Joel L. Kaar

Use of Salt Hydrate Pairs to Control Water Activity for Enzyme Catalysis in Ionic Liquids

Salt hydrate pairs were used to control water activity in the ionic liquid 1‐butyl‐3‐methylimidazolium hexafluorophosphate. It was shown that salt hydrate pairs behave essentially the same in ionic liquids as they do in organic solvents as long as they do not dissolve. Initial rate‐water activity profiles were prepared for the immobilized Candida antarctica lipase catalyzed synthesis of 2‐ethylhexyl methacrylate. The ability to use salt hydrate pairs for the control of water activity in ionic liquids should allow for improved comparison of enzyme activity and specificity in ionic liquids and conventional solvents.

Matrix metalloproteinase-1 treatment of muscle fibrosis.

The onset of scarring after injury may impede the regeneration and functional recovery of skeletal muscle. Matrix metalloproteinase-1 (MMP-1) hydrolyzes type I collagen and thus may improve muscle regeneration by resolving fibrotic tissue. We examined the effect of recombinant human MMP-1 on fibrosis in the lacerated gastrocnemius muscle of NOD/scid mice, allowing treatment potential to be ascertained in isolation from immune response. The efficacy of proMMP-1 and active MMP-1 were compared with or without poly(ethylene glycol) (PEG) modification, which was intended to increase the enzymes stability. Active MMP-1 was most effective in reducing fibrosis, although treatment with proMMP-1 was also beneficial relative to controls. PEG-modified MMP-1 had minimal activity in vivo, despite retaining activity towards a thioester substrate. Moreover, the modified enzyme was inactivated by trypsin and subtilisin at rates comparable to that of native MMP-1. These results and those of computational structural studies suggest that modification occurs at the C-terminal hemopexin domain of MMP-1, which plays a critical role in collagen turnover. Site-specific modifications that spares catalytic and substrate binding sites while protecting susceptible proteolytic digestion sites may be beneficial. We conclude that active MMP-1 can effectively reduce muscle scarring and that its activity is related to the ability of the enzyme to digest collagen, thereby facilitating remodeling of the injured muscle.

Stabilization of enzymes in ionic liquids via modification of enzyme charge

Due to the propensity of ionic liquids (ILs) to inactivate enzymes, the development of strategies to improve enzyme utility in these solvents is critical to fully exploit ILs for biocatalysis. We have developed a strategy to broadly improve enzyme utility in ILs based on elucidating the effect of charge modifications on the function of enzymes in IL environments. Results of stability studies in aqueous‐IL mixtures indicated a clear connection between the ratio of enzyme‐containing positive‐to‐negative sites and enzyme stability in ILs. Stability studies of the effect of [BMIM][Cl] and [EMIM][EtSO4] on chymotrypsin specifically found an optimum ratio of positively‐charged amine‐to‐negatively‐charged acid groups (0.39). At this ratio, the half‐life of chymotrypsin was increased 1.6‐ and 4.3‐fold relative to wild‐type chymotrypsin in [BMIM][Cl] and [EMIM][EtSO4], respectively. The half‐lives of lipase and papain were similarly increased as much as 4.0 and 2.4‐fold, respectively, in [BMIM][Cl] by modifying the ratio of positive‐to‐negative sites of each enzyme. More generally, the results of stability studies found that modifications that reduce the ratio of enzyme‐containing positive‐to‐negative sites improve enzyme stability in ILs. Understanding the impact of charge modification on enzyme stability in ILs may ultimately be exploited to rationally engineer enzymes for improved function in IL environments. Biotechnol. Bioeng. 2013; 110:2352–2360.

