A bottom-up approach to understanding protein layer formation at solid-liquid interfaces

Phosphate-Driven Interfacial Self-Assembly of Silk Fibroin for Continuous Noncovalent Growth of Nanothin Defect-Free Coatings

Silk fibroin is a fiber-forming protein derived from the thread of Bombyx mori silkworm cocoons. This biocompatible protein, under the kosmotropic influence of potassium phosphate, can undergo supramolecular self-assembly driven by a random coil to β-sheet secondary structure transition. By leveraging concurrent nonspecific adsorption and self-assembly of silk fibroin, we demonstrate an interfacial phenomenon that yields adherent, defect-free nanothin protein coatings that grow continuously in time, without observable saturation in mass deposition. This noncovalent growth of silk fibroin coatings is a departure from traditionally studied protein adsorption phenomena, which generally yield adsorbed layers that saturate in mass with time and often do not completely cover the surface. Here, we explore the fundamental mechanisms of coating growth by examining the effects of coating solution parameters that promote or inhibit silk fibroin self-assembly. Results show a strong dependence of coating kinetics and structure on solution pH, salt species, and salt concentration. Moreover, coating growth was observed to occur in two stages: an early stage driven by protein-surface interactions and a late stage driven by protein-protein interactions. To describe this phenomenon, we developed a kinetic adsorption model with Langmuir-like behavior at early times and a constant steady-state growth rate at later times. Structural analysis by FTIR and photoinduced force microscopy show that small β-sheet-rich structures serve as anchoring sites for absorbing protein nanoaggregates, which is critical for coating formation. Additionally, β-sheets are preferentially located at the interface between protein nanoaggregates in the coating, suggesting their role in forming stable, robust coatings.

Differential effects of the N-terminal helix of FGF8b on the activity of a small-molecule FGFR inhibitor in cell culture and for the extracellular domain of FGFR3c in solution

SSR128129E (SSR) is a unique small-molecule inhibitor of fibroblast growth factor receptors (FGFRs). SSR is a high-affinity allosteric binder that selectively blocks one of the two major FGFR-mediated pathways. The mechanisms of SSR activity were studied previously in much detail, allowing the identification of its binding site, located in the hydrophobic groove of the receptor D3 domain. The binding site overlaps with the position of an N-terminal helix, an element exclusive for the FGF8b growth factor, which could potentially convert SSR from an allosteric inhibitor into an orthosteric blocker for the particular FGFR/FGF8b system. In this regard, we report here on the structural and functional investigation of FGF8b/FGFR3c system and the effects imposed on it by SSR. We show that SSR is equally or more potent in inhibiting FGF8b-induced FGFR signaling compared to FGF2-induced activation. On the other hand, when studied in the context of separate extracellular domains of FGFR3c in solution with NMR spectroscopy, SSR is unable to displace the N-terminal helix of FGF8b from its binding site on FGFR3c and behaves as a weak orthosteric inhibitor. The substantial inconsistency between the results obtained with cell culture and for the individual water-soluble subdomains of the FGFR proteins points to the important role played by the cell membrane.

The importance of the simulated wound fluid composition and properties in the determination of the fluid handling performance of wound dressings

Effective fluid handling by wound dressings is crucial in the management of exuding wounds through maintaining a clean, moist environment, facilitating healing by removing excess exudate and promoting tissue regeneration. In this context, the availability of reliable and clinically relevant standardised testing methods for wound dressings are critical for informed decision making by clinicians, healthcare administrators, regulatory/reimbursement bodies and product developers. The widely used standard EN 13726 specifies the use of Solution A, an aqueous protein-free salt solution, for determining fluid-handling capacity (FHC). However, a simulated wound fluid (SWF) with a more complex composition, resembling the protein, salt, and buffer concentrations found in real-world clinical exudate, would provide a more clinically relevant dressing performance assessment. This study compared selected physicochemical parameters of Solution A, an alternative, novel simulated wound fluid (SWF A), and a benchmark reference serum-containing solution (SCS) simulating chronic wound exudate. Additionally, FHC values for eight advanced bordered and non-bordered foam dressings were determined for all three test fluids, following EN 13726. Our findings demonstrate a close resemblance between SWF A and SCS. This study highlights the critical importance of selecting a physiochemically appropriate test fluid for accurate FHC testing resulting in clinically meaningful evaluation of dressing performance.

An Up-to-Date Review on the Remediation of Dyes and Phenolic Compounds from Wastewaters Using Enzymes Immobilized on Emerging and Nanostructured Materials: Promises and Challenges

Addressing the critical issue of water pollution, this review article emphasizes the need to remove hazardous dyes and phenolic compounds from wastewater. These pollutants pose severe risks due to their toxic, mutagenic, and carcinogenic properties. The study explores various techniques for the remediation of organic contaminants from wastewater, including an enzymatic approach. A significant challenge in enzymatic wastewater treatment is the loss of enzyme activity and difficulty in recovery post-treatment. To mitigate these issues, this review examines the strategy of immobilizing enzymes on newly developed nanostructured materials like graphene, carbon nanotubes (CNTs), and metal-organic frameworks (MOFs). These materials offer high surface areas, excellent porosity, and ample anchoring sites for effective enzyme immobilization. The review evaluates recent research on enzyme immobilization on these supports and their applications in biocatalytic nanoparticles. It also analyzes the impact of operational factors (e.g., time, pH, and temperature) on dye and phenolic compound removal from wastewater using these enzymes. Despite promising outcomes, this review acknowledges the challenges for large-scale implementation and offers recommendations for future research to tackle these obstacles. This review concludes by suggesting that enzyme immobilization on these emerging materials could present a sustainable, environmentally friendly solution to the escalating water pollution crisis.

