Insight into the Structure and Activity of Surface-Engineered Lipase Biofluids

Lipases for targeted industrial applications, focusing on the development of biotechnologically significant aspects: A comprehensive review of recent trends in protein engineering

Lipases are remarkable biocatalysts, adept at catalyzing the breakdown of diverse compounds into glycerol, fatty acids, and mono- and di-glycerides via hydrolysis. Beyond this, they facilitate esterification, transesterification, alcoholysis, acidolysis, and more, making them versatile in industrial applications. In industrial processes, lipases that exhibit high stability are favored as they can withstand harsh conditions. However, most native lipases are unable to endure adverse conditions, making them unsuitable for industrial use. Protein engineering proves to be a potent technology in the development of lipases that can function effectively under challenging conditions and fulfill criteria for various industrial processes. This review concentrated on new trends in protein engineering to enhance the diversity of lipase genes and employed in silico methods for predicting and comprehensively analyzing target mutations in lipases. Additionally, key molecular factors associated with industrial characteristics of lipases, including thermostability, solvent tolerance, catalytic activity, and substrate preference have been elucidated. The present review delved into how industrial traits can be enhanced through directed evolution (epPCR, gene shuffling), rational design (FRESCO, ASR), combined engineering strategies (i.e. CAST, ISM, and FRISM) as protein engineering methodologies in contexts of biodiesel production, food processing, and applications of detergent, pharmaceutics, and plastic degradation.

Designing surface exposed sites on Bacillus subtilis lipase A for spin-labeling and hydration studies

Spin-labeling with electron paramagnetic resonance spectroscopy (EPR) is a facile method for interrogating macromolecular flexibility, conformational changes, accessibility, and hydration. Within we present a computationally based approach for the rational selection of reporter sites in Bacillus subtilis lipase A (BSLA) for substitution to cysteine residues with subsequent modification with a spin-label that are expected to not significantly perturb the wild-type structure, dynamics, or enzymatic function. Experimental circular dichroism spectroscopy, Michaelis-Menten kinetic parameters and EPR spectroscopy data validate the success of this approach to computationally select reporter sites for future magnetic resonance investigations of hydration and hydration changes induced by polymer conjugation, tethering, immobilization, or amino acid substitution in BSLA. Analysis of molecular dynamic simulations of the impact of substitutions on the secondary structure agree well with experimental findings. We propose that this computationally guided approach for choosing spin-labeled EPR reporter sites, which evaluates relative surface accessibility coupled with hydrogen bonding occupancy of amino acids to the catalytic pocket via atomistic simulations, should be readily transferable to other macromolecular systems of interest including selecting sites for paramagnetic relaxation enhancement NMR studies, other spin-labeling EPR studies or any method requiring a tagging method where it is desirable to not alter enzyme stability or activity.

Hydrophobic Clusters Regulate Surface Hydration Dynamics of Bacillus subtilis Lipase A

The surface hydration diffusivity of Bacillus subtilis Lipase A (BSLA) has been characterized by low-field Overhauser dynamic nuclear polarization (ODNP) relaxometry using a series of spin-labeled constructs. Sites for spin-label incorporation were previously designed via an atomistic computational approach that screened for surface exposure, reflective of the surface hydration comparable to other proteins studied by this method, as well as minimal impact on protein function, dynamics, and structure of BSLA by excluding any surface site that participated in greater than 30% occupancy of a hydrogen bonding network within BSLA. Experimental ODNP relaxometry coupling factor results verify the overall surface hydration behavior for these BSLA spin-labeled sites similar to other globular proteins. Here, by plotting the ODNP parameters of relative diffusive water versus the relative bound water, we introduce an effective "phase-space" analysis, which provides a facile visual comparison of the ODNP parameters of various biomolecular systems studied to date. We find notable differences when comparing BSLA to other systems, as well as when comparing different clusters on the surface of BSLA. Specifically, we find a grouping of sites that correspond to the spin-label surface location within the two main hydrophobic core clusters of the branched aliphatic amino acids isoleucine, leucine, and valine cores observed in the BSLA crystal structure. The results imply that hydrophobic clustering may dictate local surface hydration properties, perhaps through modulation of protein conformations and samplings of the unfolded states, providing insights into how the dynamics of the hydration shell is coupled to protein motion and fluctuations.

Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid

Protein-ligand binding studies are crucial for understanding the molecular basis of biological processes and for further advancing industrial biocatalysis and drug discovery. Using computational modeling and molecular dynamics simulations, we investigated the binding of a butyrate ester substrate to the lipase A (LipA) enzyme of Bacillus subtilis. Besides obtaining a close agreement of the binding free energy with the experimental value, the study reveals a remarkable reorganization of the catalytic triad upon substrate binding, leading to increased essential hydrogen bond populations. The investigation shows the distortion of the oxyanion hole in both the substrate-bound and unbound states of LipA and highlights the strengthening of the same in the tetrahedral intermediate complex. Principal component analysis of the unbound ensemble reveals the dominant motion in LipA to be the movement of Loop-1 (Tyr129-Arg142) between two states that cover and uncover the active site, mirroring that of a lid prevalent in several lipases. This lid-like motion of Loop-1 is also supported by its tendency to spontaneously open up at an oil-water interface. Overall, this study provides valuable insights into the impact of substrate binding on the structure, flexibility, and conformational dynamics of the LipA enzyme.