Charge engineering of cellulases improves ionic liquid tolerance and reduces lignin inhibition

We report a novel approach to concurrently improve the tolerance to ionic liquids (ILs) as well as reduce lignin inhibition of Trichoderma reesei cellulase via engineering enzyme charge. Succinylation of the cellulase enzymes led to a nearly twofold enhancement in cellulose conversion in 15% (v/v) 1‐butyl‐3‐methylimidazolium chloride ([BMIM][Cl]). The improvement in activity upon succinylation correlated with the apparent preferential exclusion of the [Cl] anion in fluorescence quenching assays. Additionally, modeling analysis of progress curves of Avicel hydrolysis in buffer indicated that succinylation had a negligible impact on the apparent KM of cellulase. As evidence of reducing lignin inhibition of T. reesei cellulase, succinylation resulted in a greater than twofold increase in Avicel conversion after 170 h in buffer with 1 wt% lignin. The impact of succinylation on lignin inhibition of cellulase further led to the reduction in apparent KM of the enzyme cocktail for Avicel by 2.7‐fold. These results provide evidence that naturally evolved cellulases with highly negative surface charge densities may similarly repel lignin, resulting in improved cellulase activity. Ultimately, these results underscore the potential of rational charge engineering as a means of enhancing cellulase function and thus conversion of whole biomass in ILs. Biotechnol. Bioeng. 2014;111: 1541–1549.

Photonic crystal kinase biosensor.

We have developed a novel biosensor for kinases that is based on a kinase-responsive polymer hydrogel, which enables label-free screening of kinase activity via changes in optical properties. The hydrogel is specifically designed to swell reversibly upon phosphorylation of a target peptide, triggering a change in optical diffraction from a crystalline colloidal array of particles impregnated into the hydrogel. Diffraction measurements, and charge staining, confirmed the responsive nature of the hydrogel. Moreover, the change in diffraction of the hydrogel upon treatment with kinase exhibited a time- and dose-dependent response. A theoretical model for ionic polymer networks describes the observed optical response well and can be used to quantify the extent of phosphorylation.

Mediating electrostatic binding of 1-butyl-3-methylimidazolium chloride to enzyme surfaces improves conformational stability.

We have recently developed a general approach to improve the utility of enzymes in ionic liquids (ILs) via tuning of the ratio of enzyme-containing positive to negative surface charges. In this work, the impact of enzyme surface charge ratio on the biophysical interaction of 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]) with chymotrypsin and lipase was investigated to understand this approach at the molecular level. Results of fluorescence quenching assays indicated that the extent of binding of the [BMIM] cation decreased (7- and 3.5-fold for chymotrypsin and lipase, respectively) as a function of increasing ratio of positive to negative surface charges. Conformational stability assays further showed a close correlation between thermodynamic stabilization and enzyme surface charge ratio as well as [BMIM] binding. As evidence of this correlation, succinylation and acetylation resulted in the stabilization of chymotrypsin in 10% (v/v) [BMIM][Cl] by 17.0 and 6.6 kJ/mol, respectively, while cationization destabilized chymotrypsin by 3.6 kJ/mol. Combined, these results indicate that altering the surface charge ratio mediates the organization of IL molecules, namely, [BMIM] and [Cl], around the enzymes. Preferential exclusion of [Cl], in particular, via lowering of the ratio of positive to negative surface charges, correlated with increased enzyme stability. Accordingly, these results more broadly provide insight into the mechanism of stabilization in ILs via charge modification.

Linking the foreign body response and protein adsorption to PEG-based hydrogels using proteomics.

Poly(ethylene glycol) (PEG) hydrogels with their highly tunable properties are promising implantable materials, but as with all non-biological materials, they elicit a foreign body response (FBR). Recent studies, however, have shown that incorporating the oligopeptide RGD into PEG hydrogels reduces the FBR. To better understand the mechanisms involved and the role of RGD in mediating the FBR, PEG, PEG-RGD and PEG-RDG hydrogels were investigated. After a 28-day subcutaneous implantation in mice, a thinner and less dense fibrous capsule formed around PEG-RGD hydrogels, while PEG and PEG-RDG hydrogels exhibited stronger, but similar FBRs. Protein adsorption to the hydrogels, which is considered the first step in the FBR, was also characterized. In vitro experiments confirmed that serum proteins adsorbed to PEG-based hydrogels and were necessary to promote macrophage adhesion to PEG and PEG-RDG, but not PEG-RGD hydrogels. Proteins adsorbed to the hydrogels in vivo were identified using liquid chromatography-tandem mass spectrometry. The majority (245) of the total proteins (≥300) that were identified was present on all hydrogels with many proteins being associated with wounding and acute inflammation. These findings suggest that the FBR to PEG hydrogels may be mediated by the presence of inflammatory-related proteins adsorbed to the surface, but that macrophages appear to sense the underlying chemistry, which for RGD improves the FBR.

