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

Mechanistic Understanding of Protein Corona Formation around Nanoparticles: Old Puzzles and New Insights

Although a wide variety of nanoparticles (NPs) have been engineered for use as disease markers or drug delivery agents, the number of nanomedicines in clinical use has hitherto remained small. A key obstacle in nanomedicine development is the lack of a deep mechanistic understanding of NP interactions in the bio-environment. Here, the focus is on the biomolecular adsorption layer (protein corona), which quickly enshrouds a pristine NP exposed to a biofluid and modifies the way the NP interacts with the bio-environment. After a brief introduction of NPs for nanomedicine, proteins, and their mutual interactions, research aimed at addressing fundamental properties of the protein corona, specifically its mono-/multilayer structure, reversibility and irreversibility, time dependence, as well as its role in NP agglomeration, is critically reviewed. It becomes quite evident that the knowledge of the protein corona is still fragmented, and conflicting results on fundamental issues call for further mechanistic studies. The article concludes with a discussion of future research directions that should be taken to advance the understanding of the protein corona around NPs. This knowledge will provide NP developers with the predictive power to account for these interactions in the design of efficacious nanomedicines.

Surface-Induced Protein Aggregation and Particle Formation in Biologics: Current Understanding of Mechanisms, Detection and Mitigation Strategies

Protein stability against aggregation is a major quality concern for the production of safe and effective biopharmaceuticals. Amongst the different drivers of protein aggregation, increasing evidence indicates that interactions between proteins and interfaces represent a major risk factor for the formation of protein aggregates in aqueous solutions. Potentially harmful surfaces relevant to biologics manufacturing and storage include air-water and silicone oil-water interfaces as well as materials from different processing units, storage containers, and delivery devices. The impact of some of these surfaces, for instance originating from impurities, can be difficult to predict and control. Moreover, aggregate formation may additionally be complicated by the simultaneous presence of interfacial, hydrodynamic and mechanical stresses, whose contributions may be difficult to deconvolute. As a consequence, it remains difficult to identify the key chemical and physical determinants and define appropriate analytical methods to monitor and predict protein instability at these interfaces. In this review, we first discuss the main mechanisms of surface-induced protein aggregation. We then review the types of contact materials identified as potentially harmful or detected as potential triggers of proteinaceous particle formation in formulations and discuss proposed mitigation strategies. Finally, we present current methods to probe surface-induced instabilities, which represent a starting point towards assays that can be implemented in early-stage screening and formulation development of biologics.

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.

The competing influence of surface roughness, hydrophobicity, and electrostatics on protein dynamics on a self-assembled monolayer

Surface morphology, in addition to hydrophobic and electrostatic effects, can alter how proteins interact with solid surfaces. Understanding the heterogeneous dynamics of protein adsorption on surfaces with varying roughness is experimentally challenging. In this work, we use single-molecule fluorescence microscopy to study the adsorption of α-lactalbumin protein on the glass substrate covered with a self-assembled monolayer (SAM) with varying surface concentrations. Two distinct interaction mechanisms are observed: localized adsorption/desorption and continuous-time random walk (CTRW). We investigate the origin of these two populations by simultaneous single-molecule imaging of substrates with both bare glass and SAM-covered regions. SAM-covered areas of substrates are found to promote CTRW, whereas glass surfaces promote localized motion. Contact angle measurements and atomic force microscopy imaging show that increasing SAM concentration results in both increasing hydrophobicity and surface roughness. These properties lead to two opposing effects: increasing hydrophobicity promotes longer protein flights, but increasing surface roughness suppresses protein dynamics resulting in shorter residence times. Our studies suggest that controlling hydrophobicity and roughness, in addition to electrostatics, as independent parameters could provide a means to tune desirable or undesirable protein interactions with surfaces.

