Impact of surface interactions on protein conformation

Single-Particle and Single-Molecule Characterization of Immobilized Enzymes: A Multiscale Path toward Optimizing Heterogeneous Biocatalysts

Heterogeneous biocatalysis is highly relevant in biotechnology as it offers several benefits and practical uses. To leverage the full potential of heterogeneous biocatalysts, the establishment of well-crafted protocols, and a deeper comprehension of enzyme immobilization on solid substrates are essential. These endeavors seek to optimize immobilized biocatalysts, ensuring maximal enzyme performance within confined spaces. For this aim, multidimensional characterization of heterogeneous biocatalysts is required. In this context, spectroscopic and microscopic methodologies conducted at different space and temporal scales can inform about the intraparticle enzyme kinetics, the enzyme spatial distribution, and the mass transport issues. In this Minireview, we identify enzyme immobilization, enzyme catalysis, and enzyme inactivation as the three main processes for which advanced characterization tools unveil fundamental information. Recent advances in operando characterization of immobilized enzymes at the single-particle (SP) and single-molecule (SM) levels inform about their functional properties, unlocking the full potential of heterogeneous biocatalysis toward biotechnological applications.

ToF-SIMS analysis of ultrathin films and their fragmentation patterns

Organic thin films are of great interest due to their intriguing interfacial and functional properties, especially for device applications such as thin-film transistors and sensors. As their thickness approaches single nanometer thickness, characterization and interpretation of the extracted data become increasingly complex. In this study, plasma polymerization is used to construct ultrathin films that range in thickness from 1 to 20 nm, and time-of-flight secondary ion mass spectrometry coupled with principal component analysis is used to investigate the effects of film thickness on the resulting spectra. We demonstrate that for these cross-linked plasma polymers, at these thicknesses, the observed trends are different from those obtained from thicker films with lower degrees of cross-linking: contributions from ambient carbon contamination start to dominate the mass spectrum; cluster-induced nonlinear enhancement in secondary ion yield is no longer observed; extent of fragmentation is higher due to confinement of the primary ion energy; and the size of the primary ion source also affects fragmentation (e.g., Bi1 versus Bi5). These differences illustrate that care must be taken in choosing the correct primary ion source as well as in interpreting the data.

Hemostatic and antibacterial calcium-copper zeolite gauze for infected wound healing

The design and development of wound dressings with excellent procoagulant and antibacterial activity to achieve high wound healing effectiveness are highly desirable in clinical applications. In this work, we develop a calcium-copper zeolite gauze (CaCu-ZG) by a two-step process involving calcium and copper ion exchange in a zeolite gauze. The CaCu-ZG exhibits remarkable procoagulant and antibacterial abilities, as well as good biocompatibility. Compared with the medical gauze, the blood clotting time of CaCu-ZG significantly decreases and the antibacterial activity increases in both in vivo and in vitro experiments. The remarkable ability of wound healing has been verified using a mouse dorsal skin-infected wound model, demonstrating its great potential for wound treatment in clinical applications.

Shish-kebab structure fiber with nano and micro diameter regulate macrophage polarization for anti-inflammatory and bone differentiation

Biopolymer grafts often have limited biocompatibility, triggering excessive inflammatory responses similar to foreign bodies. Macrophage phenotype shifts are pivotal in the inflammatory response and graft success. The effects of the morphology and physical attributes of the material itself on macrophage polarization should be the focus. In this study, we prepared electrospun fibers with diverse diameters and formed a shish-kebab (SK) structure on the material surface by solution-induced crystallization, forming electrospun fiber scaffolds with diverse pore sizes and roughness. In vitro cell culture experiments demonstrated that SK structure fibers could regulate macrophage differentiation toward M2 phenotype, and the results of in vitro simulation of in vivo tissue reconstruction by the microenvironment demonstrated that the paracrine role of M2 phenotype macrophages could promote bone marrow mesenchymal stem cells (BMSCs) to differentiate into osteoblasts. In rats implanted with a subcutaneous SK-structured fiber scaffold, the large-pore size and low-stiffness SK fiber scaffolds demonstrated superior immune performance, less macrophage aggregation, and easier differentiation to the anti-inflammatory M2 phenotype. Large pore sizes and low-stiffness SK fiber scaffolds guide the morphological design of biological scaffolds implanted in vivo, which is expected to be an effective strategy for reducing inflammation when applied to graft materials in clinical settings.

Exploring Enzymatic Conformational Dynamics at Surfaces through μ-FTIR Spectromicroscopy

Immobilization of proteins onto solid supports has critical industrial, technological, and medical applications, and is a daily task in chemical research. Significant conformational rearrangements often occur due to enzyme-surface interactions, and it is of broad interest to develop methods to probe and better understand these molecular-level changes that contribute to the enzyme's catalytic activity and stability. While circular dichroism is a common method for solution-phase conformational study, the application to surface-supported proteins is not trivial and spatial mapping is not viable. On the other hand, a nonlinear laser spectroscopy technique used to analyze surfaces and interfaces is not often found in most laboratories, therefore requiring an alternative and reliable method. Here, we employed high-dimensional data spectromicroscopy analysis in the infrared region (μ-FTIR) to investigate the enzyme's conformational change when adsorbed onto solid matrices, across a ca. 20 mm2 area. Alcohol dehydrogenase (ADH) enzyme was adopted as a model enzyme to interact with CaF2, Au, and Au-thiol model substrates, strategically chosen for mapping the enzyme dynamics on solid surfaces with different polarity/hydrophobicity properties and extendable to other materials. Two-dimensional chemical maps indicate that the enzyme adsorbs with different patterns in which secondary structures dynamically adjust to optimize interprotein and enzyme-surface interactions. The results suggest an experimental approach to identify and map enzyme conformational dynamics onto different solid surfaces across space and provide insights into immobilized protein structure investigations for areas such as biosensing and bioenergy.

