Thermal stability, mechanical properties and content of bacterial protein layers recrystallized on polyelectrolyte multilayers

Quantifying the Extent of Hydration of a Surface-Bound Peptide Using Neutron Reflectometry

Establishing how water, or the absence of water, affects the structure, dynamics, and function of proteins in contact with inorganic surfaces is critical to developing successful protein immobilization strategies. In the present article, the quantity of water hydrating a monolayer of helical peptides covalently attached to self-assembled monolayers (SAMs) of alkyl thiols on Au was measured using neutron reflectometry (NR). The peptide sequence was composed of repeating LLKK units in which the leucines were aligned to face the SAM. When immersed in water, NR measured 2.7 ± 0.9 water molecules per thiol in the SAM layer and between 75 ± 13 and 111 ± 13 waters around each peptide. The quantity of water in the SAM was nearly twice that measured prior to peptide functionalization, suggesting that the peptide disrupted the structure of the SAM. To identify the location of water molecules around the peptide, we compared our NR data to previously published molecular dynamics simulations of the same peptide on a hydrophobic SAM in water, revealing that 49 ± 5 of 95 ± 8 total nearby water molecules were directly hydrogen-bound to the peptide. Finally, we show that immersing the peptide in water compressed its structure into the SAM surface. Together, these results demonstrate that there is sufficient water to fully hydrate a surface-bound peptide even at hydrophobic interfaces. Given the critical role that water plays in biomolecular structure and function, these results are expected to be informative for a broad array of applications involving proteins at the bio/abio interface.

X-ray and Neutron Reflectometry of Thin Films at Liquid Interfaces

In the 1980s, Helmuth Möhwald studied lipid monolayers at the air/water interface to understand the thermodynamically characterized phases at the molecular level. In collaboration with Jens Als-Nielsen, X-ray reflectometry was used and further developed to determine the electron density profile perpendicular to the water surface. Using a slab model, parameters such as thickness and density of the individual molecular regions, as well as the roughness of the individual interfaces, were determined. Later, X-ray and neutron reflectometry helped to understand the coverage and conformation of anchored and adsorbed polymers. Nowadays, they resolve molecular properties in emerging topics such as liquid metals and ionic liquids. Much is still to be learned about buried interfaces (e.g., liquid/liquid interfaces). In this Article, a historical and theoretical background of X-ray reflectivity is given, recent developments of X-ray and neutron reflectometry for polymers at interfaces and thin layers are highlighted, and emerging research topics involving these techniques are emphasized.

Lysine residues control the conformational dynamics of beta 2-glycoprotein I

One of the major problems in the study of the dynamics of proteins is the visualization of changing conformations that are important for processes ranging from enzyme catalysis to signaling. A protein exhibiting conformational dynamics is the soluble blood protein beta 2-glycoprotein I (beta2GPI), which exists in two conformations: the closed (circular) form and the open (linear) form. It is hypothesized that an increased proportion of the open conformation leads to the autoimmune disease antiphospholipid syndrome (APS). A characteristic feature of beta2GPI is the high content of lysine residues. However, the potential role of lysine in the conformational dynamics of beta2GPI has been poorly investigated. Here, we report on a strategy to permanently open up the closed protein conformation by chemical acetylation of lysine residues using acetic acid N-hydroxysuccinimide ester (NHS-Ac). Specific and complete acetylation was demonstrated by the quantification of primary amino groups with fluoraldehyde o-phthalaldehyde (OPA) reagent, as well as western blot analysis with an anti-acetylated lysine antibody. Our results demonstrate that acetylated beta2GPI preserves its secondary and tertiary structures, as shown by circular dichroism spectroscopy. We found that after lysine acetylation, the majority of proteins are in the open conformation as revealed by atomic force microscopy high-resolution images. Using this strategy, we proved that the electrostatic interaction of lysine residues plays a major role in stabilizing the beta2GPI closed conformation, as confirmed by lysine charge distribution calculations. We foresee that our approach will be applied to other lysine-rich proteins (e.g. histones) undergoing conformational transitions. For instance, conformational dynamics can be triggered by environmental conditions (e.g. pH, ion concentration, post-translational modifications, and binding of ligands). Therefore, our study may be relevant for investigating the equilibrium of protein conformations causing diseases.

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.

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.