Molecular dynamics investigation of the ionic liquid/enzyme interface: application to engineering enzyme surface charge.

Molecular simulations of the enzymes Candida rugosa lipase and Bos taurus α‐chymotrypsin in aqueous ionic liquids 1‐butyl‐3‐methylimidazolium chloride and 1‐ethyl‐3‐methylimidazolium ethyl sulfate were used to study the change in enzyme–solvent interactions induced by modification of the enzyme surface charge. The enzymes were altered by randomly mutating lysine surface residues to glutamate, effectively decreasing the net surface charge by two for each mutation. These mutations resemble succinylation of the enzyme by chemical modification, which has been shown to enhance the stability of both enzymes in ILs. After establishing that the enzymes were stable on the simulated time scales, we focused the analysis on the organization of the ionic liquid substituents about the enzyme surface. Calculated solvent charge densities show that for both enzymes and in both solvents that changing positively charged residues to negative charge does indeed increase the charge density of the solvent near the enzyme surface. The radial distribution of IL constituents with respect to the enzyme reveals decreased interactions with the anion are prevalent in the modified systems when compared to the wild type, which is largely accompanied by an increase in cation contact. Additionally, the radial dependence of the charge density and ion distribution indicates that the effect of altering enzyme charge is confined to short range (≤1 nm) ordering of the IL. Ultimately, these results, which are consistent with that from prior experiments, provide molecular insight into the effect of enzyme surface charge on enzyme stability in ILs. Proteins 2015; 83:670–680.

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

Significance Understanding the effect of near-surface environments on protein conformation is critical in many fields, including biosensing, cell culture, tissue engineering, biocatalysis, and pharmaceutical formulation. However, methods to elucidate both protein structure and interfacial dynamics in heterogeneous near-surface environments are virtually nonexistent. This article describes an approach to characterize changes in protein structure on surfaces using dynamic single-molecule microscopy. Specifically, this approach exploits single-molecule Förster resonance energy transfer tracking to elucidate changes in protein structure at the single-molecule level. Using this approach, structural changes in the protein organophosphorus hydrolase were monitored upon adsorption to fused silica in the presence of BSA on a molecule-by-molecule basis. This method, which is widely applicable to virtually any protein, provides the framework for developing surfaces and surface modifications with improved biocompatibility. A method was developed to monitor dynamic changes in protein structure and interfacial behavior on surfaces by single-molecule Förster resonance energy transfer. This method entails the incorporation of unnatural amino acids to site-specifically label proteins with single-molecule Förster resonance energy transfer probes for high-throughput dynamic fluorescence tracking microscopy on surfaces. Structural changes in the enzyme organophosphorus hydrolase (OPH) were monitored upon adsorption to fused silica (FS) surfaces in the presence of BSA on a molecule-by-molecule basis. Analysis of >30,000 individual trajectories enabled the observation of heterogeneities in the kinetics of surface-induced OPH unfolding with unprecedented resolution. In particular, two distinct pathways were observed: a majority population (∼ 85%) unfolded with a characteristic time scale of 0.10 s, and the remainder unfolded more slowly with a time scale of 0.7 s. Importantly, even after unfolding, OPH readily desorbed from FS surfaces, challenging the common notion that surface-induced unfolding leads to irreversible protein binding. This suggests that protein fouling of surfaces is a highly dynamic process because of subtle differences in the adsorption/desorption rates of folded and unfolded species. Moreover, such observations imply that surfaces may act as a source of unfolded (i.e., aggregation-prone) protein back into solution. Continuing study of other proteins and surfaces will examine whether these conclusions are general or specific to OPH in contact with FS. Ultimately, this method, which is widely applicable to virtually any protein, provides the framework to develop surfaces and surface modifications with improved biocompatibility.

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.