Enhanced surface nanoanalytics of transient biomolecular processes

Fundamental knowledge of the physical and chemical properties of biomolecules is key to understanding molecular processes in health and disease. Bulk and single-molecule analytical methods provide rich information about biomolecules but often require high concentrations and sample preparation away from physiologically relevant conditions. Here, we present the development and application of a lab-on-a-chip spray approach that combines rapid sample preparation, mixing, and deposition to integrate with a range of nanoanalytical methods in chemistry and biology, providing enhanced spectroscopic sensitivity and single-molecule spatial resolution. We demonstrate that this method enables multidimensional study of heterogeneous biomolecular systems over multiple length scales by nanoscopy and vibrational spectroscopy. We then illustrate the capabilities of this platform by capturing and analyzing the structural conformations of transient oligomeric species formed at the early stages of the self-assembly of α-synuclein, which are associated with the onset of Parkinson's disease.

Protein Desorption Kinetics Depends on the Timescale of Observation

The presence of so-called reversible and irreversible protein adsorption on solid surfaces is well documented in the literature and represents the basis for the development of nanoparticles and implant materials to control interactions in physiological environments. Here, using a series of complementary single-molecule tracking approaches appropriate for different timescales, we show that protein desorption kinetics is much more complex than the traditional reversible-irreversible binary picture. Instead, we find that the surface residence time distribution of adsorbed proteins transitions from power law to exponential behavior when measured over a large range of timescales (10^-2-10⁶ s). A comparison with macroscopic results obtained using a quartz crystal microbalance suggested that macroscopic measurements have generally failed to observe such nonequilibrium phenomena because they are obscured by ensemble-averaging effects. These findings provide new insights into the complex phenomena associated with protein adsorption and desorption.

Is enzyme immobilization a mature discipline? Some critical considerations to capitalize on the benefits of immobilization

Enzyme immobilization has been developing since the 1960s and although many industrial biocatalytic processes use the technology to improve enzyme performance, still today we are far from full exploitation of the field. One clear reason is that many evaluate immobilization based on only a few experiments that are not always well-designed. In contrast to many other reviews on the subject, here we highlight the pitfalls of using incorrectly designed immobilization protocols and explain why in many cases sub-optimal results are obtained. We also describe solutions to overcome these challenges and come to the conclusion that recent developments in material science, bioprocess engineering and protein science continue to open new opportunities for the future. In this way, enzyme immobilization, far from being a mature discipline, remains as a subject of high interest and where intense research is still necessary to take full advantage of the possibilities.

Insulin aggregation starts at dynamic triple interfaces, originating from solution agitation

The consequences of agitation on protein stability are particularly relevant to therapeutic proteins. However, the precise contribution of the different effects induced by agitation in pathways leading to protein denaturation and aggregation at interfaces is not entirely understood. In particular, the contribution of a moving triple line, induced by the sweeping of a solution meniscus on a container wall upon agitation, has only been rarely assessed. In this article, we therefore designed experimental setups to analyze how mixing, shear stress, and dynamic triple interfaces influence insulin aggregation in physiological conditions. This has been achieved by controlling agitation speed, shear stress, and the extension of triple interfaces in order to shed light on the contribution of different agitation-induced effects on insulin aggregation in physiological conditions. We demonstrate that strong agitation is necessary for the onset of insulin aggregation, while the growth of the aggregates is sustained even under weak agitation. Kinetic insulin aggregation studies in conditions of intermittent wetting show that the aggregation rate correlates with the amount of dynamic triple interfaces that the proteins are exposed to. Finally, we demonstrate that the triple line, where the protein solution, the air, and a hydrophobic surface meet constitutes a preferential early aggregation site.

Effect of Microgroove Structure in PDMS-Based Silicone Implants on Biocompatibility

Capsule and capsule contracture around implants are important concerns in a clinic. The physical topology of the material surface regulates the formation of the capsule, but the specific regulatory mechanism is unclear. In this study, four types of silicone implant materials with different microgroove structures (groove depths of 10 and 50 μm and widths of 50 and 200 μm) were constructed using lithography to form different gradient surface topologies. Mass spectrometry, Cell Counting Kit-8, 5-ethynyl-2′-deoxycytidine (EdU), enzyme-linked immunosorbent assay, western blot, immunofluorescence, and immunohistochemistry were used to explore the changes in protein adsorption, cell adhesion, cell proliferation, and collagen deposition on the surface of the materials. At the same time, RNA-seq was used to detect transcriptome differences caused by different structures. Furthermore, collagen deposition and capsule formation were observed in the rats. The groove structure was observed to significantly increase the surface roughness of the material. The deeper groove and the narrower width of the polydimethylsiloxane would increase the surface roughness of the material and the surface water contact angle but reduce the total amount of adsorbed protein in the first two hours. In vitro cell experiments revealed that microtopology affected cell proliferation and adhesion and regulated collagen secretion. Further analysis indicated the deeper and narrower groove (group 50–50) on the surface of the material caused more evident collagen deposition around the material, forming a thicker envelope. Surface roughness of the material was thus related to collagen deposition and envelope thickness. The thickness of the envelope tissue around smooth materials does not exceed that of the materials with surface roughness. In conclusion, the narrower and deeper grooves in the micron range exhibited poor histocompatibility and led to formation of thicker envelopes around the materials. The appropriate grooves can reduce envelope thickness.

