Molecular simulation of protein adsorption and conformation at gas-liquid, liquid–liquid and solid–liquid interfaces

Exploring proteins at soft interfaces and in thin liquid films - From classical methods to advanced applications of reflectometry

The history of the topic of proteins at soft interfaces dates back to the 19th century, and until the present day, it has continuously attracted great scientific interest. A multitude of experimental methods and theoretical approaches have been developed to serve the research progress in this large domain of colloid and interface science, including the area of soft colloids such as foams and emulsions. From classical methods like surface tension adsorption isotherms, surface pressure-area measurements for spread layers, and surface rheology probing the dynamics of adsorption, nowadays, advanced surface-sensitive techniques based on spectroscopy, microscopy, and the reflection of light, X-rays and neutrons at liquid/fluid interfaces offers important complementary sources of information. Apart from the fundamental characteristics of protein adsorption layers, i.e., surface tension and surface excess, the nanoscale structure of such layers and the interfacial protein conformations and morphologies are of pivotal importance for extending the depth of understanding on the topic. In this review article, we provide an extensive overview of the application of three methods, namely, ellipsometry, X-ray reflectometry and neutron reflectometry, for adsorption and structural studies on proteins at water/air and water/oil interfaces. The main attention is placed on the development of experimental approaches and on a discussion of the relevant achievements in terms of notable experimental results. We have attempted to cover the whole history of protein studies with these techniques, and thus, we believe the review should serve as a valuable reference to fuel ideas for a wide spectrum of researchers in different scientific fields where proteins at soft interface may be of relevance.

Whey protein isolate and inulin-glycosylated conjugate affect the physicochemical properties and oxidative stability of pomegranate seed oil emulsion

Glycosylated protein was obtained by the reaction of whey protein isolate(WPI) with inulin of different polymerization degrees and was used to stabilize a pomegranate seed oil emulsion. The physicochemical and antioxidative properties of the emulsions were assessed, and the impacts of accelerated oxidation on pomegranate seed oil were examined. The interfacial tension of WPI and short-chain inulin (SCI)-glycosylated conjugate (WPI-SCI) gradually decreased with increasing glycosylation reaction time. Emulsions stabilized by WPI-SCI (72 h) were the most stable, with a thick interfacial film on the surface of the droplets. After accelerated oxidation for 72 h, WPI-SCI inhibited the oxidation of oil in the emulsion. GC-IMS results showed that the production of harmful volatile components in oil was inhibited, and the peroxide strength was less than 30 mmol/kg oil. This study contributes to understanding of stable storage of lipids.

Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability

Understanding the mechanisms influencing poly(ethylene terephthalate) (PET) biodegradation is crucial for developing innovative strategies to accelerate the breakdown of this persistent plastic. In this study, we employed all-atom molecular dynamics simulation to investigate the adsorption process of the LCC-ICCG cutinase enzyme onto the PET surface. Our results revealed that hydrophobic, π-π, and H bond interactions, specifically involving aliphatic, aromatic, and polar uncharged amino acids, were the primary driving forces for the adsorption of the cutinase enzyme onto PET. Additionally, we observed a negligible change in the enzyme's tertiary structure during the interaction with PET (RMSD = 1.35 Å), while its secondary structures remained remarkably stable. Quantitative analysis further demonstrated that there is about a 24% decrease in the number of enzyme-water hydrogen bonds upon adsorption onto the PET surface. The significance of this study lies in unraveling the molecular intricacies of the adsorption process, providing valuable insights into the initial steps of enzymatic PET degradation.

Insights into the emulsification mechanism of the surfactant-like protein oleosin

Oleosins are proteins with a unique central hydrophobic hairpin designed to stabilize lipid droplets (oleosomes) in plant seeds. For efficient droplet stabilization, the hydrophobic hairpin with a strong affinity for the apolar droplet core is flanked by hydrophilic arms on each side. This gives oleosins a unique surfactant-like shape making them a very interesting protein. In this study, we tested if isolated oleosins retain their ability to stabilize oil-in-water emulsions, and investigated the underlying stabilization mechanism. Due to their surfactant-like shape, oleosins when dispersed in aqueous buffers associated to micelle-like nanoparticles with a size of ∼33 nm. These micelles, in turn, clustered into larger aggregates of up to 20 µm. Micelle aggregation was more extensive when oleosins lacked charge. During emulsification, oleosin micelles and micelle aggregates dissociated and mostly individual oleosins adsorbed on the oil droplet interface. Oleosins prevented the coalescence of the oil droplets and if sufficiently charged, droplet flocculation as well.

