Molecular Orientation of Enzymes Attached to Surfaces through Defined Chemical Linkages at the Solid–Liquid Interface

Review on sterilization techniques, and the application potential of phage lyase and lyase immobilization in fighting drug-resistant bacteria

Many human health problems and property losses caused by pathogenic contamination cannot be underestimated. Bactericidal techniques have been extensively studied to address this issue of public health and economy. Bacterial resistance develops as a result of the extensive use of single or multiple but persistent usage of sterilizing drugs, and the emergence of super-resistant bacteria brings new challenges. Therefore, it is crucial to control pathogen contamination by applying innovative and effective sterilization techniques. As organisms that exist in nature and can specifically kill bacteria, phages have become the focus as an alternative to antibacterial agents. Furthermore, phage-encoded lyases are proteins that play important roles in phage sterilization. The in vitro sterilization of phage lyase has been developed as a novel biosterilization technique to reduce bacterial resistance and is more environmentally friendly than conventional sterilization treatments. For the shortcomings of enzyme applications, this review discusses the enzyme immobilization methods and the application potential of immobilized lyases for sterilization. Although some techniques provide effective solutions, immobilized lyase sterilization technology has been proven to be a more effective innovation for efficient pathogen killing and reducing bacterial resistance. We hope that this review can provide new insights for the development of sterilization techniques.

Site-directed immobilization of enzymes on nanoparticles using self-assembly systems

Enzyme immobilization is an effective method for improving the stability and reusability. However, linking at random sites on the enzyme results in low catalytic efficiency due to blockage of the active site or conformational changes. Therefore, controlling the orientation of enzymes on the carrier has been developed. Here, the site-specific mutation and the SpyTag/SpyCatcher systems were used to prepare a site-directed immobilized enzyme. The thermal stability of the immobilized enzyme was better than that of the free enzyme, and ≥80 % of the catalytic activity was retained after 30 days of storage. Furthermore, the Michaelis constant (Km) and the turnover number (kcat) of the immobilized enzyme were 5.23-fold lower and 6.11-fold higher than those of the free enzyme, respectively, which appeared to be related to changes in secondary structure after immobilization. These findings provide a new and effective option for enzyme-directed immobilization.

Electrochemical transformations catalyzed by cytochrome P450s and peroxidases

Cytochrome P450s (Cyt P450s) and peroxidases are enzymes featuring iron heme cofactors that have wide applicability as biocatalysts in chemical syntheses. Cyt P450s are a family of monooxygenases that oxidize fatty acids, steroids, and xenobiotics, synthesize hormones, and convert drugs and other chemicals to metabolites. Peroxidases are involved in breaking down hydrogen peroxide and can oxidize organic compounds during this process. Both heme-containing enzymes utilize active Fe^IVO intermediates to oxidize reactants. By incorporating these enzymes in stable thin films on electrodes, Cyt P450s and peroxidases can accept electrons from an electrode, albeit by different mechanisms, and catalyze organic transformations in a feasible and cost-effective way. This is an advantageous approach, often called bioelectrocatalysis, compared to their biological pathways in solution that require expensive biochemical reductants such as NADPH or additional enzymes to recycle NADPH for Cyt P450s. Bioelectrocatalysis also serves as an ex situ platform to investigate metabolism of drugs and bio-relevant chemicals. In this paper we review biocatalytic electrochemical reactions using Cyt P450s including C-H activation, S-oxidation, epoxidation, N-hydroxylation, and oxidative N-, and O-dealkylation; as well as reactions catalyzed by peroxidases including synthetically important oxidations of organic compounds. Design aspects of these bioelectrocatalytic reactions are presented and discussed, including enzyme film formation on electrodes, temperature, pH, solvents, and activation of the enzymes. Finally, we discuss challenges and future perspective of these two important bioelectrocatalytic systems.

Grafting of proteins onto polymeric surfaces: A synthesis and characterization challenge

This review aims at answering the following question: how can a researcher be sure to succeed in grafting a protein onto a polymer surface? Even if protein immobilization on solid supports has been used industrially for a long time, hence enabling natural enzymes to serve as a powerful tool, emergence of new supports such as polymeric surfaces for the development of so-called intelligent materials requires new approaches. In this review, we introduce the challenges in grafting protein on synthetic polymers, mainly because compared to hard surfaces, polymers may be sensitive to various aqueous media, depending on the pH or reductive molecules, or may exhibit state transitions with temperature. Then, the specificity of grafting on synthetic polymers due to difference of chemical functions availability or difference of physical properties are summarized. We present next the various available routes to covalently bond the protein onto the polymeric substrates considering the functional groups coming from the monomers used during polymerization reaction or post-modification of the surfaces. We also focus our review on a major concern of grafting protein, which is avoiding the potential loss of function of the immobilized protein. Meanwhile, this review considers the different methods of characterization used to determine the grafting efficiency but also the behavior of enzymes once grafted. We finally dedicate the last part of this review to industrial application and future prospective, considering the sustainable processes based on green chemistry.