Ultrasound-enhanced interfacial adsorption and inactivation of soy trypsin inhibitors

In this study, liquid-liquid interfacial protein adsorption was proposed as a means of inactivating soy trypsin inhibitors (TIs, including Kunitz (KTI) and Bowman-Birk inhibitor (BBI)). Hexane-water was first selected as a model system to compare three emulsification methods (hand shaking, rotor-stator and ultrasound mixing). Ultrasound could generate the smallest and least polydisperse emulsion droplets, resulting in highest interfacial adsorption amount of KTI and BBI as well as the highest inactivation percentage of TIs (p < 0.05). Therefore, ultrasound was selected to further explore the effect of the non-aqueous phase on interfacial adsorption and inactivation kinetics of TIs in a food emulsion system containing vegetable oil (VTO). The adsorption amounts of KTI and BBI in the VTO-aqueous emulsion increased by ∼ 25 % compared to the hexane-aqueous emulsion. In addition, the adsorption amounts of KTI and BBI were rapidly increased as a function of sonication time, especially for the hexane-aqueous emulsion system. This result suggests that such inactivation of TIs could be implemented in continuous systems for large-scale processing. Finally, the pathways of interface-induced inactivation of BBI and KTI were investigated based on separate experiments on individual BBI and KTI systems. The results showed that the interface adsorption caused the changes in the secondary and tertiary structure of KTI that led to its activitation. However, BBI was quite stable at the liquid-liquid interface without significant conformational change. Overall, ultrasound-assisted interfacial adsorption can be considered a rapid and highly efficient method to inactivate KTI.

Effects of the molecular weight of hyaluronan on the conformation and release kinetics of self-assembled 5-fluorouracil-loaded lysozyme-hyaluronan colloidal nanoparticles

Lysozyme (LYS) and hyaluronan with low (HA1: 3 kDa), medium (HA2: 120 kDa), and high (HA3: 1200 kDa) molecular weights were used to fabricate lysozyme-hyaluronan colloidal nanoparticles using a green self-assembly method. Fourier transform infrared spectroscopy indicated that hydrogen bonding, hydrophobic and electrostatic interactions promoted the formation of the colloidal nanoparticles. The hydrophobic area of prepared colloidal nanoparticles was quantified using a pyrene fluorescent probe, and the results showed that the LYS-HA3 nanoparticles had the strongest hydrophobic capacity. Furthermore, 5-fluorouracil (5-Fu) was used to evaluate encapsulation performance, demonstrating that the LYS-HA3 nanoparticles had the highest encapsulation ability (>90 %). All prepared 5-Fu-loaded lysozyme-hyaluronan (5-Fu@LYS-HA) colloidal nanoparticles exhibited excellent long-term storage stability at 4 °C for 60 days. Cellular uptake and in vitro release results indicated that the LYS-HA2 nanoparticles exhibited the highest cellular uptake efficiency, and the LYS-HA3 nanoparticles had the best slow-release effect, while the release process was mainly controlled by the combination of Fickian diffusion and structural relaxation, respectively. This study demonstrates the influence of molecular weight on the conformational and structural properties of colloidal nanoparticles, which has implications for the design of insoluble drug self-assembly systems.

Tuning the surface charge of phospholipid bilayers inhibits insulin fibrilization

The interactions between proteins and materials, in particular lipid bilayers, have been studied extensively for their relevance in diseases and for the formulation of protein-based therapeutics and vaccines. However, the precise rules by which material properties induce favorable or unfavorable structural states in biomolecules are incompletely understood, and as a result, the rational design of materials remains challenging. Here, we investigated the influence of lipid bilayers (in the form of small unilamellar vesicles) on the formation of insulin amyloid fibrils using a fibril-specific assay (thioflavin T), polyacrylamide gel electrophoresis, and circular dichroism spectroscopy. Lipid bilayers composed of equal mixtures of cationic and anionic lipids effectively inhibited fibril formation and stabilized insulin in its native conformation. However, other lipid bilayer compositions failed to inhibit fibril formation or even destabilized insulin, exacerbating fibrilization and/or non-amyloid aggregation. Our findings suggest that electrostatic interactions with lipid bilayers can play a critical role in stabilizing or destabilizing insulin, and preventing the conversion of insulin to its amyloidogenic, disease-associated state.

Aptamer/Hydroxyapatite-Functionalized Titanium Substrate Promotes Implant Osseointegration via Recruiting Mesenchymal Stem Cells

Endowing bone regeneration materials with both stem cell recruitment and osteoinduction properties is a key factor in promoting osseointegration of titanium (Ti) implants. In this study, Apt19s-grafted oxidized hyaluronic acid (OHA) was deposited onto a protein-mediated biomineralization hydroxyapatite (HAp) coating of Ti. HAp was achieved by the treatment of lysozyme and tris(2-carboxyethyl) phosphonate mixture and then soaked in calcium ion (Ca²⁺) solution to obtain functional Ti substrate (Ti/HAp/OHA-Apt). In vitro studies confirmed that Ti/HAp/OHA-Apt could effectively maintain the sustained release of Apt19s from Ti for 7 days. The released Apt19s significantly enhanced the migration of bone marrow mesenchymal stem cells (MSCs), which was reflected by the experiment of transwell assay, wound healing, and zymogram detection. Compared with pure Ti, Ti/HAp/OHA-Apt was able to adjust the adsorption of functional proteins at the Ti-based interface to expose their active sites, which significantly increased the expression of adhesion-associated proteins (vinculin and tensin) in MSCs to promote their adhesion on Ti-based interface. In vitro cell experiments of alkaline phosphatase activity staining, mineralization detection, and expression of osteogenesis-related genes showed that Ti/HAp/OHA-Apt significantly enhanced the osteogenic differentiation ability of MSCs, which may be highly related to the porous structure of hydroxyapatite on Ti interface. In vivo test of Micro-CT, H&E staining, and histochemical staining further confirmed that Ti/HAp/OHA-Apt was able to promote MSC recruitment at the peri-implant interface to form new bone. This work provides a new approach to develop functional Ti-based materials for bone defect repair.

