Single-molecule resolution of protein structure and interfacial dynamics on biomaterial surfaces

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.

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.

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.

Dissection of Interaction Kinetics through Single-Molecule Interaction Simulation

The ability to extract kinetic interaction parameters from single-molecule fluorescence resonance energy transfer trajectories without the need for solving complex single-molecule differential equations has the potential to address some of the critical biophysical questions. Here, we provide a noise-free single-molecule interaction simulation (SMIS) tool to give the expected dwell-time distributions and relative populations of each FRET level based on the assigned kinetic model and to dissect kinetic interaction parameters from single-molecule FRET trajectories. The method provides the expected dwell-time distributions, average transition rates, and relative populations of each FRET level based on the assigned kinetic model. By comparing with ground truth data and experimental data, we demonstrated that SMIS is useful to quantify the interaction kinetic rate constants without using the traditional single-molecule analytical solution approach.

Inflammation via myeloid differentiation primary response gene 88 signaling mediates the fibrotic response to implantable synthetic poly(ethylene glycol) hydrogels

Synthetic hydrogels, such as poly(ethylene glycol) (PEG), are promising for a range of in vivo applications. However, like all non-biological biomaterials, synthetic hydrogels including PEG elicit a foreign body response (FBR). The FBR is thought to be initiated by adsorbed protein that is recognized by and subsequently activates inflammatory cells, notably macrophages, and culminates with fibrotic encapsulation. However, the molecular mechanisms that drive the FBR are not well understood. Toll-like receptors (TLRs) are key receptors that recognize pathogens, but also recognize altered host proteins that display damage-associated molecular patterns (DAMPs). Thus TLRs may play a role in the FBR. Here, we investigated myeloid differentiation primary response gene 88 (MyD88), a signaling adaptor protein that mediates inflammatory cytokine production induced by most TLRs. An in vitro model was used consisting of macrophages cultured on the surface of synthetic hydrogels, specifically PEG, with pre-adsorbed serum proteins. Our in vitro findings demonstrate that MyD88-dependent signaling is the predominant inflammatory pathway in macrophage activation to synthetic hydrogels. When stimulated with TLR agonists to mimic additional DAMPs present in vivo, MyD88-dependent signaling was also the predominant pathway in macrophage activation. An in vivo model of PEG hydrogels implanted subcutaneously in wild-type and MyD88^-/- mice also demonstrated that MyD88 is the key contributor to the recruitment of inflammatory cells and formation of the fibrous capsule surrounding the implanted hydrogel. Taken together, findings from this study identify MyD88-mediated inflammation as being a critical pathway involved not only in the inflammatory response, but in formation of the fibrous capsule to PEG hydrogels. STATEMENT OF SIGNIFICANCE: Synthetic hydrogels are promising for in vivo applications but, like all non-biological biomaterials, synthetic hydrogels elicit a foreign body response (FBR). The molecular mechanisms that drive the FBR are not well understood. This work identifies the myeloid differentiation primary response gene 88 (MyD88) as a central mediator to macrophage activation in response to a poly(ethylene glycol) hydrogel with pre-adsorbed proteins in vitro. Moreover, MyD88 was also central to the recruitment of inflammatory cells, which included neutrophils, monocytes, and macrophages, to implanted PEG hydrogels and to fibrous encapsulation. These findings demonstrate that MyD88-mediated inflammation is responsible in part for the formation of the fibrous capsule of the FBR.

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.

Single-Molecule FRET Methods to Study Glutamate Receptors

Single-molecule fluorescence energy transfer methods allow us to determine the complete structural landscape between the donor and acceptor fluorophores introduced on the protein of interest. This method is particularly attractive to study ion channel proteins as single-molecule current recordings have been used to study the function of these proteins for several decades. Here we describe the smFRET method used to study glutamate receptors.

