Because of the imperfect formation of hydrophobin films, a high variation in surface properties is observed. In this study, we report on the relation between the film thickness of hydrophobin-coated solid surfaces and their wettability. We found that the wettability of protein-coated surfaces strictly depends on the amount of adsorbed protein, as reflected in an oscillation of the contact angles of hydrophobin-coated silicon wafers. Fusion proteins of Ccg2 and HFBI, representatives of class I and II hydrophobins, document the influence of fused peptide tags on the wettability. The orientation of the first crystal nuclei plays a decisive role in the formation of the growing hydrophobin layers. Here, a simple method of deducing the film thickness of hydrophobin assemblies on solid surfaces is presented. The determination of the static contact angle allows the prediction of which part of the protein is exposed to possible analytes.

Influence of surface chemistry and protein concentration on the adsorption rate and S-layer crystal formation

Bacterial crystalline surface layers (S-layers) are the outermost envelope of prokaryotic organisms representing the simplest biological membranes developed during evolution. In this context, the bacterial protein SbpA has already shown its intrinsic ability to reassemble on different substrates forming protein crystals of square lattice symmetry. In this work, we present the interaction between the bacterial protein SbpA and five self-assembled monolayers carrying methyl (CH(3)), hydroxyl (OH), carboxylic acid (COOH) and mannose (C(6)H(12)O(6)) as functional groups. Protein adsorption and S-layer formation have been characterized by atomic force microscopy (AFM) while protein adsorption kinetics, mass uptake and the protein layer viscoelastic properties were investigated with quartz crystal microbalance with dissipation monitoring (QCM-D). The results indicate that the protein adsorption rate and crystalline domain area depend on surface chemistry and protein concentration. Furthermore, electrostatic interactions tune different protein rate adsorption and S-layer recrystallization pathways. Electrostatic interactions induce faster adsorption rate than hydrophobic or hydrophilic interactions. Finally, the shear modulus and the viscosity of the recrystallized S-layer on CH(3)C(6)S, CH(3)C(11)S and COOHC(11)S substrates were calculated from QCM-D measurements. Protein-protein interactions seem to play a main role in the mechanical stability of the formed protein (crystal) bilayer.

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.