Brave new surfactant world revisited by thermoalkalophilic lipases: computational insights into the role of SDS as a substrate analog

Non-ionic surfactants were shown to stabilize the active conformation of thermoalkalophilic lipases by mimicking the lipid substrate while the catalytic interactions formed by anionic surfactants have not been well characterized. In this study, we combined μs-scale molecular dynamics (MD) simulations and lipase activity assays to analyze the effect of ionic surfactant, sodium dodecyl sulfate (SDS), on the structure and activity of thermoalkalophilic lipases. Both the open and closed lipase conformations that differ in geometry were recruited to the MD analysis to provide a broader understanding of the molecular effect of SDS on the lipase structure. Simulations at 298 K showed the potential of SDS for maintaining the active lipase through binding to the sn-1 acyl-chain binding pocket in the open conformation or transforming the closed conformation to an open-like state. Consistent with MD findings, experimental analysis showed increased lipase activity upon SDS incubation at ambient temperature. Notably, the lipase cores stayed intact throughout 2 μs regardless of an increase in the simulation temperature or SDS concentration. However, the surface structures were unfolded in the presence of SDS and at elevated temperature for both conformations. Simulations of the dimeric lipase were also carried out and showed reduced flexibility of the surface structures which were unfolded in the monomer, indicating the insulating role of dimer interactions against SDS. Taken together, this study provides insights into the possible substrate mimicry by the ionic surfactant SDS for the thermoalkalophilic lipases without temperature elevation, underscoring SDS's potential for interfacial activation at ambient temperatures.

Superanionic Solvent-Free Liquid Enzymes Exhibit Enhanced Structures and Activities

The surface of a carboxylate-enriched octuple mutant of Bacillus subtilis lipase A (8M) is chemically anionized to produce core (8M)-shell (cationic polymer surfactants) bionanoconjugates in protein liquid form, which are termed anion-type biofluids. The resultant lipase biofluids exhibit a 2.5-fold increase in hydrolytic activity when compared with analogous lipase biofluids based on anionic polymer surfactants. In addition, the applicability of the anion-type biofluid using Myoglobin (Mb) that is well studied in anion-type solvent-free liquid proteins is evaluated. Although anionization resulted in the complete unfolding of Mb, the active α-helix level is partially recovered in the anion-type biofluids, and the effect is accentuated in the cation-type Mb biofluids. These highly active anion-type solvent-free liquid enzymes exhibit increased thermal stability and provide a new direction in solvent-free liquid protein research.

Molecular simulations explain the exceptional thermal stability, solvent tolerance and solubility of protein-polymer surfactant bioconjugates in ionic liquids

Proteins complexed electrostatically with polymer surfactants constitute a viscous liquid by themselves, called the solvent-free protein liquid (SFPL). A solution of SFPL in a room temperature ionic liquid (PS-IL) offers the protein hyperthermal stability, higher solubility and greater IL tolerance. A generic understanding of these protein-polymer systems is obtained herein through extensive atomistic molecular dynamics simulations of three different enzymes (lipase A, lysozyme and myoglobin) under various conditions. Along with increased intra-protein hydrogen bonding, the surfactant coating around the proteins imparts greater thermal stability, and also aids in screening protein-IL interactions, endowing them IL tolerance. The reduced surface polarity of the protein-polymer bioconjugate and hydrogen bonding between the ethylene glycol groups of the surfactant and the IL cation contribute to the facile solvation of the protein in its PS-IL form. The results presented here rationalize several experimental observations and will aid in the improved design of such hybrid materials for sustainable catalysis.

Insights into substrate behavior in a solvent-free protein liquid to rationalize its reduced catalytic rate

When proteins are engineered with a polymer surfactant coating on their surface, they can form a liquid phase by themselves, without the need for a solvent, such as, say, water. However, such solvent-free protein liquids (SFPL), despite their capability to function at temperatures above those in aqueous solutions, exhibit much reduced catalytic rates. A comprehensive understanding of the nature of substrates in such liquids is crucial to reason out the reduced catalytic activity of enzymes as SFPL media, and thus identify the means to improve the same. Employing atomistic molecular dynamics simulations of lipase A from Bacillus subtilis in its SFPL form, we demonstrate that at low concentrations, the substrate molecules are located mostly in the hydrophilic layer of the surfactant shell that ensheaths the enzyme; substrates in this SFPL are present in various conformations with similar propensities as in the aqueous solution. Slower translational diffusion and reorientational dynamics, as well as the reduced tendency of a substrate molecule to closely interact with the enzymes in the SFPL medium have been identified herein as the contributing factors for the reduced activity of enzymes in this hybrid liquid. At high concentrations of substrates corresponding to those used in in vitro experiments, the formation of an enzyme-substrate complex is observed. Microscopic insights reported here can aid in the choice of surfactants to improve the catalytic rate of enzymes in SFPL.