Surface-Templated Nanobubbles Protect Proteins from Surface-Mediated Denaturation

In this Letter, we report that surface-bound nanobubbles reduce protein denaturation on methylated glass by irreversible protein shell formation. Single-molecule total internal reflection fluorescence (SM-TIRF) microscopy was combined with intramolecular Förster resonance energy transfer (FRET) to study the conformational dynamics of nitroreductase (NfsB) on nanobubble-laden methylated glass surfaces, using reflection brightfield microscopy to register nanobubble locations with NfsB adsorption. First, NfsB adsorbed irreversibly to nanobubbles with no apparent desorption after 5 h. Moreover, virtually all (96%) of the NfsB molecules that interacted with nanobubbles remained folded, whereas less than 50% of NfsB molecules remained folded in the absence of nanobubbles on unmodified silica or methylated glass surfaces. This trend was confirmed by ensemble-average fluorometer TIRF experiments. We hypothesize that nanobubbles reduce protein damage by passivating strongly denaturing topographical surface defects. Thus, nanobubble stabilization on surfaces may have important implications for antifouling surfaces and improving therapeutic protein storage.

Conformational Dynamics, Intramolecular Domain Conformation Signaling, and Activation of Apo-FimD Revealed by Single-Molecule Fluorescence Resonance Energy Transfer Studies

The chaperone-usher secretion pathway is a conserved bacterial protein secretion system dedicated to the biogenesis of adhesive fibers. Usher, a multidomain-containing outer membrane protein, plays a central role in this process by acting as a molecular machine that recruits different chaperone-subunit complexes, catalyzes subunit polymerization, and forms a channel for secretion of the assembled subunits. While recent crystal structural studies have greatly advanced our understanding of the structure and function of ushers, the overall architecture of the full-length apo-usher, the molecular events that dictate conformational changes in usher during pilus biogenesis, and its activation by the specific chaperone-adhesin complex remain largely elusive. Using single-molecule fluorescence resonance energy transfer studies, we found that the substrate-free usher FimD (apo-FimD) adopts a contracted conformation that is distinct from its substrate-bound states; both the N-terminal domain (NTD) and the C-terminal domain (CTD) of apo-FimD are highly dynamic, and FimD coordinates its domain conformational changes via intramolecular domain conformation signaling. By combining these studies with in vitro photo-cross-linking studies, we further show that only the chaperone-bound adhesin (FimC:FimH) can be transferred to the CTD, dislocates the plug domain, and triggers conformational changes in the remaining FimD domains. Taken together, these studies delineate an overall architecture of the full-length apo-FimD, provide detailed mechanic insight into the activation of apo-FimD, and explain why FimD could adjust its conformational states to perform multiple functions in each cycle of pilus subunit addition and ensure that pilus assembly proceeds progressively in a cellular energy-free environment.

Zwitterionic PEG-PC Hydrogels Modulate the Foreign Body Response in a Modulus-Dependent Manner

Reducing the foreign body response (FBR) to implanted biomaterials will enhance their performance in tissue engineering. Poly(ethylene glycol) (PEG) hydrogels are increasingly popular for this application due to their low cost, ease of use, and the ability to tune their compliance via molecular weight and cross-linking densities. PEG hydrogels can elicit chronic inflammation in vivo, but recent evidence has suggested that extremely hydrophilic, zwitterionic materials and particles can evade the immune system. To combine the advantages of PEG-based hydrogels with the hydrophilicity of zwitterions, we synthesized hydrogels with comonomers PEG and the zwitterion phosphorylcholine (PC). Recent evidence suggests that stiff hydrogels elicit increased immune cell adhesion to hydrogels, which we attempted to reduce by increasing hydrogel hydrophilicity. Surprisingly, hydrogels with the highest amount of zwitterionic comonomer elicited the highest FBR. Lowering the hydrogel modulus (165 to 3 kPa), or PC content (20 to 0 wt %), mitigated this effect. A high density of macrophages was found at the surface of implants associated with a high FBR, and mass spectrometry analysis of the proteins adsorbed to these gels implicated extracellular matrix, immune response, and cell adhesion protein categories as drivers of macrophage recruitment. Overall, we show that modulus regulates macrophage adhesion to zwitterionic-PEG hydrogels, and demonstrate that chemical modifications to hydrogels should be studied in parallel with their physical properties to optimize implant design.