Conformation and Orientation of Antimicrobial Peptides MSI-594 and MSI-594A in a Lipid Membrane

There is significant interest in the development of antimicrobial compounds to overcome the increasing bacterial resistance to conventional antibiotics. Studies have shown that naturally occurring and de novo-designed antimicrobial peptides could be promising candidates. MSI-594 is a synthetic linear, cationic peptide that has been reported to exhibit a broad spectrum of antimicrobial activities. Investigation into how MSI-594 disrupts the cell membrane is important for better understanding the details of this antimicrobial peptide (AMP)'s action against bacterial cells. In this study, we used two different synthetic lipid bilayers: zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and anionic 7:3 POPC/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho(1'-rac-glycerol) (POPG). Sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) were used to determine the orientations of MSI-594 and its analogue MSI-594A associated with zwitterionic POPC and anionic 7:3 POPC/POPG lipid bilayers. The simulated ATR-FTIR and SFG spectra using nuclear magnetic resonance (NMR)-determined structures were compared with experimental spectra to optimize the bent angle between the N- (1-11) and C- (12-24) termini helices and the membrane orientations of the helices; since the NMR structure of the peptide was determined from lipopolysaccharide (LPS) micelles, the optimization was needed to find the most suitable conformation and orientation in lipid bilayers. The reported experimental results indicate that the optimized MSI-594 helical hairpin structure adopts a complete lipid bilayer surface-bound orientation (denoted "face-on") in both POPC and 7:3 POPC/POPG lipid bilayers. The analogue peptide, MSI-584A, on the other hand, exhibited a larger bent angle between the N- (1-11) and C- (12-24) termini helices with the hydrophobic C-terminal helix inserted into the hydrophobic region of the bilayer (denoted "membrane-inserted") when interacting with both POPC and 7:3 POPC/POPG lipid bilayers. These experimental findings on the membrane orientations suggest that both peptides are likely to disrupt the cell membrane through the carpet mechanism.

Activity of AC electrokinetically immobilized horseradish peroxidase

Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H₂ O₂ to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.

Ceruloplasmin in flatland: the relationship between enzyme catalytic activity and surface hydrophilicity

The effective immobilization of the enzyme on the substrate surface plays a key role especially in biocatalysis, medicine or industry. Herein, we showed the influence of substrate hydrophilicity on the activity of the physically immobilized ceruloplasmin. To control the hydrophilicity of the substrate, thiols with various terminal groups were used. We have found that the effectiveness of the catalytic process of multimeric protein is the highest in the situation of application of the highly hydrophilic substrate. In the case of physical adsorption, the orientation of the enzyme is random, however the application of the appropriate modifying layer enforces the desired enzyme orientation. The quartz crystal microbalance with dissipation (QCM-D) results showed that the crucial parameter for the highest and most durable catalytic activity of the enzyme is the orientation, not the amount of the physically adsorbed enzyme.

Surface hydrophilicity – the way to control the activity of the immobilized enzyme.

Optimized Silica-Binding Peptide-Mediated Delivery of Bactericidal Lysin Efficiently Prevents Staphylococcus aureus from Adhering to Device Surfaces

Staphylococcal-associated device-related infections (DRIs) represent a significant clinical challenge causing major medical and economic sequelae. Bacterial colonization, proliferation, and biofilm formation after adherence to surfaces of the indwelling device are probably the primary cause of DRIs. To address this issue, we incorporated constructs of silica-binding peptide (SiBP) with ClyF, an anti-staphylococcal lysin, into functionalized coatings to impart bactericidal activity against planktonic and sessile Staphylococcus aureus. An optimized construct, SiBP1-ClyF, exhibited improved thermostability and staphylolytic activity compared to its parental lysin ClyF. SiBP1-ClyF-functionalized coatings were efficient in killing MRSA strain N315 (>99.999% within 1 h) and preventing the growth of static and dynamic S. aureus biofilms on various surfaces, including siliconized glass, silicone-coated latex catheter, and silicone catheter. Additionally, SiBP1-ClyF-immobilized surfaces supported normal attachment and growth of mammalian cells. Although the recycling potential and long-term stability of lysin-immobilized surfaces are still affected by the fragility of biological protein molecules, the present study provides a generic strategy for efficient delivery of bactericidal lysin to solid surfaces, which serves as a new approach to prevent the growth of antibiotic-resistant microorganisms on surfaces in hospital settings and could be adapted for other target pathogens as well.