Multiscale Simulation of Protein Corona Formation on Silver Nanoparticles: Study of Ovispirin-1 Peptide Adsorption

The exposure of nanoparticles (NPs) to biofluids leads to the rapid coverage of proteins, named protein corona, which alters the NPs' chemicophysical and biological properties. Fundamental studies of the protein corona are thus critical to the increasing applications of NPs in nanotechnology and nanomedicines. The present work utilizes multiscale simulations of a model biological system, small ovispirin-1 peptides, and bare silver nanoparticles (AgNPs) to examine the NPs' size and surface hydrophilicity effects on formation dynamics and the structure of the peptide corona. Our simulations revealed the different adsorption dynamics of ovispirin-1 peptides on the NPs, including the direct adsorption of a single peptide and peptide aggregates and multistep adsorption, as well as an intermediate cycle of desorption and readsorption. Notably, the whole process of peptide adsorption on hydrophilic AgNP surfaces can be generalized as three stages: diffusion to the surface, initial landing via hydrophilic residues, and the final attachment. The decrease in AgNP's size leads to faster adsorption with more heterogeneous peptide interfacial dynamics, a denser and inhomogeneous peptide packing structure, and a wider distribution of adsorption orientations. Subsequent atomistic molecular dynamics simulations demonstrated that on the hydrophilic AgNP surfaces, adsorbed peptides display moderate changes in their secondary structure, resulting in further changes of corona composition, i.e., amino acid residue distribution on the surface.

Lipid bilayer coatings for rapid enzyme-linked immunosorbent assay

The enzyme-linked immunosorbent assay (ELISA) is a widely used method for protein detection and relies on the specific capture of target proteins while minimizing the nonspecific binding of other interfering proteins and biomolecules. To prevent nonspecific binding events, blocking agents such as bovine serum albumin (BSA) protein, mixtures of proteins in media such as milk or serum, and/or surfactants are typically added to ELISA plates after probe attachment and before analyte capture. Herein, we developed a streamlined ELISA strategy in which readily prepared lipid nanoparticles are utilized as the blocking agent and are added together with the probe molecule to the ELISA plate, resulting in fewer processing steps, quicker protocol time, and superior detection performance compared to conventional BSA blocking. These measurement capabilities were established for coronavirus disease-2019 (COVID-19) antibody detection in saline and human serum conditions and are broadly applicable for developing rapid ELISA diagnostics.

Adsorption rate constants of therapeutic proteins and surfactants for material surfaces

Adsorption of therapeutic proteins to material surfaces can be a pivotal issue in drug development, especially for low concentration products. Surfactants are used to limit adsorption losses. For each formulation component, surface adsorption is the result of a combination of its diffusion and surface adsorption rates. The latter are difficult to measure accurately because a depletion layer forms rapidly in the bulk solution above a bare surface, slowing down adsorption. Adapting flow conditions and local surface chemistry, we are able to minimize depletion limitations and measure apparent adsorption rate constants of three monoclonal antibodies, other proteins and surfactants with a hydrophobic surface. We show that surface adsorption rates scale with the molecular mass of the molecule, with polysorbates therefore showing thousand times slower rates than antibodies. Moreover, we observed that the desorption dynamic of polysorbates from a given hydrophobic surface depends on surface coverage, whereas this is not the case for Poloxamer 188. These novel contributions to surface adsorption dynamics enable a new perspective on the evaluation of drug surface compatibility and can, together with diffusion rates, be used to predict the protective potential of surfactants in given conditions.

Elastic compliance and adsorption profiles of Bovine serum albumin at fluid/solid interface in the presence of electrolytes

Non-trivial topology of proteins under shear suggests that even small structural changes in proteins result in dramatic variations in the mechanical properties and stability. In this study, we have analysed the elastic compliance of solvated bovine serum albumin (BSA) with NaCl,MgCl2, FeCl3 of concentration-ranging from 50 mM to 250 mM using Quartz crystal microbalance with dissipation. The compliance shows a reverse Hofmeister trend (Na +  Collapse

Key Words

• BSA
• Elastic compliance
• FRET
• Intra molecular interaction
• Ion cloud

Collapse

MESH Headings

• Elasticity
• Absorption
• Serum Albumin, Bovine/chemistry
• Electrolytes
• Spectrum Analysis
• Sodium Chloride/chemistry
• Magnesium Chloride
• Ferric Compounds/chemistry
• Chlorides/chemistry
• Shear Strength
• Scattering, Small Angle
• X-Ray Diffraction

Collapse

Grants Collapse

Affiliation(s)

A Bruntha Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
R Radhipriya Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India
Thanikaivelan Palanisamy Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
A Dhathathreyan Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.

Collapse

Advanced protein adsorption properties of a novel silicate-based bioceramic: A proteomic analysis

Silicate bioceramics have been shown to possess excellent cytocompatibility and osteogenic activity, but the exact mechanism is still unclear. Protein adsorption is the first event taking place at the biomaterial-tissue interface, which is vital to the subsequent cellular behavior and further influence the biomaterial-tissue interaction. In this work, the protein adsorption behavior of a novel CPS bioceramic was evaluated using the proteomics technology. The results showed that CPS adsorbed more amount and types of serum proteins than HA. FN1 and IGF1 proteins selected from proteomics results were validated by Western-blot experiment. Pathway analysis also revealed mechanistic insights how these absorbed proteins by CPS help mediate cell adhesion and promotes osteogenic activity. Firstly, the dramatically enhanced adsorption of FN1 could greatly promote cell adhesion and growth. Secondly, IGF1 was uniquely adsorbed on CPS bioceramic and IGF1 could activate Rap1 signaling pathway to promote cell adhesion. Thirdly, the increased adsorption of FN1, IGF1 and COL1A2 proteins on CPS explains its better ability on bone regeneration than HA. Fourthly, the increased adsorption of IGF1, CHAD, COL2A1 and THBS4 proteins on CPS explains its ability on cartilage formation. Lastly, the increased adsorption of immunological related proteins on CPS may also play a positive role in bone regeneration. In addition, CPS had a much better cell adhesion ability than HA, proving that more adsorbed proteins really had a positive effect on cell behavior. The more adsorbed proteins on CPS than HA might indicated a better bone regeneration rate at early stage of implantation.