Revealing the principal attributes of protein adsorption on block copolymer surfaces with direct experimental evidence at the single protein level

Understanding protein adsorption onto polymer surfaces is of great importance in designing biomaterials, improving bioanalytical devices, and controlling biofouling, to name a few examples. Although steady research efforts have been advancing this field, our knowledge of this ubiquitous and complex phenomenon is still limited. In this study, we elucidate competitive protein adsorption behaviors sequentially occurring onto nanoscale block copolymer (BCP) surfaces via combined experimental and computer simulation approaches. The model systems chosen for our investigation are immunoglobulin G and fibrinogen introduced in different orders into the self-assembled nanodomains of poly(styrene)-block-poly(methylmethacrylate). We unambiguously reveal the adsorption, desorption, and replacement events of the same protein molecules via single protein tracking with atomic force microscopy. We then ascertain adsorption-related behaviors such as lateral mobility and self-association of proteins. We provide the much-needed, direct experimental proof of sequential adsorption events at the biomolecular level, which was virtually nonexistent before. We determine key protein adsorption pathways and dominant tendencies of sequential protein adsorption. We also reveal preadsorbed surface-associated behaviors in sequential adsorption, distinct from situations involving initially empty surfaces. We perform Monte-Carlo simulations to further substantiate our experimental outcomes. Our endeavors in this study may facilitate a well-guided mechanistic understanding of protein-polymer interactions by providing definite experimental evidence of competitive, sequential adsorption at the nanoscale. Increasingly, biomaterial and biomedical applications rely on systems of multicomponent proteins and chemically intricate, nanoscale polymer surfaces. Hence, our findings can also be beneficial for the development of next-generation nanobiomaterials and nanobiosensors exploiting self-assembled BCP nanodomain surfaces.

Enhancing Analytical Separations Using Super-Resolution Microscopy

Super-resolution microscopy is becoming an invaluable tool to investigate structure and dynamics driving protein interactions at interfaces. In this review, we highlight the applications of super-resolution microscopy for quantifying the physics and chemistry that occur between target proteins and stationary-phase supports during chromatographic separations. Our discussion concentrates on the newfound ability of super-resolved single-protein spectroscopy to inform theoretical parameters via quantification of adsorption-desorption dynamics, protein unfolding, and nanoconfined transport.

Bacterial Adhesion to Ultrafiltration Membranes: Role of Hydrophilicity, Natural Organic Matter, and Cell-Surface Macromolecules

Insight into the mechanisms underlying bacterial adhesion is critical to the formulation of membrane biofouling control strategies. Using AFM-based single-cell force spectroscopy, we investigated the interaction between Pseudomonas fluorescens, a biofilm-forming bacterium, and polysulfone (PSF) ultrafiltration (UF) membranes to unravel the mechanisms underlying early stage membrane biofouling. We show that hydrophilic polydopamine (PDA) coatings decrease bacterial adhesion forces at short bacterium-membrane contact times. Further, we find that adhesion forces are weakened by the presence of natural organic matter (NOM) conditioning films, owing to the hydrophilicity of NOM. Investigation of the effect of adhesion contact time revealed that PDA coatings are less effective at preventing bioadhesion when the contact time is prolonged to 2-5 s, or when the membranes are exposed to bacterial suspensions under stirring. These results therefore challenge the notion that simple hydrophilic surface coatings are effective as a biofouling control strategy. Finally, we present evidence that adhesion to the UF membrane surface is mediated by cell-surface macromolecules (likely to be outer membrane proteins and pili) which, upon contacting the membrane, undergo surface-induced unfolding.

Surface-Mediated DNA Hybridization: Effects of DNA Conformation, Surface Chemistry, and Electrostatics

Single-molecule Förster Resonance Energy Transfer (FRET) was used to study the dynamic association of mobile donor-labeled ssDNA oligonucleotides ("target") with covalently immobilized complementary acceptor-labeled ssDNA oligonucleotides ("probe"). While probe-target association events were resolved for all experiments, such FRET events were far more likely to occur in systems with complementarity and on hydrophobic, as compared to hydrophilic, surfaces. The distribution of donor-acceptor association-time intervals did not exhibit simple first-order kinetics, and when decomposed into a superposition of first-order processes, only a small fraction of events corresponded to a long-lived state that was presumed to represent true DNA hybridization, while the majority of association events were transient, representing nonspecific associations or partial hybridization. The structure of the DNA target and probe affected both the stability of the hybridized state, as well as the likelihood that an association between the two led to hybridization. In particular, the likelihood of hybridization decreased for longer target strands and for targets with stem-loop secondary structure. The presence of oligonucleotide secondary structure reduced the stability of hybridization, while greater complementarity increased stability of the hybridized state. Interestingly, increased ionic strength (i.e., greater electrostatic screening) increased the probability of hybridization but did not influence the lifetime of the hybridized state. Combined, these observations provide a nuanced view of surface-mediated DNA hybridization, where various factors independently influence the probability and stability of hybridization.