Probing Orientations and Conformations of Peptides and Proteins at Buried Interfaces

Molecular structures of peptides/proteins at interfaces determine their interfacial properties, which play important roles in many applications. It is difficult to probe interfacial peptide/protein structures because of the lack of appropriate tools. Sum frequency generation (SFG) vibrational spectroscopy has been developed into a powerful technique to elucidate molecular structures of peptides/proteins at buried solid/liquid and liquid/liquid interfaces. SFG has been successfully applied to study molecular interactions between model cell membranes and antimicrobial peptides/membrane proteins, surface-immobilized peptides/enzymes, and physically adsorbed peptides/proteins on polymers and 2D materials. A variety of other analytical techniques and computational simulations provide supporting information to SFG studies, leading to more complete understanding of structure-function relationships of interfacial peptides/proteins. With the advance of SFG techniques and data analysis methods, along with newly developed supplemental tools and simulation methodology, SFG research on interfacial peptides/proteins will further impact research in fields like chemistry, biology, biophysics, engineering, and beyond.

Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein

Recently, a super uranyl binding protein (SUP) was developed, which exhibits excellent sensitivity/selectivity to bind uranyl ions. It can be immobilized onto a surface in sensing devices to detect uranyl ions. Here, sum frequency generation (SFG) vibrational spectroscopy was applied to probe the interfacial structures of surface-immobilized SUP. The collected SFG spectra were compared to the calculated orientation-dependent SUP SFG spectra using a one-excitonic Hamiltonian approach based on the SUP crystal structures to deduce the most likely surface-immobilized SUP orientation(s). Furthermore, discrete molecular dynamics (DMD) simulation was applied to refine the surface-immobilized SUP conformations and orientations. The immobilized SUP structures calculated from DMD simulations confirmed the SUP orientations obtained from SFG data analyzed based on the crystal structures and were then used for a new round of SFG orientation analysis to more accurately determine the interfacial orientations and conformations of immobilized SUP before and after uranyl ion binding, providing an in-depth understanding of molecular interactions between SUP and the surface and the effect of uranyl ion binding on the SUP interfacial structures. We believe that the developed method of combining SFG measurements, DMD simulation, and Hamiltonian data analysis approach is widely applicable to study biomolecules at solid/liquid interfaces.

Metal-Organic Frameworks for Enzyme Immobilization: Beyond Host Matrix Materials

Enzyme immobilization in metal-organic frameworks (MOFs) as a promising strategy is attracting the interest of scientists from different disciplines with the expansion of MOFs' development. Different from other traditional host materials, their unique strengths of high surface areas, large yet adjustable pore sizes, functionalizable pore walls, and diverse architectures make MOFs an ideal platform to investigate hosted enzymes, which is critical to the industrial and commercial process. In addition to the protective function of MOFs, the extensive roles of MOFs in the enzyme immobilization are being well-explored by making full use of their remarkable properties like well-defined structure, high porosity, and tunable functionality. Such development shifts the focus from the exploration of immobilization strategies toward functionalization. Meanwhile, this would undoubtedly contribute to a better understanding of enzymes in regards to the structural transformation after being hosted in a confinement environment, particularly to the orientation and conformation change as well as the interplay between enzyme and matrix MOFs. In this Outlook, we target a comprehensive review of the role diversities of the host matrix MOF based on the current enzyme immobilization research, along with proposing an outlook toward the future development of this field, including the representatives of potential techniques and methodologies being capable of studying the hosted enzymes.

Lignin nanoparticles are renewable and functional platforms for the concanavalin a oriented immobilization of glucose oxidase-peroxidase in cascade bio-sensing

Lignin nanoparticles (LNPs) acted as a renewable and efficient platform for the immobilization of horseradish peroxidase (HRP) and glucose oxidase (GOX) by a layer by layer procedure. The use of concanavalin A as a molecular spacer ensured the correct orientation and distance between the two enzymes as confirmed by Förster resonance energy transfer measurement. Layers with different chemo–physical properties tuned in a different way the activity and kinetic parameters of the enzymatic cascade, with cationic lignin performing as the best polyelectrolyte in the retention of the optimal Con A aggregation state. Electrochemical properties, temperature and pH stability, and reusability of the novel systems have been studied, as well as their capacity to perform as colorimetric biosensors in the detection of glucose using ABTS and dopamine as chromogenic substrates. A boosting effect of LNPs was observed during cyclovoltammetry analysis. The limit of detection (LOD) was found to be better than, or comparable to, that previously reported for other HRP–GOX immobilized systems, the best results being again obtained in the presence of a cationic lignin polyelectrolyte. Thus renewable lignin platforms worked as smart and functional devices for the preparation of green biosensors in the detection of glucose.