An atomistic view of solvent-free protein liquids: the case of Lipase A

Solvent-free enzymes hold the promise of being able to deliver higher activity at elevated temperatures by virtue of them being not limited by the boiling point of the solvent. They have been realized in the liquid phase through a polymer surfactant coating on the protein surface. However, a clear understanding of intermolecular interactions, structure, dynamics, and the behaviour of the minuscule amount of water present in the solvent-free protein liquid is essential to enhance the activity of these biofluids. Using atomistic molecular dynamics simulations, we demonstrate that the scaled spatial correlations between proteins in the hybrid liquid phase of Lipase A enzymes are comparable to the inter-particle correlations in a noble gas fluid. The hydrophilic region of the surfactants forms a coronal layer around each enzyme which percolates throughout the liquid, while the hydrophobic parts are present as disjointed clusters. Inter-surfactant interactions, determined to be attractive and in the range of -200 to -300 kcal mol^-1, stabilize the liquid state. While the protein retains its native state conformational dynamics in the solvent-free form, the fluxionality of its side chains is much reduced; at 333 K, the latter is found to be equivalent to that of the enzyme in an aqueous solution at 249 K. Despite the sluggishness of the solvent-free enzyme, some water molecules exhibit high mobility and transit between enzymes primarily via the interspersed hydrophilic regions. These microscopic insights offer ideas to improve substrate diffusion in the liquid to enable the enhancement of catalytic activity.

Single Enzyme Nanoparticles with Improved Biocatalytic Activity through Protein Entrapment in a Surfactant Shell

A polymeric corona consisting of an alkyl-glycolic acid ethoxylate (C_XEO_Y) surfactant offers a promising approach toward endowing proteins with thermotropic phase behavior and hyperthermal activity. Typically, preparation of protein–surfactant biohybrids is performed via chemical modification of acidic residues followed by electrostatic conjugation of an anionic surfactant to encapsulate single proteins. While this procedure has been applied to a broad range of proteins, modification of acidic residues may be detrimental to function for specific enzymes. Herein, we report on the one-pot preparation of biohybrids via covalent conjugation of surfactants to accessible lysine residues. We entrap the model enzyme hen egg-white lysozyme (HEWL) in a shell of carboxyl-functionalized C₁₂EO₁₀ or C₁₂EO₂₂ surfactants. With fewer surfactants, our covalent biohybrids display similar thermotropic phase behavior to their electrostatically conjugated analogues. Through a combination of small-angle X-ray scattering and circular dichroism spectroscopy, we find that both classes of biohybrids consist of a folded single-protein core decorated by surfactants. Whilst traditional biohybrids retain densely packed surfactant coronas, our biohybrids display a less dense and heterogeneously distributed surfactant coverage located opposite to the catalytic cleft of HEWL. In solution, this surfactant coating permits 7- or 3.5-fold improvements in activity retention for biohybrids containing C₁₂EO₁₀ or C₁₂EO₂₂, respectively. The reported alternative pathway for biohybrid preparation offers a new horizon to expand upon the library of proteins for which functional biohybrid materials can be prepared. We also expect that an improved understanding of the distribution of tethered surfactants in the corona will be crucial for future structure–function investigations.

Preparation and application of solvent-free liquid proteins with enhanced thermal and anhydrous stabilities

This perspective details a robust chemical modification strategy to protect proteins from temperature, aggregation, and non-aqueous environments.

Solvent-free liquid avidin as a step toward cold chain elimination

The temperature sensitivity of vaccines and therapeutic proteins forces the distribution of life-saving treatments to rely heavily on the temperature-controlled (usually 2-8°C) supply and distribution network known as the cold chain. Here, using avidin as a model, we demonstrate how surface engineering could significantly increase the thermal stability of therapeutic proteins. A combination of spectroscopic (Fourier transform infrared, circular dichroism, and ultraviolet-visible) and scattering techniques (dynamic light scattering, small-angle, and wide-angle X-ray scattering) were deployed to probe the activity, structure, and stability of the model protein. Temperature-dependent synchrotron radiation circular dichroism spectroscopy was used to demonstrate a significant increase in thermal stability, with a half denaturation temperature of 139.0°C and reversible unfolding with modified avidin returning to a 90% folded state when heated to temperatures below 100°C. Accelerated aging studies revealed that modified avidin retained its secondary structure after storage at 40°C for 56 days, equivalent to 160 days at 25°C. Furthermore, binding studies with multiple ligands revealed that the binding site remained functional after modification. As a result, this approach has potential as a storage technology for therapeutic proteins and the elimination of the cold chain, enabling the dissemination of life-saving vaccines worldwide.