Stabilization and Kinetics of an Adsorbed Protein Depends on the Poly(N-isopropylacrylamide) Grafting Density

The solubility transition at the lower critical solution temperature (LCST, 32 °C) of poly(N-isopropylacrylamide) (PNIPAM) is widely used as a thermal switch to rapidly and reversibly capture and release proteins and cells. It is generally assumed that proteins adsorbed to PNIPAM above the LCST are unaffected by polymer interactions. Here we show that the folding stability of the enzyme phosphoglycerate kinase (PGK) is increased by interactions with end-grafted PNIPAM films above the LCST. We systematically compare two protein mutants with different stabilities. The stabilization mirrors the degree of protein adsorption under grafting conditions studied previously. Maximum stabilization occurs when proteins adsorb to low density, collapsed polymer "mushrooms". In the denser polymer "brush" regime, protein stabilization decreases back to a value indistinguishable from the bulk solution, consistent with low protein adsorption on dense, collapsed brushes. The temperature-dependent kinetics measured by Fast Relaxation Imaging reveals that PNIPAM does not affect the overall folding/unfolding mechanism. Based on the different stabilizations of two mutants and the relaxation kinetics, we hypothesize that the polymer acts mainly by increasing the conformational entropy of the folded protein by interacting with the protein surface and less by crowding the unfolded state of PGK.

Single-Molecule Study of Thermomyces lanuginosus Lipase in a Detergency Application System Reveals Diffusion Pattern Remodeling by Surfactants and Calcium

Lipases comprise one of the major enzyme classes in biotechnology with applications within, e.g., baking, brewing, biocatalysis, and the detergent industry. Understanding the mechanisms of lipase function and regulation is therefore important to facilitate the optimization of their function by protein engineering. Advances in single-molecule studies in model systems have provided deep mechanistic insights on lipase function, such as the existence of functional states, their dependence on regulatory cues, and their correlation to activity. However, it is unclear how these observations translate to enzyme behavior in applied settings. Here, single-molecule tracking of individual Thermomyces lanuginosus lipase (TLL) enzymes in a detergency application system allowed real-time direct observation of spatiotemporal localization, and thus diffusional behavior, of TLL enzymes on a lard substrate. Parallelized imaging of thousands of individual enzymes allowed us to observe directly the existence and quantify the abundance and interconversion kinetics between three diffusional states that we recently provided evidence to correlate with function. We observe redistribution of the enzyme's diffusional pattern at the lipid-water interface as well as variations in binding efficiency in response to surfactants and calcium, demonstrating that detergency effectors can drive the sampling of lipase functional states. Our single-molecule results combined with ensemble activity assays and enzyme surface binding efficiency readouts allowed us to deconvolute how application conditions can significantly alter protein functional dynamics and/or surface binding, both of which underpin enzyme performance. We anticipate that our results will inspire further efforts to decipher and integrate the dynamic nature of lipases, and other enzymes, in the design of new biotechnological solutions.

Understanding Design Rules for Optimizing the Interface between Immobilized Enzymes and Random Copolymer Brushes

A long-standing goal in the field of biotechnology is to develop and understand design rules for the stabilization of enzymes upon immobilization to materials. While immobilization has sometimes been successful as a strategy to stabilize enzymes, the design of synthetic materials that stabilize enzymes remains largely empirical. We sought to overcome this challenge by investigating the mechanistic basis for the stabilization of immobilized lipases on random copolymer brush surfaces comprised of poly(ethylene glycol) methacrylate (PEGMA) and sulfobetaine methacrylate (SBMA), which represent novel heterogeneous supports for immobilized enzymes. Using several related but structurally diverse lipases, including Bacillus subtilis lipase A (LipA), Rhizomucor miehei lipase, Candida rugosa lipase, and Candida antarctica lipase B (CALB), we showed that the stability of each lipase at elevated temperatures was strongly dependent on the fraction of PEGMA in the brush layer. This dependence was explained by developing and applying a new algorithm to quantify protein surface hydrophobicity, which involved using unsupervised cluster analysis to identify clusters of hydrophobic atoms. Characterization of the lipases showed that the optimal brush composition correlated with the free energy of solvation per enzyme surface area, which ranged from -17.1 kJ/mol·nm² for LipA to -11.8 kJ/mol·nm² for CALB. Additionally, using this algorithm, we found that hydrophobic patches consisting of aliphatic residues had a higher free energy than patches consisting of aromatic residues. By providing the basis for rationally tuning the interface between enzymes and materials, this understanding will transform the use of materials to reliably ruggedize enzymes under extreme conditions.