Lignin nanoparticles as functional renewable nanoplatform for the immobilization of cascade process in colorimetric biosensing of β-d-glucose.

Control of Protein Conformation and Orientation on Graphene

Graphene-based biosensors have attracted considerable attention due to their advantages of label-free detection and high sensitivity. Many such biosensors utilize noncovalent van der Waals force to attach proteins onto graphene surface while preserving graphene's high conductivity. Maintaining the protein structure without denaturation/substantial conformational change and controlling proper protein orientation on the graphene surface are critical for biosensing applications of these biosensors fabricated with proteins on graphene. Based on the knowledge we obtained from our previous experimental study and computer modeling of amino acid residual level interactions between graphene and peptides, here we systemically redesigned an important protein for better conformational stability and desirable orientation on graphene. In this paper, immunoglobulin G (IgG) antibody-binding domain of protein G (protein GB1) was studied to demonstrate how we can preserve the protein native structure and control the protein orientation on graphene surface by redesigning protein mutants. Various experimental tools including sum frequency generation vibrational spectroscopy, attenuated total refection-Fourier transform infrared spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy were used to study the protein GB1 structure on graphene, supplemented by molecular dynamics simulations. By carefully designing the protein GB1 mutant, we can avoid strong unfavorable interactions between protein and graphene to preserve protein conformation and to enable the protein to adopt a preferred orientation. The methodology developed in this study is general and can be applied to study different proteins on graphene and beyond. With the knowledge obtained from this research, one could apply this method to optimize protein function on surfaces (e.g., to enhance biosensor sensitivity).

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.

Vibrational Sum-Frequency Scattering as a Sensitive Approach to Detect Structural Changes in Collagen Fibers Treated with Surfactants

Optimizing protocols so that the structure of the collagen fibers in the extracellular matrix remains intact during the decellularization process requires techniques with high structural sensitivity, especially for the surface region of the collagen fibers. Here, we demonstrate that vibrational sum-frequency scattering (SFS) spectroscopy in the protein-specific amide I region provides vibrational spectra and scattering patterns characteristic of protein fiber networks self-assembled in vitro from collagen type I, which are kept in aqueous environments during the analysis. At scattering angles away from the phase-matched direction, the relative strengths of various polarization combinations are highly reproducible, and changes in their ratios can be followed in real time during exposure to sodium dodecyl sulfate surfactant solutions. For the fibers in this work, a scattering angle of about 22° provided specificity for the surface region of the fibers, as it allowed monitoring of immediate structural changes during the surfactant exposure. With further development, we hypothesize that the information from the SFS characterization of collagen fibers may complement information from other techniques with sensitivity to the overall structure, such as second-harmonic generation imaging and infrared spectroscopy, and provide a more complete understanding of fiber molecular structures and interactions during exposure to various environments and conditions.

Molecular Mechanisms of Interactions between Monolayered Transition Metal Dichalcogenides and Biological Molecules

Single layered two-dimensional (2D) materials such as transition metal dichalcogenides (TMDs) show great potential in many microelectronic or nanoelectronic applications. For example, because of extremely high sensitivity, TMD-based biosensors have become promising candidates for next-generation label-free detection. However, very few studies have been conducted on understanding the fundamental interactions between TMDs and other molecules including biological molecules, making the rational design of TMD-based sensors (including biosensors) difficult. This study focuses on the investigations of the fundamental interactions between proteins and two widely researched single-layered TMDs, MoS₂, and WS₂ using a combined study with linear vibrational spectroscopy attenuated total reflectance FTIR and nonlinear vibrational spectroscopy sum frequency generation vibrational spectroscopy, supplemented by molecular dynamics simulations. It was concluded that a large surface hydrophobic region in a relatively flat location on the protein surface is required for the protein to adsorb onto a monolayered MoS₂ or WS₂ surface with preferred orientation. No disulfide bond formation between cysteine groups on the protein and MoS₂ or WS₂ was found. The conclusions are general and can be used as guiding principles to engineer proteins to attach to TMDs. The approach adopted here is also applicable to study interactions between other 2D materials and biomolecules.