Power Law Behavior in Protein Desorption Kinetics Originating from Sequential Binding and Unbinding

The study of protein adsorption at the single molecule level has recently revealed that the adsorption is reversible, but with a long-tailed residence time distribution which can be approximated with a sum of exponential functions putatively related to distinct adsorption sites. Here it is proposed that the shape of the residence time distribution results from an adsorption process with sequential and reversible steps that contribute to overall binding strength resembling "zippering". In this model, the survival function of the residence time distribution of single proteins varies from an exponential distribution for a single adsorption step to a power law distribution with exponent -1/2 for a large number of adsorption steps. The adsorption of fluorescently labeled fibrinogen to glass surfaces is experimentally studied with single molecule imaging. The experimental residence time distribution can be readily fit by the proposed model. This demonstrates that the observed long residence times can arise from stepwise adsorption rather than rare but strong binding sites and provides guidance for the control of protein adsorption to biomaterials.

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.

Characterization of Sample Loss Caused by Competitive Adsorption of Proteins in Vials Using Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis

Sample loss caused by competitive protein adsorption on solid surfaces from complex samples remains to be a major hurdle in sensitive analyses of proteins. No label-free techniques can easily quantify individual proteins adsorbed on irregular surfaces of Eppendorf vials or Falcon tubes, which are commonly used to contain complex biological samples. Multiplexed characterization of such adsorption by different proteins is technically challenging. Herein, we developed a direct protein analysis based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the characterization of sample loss occurred on the curved surface with limited area. Using this simple and easily accessible method, we discovered the effect of ethylenediaminetetraacetic acid on surface adsorption of different milk proteins, specifically an augmented loss of milk proteins in low-binding sample vials. In this study, we also identified severe biases of silver staining and established proteomics-based mapping of protein distribution in biological samples for absolute quantification of competitive protein adsorption on irregular surfaces.

In Situ Characterization of Protein Corona Formation on Silica Microparticles Using Confocal Laser Scanning Microscopy Combined with Microfluidics

In biological fluids, proteins bind to particles, forming so-called protein coronas. Such adsorbed protein layers significantly influence the biological interactions of particles, both in vitro and in vivo. The adsorbed protein layer is generally described as a two-component system comprising "hard" and "soft" protein coronas. However, a comprehensive picture regarding the protein corona structure is lacking. Herein, we introduce an experimental approach that allows for in situ monitoring of protein adsorption onto silica microparticles. The technique, which mimics flow in vascularized tumors, combines confocal laser scanning microscopy with microfluidics and allows the study of the time-evolution of protein corona formation. Our results show that protein corona formation is kinetically divided into three different phases: phase 1, proteins irreversibly and directly bound (under physiologically relevant conditions) to the particle surface; phase 2, irreversibly bound proteins interacting with preadsorbed proteins, and phase 3, reversibly bound "soft" protein corona proteins. Additionally, we investigate particle-protein interactions on low-fouling zwitterionic-coated particles where the adsorption of irreversibly bound proteins does not occur, and on such particles, only a "soft" protein corona is formed. The reported approach offers the potential to define new state-of-the art procedures for kinetics and protein fouling experiments.

Surface Characteristics Control the Attachment and Functionality of (Chimeric) Avidin

The physical adsorption (physisorption) of proteins to surfaces is an important but incompletely understood factor in many biological processes and is of increasing significance in bionanotechnology as well. Avidin is an important protein because of strong avidin-biotin binding, which has been exploited in numerous applications. We have undertaken thorough experimentation on the physisorption of avidin, to chemically different flat surfaces of Si and graphite and also to the curved version of the latter, on multiwalled carbon nanotubes (MWNTs) of different diameters. The difference in the behavior of avidin on Si versus graphite is drastic; on Si, avidin deposits as single globular tetrameric units and maintains functionality, whereas on graphite, it forms irregular networks of two-layer thick filaments, where the first layer has lost its biological activity. On MWNTs, avidin also deposits as one-dimensional formations, or stripes, but these appear to order in a perpendicular arrangement to the MWNT axis. A better understanding of protein-surface interactions is essential for the development of robust and reliable methods for biofunctionalization of materials. This work also provides insights into the importance of the nanoscale surface architecture.

Practical guide to characterize biomolecule adsorption on solid surfaces (Review)

The control over the adsorption or grafting of biomolecules from a liquid to a solid interface is of fundamental importance in different fields, such as drug delivery, pharmaceutics, diagnostics, and tissue engineering. It is thus important to understand and characterize how biomolecules interact with surfaces and to quantitatively measure parameters such as adsorbed amount, kinetics of adsorption and desorption, conformation of the adsorbed biomolecules, orientation, and aggregation state. A better understanding of these interfacial phenomena will help optimize the engineering of biofunctional surfaces, preserving the activity of biomolecules and avoiding unwanted side effects. The characterization of molecular adsorption on a solid surface requires the use of analytical techniques, which are able to detect very low quantities of material in a liquid environment without modifying the adsorption process during acquisition. In general, the combination of different techniques will give a more complete characterization of the layers adsorbed onto a substrate. In this review, the authors will introduce the context, then the different factors influencing the adsorption of biomolecules, as well as relevant parameters that characterize their adsorption. They review surface-sensitive techniques which are able to describe different properties of proteins and polymeric films on solid two-dimensional materials and compare these techniques in terms of sensitivity, penetration depth, ease of use, and ability to perform "parallel measurements."