Faster Surface Ligation Reactions Improve Immobilized Enzyme Structure and Activity

During integration into materials, the inactivation of enzymes as a result of their interaction with nanometer size denaturing "hotspots" on surfaces represents a critical challenge. This challenge, which has received far less attention than improving the long-term stability of enzymes, may be overcome by limiting the exploration of surfaces by enzymes. One way this may be accomplished is through increasing the rate constant of the surface ligation reaction and thus the probability of immobilization with reactive surface sites (i.e., ligation efficiency). Here, the connection between ligation reaction efficiency and the retention of enzyme structure and activity was investigated by leveraging the extremely fast reaction of strained trans-cyclooctene (sTCOs) and tetrazines (Tet). Remarkably, upon immobilization via Tet-sTCO chemistry, carbonic anhydrase (CA) retained 77% of its solution-phase activity, while immobilization via less efficient reaction chemistries, such as thiol-maleimide and azide-dibenzocyclooctyne, led to activity retention of only 46% and 27%, respectively. Dynamic single-molecule fluorescence tracking methods further revealed that longer surface search distances prior to immobilization (>0.5 μm) dramatically increased the probability of CA unfolding. Notably, the CA distance to immobilization was significantly reduced through the use of Tet-sTCO chemistry, which correlated with the increased retention of structure and activity of immobilized CA compared to the use of slower ligation chemistries. These findings provide an unprecedented insight into the role of ligation reaction efficiency in mediating the exploration of denaturing hotspots on surfaces by enzymes, which, in turn, may have major ramifications in the creation of functional biohybrid materials.

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.

Single-Particle Kinetics of Immobilized Enzymes by Harnessing the Autofluorescence of Co-Immobilized Cofactors

The co-immobilized enzymes and cofactors onto porous microparticles work as self-sufficient heterogeneous biocatalysts whose catalytic activity can be easily monitored by means of the cofactors autofluorescence. The reduction step of some cofactors as NAD⁺ and FAD⁺ to NADH and FADH₂, respectively, involves an increase of its autofluorescence. This phenomenon is harnessed to image and analyze the enzymatic reactions catalyzed by cofactor-dependent enzymes at real time and single-particle level during the operational process. Due to the universality and highly accessibility of fluorescence microscopy, the strategy described here allows a straightforward and more accurate analysis at micro-scale of heterogeneous biocatalysts. These studies promote and support the rational design and optimization of biocatalysts toward highly efficient heterogeneous biocatalytic reactions.

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

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

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.

Transforming Separation Science with Single-Molecule Methods

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

Polymer Free Volume Effects on Protein Dynamics in Polystyrene Revealed by Single-Molecule Spectroscopy

Protein-polymer interactions are critical to applications ranging from biomedical devices to chromatographic separations. The mechanistic relationship between the microstructure of polymer chains and protein interactions is challenging to quantify and not well studied. Here, single-molecule microscopy is used to compare the dynamics of two model proteins, α-lactalbumin and lysozyme, at the interface of uncharged polystyrene with varied molecular weights. The two proteins exhibit different surface interaction mechanisms despite having a similar size and structure. α-Lactalbumin exhibits interfacial adsorption-desorption with residence times that depend on polymer molecular weight. Lysozyme undergoes a continuous time random walk at the polystyrene surface with residence times that also depend on the molecular weight of polystyrene. Single-molecule observables suggest that the hindered continuous time random walk dynamics displayed by lysozyme are determined by the polystyrene free volume, a finding supported by thermal annealing and solvent quality studies. Hindered dynamics are dominated by short-range hydrophobic interactions where the contributions of electrostatic forces are negligible. This work establishes a relationship between the microscale structure (i.e., free volume) of polystyrene polymer chains to nanoscale interfacial protein dynamics.