Flexible Peptide Linkers Enhance the Antimicrobial Activity of Surface-Immobilized Bacteriolytic Enzymes

Chemical linkers are frequently used in enzyme immobilization to improve enzyme flexibility and activity, whereas peptide linkers, although ubiquitous in protein engineering, are much less explored in enzyme immobilization. Here, we report peptide-linker-assisted noncovalent immobilization of the bacteriolytic enzyme lysostaphin (Lst) to generate anti- Staphylococcus aureus surfaces. Lst was immobilized through affinity tags onto a silica surface (glass slides) and nickel nitrilotriacetic acid (NiNTA) agarose beads via silica-binding peptides (SiBPs) or a hexahistidine tag (His-tag) fused at the C-terminus of Lst, respectively. By inserting specific peptide linkers upstream of the SiBP or His-tag, the immobilized enzymes killed >99.5% of S. aureus ATCC 6538 cells (10⁸ CFU/mL) within 3 h in buffer and could be reused multiple times without significant loss of activity. In contrast, immobilized Lst without a peptide linker was less active/stable. Molecular modeling of Lst-linker-affinity tag constructs illustrated that the presence of the peptide linkers enhanced the molecular flexibility of the proximal Lst binding domain, which interacts with the bacterial substrate, and such increased flexibility correlated with increased antimicrobial activity. We further show that Lst immobilized onto NiNTA beads retained the ability to kill ∼99% of a 10⁸ CFU/mL microbial challenge even in the presence of 1% of a commercial anionic surfactant, C12-14 alcohol EO 3:1 sodium sulfate, when the Lst construct contained a decapeptide linker containing glycine, serine, and alanine residues. This linker-assisted immobilization strategy could be extended to an unrelated lytic enzyme, the endolysin PlyPH, to target Bacillus anthracis Sterne cells either in buffer or in the presence of anionic surfactants. Our approach, therefore, provides a facile route to the use of antimicrobial enzymes on surfaces.

Simultaneous Observation of the Orientation and Activity of Surface-Immobilized Enzymes

Surface immobilized enzymes have been widely used in many applications such as biosensors, biochips, biofuel production, and biofuel cell construction. Many factors dictate how enzymes' structure, activity, and stability may change when immobilized, including surface functionalization, immobilization chemistry, nature of the solid support, and enzyme surface density. To better understand how immobilization affects enzyme structure and activity, we have developed a method to measure both surface-sensitive protein vibrational spectra and enzymatic activity simultaneously. To accomplish this, an optical/fluorescence microscope was incorporated into a sum frequency generation (SFG) spectrometer. Using β-glucosidase (β-Glu) as a model system, enzymes were covalently tethered to a self-assembled monolayer surface using cysteine-maleimide chemistry. Their orientations were determined by SFG spectroscopy, with a single native cysteine residue oriented toward the functionalized surface, and activity measured simultaneously using a fluorogenic substrate resorufin β-d-glucopyranoside, with a loss of activity of 53% as compared to comparable solution measurements. Measuring β-Glu activity and orientation simultaneously provides more accurate information for designing and further improving enzymatic activity of surface-bound enzymes.

Nonlinear Optical Methods for Characterization of Molecular Structure and Surface Chemistry

The principles, strengths and limitations of several nonlinear optical (NLO) methods for characterizing biological systems are reviewed. NLO methods encompass a wide range of approaches that can be used for real-time, in-situ characterization of biological systems, typically in a label-free mode. Multiphoton excitation fluorescence (MPEF) is widely used for high-quality imaging based on electronic transitions, but lacks interface specificity. Second harmonic generation (SHG) is a parametric process that has all the virtues of the two-photon version of MPEF, yielding a signal at twice the frequency of the excitation light, which provides interface specificity. Both SHG and MPEF can provide images with high structural contrast, but they typically lack molecular or chemical specificity. Other NLO methods such as coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) can provide high-sensitivity imaging with chemical information since Raman active vibrations are probed. However, CARS and SRS lack interface and surface specificity. A NLO method that provides both interface/surface specificity as well as molecular specificity is vibrational sum frequency generation (SFG) spectroscopy. Vibration modes that are both Raman and IR active are probed in the SFG process, providing the molecular specificity. SFG, like SHG, is a parametric process, which provides the interface and surface specificity. SFG is typically done in the reflection mode from planar samples. This has yielded rich and detailed information about the molecular structure of biomaterial interfaces and biomolecules interacting with their surfaces. However, 2-D systems have limitations for understanding the interactions of biomolecules and interfaces in the 3-D biological environment. The recent advances made in instrumentation and analysis methods for sum frequency scattering (SFS) now present the opportunity for SFS to be used to directly study biological solutions. By detecting the scattering at angles away from the phase-matched direction even centrosymmetric structures that are isotropic (e.g., spherical nanoparticles functionalized with self-assembled monolayers or biomolecules) can be probed. Often a combination of multiple NLO methods or a combination of a NLO method with other spectroscopic methods is required to obtain a full understanding of the molecular structure and surface chemistry of biomaterials and the biomolecules that interact with them. Using the right combination methods provides a powerful approach for characterizing biological materials.