Microfluidic deposition for resolving single-molecule protein architecture and heterogeneity

Scanning probe microscopy provides a unique window into the morphology, mechanics, and structure of proteins and their complexes on the nanoscale. Such measurements require, however, deposition of samples onto substrates. This process can affect conformations and assembly states of the molecular species under investigation and can bias the molecular populations observed in heterogeneous samples through differential adsorption. Here, we show that these limitations can be overcome with a single-step microfluidic spray deposition platform. This method transfers biological solutions to substrates as microdroplets with subpicoliter volume, drying in milliseconds, a timescale that is shorter than typical diffusion times of proteins on liquid–solid interfaces, thus avoiding surface mass transport and change to the assembly state. Finally, the single-step deposition ensures the attachment of the full molecular content of the sample to the substrate, allowing quantitative measurements of different molecular populations within heterogeneous systems, including protein aggregates.

Manual sample deposition on a substrate can introduce artifacts in quantitative AFM measurements. Here the authors present a microfluidic spray device for reliable deposition of subpicoliter droplets which dry out in milliseconds after landing on the surface, thereby avoiding protein self-assembly.

Understanding interactions between biomaterials and biological systems using proteomics

The role that biomaterials play in the clinical treatment of damaged organs and tissues is changing. While biomaterials used in permanent medical devices were required to passively take over the function of a damaged tissue in the long term, current biomaterials are expected to trigger and harness the self-regenerative potential of the body in situ and then to degrade, the foundation of regenerative medicine. To meet these different requirements, it is imperative to fully understand the interactions biomaterials have with biological systems, in space and in time. This knowledge will lead to a better understanding of the regenerative capabilities of biomaterials aiding their design with improved functionalities (e.g. biocompatibility, bioactivity). Proteins play a pivotal role in the interaction between biomaterials and cells or tissues. Protein adsorption on the material surface is the very first event of this interaction, which is determinant for the subsequent processes of cell growth, differentiation, and extracellular matrix formation. Against this background, the aim of the current review is to provide insight in the current knowledge of the role of proteins in cell-biomaterial and tissue-biomaterial interactions. In particular, the focus is on proteomics studies, mainly using mass spectrometry, and the knowledge they have generated on protein adsorption of biomaterials, protein production by cells cultured on materials, safety and efficacy of new materials based on nanoparticles and the analysis of extracellular matrices and extracellular matrix-derived products. In the outlook, the potential and limitations of this approach are discussed and mass spectrometry imaging is presented as a powerful technique that complements existing mass spectrometry techniques by providing spatial molecular information about the material-biological system interactions.

Quantitation of nonspecific protein adsorption at solid–liquid interfaces for single-cell proteomics

Protein nonspecific adsorption that occurred at the solid–liquid interface has been subjected to intense physical and chemical characterizations due to its crucial role in a wide range of applications, including food and pharmaceutical industries, medical implants, biosensing, and so on. Protein-adsorption caused sample loss has largely hindered the studies of single-cell proteomics; the prevention of such loss requires the understanding of protein–surface adsorption at the proteome level, in which the competitive adsorption of thousands and millions of proteins with vast dynamic range occurs. To this end, we feel the necessity to review current methodologies on their potentials to characterize — more specifically to quantify — the proteome-wide adsorption. We hope this effort can help advancing single-cell proteomics and trace proteomics.

Nanoconfined water can orient and cause long-range dipolar interactions with biomolecules

Surface properties are generally determined by the top most surface layer also defining how molecules adsorb onto it. By exploring effects due to interactions with deeper subsurface layers, however, long-range interaction forces were found to also significantly contribute to molecular adsorption, in which hydration of the subsurface region is the key factor. Water molecules confined to a subsurface amphiphilic gradient are confirmed to cause these long-range dipolar interactions by preferential orientation, thus significantly changing the way how a protein interacts with the surface. These findings imply future exploitation of an additional factor to modulate adsorption processes.

Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking

Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking information have been devised, each with their own strengths and weaknesses. These include imaging of multiple focal planes, point-spread-function engineering, and interferometric detection. These methods may be compared based on their ability to provide accurate and precise position information on single-molecule emitters with limited photons. To successfully apply and further develop these methods, it is essential to consider many practical concerns, including the effects of optical aberrations, field dependence in the imaging system, fluorophore labeling density, and registration between different color channels. Selected examples of 3D super-resolution imaging and tracking are described for illustration from a variety of biological contexts and with a variety of methods, demonstrating the power of 3D localization for understanding complex systems.

Single Particle Tracking: From Theory to Biophysical Applications

After three decades of developments, single particle tracking (SPT) has become a powerful tool to interrogate dynamics in a range of materials including live cells and novel catalytic supports because of its ability to reveal dynamics in the structure-function relationships underlying the heterogeneous nature of such systems. In this review, we summarize the algorithms behind, and practical applications of, SPT. We first cover the theoretical background including particle identification, localization, and trajectory reconstruction. General instrumentation and recent developments to achieve two- and three-dimensional subdiffraction localization and SPT are discussed. We then highlight some applications of SPT to study various biological and synthetic materials systems. Finally, we provide our perspective regarding several directions for future advancements in the theory and application of SPT.