Anomalous protein kinetics on low-fouling surfaces

In this work, protein-surface interactions were probed in terms of adsorption and desorption of a model protein, bovine serum albumin, on a low-fouling surface with single-molecule localization microscopy. Single-molecule experiments enable precise determination of both adsorption and desorption rates. Strikingly the experimental data show anomalous desorption kinetics, evident as a surface dwell time that exhibits a power-law distribution, i.e. a heavy-tailed rather than the expected exponential distribution. As a direct consequence of this heavy-tailed distribution, the average desorption rate depends upon the time scale of the experiment and the protein surface concentration does not reach equilibrium. Further analysis reveals that the observed anomalous desorption emerges due to the reversible formation of a small fraction of soluble protein multimers (small oligomers), such that each one desorbs from the surface with a different rate. The overall kinetics can be described by a series of elementary reactions, yielding simple scaling relations that predict experimental observations. This work reveals a mechanistic origin for anomalous desorption kinetics that can be employed to interpret observations where low-protein fouling surfaces eventually foul when in long-term contact with protein solutions. The work also provides new insights that can be used to define design principles for non-fouling surfaces and to predict their performance.

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

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

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

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

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

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

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.

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

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

Advances in surface-enhanced Raman spectroscopy (SERS) substrates for lipid and protein characterization: sensing and beyond

Surface-enhanced Raman spectroscopy (SERS) has become an essential ultrasensitive analytical tool for biomolecular analysis of small molecules, macromolecular proteins, and even cells. SERS enables label-free, direct detection of molecules through their intrinsic Raman fingerprint. In particular, protein and lipid bilayers are dynamic three-dimensional structures that necessitate label-free methods of characterization. Beyond direct detection and quantitation, the structural information contained in SERS spectra also enables deeper biophysical characterization of biomolecules near metallic surfaces. Therefore, SERS offers enormous potential for such systems, although making measurements in a nonperturbative manner that captures the full range of interactions and activity remains a challenge. Many of these challenges have been overcome through advances in SERS substrate development, which have expanded the applications and targets of SERS for direct biomolecular quantitation and biophysical characterization. In this review, we will first discuss different categories of SERS substrates including solution-phase, solid-supported, tip-enhanced Raman spectroscopy (TERS), and single-molecule substrates for biomolecular analysis. We then discuss detection of protein and biological lipid membranes. Lastly, biophysical insights into proteins, lipids and live cells gained through SERS measurements of these systems are reviewed.

Correlating Structural and Functional Heterogeneity of Immobilized Enzymes

Many nanobiotechnology applications rely on stable and efficient integration of functional biomacromolecules with synthetic nanomaterials. Unfortunately, the reasons for the ubiquitous loss of activity of immobilized enzymes remain poorly understood due to the difficulty in distinguishing between distinct molecular-level mechanisms. Here, we employ complementary single-molecule fluorescence methods that independently measure the impact of immobilization on the structure and function ( i. e., substrate binding kinetics) of nitroreductase (NfsB). Stochastic statistical modeling methods were used to unambiguously quantify the effects of immobilized NfsB structural dynamics on function, allowing us to explicitly separate effects due to conformation and accessibility. Interestingly, we found that nonspecifically tethered NfsB exhibited enhanced stability compared to site-specifically tethered NfsB; however, the folded state of site-specifically tethered NfsB had faster substrate binding rates, suggesting improved active site accessibility. This demonstrated an unexpected intrinsic trade-off associated with competing bioconjugation methods, suggesting that it may be necessary to balance conformational stability versus active site accessibility. This nuanced view of the impact of immobilization will facilitate a rational approach to the integration of enzymes with synthetic nanomaterials.