Monitoring Antimicrobial Mechanisms of Surface-Immobilized Peptides in Situ

Antimicrobial peptides (AMPs) in free solution can kill bacteria by disrupting bacterial cell membranes. Their modes of action have been extensively studied, and various models ranging from pore formation to carpet-like mechanisms were proposed. Surface-immobilized AMPs have been used as coatings to kill bacteria and as sensors to capture bacteria, but the interaction mechanisms of surface-immobilized AMPs and bacteria are not fully understood. In this research, an analytical platform, sum frequency generation (SFG) microscope, which is composed of an SFG vibrational spectrometer and a fluorescence microscope, was used to probe molecular interactions between surface-immobilized AMPs and bacteria in situ in real time at the solid/liquid interface. SFG probed the molecular structure of surface-immobilized AMPs while interacting with bacteria, and fluorescence images of dead bacteria were monitored as a function of time during the peptide-bacteria interaction. It was believed that upon bacteria contact, the surface-immobilized peptides changed their orientation and killed bacteria. This research demonstrated that the SFG microscope platform can examine the structure and function (bacterial killing) at the same time in the same sample environment, providing in-depth understanding on the structure-activity relationships of surface-immobilized AMPs.

Effect of immobilization site on the orientation and activity of surface-tethered enzymes

Tethering peptides and proteins to abiotic surfaces has the potential to create biomolecule-functionalized surfaces with useful properties.

Attachment of enzymes to hydrophilic magnetic nanoparticles through DNA-directed immobilization with enhanced stability and catalytic activity

An efficient enzyme immobilization strategy based on DNA directed immobilization on hydrophilic polydopamine (PDA) modified magnetic nanoparticles was developed in this study.

Effect of Surface Crowding and Surface Hydrophilicity on the Activity, Stability and Molecular Orientation of a Covalently Tethered Enzyme

We have investigated two surface properties that are generally thought to have an important influence of enzyme activity and stability: surface hydrophobicity and surface crowding. Here two variants of an engineered bacterial nitro-reductase were covalently tethered to orient the protein's pseudo-2-fold symmetry axis either parallel or perpendicular to the surface. The surface hydrophobicity was systematically varied by changing the ratio of methyl- to hydroxyl-groups displayed on the SAM surface, and the effects on enzyme activity, thermal stability, and structure investigated. Increasing surface hydrophobicity progressively decreased enzyme activity, but had no effect on thermal stability. Surface-sensitive sum frequency generation and attenuated total reflectance Fourier transform IR spectroscopies indicated that the enzyme is not denatured by the more hydrophobic surface, but is more likely trapped in less active conformations by transient hydrophobic interactions. In contrast, increasing enzyme surface concentration increased the specific activity of the parallel oriented enzyme, but had no effect on the activity of the perpendicularly oriented enzyme, suggesting that crowding effects are highly context dependent.

Engineered Surface-Immobilized Enzyme that Retains High Levels of Catalytic Activity in Air

In the absence of aqueous buffer, most enzymes retain little or no activity; however, "water-free" enzymes would have many diverse applications. Here, we describe the chemically precise immobilization of an enzyme on an engineered surface designed to support catalytic activity in air at ambient humidity. Covalent immobilization of haloalkane dehalogenase on a surface support displaying poly(sorbitol methacrylate) chains resulted in ∼40-fold increase in activity over lyophilized enzyme powders for the gas-phase dehalogenation of 1-bromopropane. The activity of the immobilized enzyme in air approaches 25% of the activity obtained in buffer for the immobilized enzyme. Poly(sorbitol methacrylate) appears to enhance activity by replacing protein-water interactions, thereby preserving the protein structure.

Immobilized enzymes: understanding enzyme – surface interactions at the molecular level

Interactions between immobilized enzymes and supporting surfaces are complex and context-dependent and can significantly alter enzyme structure, stability and activity.

Engineering and Characterization of Peptides and Proteins at Surfaces and Interfaces: A Case Study in Surface-Sensitive Vibrational Spectroscopy