Recycling protein selective adsorption on fluorine-modified surface through fluorine-fluorine interaction

Low surface energy materials with micro-nano structures have been widely developed to prevent non-specific adhesion of biomolecules. Herein we put forward a new approach based on the antifouling and self-assembly properties of fluorine components, to construct a non-specific protein resistance surface with selective protein adsorption property. Briefly, the antifouling surface (SN-F) was obtained by a simple one-step modification on silicon nanowire arrays (SiNWAs) with fluorine coupling agent 1 H,1 H,2 H,2 H-perfluorodecyltrimethoxysilane (FAS). And protein was fluorinated by conjugation with an amphiphilic fluoro-copolymer, produced from 2-methacrylamido glucopyranose (MAG) and trifluoroethyl methacrylate (TFEMA) via RAFT polymerization. The properties of the materials were characterized by ¹H nuclear magnetic resonance (¹H NMR), infrared spectroscopy (FTIR), water contact angle, and X-ray photoelectron spectroscopy (XPS) etc., and protein adsorption was investigated by protein content measurement, fluorescence detection, and electrophoresis. It was observed that the adsorption for native proteins on SN-F was at an extremely low level, while the adsorption for the fluoro-copolymer conjugated protein (PFG-BSA) was significantly increased. When the percentage of TFEMA in the fluoro-copolymer was as high as 52.0%, the fluorinated protein adsorbed on SN-F was more than 35 times of native proteins on the surface. Moreover, the platform could resist IgG adhesion in serum after the adsorption of fluorinated protein, and it could be recycled three times after 75% ethanol treatment. In conclusion, SN-F showed non-specific protein resistance through low surface energy and specific protein adsorption by fluorine-fluorine self-assembly. The fluorinated nanostructured platform has a great potential in controlling protein adsorption and release.

In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold

The influence of the properties of different solid substrates on the tethering of two antibodies, IgG1-CR3022 and IgG1-S309, which were specifically engineered for the detection of SARS-CoV-2, has been examined at the molecular level using conventional and accelerated Molecular Dynamics (cMD and aMD, respectively). Two surfaces with very different properties and widely used in immunosensors for diagnosis, amorphous silica and the most stable facet of the face-centered cubic gold structure, have been considered. The effects of such surfaces on the structure and orientation of the immobilized antibodies have been determined by quantifying the tilt and hinge angles that describe the orientation and shape of the antibody, respectively, and the dihedrals that measure the relative position of the antibody arms with respect to the surface. Results show that the interactions with amorphous silica, which are mainly electrostatic due to the charged nature of the surface, help to preserve the orientation and structure of the antibodies, especially of the IgG1-CR3022, indicating that the primary sequence of those antibodies also plays some role. Instead, short-range van der Waals interactions with the inert gold surface cause a higher degree tilting and fraying of the antibodies with respect to amorphous silica. The interactions between the antibodies and the surface also affect the correlation among the different angles and dihedrals, which increases with their strength. Overall, results explain why amorphous silica substrates are frequently used to immobilize antibodies in immunosensors.

Combining a Genetically Engineered Oxidase with Hydrogen-Bonded Organic Frameworks (HOFs) for Highly Efficient Biocomposites

Enzymes incorporated into hydrogen‐bonded organic frameworks (HOFs) via bottom‐up synthesis are promising biocomposites for applications in catalysis and sensing. Here, we explored synthetic incorporation of d‐amino acid oxidase (DAAO) with the metal‐free tetraamidine/tetracarboxylate‐based BioHOF‐1 in water. N‐terminal enzyme fusion with the positively charged module Z_basic2 strongly boosted the loading (2.5‐fold; ≈500 mg enzyme g_material⁻¹) and the specific activity (6.5‐fold; 23 U mg⁻¹). The DAAO@BioHOF‐1 composites showed superior activity with respect to every reported carrier for the same enzyme and excellent stability during catalyst recycling. Further, extension to other enzymes, including cytochrome P450 BM3 (used in the production of high‐value oxyfunctionalized compounds), points to the versatility of genetic engineering as a strategy for the preparation of biohybrid systems with unprecedented properties.

Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalized Gold Surfaces

The efficient immobilization of enzymes on surfaces remains a complex but central issue in the biomaterials field, which requires us to understand this process at the atomic level. Using a multiscale approach combining all-atom molecular dynamics and coarse-grain Brownian dynamics simulations, we investigated the adsorption behavior of β-glucosidase A (βGA) on bare and self-assembled monolayer (SAM)-functionalized gold surfaces. We monitored the enzyme position and orientation during the molecular dynamics (MD) trajectories and measured the contacts it forms with both surfaces. While the adsorption process has little impact on the protein conformation, it can nonetheless perturb its mechanical properties and catalytic activity. Our results show that compared to the SAM-functionalized surface, the adsorption of βGA on bare gold is more stable, but less specific, and more likely to disrupt the enzyme's function. This observation emphasizes the fact that the structural organization of proteins at the solid interface is a key point when designing devices based on enzyme immobilization, as one must find an acceptable stability-activity trade-off.