Controlling adsorption and passivation properties of bovine serum albumin on silica surfaces by ionic strength modulation and cross-linking

Understanding the physicochemical factors that influence protein adsorption onto solid supports holds wide relevance for fundamental insights into protein structure and function as well as for applications such as surface passivation.

pH-Dependent Ordered Fibrinogen Adsorption on Polyethylene Single Crystals

Nanostructured surfaces have the potential to influence the assembly as well as the orientation of adsorbed proteins and may, thus, strongly influence the biomaterials' performance. For the class of polymeric (bio)materials a reproducible and well-characterized nanostructure is the ordered chain folded surface of a polyethylene single crystal (PE-SC). We tested the hypothesis that the trinodal-rod-shaped protein human plasma fibrinogen (HPF) adsorbs on the (001) surface of PE-SCs along specific crystallographic directions. The PE-SC samples were prepared by isothermal crystallization in dilute solution and characterized by atomic force microscopy (AFM) before as well as after HPF adsorption at different concentrations and pH values. At a physiological pH of 7.4, connected HPF molecules, or e.g., fibrils, fibril networks, or sponge-like structures, were observed on PE-SC surfaces that featured no preferential orientation. The observation of these nonoriented multiprotein assemblies was explained by predominant protein-protein interactions and limited surface diffusion. However, at an increased pH of 9.2, single HPF molecules, e.g., spherical-shaped and trinodal-rod-shaped HPF molecules as well as agglomerates, were observed on the PE-SC surface. The presence of single HPF molecules at increased pH was explained by decreased protein-protein interactions. These single trinodal-rod-shaped HPF molecules oriented preferentially along crystallographic [100] and [010] directions on the PE-SC surface which was explained by an increased amount of intermolecular bonds along these crystallographic directions with increased surface atom density. The study established that HPF molecules can align on chemically homogeneous surface topographies one order of magnitude smaller than the dimension of the protein. This advances the understanding of how to control the assembly and orientation of proteins on nanostructured polymer surfaces. Controlled protein adsorption is a crucial key to improve the surface functionality of future implants and biosensors.

Improved scaffold biocompatibility through anti-Fibronectin aptamer functionalization

Protein adsorption is the first and decisive step to define cell-biomaterial interaction. Guiding the adsorption of desired protein species may represent a viable approach to promote cell activities conducive to tissue regeneration. The aim of the present study was to investigate whether immobilized anti-Fibronectin aptamers could promote the attachment and growth of osteoblastic cells. Polyethyleneglycole diacrylate/thiolated Hyaluronic Acid hydrogels (PEGDA/tHA) were coated with anti-Fibronectin aptamers. Hydrogel loading and Fibronectin bonding were investigated, through spectrophotometry and Bradford assay. Subsequently, human osteoblasts (hOBs) were cultured on hydrogels for 10days in 2D and 3D cultures. Cells were monitored through microscopy and stained for focal adhesions, microfilaments and nuclei using fluorescence microscopy. Samples were also included in paraffin and stained with Hematoxylin-Eosin. Cell number on hydrogels was quantitated over time. Cell migration into the hydrogels was also studied through Calcein AM staining. Aptamers increased the number of adherent hOBs and their cytoplasm appeared more spread and richer in adhesion complexes than on control hydrogels. Viability assays confirmed that significantly more cells were present on hydrogels in the presence of aptamers, already after 48h of culture. When hOBs were encapsulated into hydrogels, cells were more numerous on aptamer-containing PEGDA-tHA. Cells migrated deeper in the gel in the presence of DNA aptamers, appearing on different focus planes. Our data demonstrate that anti-Fibronectin aptamers promote scaffold enrichment for this protein, thus improving cell adhesion and scaffold colonization.

STATEMENT OF SIGNIFICANCE

We believe aptamer coating of biomaterials is a useful and viable approach to improve the performance of scaffold materials for both research and possibly clinical purposes, because different medical devices could be envisaged able to capture bioactive mediators from the patients' blood and concentrate them where they are needed, on the biomaterial itself. At the same time, this technology could be used to confer 3D cell culture scaffold with the ability to store proteins, such as Fibronectin, taking it from the medium and capture what is produced by cells. This is an improvement of traditional biomaterials that can be enriched with exogenous molecules but are not able to selectively capture a desired molecule.

Reversible Adsorption Kinetics of Near Surface Dimer Colloids

We investigate the effect of shape on reversible adsorption kinetics using colloidal polystyrene dimers near a solid glass surface as a model system. The interaction between colloid and wall is tuned using electrostatic, depletion, and gravity forces to produce a double-well potential. The dwell time in each of the potential wells is measured from long duration particle trajectories. The height of each monomer relative to the glass surface is measured to a resolution of <20 nm by in-line holographic microscopy. The measured transition probability distributions are used in kinetic equations to describe the flux of particles to and from the surface. The dimers are compared to independent isolated monomers to determine the effects of shape on adsorption equilibria and kinetics. To elucidate these differences, we consider both mass and surface coverage and two definitions of surface coverage. The results show that dimers with single coverage produce slower adsorption, lower surface coverage, and higher mass coverage in comparison to those of monomers, while dimers with double coverage adsorb faster and result in higher surface coverage.