Understanding molecular structures of interfacial peptides and proteins impacts many research fields by guiding the advancement of biocompatible materials, new and improved marine antifouling coatings, ultrasensitive and highly specific biosensors and biochips, therapies for diseases related to protein amyloid formation, and knowledge on mechanisms for various membrane proteins and their interactions with ligands. Developing methods for measuring such unique systems, as well as elucidating the structure and function relationship of such biomolecules, has been the goal of our lab at the University of Michigan. We have made substantial progress to develop sum frequency generation (SFG) vibrational spectroscopy into a powerful technique to study interfacial peptides and proteins, which lays a foundation to obtain unique and valuable insights when using SFG to probe various biologically relevant systems at the solid/liquid interface in situ in real time. One highlighting feature of this Account is the demonstration of the power of combining SFG with other techniques and methods such as ATR-FTIR, surface engineering, MD simulation, liquid crystal sensing, and isotope labeling in order to study peptides and proteins at interfaces. It is necessary to emphasize that SFG plays a major role in these studies, while other techniques and methods are supplemental. The central role of SFG is to provide critical information on interfacial peptide and protein structure (e.g., conformation and orientation) in order to elucidate how surface engineering (e.g., to vary the structure) can ultimately affect surface function (e.g., to optimize the activity). This Account focuses on the most significant recent progress in research on interfacial peptides and proteins carried out by our group including (1) the development of SFG analysis methods to determine orientations of regular as well as disrupted secondary structures, and the successful demonstration and application of an isotope labeling method with SFG to probe the detailed local structure and microenvironment of peptides at buried interfaces, (2) systematic research on cell membrane associated peptides and proteins including antimicrobial peptides, cell penetrating peptides, G proteins, and other membrane proteins, discussing the factors that influence interfacial peptide and protein structures such as lipid charge, membrane fluidity, and biomolecule solution concentration, and (3) in-depth discussion on solid surface immobilized antimicrobial peptides and enzymes. The effects of immobilization method, substrate surface, immobilization site on the peptide or protein, and surrounding environment are presented. Several examples leading to high impact new research are also briefly introduced: The orientation change of alamethicin detected while varying the model cell membrane potential demonstrates the feasibility to apply SFG to study ion channel protein gating mechanisms. The elucidation of peptide secondary structures at liquid crystal interfaces shows promising results that liquid crystal can detect and recognize different peptides and proteins. The method of retaining the native structure of surface immobilized peptides or proteins in air demonstrates the feasibility to protect and preserve such structures via the use of hydromimetic functionalities when there is no bulk water. We hope that readers in many different disciplines will benefit from the research progress reported in this Account on SFG studies of interfacial structure-function relationships of peptides and proteins and apply this powerful technique to study interfacial biomolecules in the future.

Effect of Lipid Composition on the Membrane Orientation of the G Protein-Coupled Receptor Kinase 2-Gβ1γ2 Complex

Interactions between proteins and cell membranes are critical for biological processes such as transmembrane signaling, and specific components of the membrane may play roles in helping to organize or mandate particular conformations of both integral and peripheral membrane proteins. One example of a signaling enzyme whose function is dependent on membrane binding and whose activity is affected by specific lipid components is G protein-coupled receptor (GPCR) kinase 2 (GRK2). Efficient GRK2-mediated phosphorylation of activated GPCRs is dependent not only on its recruitment to the membrane by heterotrimeric Gβγ subunits but also on the presence of highly negatively charged lipids, in particular phosphatidylinositol 4',5'-bisphosphate (PIP2). We hypothesized that PIP2 may favor a distinct orientation of the GRK2-Gβγ complex on the membrane that is more optimal for function. In this study, we compared the possible orientations of the GRK2-Gβγ complex and Gβγ alone on model cell membranes prepared with various anionic phospholipids as deduced from sum frequency generation vibrational and attenuated total reflectance Fourier transform infrared spectroscopic methods. Our results indicate that PIP2 affects the membrane orientation of the GRK2-Gβ1γ2 complex but not that of complexes formed with anionic phospholipid binding deficient mutations in the GRK2 pleckstrin homology (PH) domain. Gβ1γ2 exhibits a similar orientation on the lipid bilayer regardless of its lipid composition. The PIP2-induced orientation of the GRK2-Gβ1γ2 complex is therefore most likely caused by specific interactions between PIP2 and the GRK2 PH domain. Thus, PIP2 not only helps recruit GRK2 to the membrane but also "fine tunes" the orientation of the GRK2-Gβγ complex so that it is better positioned to phosphorylate activated GPCRs.

In situ regeneration of bioactive coatings enabled by an evolved Staphylococcus aureus sortase A

Surface immobilization of bioactive molecules is a central paradigm in the design of implantable devices and biosensors with improved clinical performance capabilities. However, in vivo degradation or denaturation of surface constituents often limits the long-term performance of bioactive films. Here we demonstrate the capacity to repeatedly regenerate a covalently immobilized monomolecular thin film of bioactive molecules through a two-step stripping and recharging cycle. Reversible transpeptidation by a laboratory evolved Staphylococcus aureus sortase A (eSrtA) enabled the rapid immobilization of an anti-thrombogenic film in the presence of whole blood and permitted multiple cycles of film regeneration in vitro that preserved its biological activity. Moreover, eSrtA transpeptidation facilitated surface re-engineering of medical devices in situ after in vivo implantation through removal and restoration film constituents. These studies establish a rapid, orthogonal and reversible biochemical scheme to regenerate selective molecular constituents with the potential to extend the lifetime of bioactive films.