Effect of Oil Polarity on the Protein Adsorption at Oil-Water Interfaces

Protein adsorption at oil-water interfaces has received much attention in applications of food emulsion and biocatalysis. The protein activity is influenced by the protein orientation and conformation. The oil polarity is expected to influence the orientation and conformation of adsorbed proteins by modulating intermolecular interactions. Hence, it is possible to tune the protein emulsion stability and activity by varying the oil polarity. Martini v3.0-based coarse-grained molecular dynamics (CGMD) simulations were employed to investigate the effect of oil polarity on the orientation and conformation of hydrophobin (HFBI) and Candida antarctica lipase B (CALB) adsorbed at triolein-water, hexadecane-water, and octanol-water interfaces for the first time. The protein adsorption orientation was predicted through the hydrophobic dipole, indicating that protein adsorption exists in preferred orientations at hydrophobic oil interfaces. The conformation of the adsorbed HFBI is well conserved, whereas relatively larger conformational changes occur during the CALB adsorption as the oil hydrophobicity increases. Comparisons on the adsorption interaction energy of proteins with oils confirm the relationship between the oil polarity and the interaction strength of proteins with oils. In addition, CGMD simulations allow longer time scale simulations of the behaviors of protein adsorption at oil-water interfaces.

pH-Dependent Changes in Structural Stabilities of Bt Cry1Ac Toxin and Contrasting Model Proteins following Adsorption on Montmorillonite

The environmental fate of insecticidal Cry proteins, including time-dependent conservation of biological properties, results from their structural stability in soils. The complex cascade of reactions involved in biological action requires Cry proteins to be in solution. However, the pH-dependent changes in conformational stability and the adsorption-desorption mechanisms of Cry protein on soil minerals remain unclear. We used Derjaguin-Landau-Verwey-Overbeek (DLVO) calculation and differential scanning calorimetry to interpret the driving forces and structural stabilities of Cry1Ac and two contrasting model proteins adsorbed by montmorillonite. The structural stability of Cry1Ac is closer to that of the "hard" protein, α-chymotrypsin, than that of the "soft" bovine serum albumin (BSA). The pH-dependent adsorption of Cry1Ac and α-chymotrypsin could be explained by DLVO theory, whereas the BSA adsorption deviated from it. Patch-controlled electrostatic attraction, hydrophobic effects, and entropy changes following protein unfolding on a mineral surface could contribute to Cry1Ac adsorption. Cry1Ac, like chymotrypsin, was partly denatured on montmorillonite, and its structural stability decreased with an increase in pH. Moreover, small changes in the conformational heterogeneity of both Cry1Ac and chymotrypsin were observed following adsorption. Conversely, adsorbed BSA was completely denatured regardless of the solution pH. The moderate conformational rearrangement of adsorbed Cry1Ac may partially explain why the insecticidal activity of Bt toxin appears to be conserved in soils, albeit for a relatively short time period.

Plasma polymerized bio-interface directs fibronectin adsorption and functionalization to enhance "epithelial barrier structure" formation via FN-ITG β1-FAK-mTOR signaling cascade

BACKGROUND

Transepithelial medical devices are increasing utilized in clinical practices. However, the damage of continuous natural epithelial barrier has become a major risk factor for the failure of epithelium-penetrating implants. How to increase the "epithelial barrier structures" (focal adhesions, hemidesmosomes, etc.) becomes one key research aim in overcoming this difficulty. Directly targeting the in situ "epithelial barrier structures" related proteins (such as fibronectin) absorption and functionalization can be a promising way to enhance interface-epithelial integration.

METHODS

Herein, we fabricated three plasma polymerized bio-interfaces possessing controllable surface chemistry. Their capacity to adsorb and functionalize fibronectin (FN) from serum protein was compared by Liquid Chromatography-Tandem Mass Spectrometry. The underlying mechanisms were revealed by molecular dynamics simulation. The response of gingival epithelial cells regarding the formation of epithelial barrier structures was tested.

RESULTS

Plasma polymerized surfaces successfully directed distinguished protein adsorption profiles from serum protein pool, in which plasma polymerized allylamine (ppAA) surface favored adsorbing adhesion related proteins and could promote FN absorption and functionalization via electrostatic interactions and hydrogen bonds, thus subsequently activating the ITG β1-FAK-mTOR signaling and promoting gingival epithelial cells adhesion.

CONCLUSION

This study offers an effective perspective to overcome the current dilemma of the inferior interface-epithelial integration by in situ protein absorption and functionalization, which may advance the development of functional transepithelial biointerfaces. Tuning the surface chemistry by plasma polymerization can control the adsorption of fibronectin and functionalize it by exposing functional protein domains. The functionalized fibronectin can bind to human gingival epithelial cell membrane integrins to activate epithelial barrier structure related signaling pathway, which eventually enhances the formation of epithelial barrier structure.