Generalized recovery algorithm for 3D super-resolution microscopy using rotating point spread functions

Super-resolution microscopy with phase masks is a promising technique for 3D imaging and tracking. Due to the complexity of the resultant point spread functions, generalized recovery algorithms are still missing. We introduce a 3D super-resolution recovery algorithm that works for a variety of phase masks generating 3D point spread functions. A fast deconvolution process generates initial guesses, which are further refined by least squares fitting. Overfitting is suppressed using a machine learning determined threshold. Preliminary results on experimental data show that our algorithm can be used to super-localize 3D adsorption events within a porous polymer film and is useful for evaluating potential phase masks. Finally, we demonstrate that parallel computation on graphics processing units can reduce the processing time required for 3D recovery. Simulations reveal that, through desktop parallelization, the ultimate limit of real-time processing is possible. Our program is the first open source recovery program for generalized 3D recovery using rotating point spread functions.

Surface-Mediated Protein Unfolding as a Search Process for Denaturing Sites

Surface-induced protein denaturation has important implications for the development of materials that are resistant and/or innocuous to biomolecules. Here, we studied the mechanism of lysozyme (T4L) unfolding on fused silica (FS) using single-molecule methods that provided direct insight into the cause of denaturation. Unfolding of T4L was monitored by Förster resonance energy transfer while simultaneously tracking the adsorption, diffusion, and desorption of individual molecules at the solid-solution interface. Results of high-throughput single-molecule analysis suggested that the unfolding of T4L on FS was mediated by surface diffusion and occurred on isolated nanoscale sites, which were relatively rare and distinct from the majority of the surface. These observations suggest that surface-mediated protein unfolding is a search process that is based on the exploration for denaturing sites by the protein. Ultimately, these findings have important implications for the design of protein-compatible surfaces.

Steering protein adsorption at charged surfaces: electric fields and ionic screening

Protein adsorption at charged surfaces is a common process in the development of functional technological devices.

Thermodynamic, kinetic and conformational analysis of proteins diffusion-sorption on a solid surface

In this paper we examine particularly some of the more fundamental properties of protein conformational changes at a solid surface coupled with diffusion from the bulk of an aqueous solution and with the adsorption-desorption processes. We focus our attention on adsorbed protein monolayers upon a solid surface using a thermodynamic and kinetic analytical development. Account is also taken of the effects on the overall rate of the conformational change on a solid surface of deviation from ideality, of protein flexibility, of surface free energy and of interaction with reactive solid sites. Our theory applied to steady states is illustrated by examples such as folding-misfolding-unfolding of RNase and SNase on a solid surface after diffusion and adsorption from an aqueous solution. For this purpose, we put forward the determining steps which shall lead to the steady state. The existence of three situations is highlighted according to the values of the typical constants relevant for the protein considered: reaction rate determining step, diffusion and sorption determining steps, mixed adsorption diffusion and reaction rate. Finally, we have tried to link the developments of our theories to a large literature based on experimental results encountered during proteins diffusion-sorption-reaction processes, fundamental topics that has been since long investigated by Miller's team in MPKG.

Molecular-level understanding of the adsorption mechanism of a graphite-binding peptide at the water/graphite interface

The association of proteins and peptides with inorganic material has vast technological potential. An understanding of the adsorption of peptides at liquid/solid interfaces on a molecular-level is fundamental to fully realising this potential. Combining our prior work along with the statistical analysis of 100+ molecular dynamics simulations of adsorption of an experimentally identified graphite binding peptide, GrBP5, at the water/graphite interface has been used here to propose a model for the adsorption of a peptide at a liquid/solid interface. This bottom-up model splits the adsorption process into three reversible phases: biased diffusion, anchoring and lockdown. Statistical analysis highlighted the distinct roles played by regions of the peptide studied here throughout the adsorption process: the hydrophobic domain plays a significant role in the biased diffusion and anchoring phases suggesting that the initial impetus for association between the peptide and the interface may be hydrophobic in origin; aromatic residues dominate the interaction between the peptide and the surface in the adsorbed state and the polar region in the middle of the peptide affords a high conformational flexibility allowing strongly interacting residues to maximise favourable interactions with the surface. Reversible adsorption was observed here, unlike in our prior work focused on a more strongly interacting surface. However, this reversibility is unlikely to be seen once the peptide-surface interaction exceeds 10 kcal mol(-1).

Electrostatic Interactions Influence Protein Adsorption (but Not Desorption) at the Silica-Aqueous Interface

High-throughput single-molecule total internal reflection fluorescence microscopy was used to investigate the effects of pH and ionic strength on bovine serum albumin (BSA) adsorption, desorption, and interfacial diffusion at the aqueous-fused silica interface. At high pH and low ionic strength, negatively charged BSA adsorbed slowly to the negatively charged fused silica surface. At low pH and low ionic strength, where BSA was positively charged, or in solutions at higher ionic strength, adsorption was approximately 1000 times faster. Interestingly, neither surface residence times nor the interfacial diffusion coefficients of BSA were influenced by pH or ionic strength. These findings suggested that adsorption kinetics were dominated by energy barriers associated with electrostatic interactions, but once adsorbed, protein-surface interactions were dominated by short-range nonelectrostatic interactions. These results highlight the ability of single-molecule techniques to isolate elementary processes (e.g., adsorption and desorption) under steady-state conditions, which would be impossible to measure using ensemble-averaging methods.