Effect of the Concentration of Cytolytic Protein Cyt2Aa2 on the Binding Mechanism on Lipid Bilayers Studied by QCM-D and AFM

Bacillus thuringiensis is known by its insecticidal property. The insecticidal proteins are produced at different growth stages, including the cytolytic protein (Cyt2Aa2), which is a bioinsecticide and an antimicrobial protein. However, the binding mechanism (and the interaction) of Cyt2Aa2 on lipid bilayers is still unclear. In this work, we have used quartz crystal microbalance with dissipation (QCM-D) and atomic force microscopy (AFM) to investigate the interaction between Cyt2Aa2 protein and (cholesterol-)lipid bilayers. We have found that the binding mechanism is concentration dependent. While at 10 μg/mL, Cyt2Aa2 binds slowly on the lipid bilayer forming a compliance protein/lipid layer with aggregates, at higher protein concentrations (100 μg/mL), the binding is fast, and the protein/lipid layer is more rigid including holes (of about a lipid bilayer thickness) in its structure. Our study suggests that the protein/lipid bilayer binding mechanism seems to be carpet-like at low protein concentrations and pore forming-like at high protein concentrations.

Recrystallized S-layer protein of a probiotic Propionibacterium: structural and nanomechanical changes upon temperature or pH shifts probed by solid-state NMR and AFM

Surface protein layers (S layers) are common constituents of the bacterial cell wall and originate from the assembly of strain-dependent surface layer proteins (Slps). These proteins are thought to play important roles in the bacteria's biology and to have very promising technological applications as biomaterials or as part of cell-host cross-talk in probiotic mechanism. The SlpA from Propionibacterium freudenreichii PFCIRM 118 strain was isolated and recrystallized to investigate organization and assembly of the protein using atomic force microscopy and solid-state (1)H and (13)C-nuclear magnetic resonance. SlpA was found to form hexagonal p1 monolayer lattices where the protein exhibited high proportions of disordered regions and of bound water. The lattice structure was maintained, but softened, upon mild heating or acidification, probably in relation with the increasing mobilities of the disordered protein regions. These results gave structural insights on the mobile protein regions exposed by S layer films, upon physiologically relevant changes of their environmental conditions.

Reassembly of S-layer proteins

Crystalline bacterial cell surface layers (S-layers) represent the outermost cell envelope component in a broad range of bacteria and archaea. They are monomolecular arrays composed of a single protein or glycoprotein species and represent the simplest biological membranes developed during evolution. They are highly porous protein mesh works with unit cell sizes in the range of 3 to 30 nm, and pore sizes of 2 to 8 nm. S-layers are usually 5 to 20 nm thick (in archaea, up to 70 nm). S-layer proteins are one of the most abundant biopolymers on earth. One of their key features, and the focus of this review, is the intrinsic capability of isolated native and recombinant S-layer proteins to form self-assembled mono- or double layers in suspension, at solid supports, the air-water interface, planar lipid films, liposomes, nanocapsules, and nanoparticles. The reassembly is entropy-driven and a fascinating example of matrix assembly following a multistage, non-classical pathway in which the process of S-layer protein folding is directly linked with assembly into extended clusters. Moreover, basic research on the structure, synthesis, genetics, assembly, and function of S-layer proteins laid the foundation for their application in novel approaches in biotechnology, biomimetics, synthetic biology, and nanotechnology.

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.

Construction of silica-enhanced S-layer protein cages

The work presented here shows for the first time that it is possible to silicify S-layer coated liposomes and to obtain stable functionalized hollow nano-containers. For this purpose, the S-layer protein of Geobacillus stearothermophilus PV72/p2 was recombinantly expressed and used for coating positively charged liposomes composed of dipalmitoylphosphatidylcholine, cholesterol and hexadecylamine in a molar ratio of 10:5:4. Subsequently, plain (uncoated) liposomes and S-layer coated liposomes were silicified. Determination of the charge of the constructs during silicification allowed the deposition process to be followed. After the particles had been silicified, lipids were dissolved by treatment with Triton X-100 with the release of previously entrapped fluorescent dyes being determined by fluorimetry. Both, ζ-potential and release experiments showed differences between silicified plain liposomes and silicified S-layer coated liposomes. The results of the individual preparation steps were examined by embedding the respective assemblies in resin, ultrathin sectioning and inspection by bright-field transmission electron microscopy (TEM). Energy filtered TEM confirmed the successful construction of S-layer based silica cages. It is anticipated that this approach will provide a key to enabling technology for the fabrication of nanoporous protein cages for applications ranging from nano medicine to materials science.

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.

Multidimensional Assembly of S-Layer Proteins on Mobility-Controlled Polyelectrolyte Multilayers

Polyelectrolyte multilayers have been vastly utilized as an assembling platform for various biomaterials because of their soft and charged surface characteristics, analogous to biomembrane systems. In particular, polyelectrolyte chains with high self-diffusivity can effectively transfer the surface mobility to the assembling biomolecular species, facilitating the ordered self-assembly. Herein, highly diffusional cationic polyelectrolyte chains of linear polyethylenimine are employed to induce direct binding with negatively charged bacterial surface layer proteins, which eventually lead to large-scale two-dimensional crystals. Notably, at the elevated incubation temperature, a transitory intermediate of one-dimensional chain structure is observed. We reveal that this one-dimensional intermediate is a stable precursor toward two-dimensional crystal arrays.