Tag-mediated single-step purification and immobilization of recombinant proteins toward protein-engineered advanced materials

Background

The potential applications of protein-engineered functional materials are so wide and exciting that the interest in these eco-friendly advanced materials will further expand in the future. Tag-mediated protein purification/immobilization technologies have emerged as green and cost-effective approaches for the fabrication of such materials. Strategies that combine the purification and immobilization of recombinant proteins/peptides onto/into natural, synthetic or hybrid materials in a single-step are arising and attracting increasing interest.

Aim of Review

This review highlights the most significant advances of the last 5 years within the scope of tag-mediated protein purification/immobilization and elucidates their contributions for the development of efficient single-step purification and immobilization strategies. Recent progresses in the field of protein-engineered materials created using innovative protein-tag combinations and future opportunities created by these new technologies are also summarized and identified herein.

Key Scientific Concepts of Review

Protein purification/immobilization tags present a remarkable ability to establish specific non-covalent/covalent interactions between solid materials and biological elements, which prompted the creation of tailor-made and advanced functional materials, and of next-generation hybrid materials. Affinity tags can bind to a wide range of materials (of synthetic, natural or hybrid nature), being most suitable for protein purification. Covalently binding tags are most suitable for long-term protein immobilization, but can only bind naturally to protein-based materials. Hybrid affinity-covalently binding tags have allowed efficient one-step purification and immobilization of proteins onto different materials, as well as the development of innovative protein-engineered materials. Self-aggregating tags have been particularly useful in combination with other tags for generating protein-engineered materials with self-assembling, flexible and/or responsive properties. While these tags have been mainly explored for independent protein purification, immobilization or functionalization purposes, efficient strategies that combine tag-mediated purification and immobilization/functionalization in a single-step will be essential to guarantee the sustainable manufacturing of advanced protein-engineered materials.

THE METHOD OF ATOMIC FORCE MICROSCOPY AS A POSSIBLE TOOL FOR TESTING THE BIOCOMPATIBILITY OF IMPLANTS IN TRAUMATOLOGY AND ORTHOPEDICS PRACTICE

OBJECTIVE

The aim: To establish the possibility of using the atomic force microscope (AFM) to predict the body's reaction to the implant.

PATIENTS AND METHODS

Materials and methods: A total of 32 patients, 22 men and 10 women, the average age of the patients was 55±6 years, were included in the study. They performed pre- and post-operative testing of the biocompatibility of orthopedic implant materials with the patient's body with the help of AFM.

RESULTS

Results: According to the research, an increase in pro-inflammatory factors was found, which may indicate a constant inflammatory process, which is probably related to the presence of the implant.

CONCLUSION

Conclusions: On the basis of atomic force spectroscopy, an express method of testing biomaterials for compatibility with the body of a specific recipient and studying the effect of the reactions of recipient tissues on the surface of various implants has been developed. The obtained results can be useful in planning further clinical studies.

Stabilization of enzymes via immobilization: Multipoint covalent attachment and other stabilization strategies

The use of enzymes in industrial processes requires the improvement of their features in many instances. Enzyme immobilization, a requirement to facilitate the recovery and reuse of these water-soluble catalysts, is one of the tools that researchers may utilize to improve many of their properties. This review is focused on how enzyme immobilization may improve enzyme stability. Starting from the stabilization effects that an enzyme may experience by the mere fact of being inside a solid particle, we detail other possibilities to stabilize enzymes: generation of favorable enzyme environments, prevention of enzyme subunit dissociation in multimeric enzymes, generation of more stable enzyme conformations, or enzyme rigidification via multipoint covalent attachment. In this last point, we will discuss the features of an "ideal" immobilization protocol to maximize the intensity of the enzyme-support interactions. The most interesting active groups in the support (glutaraldehyde, epoxide, glyoxyl and vinyl sulfone) will be also presented, discussing their main properties and uses. Some instances in which the number of enzyme-support bonds is not directly related to a higher stabilization will be also presented. Finally, the possibility of coupling site-directed mutagenesis or chemical modification to get a more intense multipoint covalent immobilization will be discussed.

Investigating the Molecular Mechanism of Protein-Polymer Binding with Direct Saturation Compensated Nuclear Magnetic Resonance

Herein, we describe a new technique, direct saturation compensated transfer (DISCO) NMR, to characterize protein-macromolecule interactions. DISCO enables the direct observation of intermolecular interactions and is used to investigate mucoadhesion, a type of polymer-protein interaction that is widely implemented in drug delivery but remains poorly understood. In a model system of bovine submaxillary mucin and poly(acrylic acid), DISCO identifies selective backbone interactions that facilitate mucoadhesion through chain interpenetration. DISCO demonstrated distinct patterns of molecular selectivity between mucoadhesive polymers when applied to hydroxypropyl cellulose and carboxymethyl cellulose and that functionalizing adhesive polymers with strongly interacting moieties may be detrimental to the overall adhesive interaction. Additionally, DISCO was used to estimate polymer-protein dissociation constants using individual proton signals as reporters. Overall, DISCO can be used as a label-free screening tool to generate polymer-specific binding fingerprints to map and quantify interactions between macromolecules.