Orientation and Conformation of Hydrophobin at the Oil-Water Interface: Insights from Molecular Dynamics Simulations

Hydrophobins, a new class of potential protein emulsifiers, have been extensively employed in the food, pharmaceutical, and chemical industries. However, the knowledge of the underlying molecular mechanism of protein adsorption at the oil-water interface remains elusive. In this study, all-atom molecular dynamics simulations were performed to probe the adsorption orientation and conformation change of class II hydrophobin HFBI at the cyclohexane-water interface. It was proposed that a hydrophobic dipole of the protein could be used to quantitatively predict the orientation of the adsorbed HFBI. Simulation results revealed that HFBI adsorbed at the interface with the patch-up orientation toward the oil phase, regardless of its initial orientations. HFBI's secondary structure was maintained to be intact in the course of simulations despite relatively significant variations in the tertiary structure observed, which could well preserve the bioactivity of HFBI. From the energy analysis, the driving force for interface adsorption was primarily determined by van der Waals interactions between HFBI and cyclohexane. Further analysis indicated that the adsorption orientation and conformation of HFBI at the oil-water interface were typically regulated by the hydrophobic patch and some key residues. This study provides some insights into the orientation, conformation, and adsorption mechanism of proteins at the oil-water interface and theoretical guidelines for the design and development of novel biological emulsifiers involved in the food, pharmaceutical, and chemical industries.

Ensuring the Sustainability of Biocatalysis

Biocatalysis offers many attractive features for the synthetic chemist. In many cases, the high selectivity and ability to tailor specific enzyme features via protein engineering already make it the catalyst of choice. From the perspective of sustainability, several features such as catalysis under mild conditions and use of a renewable and biodegradable catalyst also look attractive. Nevertheless, to be sustainable at a larger scale it will be essential to develop processes operating at far higher concentrations of product, and which make better use of the enzyme via improved stability. In this Concept, it is argued that a particular emphasis on these specific metrics is of particular importance for the future implementation of biocatalysis in industry, at a level that fulfills its true potential.

Stabilization of enzymes via immobilization: Multipoint covalent attachment and other stabilization strategies

The use of enzymes in industrial processes requires the improvement of their features in many instances. Enzyme immobilization, a requirement to facilitate the recovery and reuse of these water-soluble catalysts, is one of the tools that researchers may utilize to improve many of their properties. This review is focused on how enzyme immobilization may improve enzyme stability. Starting from the stabilization effects that an enzyme may experience by the mere fact of being inside a solid particle, we detail other possibilities to stabilize enzymes: generation of favorable enzyme environments, prevention of enzyme subunit dissociation in multimeric enzymes, generation of more stable enzyme conformations, or enzyme rigidification via multipoint covalent attachment. In this last point, we will discuss the features of an "ideal" immobilization protocol to maximize the intensity of the enzyme-support interactions. The most interesting active groups in the support (glutaraldehyde, epoxide, glyoxyl and vinyl sulfone) will be also presented, discussing their main properties and uses. Some instances in which the number of enzyme-support bonds is not directly related to a higher stabilization will be also presented. Finally, the possibility of coupling site-directed mutagenesis or chemical modification to get a more intense multipoint covalent immobilization will be discussed.

Molecular Dynamics Simulations of Nanostructures Formed by Hydrophobins and Oil in Seawater

Classical molecular dynamics simulations using the Martini coarse-grained force field were performed to study oil nanodroplets surrounded by fungal hydrophobin (HP) proteins in seawater. The class I EAS and the class II HFBII HPs were studied along with two model oils, namely, benzene and n-decane. Both HPs exhibit free energy minima at the oil-seawater interface, which is deeper in benzene compared to the n-decane systems. Larger constraint forces are required to keep both HPs within the n-decane phase compared to inside benzene, with HFBII being more affine to benzene compared to EAS. Smaller surface tensions are observed at benzene-seawater interfaces coated with HPs compared to their n-decane counterparts. In the latter the surface tension remains unchanged upon increases in the concentration of HPs, whereas in benzene systems adding more HPs lead to decreases in surface tension. EAS has a larger tendency to cluster together in the interface compared to HFBII, with both HPs having larger coordination numbers when surrounding benzene droplets compared to when they are around n-decane nanoblobs. The HP-oil nanostructures in seawater examined have radii of gyration ranging between 2 and 12 nm, where the n-decane structures are larger and have more irregular shapes compared to the benzene systems. The n-decane molecules within the nanostructures form a compact spherical core, with the HPs partially covering its surface and clustering together, conferring irregular shapes to the nanostructures. The EAS with n-decane structures are larger and have more irregular shapes compared to their HFBII counterparts. In contrast, in the HP-benzene structures both HPs tend to penetrate the oil part of the droplet. The HFBII-benzene structures having the larger oil/HP ratios examined tend to be more compact and spherical compared to their EAS counterparts; however, some of the HFBII-benzene systems that have smaller oil/HP ratios have a more elongated structure compared to their EAS counterparts. This simulation study provides insights into HP-oil nanostructures that are smaller than the oil droplets and gas bubbles recently studied in experiments and, thus, might be challenging to examine with experimental techniques.

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.