Molecular trajectories provide signatures of protein clustering and crowding at the oil/water interface

Using high throughput single-molecule total internal reflection fluorescence microscopy (TIRFM), we have acquired molecular trajectories of bovine serum albumin (BSA) and hen egg white lysozyme during protein layer formation at the silicone oil-water interface. These trajectories were analyzed to determine the distribution of molecular diffusion coefficients, and for signatures of molecular crowding/caging, including subdiffusive motion and temporal anticorrelation of the instantaneous velocity vector. The evolution of these properties with aging time of the interface was compared with dynamic interfacial tension measurements. For both lysozyme and BSA, we observed an overall slowing of protein objects, the onset of both subdiffusive and anticorrelated motion (associated with crowding), and a decrease in the interfacial tension with aging time. For lysozyme, all of these phenomena occurred virtually simultaneously, consistent with a homogeneous model of layer formation that involves gradual crowding of weakly interacting proteins. For BSA, however, the slowing occurred first, followed by the signatures of crowding/caging, followed by a decrease in interfacial tension, consistent with a heterogeneous model of layer formation involving the formation of protein clusters. The application of microrheological methods to single molecule trajectories described here provides an unprecedented level of mechanistic interpretation of interfacial events that occurred over a wide range of interfacial protein coverage.

Experimental characterization of adsorbed protein orientation, conformation, and bioactivity

Protein adsorption on material surfaces is a common phenomenon that is of critical importance in many biotechnological applications. The structure and function of adsorbed proteins are tightly interrelated and play a key role in the communication and interaction of the adsorbed proteins with the surrounding environment. Because the bioactive state of a protein on a surface is a function of the orientation, conformation, and accessibility of its bioactive site(s), the isolated determination of just one or two of these factors will typically not be sufficient to understand the structure-function relationships of the adsorbed layer. Rather a combination of methods is needed to address each of these factors in a synergistic manner to provide a complementary dataset to characterize and understand the bioactive state of adsorbed protein. Over the past several years, the authors have focused on the development of such a set of complementary methods to address this need. These methods include adsorbed-state circular dichroism spectropolarimetry to determine adsorption-induced changes in protein secondary structure, amino-acid labeling/mass spectrometry to assess adsorbed protein orientation and tertiary structure by monitoring adsorption-induced changes in residue solvent accessibility, and bioactivity assays to assess adsorption-induced changes in protein bioactivity. In this paper, the authors describe the methods that they have developed and/or adapted for each of these assays. The authors then provide an example of their application to characterize how adsorption-induced changes in protein structure influence the enzymatic activity of hen egg-white lysozyme on fused silica glass, high density polyethylene, and poly(methyl-methacrylate) as a set of model systems.

Single-molecule resolution of protein dynamics on polymeric membrane surfaces: the roles of spatial and population heterogeneity

Although polymeric membranes are widely used in the purification of protein pharmaceuticals, interactions between biomolecules and membrane surfaces can lead to reduced membrane performance and damage to the product. In this study, single-molecule fluorescence microscopy provided direct observation of bovine serum albumin (BSA) and human monoclonal antibody (IgG) dynamics at the interface between aqueous buffer and polymeric membrane materials including regenerated cellulose and unmodified poly(ether sulfone) (PES) blended with either polyvinylpyrrolidone (PVP), polyvinyl acetate-co-polyvinylpyrrolidone (PVAc-PVP), or polyethylene glycol methacrylate (PEGM) before casting. These polymer surfaces were compared with model surfaces composed of hydrophilic bare fused silica and hydrophobic trimethylsilane-coated fused silica. At extremely dilute protein concentrations (10(-3)-10(-7) mg/mL), protein surface exchange was highly dynamic with protein monomers desorbing from the surface within ∼1 s after adsorption. Protein oligomers (e.g., nonspecific dimers, trimers, or larger aggregates), although less common, remained on the surface for 5 times longer than monomers. Using newly developed super-resolution methods, we could localize adsorption sites with ∼50 nm resolution and quantify the spatial heterogeneity of the various surfaces. On a small anomalous subset of the adsorption sites, proteins adsorbed preferentially and tended to reside for significantly longer times (i.e., on "strong" sites). Proteins resided for shorter times overall on surfaces that were more homogeneous and exhibited fewer strong sites (e.g., PVAc-PVP/PES). We propose that strong surface sites may nucleate protein aggregation, initiated preferentially by protein oligomers, and accelerate ultrafiltration membrane fouling. At high protein concentrations (0.3-1.0 mg/mL), fewer strong adsorption sites were observed, and surface residence times were reduced. This suggests that at high concentrations, adsorbed proteins block strong sites from further protein adsorption. Importantly, this demonstrates that strong binding sites can be modified by changing solution conditions. Membrane surfaces are intrinsically heterogeneous; by employing single-molecule techniques, we have provided a new framework for understanding protein interactions with such surfaces.

Adsorption-induced changes in ribonuclease A structure and enzymatic activity on solid surfaces

Ribonuclease A (RNase A) is a small globular enzyme that lyses RNA. The remarkable solution stability of its structure and enzymatic activity has led to its investigation to develop a new class of drugs for cancer chemotherapeutics. However, the successful clinical application of RNase A has been reported to be limited by insufficient stability and loss of enzymatic activity when it was coupled with a biomaterial carrier for drug delivery. The objective of this study was to characterize the structural stability and enzymatic activity of RNase A when it was adsorbed on different surface chemistries (represented by fused silica glass, high-density polyethylene, and poly(methyl-methacrylate)). Changes in protein structure were measured by circular dichroism, amino acid labeling with mass spectrometry, and in vitro assays of its enzymatic activity. Our results indicated that the process of adsorption caused RNase A to undergo a substantial degree of unfolding with significant differences in its adsorbed structure on each material surface. Adsorption caused RNase A to lose about 60% of its native-state enzymatic activity independent of the material on which it was adsorbed. These results indicate that the native-state structure of RNase A is greatly altered when it is adsorbed on a wide range of surface chemistries, especially at the catalytic site. Therefore, drug delivery systems must focus on retaining the native structure of RNase A in order to maintain a high level of enzymatic activity for applications such as antitumor chemotherapy.