Isoelectric Point of Proteins at Hydrophobic Interfaces

Structural and colloidal stability of proteins at different surfaces and interfaces is of great importance in many fields including medical, pharmaceutical, or material science. Due to their flexibility, proteins tend to respond to their environmental conditions and can undergo structural and conformational changes. For instance, alterations in physiological factors such as temperature, ions concentration, or pH as well as the adsorption to an interface can initiate protein aggregation. Therefore, at different surfaces and interfaces the characterization of the structural and colloidal stability of proteins, which is mainly influenced by their electrostatic and hydrophobic interactions, is of fundamental importance. In this study, we utilized sum frequency generation (SFG) spectroscopy to assess the role of solution pH on the polarity and magnitude of the electric field within the hydration shell of selected model proteins adsorbed to a hydrophobic surface. We used polystyrene (PS) as a model hydrophobic surface and determined the isoelectric point (IEP) of four structurally different model proteins. Comparing the measured IEP of proteins at the PS/solution or air/solution interface with that determined in the bulk solution via zeta potential measurement, we found significant similarities between the IEP of surface adsorbed proteins and those in the bulk aqueous phase. The pH dependence behavior of proteins was correlated to their amino acid composition and degree of hydrophobicity.

Toward the Specificity of Bare Nanomaterial Surfaces for Protein Corona Formation

Aiming at creating smart nanomaterials for biomedical applications, nanotechnology aspires to develop a new generation of nanomaterials with the ability to recognize different biological components in a complex environment. It is common opinion that nanomaterials must be coated with organic or inorganic layers as a mandatory prerequisite for applications in biological systems. Thus, it is the nanomaterial surface coating that predominantly controls the nanomaterial fate in the biological environment. In the last decades, interdisciplinary studies involving not only life sciences, but all branches of scientific research, provided hints for obtaining uncoated inorganic materials able to interact with biological systems with high complexity and selectivity. Herein, the fragmentary literature on the interactions between bare abiotic materials and biological components is reviewed. Moreover, the most relevant examples of selective binding and the conceptualization of the general principles behind recognition mechanisms were provided. Nanoparticle features, such as crystalline facets, density and distribution of surface chemical groups, and surface roughness and topography were encompassed for deepening the comprehension of the general concept of recognition patterns.

Solvent-induced conformational tuning of lysozyme protein adlayers on silica surfaces: A QCM-D and LSPR study

There is broad interest in functionalizing solid surfaces with lysozyme, which is a widely studied antimicrobial protein. To date, most efforts have focused on developing more effective immobilization schemes to promote lysozyme attachment in fully aqueous conditions, while there remains an outstanding need to understand how tuning the solution-phase conformational stability of lysozyme proteins can modulate adsorption behavior and resulting adlayer properties. Inspired by the unique conformational behavior of lysozyme proteins in water-ethanol mixtures, we conducted quartz crystal microbalance-dissipation (QCM-D) and localized surface plasmon resonance (LSPR) measurements to systematically investigate the adsorption behavior of lysozyme proteins onto silica surfaces across a wide range of water-ethanol mixtures. Our findings revealed that lysozyme adsorption behavior strongly depended on the ethanol fraction in a non-monotonic fashion and this trend could be rationalized by taking into account how competing effects of water and ethanol solvation influence solution-phase protein size and conformational stability. Integrated analysis of the QCM-D and LSPR measurement trends enabled quantitative determination of the solvent mass within lysozyme adlayers, which tended to decrease at higher ethanol fractions and supported that the hydrodynamic properties of lysozyme adlayers are mainly influenced by the degree of protein conformational flexibility as opposed to solvation effects alone.

Mechanism of Myoglobin Molecule Adsorption on Silica: QCM, OWLS and AFM Investigations

Adsorption kinetics of myoglobin on silica was investigated using the quartz crystal microbalance (QCM) and the optical waveguide light-mode spectroscopy (OWLS). Measurements were carried out for the NaCl concentration of 0.01 M and 0.15 M. A quantitative analysis of the kinetic adsorption and desorption runs acquired from QCM allowed to determine the maximum coverage of irreversibly bound myoglobin molecules. At a pH of 3.5-4 this was equal to 0.60 mg m^-2 and 1.3 mg m^-2 for a NaCl concentration of 0.01 M and 0.15 M, respectively, which agrees with the OWLS measurements. The latter value corresponds to the closely packed monolayer of molecules predicted from the random sequential adsorption approach. The fraction of reversibly bound protein molecules and their biding energy were also determined. It is observed that at larger pHs, the myoglobin adsorption kinetics was much slower. This behavior was attributed to the vanishing net charge that decreased the binding energy of molecules with the substrate. These results can be exploited to develop procedures for preparing myoglobin layers at silica substrates of well-controlled coverage useful for biosensing purposes.

Unfolding and Aggregation of Lysozyme under the Combined Action of Dithiothreitol and Guanidine Hydrochloride: Optical Studies

Using a number of optical techniques (interferometry, dynamic light scattering, and spectroscopy), denaturation of hen egg white lysozyme (HEWL) by treatment with a combination of dithiothreitol (DTT) and guanidine hydrochloride (GdnHCl) has been investigated. The denaturing solutions were selected so that protein denaturation occurred with aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM) or without aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM, GdnHCl 6 M) and can be evaluated after 60 min of treatment. It has been found that denatured by solution with 6 M GdnHCl lysozyme completely loses its enzymatic activity after 30 min and the size of the protein molecule increases by 1.5 times, from 3.8 nm to 5.7 nm. Denaturation without of GdnHCl led to aggregation with preserving about 50% of its enzymatic activity. Denaturation of HEWL was examined using interferometry. Previously, it has been shown that protein denaturation that occurs without subsequent aggregation leads to an increase in the refractive index (Δn ~ 4.5 × 10-5). This is most likely due to variations in the HEWL-solvent interface area. By applying modern optical techniques conjointly, it has been possible to obtain information on the nature of time-dependent changes that occur inside a protein and its hydration shell as it undergoes denaturation.