Stabilization of Immobilized Enzymes via the Chaperone-Like Activity of Mixed Lipid Bilayers

Biomimetic lipid bilayers represent intriguing materials for enzyme immobilization, which is critical for many biotechnological applications. Here, through the creation of mixed lipid bilayers, the retention of immobilized enzyme structures and catalytic activity are dramatically enhanced. The enhancement in the retention of enzyme structures, which correlated with an increase in enzyme activity, is observed using dynamic single-molecule (SM) fluorescence methods. The results of SM analysis specifically show that lipid bilayers composed of mixtures of 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC) and 1,2-dioleoyl- sn-glycero-3-phospho-(1'- rac-glycerol) (DOPG) stabilize the folded state of nitroreductase (NfsB), increasing the rate of refolding relative to unfolding of enzyme molecules on the bilayer surface. Remarkably, for optimal compositions with 15-50% DOPG, over 95% of NfsB remains folded while the activity of the enzyme is increased as much as 2 times over that in solution. Within this range of DOPG, the strength of the interaction of folded and unfolded NfsB with the bilayer surface was also significantly altered, which was evident by the change in the diffusion of folded and unfolded NfsB in the bilayer. Ultimately, these findings provide direct evidence for the chaperone-like activity of mixed DOPG/DOPC lipid bilayers, which can be controlled by tuning the fraction of DOPG in the bilayer.

Super-Temporal-Resolved Microscopy Reveals Multistep Desorption Kinetics of α-Lactalbumin from Nylon

Insight into the mechanisms driving protein-polymer interactions is constantly improving due to advances in experimental and computational methods. In this study, we used super-temporal-resolved microscopy (STReM) to study the interfacial kinetics of a globular protein, α-lactalbumin (α-LA), adsorbing at the water-nylon 6,6 interface. The improved temporal resolution of STReM revealed that residence time distributions involve an additional step in the desorption process. Increasing the ionic strength in the bulk solution accelerated the desorption rate of α-LA, attributed to adsorption-induced conformational changes. Ensemble circular dichroism measurements were used to support a consecutive reaction mechanism. Without the improved temporal resolution of STReM, the desorption intermediate was not resolvable, highlighting both STReM's potential to uncover new kinetic mechanisms and the continuing need to push for better time and space resolution.

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.

Mechanistic Origin of the Combined Effect of Surfaces and Mechanical Agitation on Amyloid Formation

Interactions between proteins and surfaces in combination with hydrodynamic flow and mechanical agitation can often trigger the conversion of soluble peptides and proteins into aggregates, including amyloid fibrils. Despite the extensive literature on the empirical effects of surfaces and mechanical forces on the formation of amyloids, the molecular details of the mechanisms underlying this behavior are still elusive. This limitation is, in part, due to the complex reaction network underlying the formation of amyloids, where several microscopic reactions of nucleation and growth can occur both at the interfaces and in bulk. In this work, we design a high-throughput assay based on nanoparticles and we apply a chemical kinetic platform to analyze the mechanisms underlying the effect of surfaces and mechanical forces on the formation of amyloid fibrils from human insulin under physiological conditions. By considering a variety of polymeric nanoparticles with different surface properties we explore a broad range of repulsive and attractive interactions between insulin and surfaces. Our analysis shows that hydrophobic interfaces induce the formation of amyloid fibrils by specifically promoting the primary heterogeneous nucleation rate. In contrast, mechanical forces accelerate the formation of amyloid fibrils by favoring mass transport and further amplify the number of fibrils by promoting fragmentation events. Thus, surfaces and agitation have a combined effect on the kinetics of protein aggregation observed at the macroscopic level but, individually, they each affect distinct microscopic reaction steps: the presence of interfaces generates primary nucleation events of fibril formation, which is then amplified by mechanical forces. These results suggest that the inhibition of surface-induced heterogeneous nucleation should be considered a primary target to suppress aggregation and explain why in many systems the simultaneous presence of surfaces and hydrodynamic flow enhances protein aggregation.