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.

Atomistic structure of monomolecular surface layer self-assemblies: toward functionalized nanostructures

The concept of self-assembly is one of the most promising strategies for the creation of defined nanostructures and therefore became an essential part of nanotechnology for the controlled bottom-up design of nanoscale structures. Surface layers (S-layers), which represent the cell envelope of a great variety of prokaryotic cells, show outstanding self-assembly features in vitro and have been successfully used as the basic matrix for molecular construction kits. Here we present the three-dimensional structure of an S-layer lattice based on tetrameric unit cells, which will help to facilitate the directed binding of various molecules on the S-layer lattice, thereby creating functional nanoarrays for applications in nanobiotechnology. Our work demonstrates the successful combination of computer simulations, electron microscopy (TEM), and small-angle X-ray scattering (SAXS) as a tool for the investigation of the structure of self-assembling or aggregating proteins, which cannot be determined by X-ray crystallography. To the best of our knowledge, this is the first structural model at an amino acid level of an S-layer unit cell that exhibits p4 lattice symmetry.

Surface dependence of protein nanocrystal formation

The self-assembly kinetics and nanocrystal formation of the bacterial surface-layer-protein SbpA are studied with a combination of quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM). Silane coupling agents, aminopropyltriethoxysilane (APTS) and octadecyltrichlorosilane (OTS), are used to vary the protein-surface interaction in order to induce new recrystallization pathways. The results show that the final S-layer crystal lattice parameters (a = b = 14 nm, gamma = 90 degrees ), the layer thickness (15 nm), and the adsorbed mass density (1700 ng cm(-2)) are independent of the surface chemistry. Nevertheless, the adsorption rate is five times faster on APTS and OTS than on SiO(2,) strongly affecting protein nucleation and growth. As a consequence, protein crystalline domains of 0.02 microm(2) for APTS and 0.05 microm(2) for OTS are formed, while for silicon dioxide the protein domains have a typical size of about 32 microm(2). In addition, more-rigid crystalline protein layers are formed on hydrophobic substrates. In situ AFM experiments reveal three different kinetic steps: adsorption, self-assembly, and crystalline-domain reorganization. These steps are corroborated by frequency-dissipation curves. Finally, it is shown that protein adsorption is a diffusion-driven process. Experiments at different protein concentrations demonstrate that protein adsorption saturates at 0.05 mg mL(-1) on silane-coated substrates and at 0.07 mg mL(-1) on hydrophilic silicon dioxide.

S-layer templated bioinspired synthesis of silica

The current understanding of the molecular mechanisms involved in the bioinspired formation of silica structures laid foundation for investigating the potential of the S-layer protein SbpA from Lysinibacillus sphaericus CCM 2177 as catalyst, template and scaffold for the generation of novel silica architectures. SbpA reassembles into monomolecular lattices with square (p4) lattice symmetry and a lattice constant of 13.1 nm. Silica layers on the S-layer lattice were formed using tetramethoxysilane (TMOS) and visualized by transmission electron microscopy. In situ quartz crystal microbalance with dissipation monitoring (QCM-D) measurements showed the adsorption of silica in dependence on the presence of phosphate in the silicate solution and on the preceding chemical modification of the S-layer. An increased amount of precipitated silica could be observed when K2HPO4/KH2PO4 was present in the solution (pH 7.2). Further on, independent of the presence of phosphate the silica deposition was higher on S-layer lattices upon activation of their carboxyl groups with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) compared to native S-layers or EDC treated S-layers when the activated carboxyl groups were blocked with ethylene diamine (EDA). Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectroscopy revealed the formation of an amorphous silica gel (SiO2)x.yH2O on the S-layer. The silica surface concentrations on the S-layer was 4 x 10(-9) to 2 x 10(-8) mol cm(-2) depending on the modification of the protein layer and corresponded to 4-21 monolayers of SiO2.

Biosensing by densely packed and optically coupled plasmonic particle arrays

Densely packed plasmonic particle arrays are investigated for biosensing applications. Such particle arrays exhibit interparticle optical coupling creating a strong field between the particles, which is useful for sensing purposes. The sensor properties, such as bulk sensitivity, layer sensitivity, and the depth of sensitivity are investigated with the aid of a multiple multipole program. Sensitivity to the analyte with low concentration is also examined by a dynamic adsorption processes. The detectable concentration limit of streptavidin within 3000 s in the detection system is expected from the signal-to-noise to be less than 150 pM.