Advancing Rational Control of Peptide-Surface Complexes

Understanding peptide-surface interactions is crucial for programming self-assembly of peptides at surfaces and in realizing their applications, such as biosensors and biomimetic materials. In this study, we developed insights into the dependence of a residue's interaction with a surface on its neighboring residue in a tripeptide using molecular dynamics simulations. This knowledge is integral for designing rational mutations to control peptide-surface complexes. Using graphene as our model surface, we estimated the free energy of adsorption (ΔA_ads) and extracted predominant conformations of 26 tripeptides with the motif LNR-CR-Gly, where LNR and CR are variable left-neighboring and central residues, respectively. We considered a combination of strongly adsorbing (Phe, Trp, and Arg) and weakly adsorbing (Ala, Val, Leu, Ser, and Thr) amino acids on graphene identified in a prior study to form the tripeptides. Our results indicate that ΔA_ads of a tripeptide cannot be estimated as the sum of ΔA_ads of each residue indicating that the residues in a tripeptide do not behave as independent entities. We observed that the contributions from the strongly adsorbing amino acids were dominant, which suggests that such residues could be used for strengthening peptide-graphene interactions irrespective of their neighboring residues. In contrast, the adsorption of weakly adsorbing central residues is dependent on their neighboring residues. Our structural analysis revealed that the dihedral angles of LNR are more correlated with that of CR in the adsorbed state than in bulk state. Together with ΔA_ads trends, this implies that different backbone structures of a given CR can be accessed for a similar ΔA_ads by varying the LNR. Therefore, incorporation of context effects in designing mutations can lead to desired peptide structure at surfaces. Our results also emphasize that these cooperative effects in ΔA_ads and structure are not easily predicted a priori. The collective results have applications in guiding rational mutagenesis techniques to control orientation of peptides at surfaces and in developing peptide structure prediction algorithms in adsorbed state from its sequence.

The role of surfaces on amyloid formation

Interfaces can strongly accelerate or inhibit protein aggregation, destabilizing proteins that are stable in solution or, conversely, stabilizing proteins that are aggregation-prone. Although this behaviour is well-known, our understanding of the molecular mechanisms underlying surface-induced protein aggregation is still largely incomplete. A major challenge is represented by the high number of physico-chemical parameters involved, which are highly specific to the considered combination of protein, surface properties, and solution conditions. The key aspect determining the role of interfaces is the relative propensity of the protein to aggregate at the surface with respect to bulk. In this review, we discuss the multiple molecular determinants that regulate this balance. We summarize current experimental techniques aimed at characterizing protein aggregation at interfaces, and highlight the need to complement experimental analysis with theoretical modelling. In particular, we illustrate how chemical kinetic analysis can be combined with experimental methods to provide insights into the molecular mechanisms underlying surface-induced protein aggregation, under both stagnant and agitation conditions. We summarize recent progress in the study of important amyloids systems, focusing on selected relevant interfaces.

Comparing Protein Adsorption onto Alumina and Silica Nanomaterial Surfaces: Clues for Vaccine Adjuvant Development

Protein adsorption onto nanomaterial surfaces is important for various nanobiotechnology applications such as biosensors and drug delivery. Within this scope, there is growing interest to develop alumina- and silica-based nanomaterial vaccine adjuvants and an outstanding need to compare protein adsorption onto alumina- and silica-based nanomaterial surfaces. Herein, using alumina- and silica-coated arrays of silver nanodisks with plasmonic properties, we conducted localized surface plasmon resonance (LSPR) experiments to evaluate real-time adsorption of bovine serum albumin (BSA) protein onto alumina and silica surfaces. BSA monomers and oligomers were prepared in different water-ethanol mixtures and both adsorbing species consistently showed quicker adsorption kinetics and more extensive adsorption-related spreading on alumina surfaces as compared to on silica surfaces. We rationalized these experimental observations in terms of the electrostatic forces governing protein-surface interactions on the two nanomaterial surfaces and the results support that more rigidly attached BSA protein-based coatings can be formed on alumina-based nanomaterial surfaces. Collectively, the findings in this study provide fundamental insight into protein-surface interactions at nanomaterial interfaces and can help to guide the development of protein-based coatings for medical and biotechnology applications such as vaccines.

Brownian motion-based nanoparticle sizing-A powerful approach for in situ analysis of nanoparticle-protein interactions

A key hurdle toward effective application of nanoparticles (NPs) in biomedicine is still the incomplete understanding of the biomolecular adsorption layer, the so-called protein corona, which inevitably forms around NPs when they are immersed in a biofluid. NP sizing techniques via the analysis of Brownian motions offer a powerful way to measure the thickness of the protein corona in situ. Here, the fundamentals of three techniques, dynamic light scattering, fluorescence correlation spectroscopy, and nanoparticle tracking analysis are briefly summarized. Then, experimental procedures for the determination of binding curves are presented in a tutorial fashion. Nanoparticle sizing experiments are illustrated with a selection of recent results on the interactions of transferrin with hydrophilic and hydrophobic polystyrene nanoparticles, and key insights gained from this work are discussed.

Transforming Separation Science with Single-Molecule Methods

Empirical optimization of the multiscale parameters underlying chromatographic and membrane separations leads to enormous resource waste and production costs. A bottom-up approach to understand the physical phenomena underlying challenges in separations is possible with single-molecule observations of solute-stationary phase interactions. We outline single-molecule fluorescence techniques that can identify key interactions under ambient conditions. Next, we describe how studying increasingly complex samples heightens the relevance of single-molecule results to industrial applications. Finally, we illustrate how separation methods that have not been studied at the single-molecule scale can be advanced, using chiral chromatography as an example case. We hope new research directions based on a molecular approach to separations will emerge based on the ideas, technologies, and open scientific questions presented in this Perspective.

Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation

Surface immobilized enzymes play a key role in numerous biotechnological applications such as biosensors, biofuel cells, or biocatalytic synthesis. As a consequence, the impact of adsorption on the enzyme structure, dynamics, and function needs to be understood on the molecular level as it is critical for the improvement of these technologies. With this perspective in mind, we used a theoretical approach for investigating local protein flexibility on the residue scale that couples a simplified protein representation with an elastic network and Brownian dynamics simulations. The impact of protein adsorption on a solid surface is implicitly modeled via additional external constraints between the residues in contact with the surface. We first performed calculations on a redox enzyme, bilirubin oxidase (BOD) from M. verrucaria, to study the impact of adsorption on its mechanical properties. The resulting rigidity profiles show that, in agreement with the available experimental data, the mechanical variations observed in the adsorbed BOD will depend on its orientation and its anchor residues (i.e., residues that are in contact with the functionalized surface). Additional calculations on ribonuclease A and nitroreductase shed light on how seemingly stable adsorbed enzymes can nonetheless display an important decrease in their catalytic activity resulting from a perturbation of their mechanics and internal dynamics.

Unraveling How Ethanol-Induced Conformational Changes Affect BSA Protein Adsorption onto Silica Surfaces

Protein adsorption at solid-liquid interfaces is highly relevant to a wide range of applications such as biosensors, drug delivery, and pharmaceuticals. Understanding how protein conformation in bulk solution impacts adsorption behavior is fundamentally important and could also lead to the development of improved protein-based coatings. To date, relevant studies have been conducted in aqueous solutions, while it remains largely unknown how organic solvents and more specifically solvent-induced conformational changes might influence protein adsorption. Herein, using the quartz crystal microbalance-dissipation (QCM-D) and localized surface plasmon resonance (LSPR) techniques, we systematically investigated the real-time adsorption behavior of bovine serum albumin (BSA) protein onto silica surfaces in different water-ethanol mixtures ranging from 0 to 60% (v/v) ethanol. The results showed that there was greater protein adsorption at higher ethanol fractions in the 10-30% range, while more complex adsorption profiles were observed in the 40-60% range. The combination of QCM-D and LSPR measurements led us to further identify specific cases in water-ethanol mixtures where washing steps caused densification of the adsorbed protein layer as opposed to typical desorption of weakly adsorbed molecules in aqueous conditions. We discuss mechanistic factors that drive these overall adsorption trends by taking into account how ethanol fraction affects BSA conformation in bulk solution. Together, our findings demonstrate that BSA proteins can adsorb onto silica surfaces across a wide range of water-ethanol mixture conditions, while specific adsorption profiles depended on the ethanol fraction in a manner closely linked to solution-phase conformational properties.

Improved Catalytic Properties of Thermomyces lanuginosus Lipase Immobilized onto Newly Fabricated Polydopamine-Functionalized Magnetic Fe3O4 Nanoparticles

In this study, magnetic Fe3O4 nanoparticles coated with polydopamine possessing abundant amino groups (Fe3O4@PDA) were conveniently prepared, detailed, and characterized, and then firstly used as a supporting matrix for immobilizing Thermomyces lanuginosus lipase (Fe3O4@PDA@TLL). The effects of some crucial factors on the immobilization efficiency were investigated and the optimal protein loading and activity recovery were found to be 156.4 mg/g and 90.9%, respectively. Characterization studies revealed that Fe3O4@PDA@TLL displayed a broader pH and temperature adaptability as compared to the free TLL, which allows its use at wider ranges of reaction conditions. With regard to the stabilities, the immobilized TLL clearly displayed improved pH, thermal, and solvent tolerance stabilities compared to the free enzyme, suggesting that the biocompatible Fe3O4@PDA might be an outstanding material for immobilizing TLL and acting as alternative support for different enzymes.

On the relationship between structure and catalytic effectiveness in solid surface-immobilized enzymes: Advances in methodology and the quest for a single-molecule perspective

The integration of enzymes with solid materials is important in many biotechnological applications, including the use of immobilized enzymes for biocatalytic synthesis. The development of functional enzyme-material composites is restrained by the lack of molecular-level insight into the behavior of enzymes in confined, surface-near environments. Here, we review recent advances in surface-sensitive spectroscopic techniques that push boundaries for the determination of enzyme structure and orientation at the solid-liquid interface. We discuss recent evidence from single-molecule studies showing that analyses sensitive to the temporal and spatial heterogeneities in immobilized enzymes can succeed in disentangling the effects of conformational stability and active-site accessibility on activity. Different immobilization methods involve distinct trade-off between these effects, thus emphasizing the need for a holistic (systems) view of immobilized enzymes for the rational development of practical biocatalysts.

A mechanistic examination of salting out in protein-polymer membrane interactions

Developing a mechanistic understanding of protein dynamics and conformational changes at polymer interfaces is critical for a range of processes including industrial protein separations. Salting out is one example of a procedure that is ubiquitous in protein separations yet is optimized empirically because there is no mechanistic description of the underlying interactions that would allow predictive modeling. Here, we investigate peak narrowing in a model transferrin-nylon system under salting out conditions using a combination of single-molecule tracking and ensemble separations. Distinct surface transport modes and protein conformational changes at the negatively charged nylon interface are quantified as a function of salt concentration. Single-molecule kinetics relate macroscale improvements in chromatographic peak broadening with microscale distributions of surface interaction mechanisms such as continuous-time random walks and simple adsorption-desorption. Monte Carlo simulations underpinned by the stochastic theory of chromatography are performed using kinetic data extracted from single-molecule observations. Simulations agree with experiment, revealing a decrease in peak broadening as the salt concentration increases. The results suggest that chemical modifications to membranes that decrease the probability of surface random walks could reduce peak broadening in full-scale protein separations. More broadly, this work represents a proof of concept for combining single-molecule experiments and a mechanistic theory to improve costly and time-consuming empirical methods of optimization.