Bioactive coatings offer a strategy to modulate host response to implants, but their translation to the clinic is hampered by their fast in vivo degradation. Here, the authors use an engineered bacterial protein to regenerate an anti-thrombogenic film in vitro and in situ after device implantation.

Molecular-Level Insights into Orientation-Dependent Changes in the Thermal Stability of Enzymes Covalently Immobilized on Surfaces

Surface-immobilized enzymes are important for a wide range of technological applications, including industrial catalysis, drug delivery, medical diagnosis, and biosensors; however, our understanding of how enzymes and proteins interact with abiological surfaces on the molecular level remains extremely limited. We have compared the structure, activity, and thermal stability of two variants of a β-galactosidase attached to a chemically well-defined maleimide-terminated self-assembled monolayer surface through a unique cysteinyl residue. In one case the enzyme is attached through an α helix and in the other case through an adjacent loop. Both enzymes exhibit similar specific activities and adopt similar orientations with respect to the surface normal, as determined by sum-frequency generation and attenuated total reflectance FT-IR spectroscopies. Surprisingly, however, the loop-tethered enzyme exhibits a thermal stability 10 °C lower than the helix-tethered enzyme and 13 °C lower than the enzyme in free solution. Using coarse-grain models, molecular dynamics simulations of the thermal unfolding of the surface-tethered enzymes were able to reproduce these differences in stability. Thus, revealing that tethering through the more flexible loop position provides more opportunity for surface residues on the protein to interact with the surface and undergo surface-induced unfolding. These observations point to the importance of the location of the attachment point in determining the performance of surface-supported biocatalysts and suggest strategies for optimizing their activity and thermal stability through molecular simulations.

Poly(L-lysine) Interfaces via Dual Click Reactions on Surface-Bound Custom-Designed Dithiol Adsorbates

Surfaces modified with poly(L-lysine) can be used to immobilize selected biomolecules electrostatically. This report describes the preparation of a set of self-assembled monolayers (SAMs) from three different azide-terminated adsorbates as platforms for performing controlled surface attachments and as a means of determining the parameters that afford stable poly(L-lysine)-modified SAM surfaces having controlled packing densities. A maleimide-terminated alkyne linker was "clicked" to the azide-terminated surfaces via a copper-catalyzed cycloaddition reaction to produce the attachment sites for the polypeptides. A thiol-Michael addition was then used to immobilize cysteine-terminated poly(L-lysine) moieties on the gold surface, avoiding adsorbate self-reactions with this two-step procedure. Each step in this process was analyzed by ellipsometry, X-ray photoelectron spectroscopy, polarization modulation infrared reflection-absorption spectroscopy, and contact angle goniometry to determine which adsorbate structure most effectively produced the targeted polypeptide interface. Additionally, a series of mixed SAMs using an azidoalkanethiol in combination with a normal alkanethiol having an equivalent alkyl chain were prepared to provide data to determine how dilution of the azide reactive site on the SAM surface influences the initial click reaction. Overall, the collected data demonstrate the advantages of an appropriately designed bidentate absorbate and its potential to form effective platforms for biomolecule surface attachment via click reactions.

Selective and Reversible Binding of Thiol-Functionalized Biomolecules on Polymers Prepared via Chemical Vapor Deposition Polymerization

We use chemical vapor deposition polymerization to prepare a novel dibromomaleimide-functionalized polymer for selective and reversible binding of thiol-containing biomolecules on a broad range of substrates. We report the synthesis and CVD polymerization of 4-(3,4-dibromomaleimide)[2.2]paracyclophane to yield nanometer thick polymer coatings. Fourier transformed infrared spectroscopy and X-ray photoelectron spectroscopy confirmed the chemical composition of the polymer coating. The reactivity of the polymer coating toward thiol-functionalized molecules was confirmed using fluorescent ligands. As a proof of concept, the binding and subsequent release of cysteine-modified peptides from the polymer coating were also demonstrated via sum frequency generation spectroscopy. This reactive polymer coating provides a flexible surface modification approach to selectively and reversibly bind biomolecules on a broad range of materials, which could open up new opportunities in many biomedical sensing and diagnostic applications where specific binding and release of target analytes are desired.

Room temperature freezing and orientational control of surface-immobilized peptides in air

The “native” structure and orientation of a surface immobilized peptide was successfully controlled in air with a sugar layer. The robust peptide structure could also be retained at high temperatures.

Interfacial ordering of thermotropic liquid crystals triggered by the secondary structures of oligopeptides

Ordering at phospholipid-decorated interfaces of liquid crystals is influenced by the secondary structure of oligopeptides.

Molecular interactions between gold nanoparticles and model cell membranes

Direct observations of the lipid flip-flop induced by Au NP – model mammalian cell membrane interactions.