Effect of size and curvature on the enzyme activity of bionanoconjugates

Biotic-abiotic hybrids comprised of globular proteins and functional nanostructures with complementary and synergistic properties are central to a number of bionanotechnological applications. A comprehensive understanding of the effect of physicochemical properties of abiotic nanostructures on the biological activity of the bionanoconjugates is critical in the design of these bio-nano hybrids. In this study, using size and curvature-controlled gold nanoparticles as a model abiotic system, we investigated the effect of hydrodynamic diameter and surface curvature on the activity of a model enzyme, horseradish peroxidase (HRP), adsorbed on the surface of the nanostructures. In contrast with the previous studies, we have employed a novel class of gold superstructures (gold nanoparticles on spheres) to deconvolute the effects of size and curvature on the catalytic activity of the bionanoconjugates. This study improves our understanding of the bio/nano interface and the design of bioinorganic hybrids with potential applications in biomimetic and bioenabled sensors, energy harvesting, optoelectronic components and devices, responsive and autonomous materials.

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.

Direct Imaging of Protein Stability and Folding Kinetics in Hydrogels

We apply fast relaxation imaging (FReI) as a novel technique for investigating the folding stability and dynamics of proteins within polyacrylamide hydrogels, which have diverse and widespread uses in biotechnology. FReI detects protein unfolding in situ by imaging changes in fluorescence resonance energy transfer (FRET) after temperature jump perturbations. Unlike bulk measurements, diffraction-limited epifluorescence imaging combined with fast temperature perturbations reveals the impact of local environment effects on protein-biomaterial compatibility. Our experiments investigated a crowding sensor protein (CrH2) and phosphoglycerate kinase (PGK), which undergoes cooperative unfolding. The crowding sensor quantifies the confinement effect of the cross-linked hydrogel: the 4% polyacrylamide hydrogel is similar to aqueous solution (no confinement), while the 10% hydrogel is strongly confining. FRAP measurements and protein concentration gradients in the 4% and 10% hydrogels further support this observation. PGK reveals that noncovalent interactions of the protein with the polymer surface are more important than confinement for determining protein properties in the gel: the mere presence of hydrogel increases protein stability, speeds up folding relaxation, and promotes irreversible binding to the polymer even at the solution-gel interface, whereas the difference between the 4% and the 10% hydrogels is negligible despite their large difference in confinement. The imaging capabilities of FReI, demonstrated to be diffraction limited, further revealed spatially homogeneous protein unfolding across the hydrogels at 500 nm length scales and revealed differences in protein properties at the gel-solution boundary.

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.

Super Temporal-Resolved Microscopy (STReM)

Super-resolution microscopy typically achieves high spatial resolution, but the temporal resolution remains low. We report super temporal-resolved microscopy (STReM) to improve the temporal resolution of 2D super-resolution microscopy by a factor of 20 compared to that of the traditional camera-limited frame rate. This is achieved by rotating a phase mask in the Fourier plane during data acquisition and then recovering the temporal information by fitting the point spread function (PSF) orientations. The feasibility of this technique is verified with both simulated and experimental 2D adsorption/desorption and 2D emitter transport. When STReM is applied to measure protein adsorption at a glass surface, previously unseen dynamics are revealed.

Polymer Surface Transport Is a Combination of in-Plane Diffusion and Desorption-Mediated Flights

Previous studies of polymer motion at solid/liquid interfaces described the transport in the context of a continuous time random walk (CTRW) process, in which diffusion switches between desorption-mediated "flights" (i.e., hopping) and surface-adsorbed waiting-time intervals. However, it has been unclear whether the waiting times represented periods of complete immobility or times during which molecules engaged in a different (e.g., slower or confined) mode of interfacial transport. Here we designed high-throughput, single-molecule tracking measurements to address this question. Specifically, we studied polymer dynamics on either chemically homogeneous or nanopatterned surfaces (hexagonal diblock copolymer films) with chemically distinct domains, where polymers were essentially excluded from the low-affinity domains, eliminating the possibility of significant continuous diffusion in the absence of desorption-mediated flights. Indeed, the step-size distributions on homogeneous surfaces exhibited an additional diffusive mode that was missing on the chemically heterogeneous nanopatterned surfaces, confirming the presence of a slow continuous mode due to 2D in-plane diffusion. Kinetic Monte Carlo simulations were performed to test this model and, with the theoretical in-plane diffusion coefficient of D_2D = 0.20 μm²/s, we found a good agreement between simulations and experimental data on both chemically homogeneous and nanopatterned surfaces.

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.