Deciphering the Effect of Microbead Size Distribution on the Kinetics of Heterogeneous Biocatalysts through Single-Particle Analysis Based on Fluorescence Microscopy

Understanding the functionality of immobilized enzymes with spatiotemporal resolution and under operando conditions is an unmet need in applied biocatalysis, as well as priceless information to guide the optimization of heterogeneous biocatalysts for industrial purposes. Unfortunately, enzyme immobilization still relies on trial-and-error approximations that prevail over rational designs. Hence, a modern fabrication process to achieve efficient and robust heterogeneous biocatalysts demands comprehensive characterization techniques to track and understand the immobilization process at the protein–material interface. Recently, our group has developed a new generation of self-sufficient heterogeneous biocatalysts based on alcohol dehydrogenases co-immobilized with nicotinamide cofactors on agarose porous microbeads. Harnessing the autofluorescence of NAD+(P)H and using time-lapse fluorescence microscopy, enzyme activity toward the redox cofactors can be monitored inside the beads. To analyze these data, herein we present an image analytical tool to quantify the apparent Michaelis–Menten parameters of alcohol dehydrogenases co-immobilized with NAD(P)+/H at the single-particle level. Using this tool, we found a strong negative correlation between the apparent catalytic performance of the immobilized enzymes and the bead radius when using exogenous bulky substrates in reduction reactions. Therefore, applying image analytics routines to microscopy studies, we can directly unravel the functional heterogeneity of different heterogeneous biocatalyst samples tested under different reaction conditions.

Formation of a Monolayer Protein Corona around Polystyrene Nanoparticles and Implications for Nanoparticle Agglomeration

Nanoparticle (NP) interactions with cells and organisms are mediated by a biomolecular adsorption layer, the so-called "protein corona." An in-depth understanding of the corona is a prerequisite to successful and safe application of NPs in biology and medicine. In this work, earlier in situ investigations on small NPs are extended to large polystyrene (PS) NPs of up to 100 nm diameter, using human transferrin (Tf) and human serum albumin (HSA) as model proteins. Direct NP sizing experiments reveal a reversibly bound monolayer protein shell (under saturating conditions) on hydrophilic, carboxyl-functionalized (PS-COOH) NPs, as was earlier observed for much smaller NPs. In contrast, protein binding on hydrophobic, sulfated (PS-OSO₃ H) NPs in solvent of low ionic strength is completely irreversible; nevertheless, the thickness of the observed protein corona again corresponds to a protein monolayer. Under conditions of reduced charge repulsion (higher ionic strength), the NPs are colloidally unstable and form large clusters below a certain protein-NP stoichiometric ratio, indicating that the adsorbed proteins induce NP agglomeration. This comprehensive characterization of the persistent protein corona on PS-OSO₃ H NPs by nanoparticle sizing and quantitative fluorescence microscopy/nanoscopy reveals mechanistic aspects of molecular interactions occurring during exposure of NPs to biofluids.

Mapping Molecular Structure of Protein Locating on Nanoparticles with Limited Proteolysis

The molecular structure of a protein could be altered when it is attached to nanoparticles (NPs), affecting the performance of NPs present in biological systems. Limited proteolysis coupled with LC-MS/MS could reveal the changes in protein structure when it binds to a variety of entities, including macro-molecules and small drugs, but it has not yet been applied to study protein-NP interaction. Herein, adsorption of proteins, transferrin, and catalase on the polystyrene (PS) or iron oxide (IO) NPs was analyzed with this method. Both increased and decreased proteolytic efficiency in certain regions on the proteins were observed. Identification of the peptides affected by protein-NP interaction led to proper prediction of alterations to protein function as well as to colloidal stability of NPs. Overall, the present work has demonstrated the utility of limited proteolysis in helping to elucidate the potential biological outcomes of the protein-NP conjugate, obtaining knowledge to guide improvement of the rational design of the protein-conjugated NPs for biomedical applications and to understand the biological behaviors of the engineered NPs.

Lipoic Acid Ligase-Promoted Bioorthogonal Protein Modification and Immobilization

Protein bioconjugation benefits from precise regional and temporal control. One notable way of achieving this control is through the enzymatic attachment of bioorthogonal reactive handles to peptide recognition sequences that are genetically fused to target proteins of interest. The lipoic acid ligase variant, LplA^W37V, functionalizes proteins by covalently attaching an azide-bearing lipoic acid derivative to a 13-amino acid recognition sequence known as the lipoic acid ligase acceptor peptide (LAP). Once attached, the azide group can be modified with diverse chemical entities through azide-alkyne click chemistry, enabling conjugation of chemical probes such as fluorophores and facilitating polymer attachment, glycosylation, and protein immobilization in addition to many other possible chemical modifications. The versatility of the attached azide group is complemented by the modular nature of the LAP sequence, which can be introduced within a protein at internal and/or terminal sites as well as at multiple sites simultaneously. In this chapter we describe the in vitro LplA^W37V-mediated ligation of 10-azidodecanoic acid to a LAP-containing target protein (i.e., green fluorescent protein (GFP)) and the characterization of the ligation reaction products. Additionally, methods for the modification and immobilization of azide-functionalized LAP-GFP are discussed.