Connecting Protein Conformation and Dynamics with Ligand-Receptor Binding Using Three-Color Förster Resonance Energy Transfer Tracking

Specific binding between biomolecules, i.e., molecular recognition, controls virtually all biological processes including the interactions between cells and biointerfaces, both natural and synthetic. Such binding often relies on the conformation of biomacromolecules, which can be highly heterogeneous and sensitive to environmental perturbations, and therefore difficult to characterize and control. An approach is demonstrated here that directly connects the binding kinetics and stability of the protein receptor integrin α_vβ₃ to the conformation of the ligand fibronectin (FN), which are believed to control cellular mechanosensing. Specifically, we investigated the influence of surface-adsorbed FN structure and dynamics on α_vβ₃ binding using high-throughput single-molecule three-color Förster resonance energy transfer (FRET) tracking methods. By controlling FN structure and dynamics through tuning surface chemistry, we found that as the conformational and translational dynamics of FN increased, the rate of binding, particularly to folded FN, and stability of the bound FN-α_vβ₃ complex decreased significantly. These findings highlight the importance of the conformational plasticity and accessibility of the arginine-glycine-aspartic acid (RGD) binding site in FN, which, in turn, mediates cell signaling in physiological and synthetic environments.

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.

Dual Unnatural Amino Acid Incorporation and Click-Chemistry Labeling to Enable Single-Molecule FRET Studies of p97 Folding

Many cellular functions are critically dependent on the folding of complex multimeric proteins, such as p97, a hexameric multidomain AAA+ chaperone. Given the complex architecture of p97, single-molecule (sm) FRET would be a powerful tool for studying folding while avoiding ensemble averaging. However, dual site-specific labeling of such a large protein for smFRET is a significant challenge. Here, we address this issue by using bioorthogonal azide-alkyne chemistry to attach an smFRET dye pair to site-specifically incorporated unnatural amino acids, allowing us to generate p97 variants reporting on inter- or intradomain structural features. An initial proof-of-principle set of smFRET results demonstrated the strengths of this labeling method. Our results highlight this as a powerful tool for structural studies of p97 and other large protein machines.

Dense Poly(ethylene glycol) Brushes Reduce Adsorption and Stabilize the Unfolded Conformation of Fibronectin

Polymer brushes, in which polymers are end-tethered densely to a grafting surface, are commonly proposed for use as stealth coatings for various biomaterials. However, although their use has received considerable attention, a mechanistic understanding of the impact of brush properties on protein adsorption and unfolding remains elusive. We investigated the effect of the grafting density of poly(ethylene glycol) (PEG) brushes on the interactions of the brush with fibronectin (FN) using high-throughput single-molecule tracking methods, which directly measure protein adsorption and unfolding within the brush. We observed that, as grafting density increased, the rate of FN adsorption decreased; however, surface-adsorbed FN unfolded more readily, and unfolded molecules were retained on the surface for longer residence times relative to those of folded molecules. These results, which are critical for the rational design of PEG brushes, suggest that there is a critical balance between protein adsorption and conformation that underlies the utility of such brushes in physiological environments.

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.

Capturing Conformation-Dependent Molecule-Surface Interactions When Surface Chemistry Is Heterogeneous

Molecular building blocks, such as carbon nanotubes and DNA origami, can be fully integrated into electronic and optical devices if they can be assembled on solid surfaces using biomolecular interactions. However, the conformation and functionality of biomolecules depend strongly on the local chemical environment, which is highly heterogeneous near a surface. To help realize the potential of biomolecular self-assembly, we introduce here a technique to spatially map molecular conformations and adsorption, based on single-molecule fluorescence microscopy. On a deliberately patterned surface, with regions of varying hydrophobicity, we characterized the conformations of adsorbed helicogenic alanine-lysine copeptides using Förster resonance energy transfer. The peptides adopted helical conformations on hydrophilic regions of the surface more often than on hydrophobic regions, consistent with previous ensemble-averaged observations of α-helix surface stability. Interestingly, this dependence on surface chemistry was not due to surface-induced unfolding, as the apparent folding and unfolding dynamics were usually much slower than desorption. The most significant effect of surface chemistry was on the adsorption rate of molecules as a function of their initial conformational state. In particular, regions with higher adsorption rates attracted more molecules in compact, disordered coil states, and this difference in adsorption rates dominated the average conformation of the ensemble. The correlation between adsorption rate and average conformation was also observed on nominally uniform surfaces. Spatial variations in the functional state of adsorbed molecules would strongly affect the success rates of surface-based molecular assembly and can be fully understood using the approach developed in this work.

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.

Site-specific bioconjugation of a murine dihydrofolate reductase enzyme by copper(I)-catalyzed azide-alkyne cycloaddition with retained activity

Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is an efficient reaction linking an azido and an alkynyl group in the presence of copper catalyst. Incorporation of a non-natural amino acid (NAA) containing either an azido or an alkynyl group into a protein allows site-specific bioconjugation in mild conditions via CuAAC. Despite its great potential, bioconjugation of an enzyme has been hampered by several issues including low yield, poor solubility of a ligand, and protein structural/functional perturbation by CuAAC components. In the present study, we incorporated an alkyne-bearing NAA into an enzyme, murine dihydrofolate reductase (mDHFR), in high cell density cultivation of Escherichia coli, and performed CuAAC conjugation with fluorescent azide dyes to evaluate enzyme compatibility of various CuAAC conditions comprising combination of commercially available Cu(I)-chelating ligands and reductants. The condensed culture improves the protein yield 19-fold based on the same amount of non-natural amino acid, and the enzyme incubation under the optimized reaction condition did not lead to any activity loss but allowed a fast and high-yield bioconjugation. Using the established conditions, a biotin-azide spacer was efficiently conjugated to mDHFR with retained activity leading to the site-specific immobilization of the biotin-conjugated mDHFR on a streptavidin-coated plate. These results demonstrate that the combination of reactive non-natural amino acid incorporation and the optimized CuAAC can be used to bioconjugate enzymes with retained enzymatic activity.

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

A common goal across different fields (e.g. separations, biosensors, biomaterials, pharmaceuticals) is to understand how protein behavior at solid-liquid interfaces is affected by environmental conditions. Temperature, pH, ionic strength, and the chemical and physical properties of the solid surface, among many factors, can control microscopic protein dynamics (e.g. adsorption, desorption, diffusion, aggregation) that contribute to macroscopic properties like time-dependent total protein surface coverage and protein structure. These relationships are typically studied through a top-down approach in which macroscopic observations are explained using analytical models that are based upon reasonable, but not universally true, simplifying assumptions about microscopic protein dynamics. Conclusions connecting microscopic dynamics to environmental factors can be heavily biased by potentially incorrect assumptions. In contrast, more complicated models avoid several of the common assumptions but require many parameters that have overlapping effects on predictions of macroscopic, average protein properties. Consequently, these models are poorly suited for the top-down approach. Because the sophistication incorporated into these models may ultimately prove essential to understanding interfacial protein behavior, this article proposes a bottom-up approach in which direct observations of microscopic protein dynamics specify parameters in complicated models, which then generate macroscopic predictions to compare with experiment. In this framework, single-molecule tracking has proven capable of making direct measurements of microscopic protein dynamics, but must be complemented by modeling to combine and extrapolate many independent microscopic observations to the macro-scale. The bottom-up approach is expected to better connect environmental factors to macroscopic protein behavior, thereby guiding rational choices that promote desirable protein behaviors.

Conformational changes of globular proteins upon adsorption on a hydrophobic surface

Coarse-grained Monte Carlo simulations are used to study thermal denaturation of small globular proteins adsorbed on a hydrophobic surface. Though helices are more stable than sheets, they are highly deformed in the adsorbed protein.

Interfacial protein-protein associations

While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on polyethylene glycol modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for longer times. The appearance of three distinct RET states suggested a spatially heterogeneous surface - with areas of high protein density (i.e., strongly interacting clusters) coexisting with mobile monomers. Distinct association states exhibited characteristic behavior, i.e., partial-RET (monomer-monomer) associations were shorter-lived than complete-RET (protein-cluster) associations. While the fractional surface area covered by regions with high protein density (i.e., clusters) increased with increasing concentration, the distribution of contact times between monomers and clusters was independent of solution concentration, suggesting that associations were a local phenomenon, and independent of the global surface coverage.