Oligohis-tags: mechanisms of binding to Ni2+-NTA surfaces

In situ cleavage-based sortase A-mediated site-specific immobilization of beta2-adrenoceptor on gold surface for surface plasmon resonance measurement

Surface Plasmon Resonance (SPR) is a pivotal technique for measuring biomolecular interactions, with the sensor surface typically made of gold or silver and requiring proteins to be immobilized in a controlled manner. Traditional methods, such as random crosslinking via covalent amide bonds (EDC/NHS strategy), resulting in diverse protein orientations. Alternatively, site-specific immobilization strategies offer better orientation control, they are still challenged by the purification needs for protein of interests and steric hindrance produced by bulk protein tags. To address these issues, we proposed a novel protein immobilization strategy relying on in situ cleavage and Sortase A (SrtA) to immobilize functional protein on SPR sensor chips. This strategy involves the β2-adrenoceptor (β2AR) as a model, incorporating an endogenous protease recognition site (EPRS) as a linker to fuse SrtA with β2AR, which contains an SrtA recognition sequence (LPXTG) at its C-terminal. When expressed in Escherichia coli (E. coli), the protease cleaves the EPRS, releasing SrtA and β2AR. When the lysate is mixed with an oligo-Gly or oligo-Gly-modified SPR chip, transpeptidation occurs, covalently immobilizing β2AR. The efficacy of the cleavage and transpeptidation reactions was validated through SDS-PAGE, Western blot, and chromatographic analysis. The SPR chip was characterized by scanning electron microscope (SEM), energy dispersive spectroscopy (EDS) mapping, X-ray photoelectron spectroscopy (XPS), and contact angle analysis, while β2AR activity was evaluated by SPR. When compared to the EDC/NHS-based random method and the haloalkane dehalogenase (HaloTag)-mediated site-specific strategy, β2AR immobilized through the SrtA-mediated method exhibited higher activity with ligands, demonstrating precision in binding affinity evaluations. This strategy meets the benchmarks for an optimal site-specific immobilization method and holds promise for applications involving the modification of other biological interfaces or biosensors.

Low pH affinity screening of peptides: An alternative to time-consuming storage experiments?

Metal-catalyzed lipid oxidation substantially reduces the shelf life of mayonnaise, thereby increasing the demand for metal-chelating antioxidants. This study, for the first time, combined Surface Plasmon Resonance (SPR) and Immobilized Metal Affinity Chromatography (IMAC) at low pH with a 28-day storage experiment in mayonnaise to screen peptides for antioxidant activity. These novel techniques could potentially replace time-consuming storage experiments in the discovery of new antioxidants. However, the application of SPR at low pH was hindered by non-specific binding, despite attempts to address this issue through various strategies. Surprisingly, IMAC experiments showed a distinct difference in affinity for Ni2+ and Fe3+ among all peptides tested, suggesting that peptide-metal ion affinity varies significantly. Nonetheless, no peptides enhanced mayonnaise's oxidative stability; some even acted as prooxidants. These findings emphasize the complexity of predicting antioxidant efficacy in food matrices and highlight the urgent need for further research to refine low pH screening methodologies.

Catalytic tunnel engineering of thermostable endoglucanase of GH7 family (W356C) from Aspergillus fumigatus gains catalytic rate

Tunnel engineering targets the access tunnels in enzymes, which is crucial for substrate binding and product release. Modifying the tunnels can lead to better biomass-degrading abilities of the lignocellulolytic enzymes. In this report, we have engineered the thermostable GH7 family endoglucanase from Aspergillus fumigatus (AfEgl7). The residues in the open tunnel having the highest bottleneck radius are mutated. Mutations are created (T229F, W356C) in the non-conserved region. The mutant W356C showed a 2-fold increase in product release rate (Vmax = 375.8 µM/min) and 2.5-fold higher catalytic activity (Kcat = 75.1 min-1) compared to wild-type (Vmax= 232 µM/min; Kcat = 30.9 min-1) using CM cellulose as substrate. The mutant T229F lost both catalytic activity and thermostability. Molecular dynamic simulations and docking studies of W356C revealed a change in structure near the product exit region, which may facilitate faster product release and account for the increased catalytic efficiency of the mutant. This study showed how redesigning the access pathways can be a promising strategy for protein engineering and de novo protein design by tailoring the open tunnel geometry to a ligand-specific manner.

Reconstructing the Motility Driven by Membrane-Bound Myosin on the Inner Surface of Cell-Sized Droplets

Molecular motors and the cytoskeleton perform essential cellular functions by interacting with the cell membrane. Reconstituting the behavior of motor proteins interacting with biological membranes and cytoskeletal filaments within a cell-sized space provides insights into their intracellular functions. A water-in-oil (W/O) emulsion droplet represents an invaluable experimental system because it offers an encapsulated space that mimics the intracellular environment. In this study, we aimed to reconstitute the actomyosin motility on the flat membrane surface of cell-sized W/O droplets using membrane-bound myosin I that anchors to and exerts force on both the cell membrane and actin cytoskeleton. Myosin IC or myosin ID, which binds specifically to the cell membrane phospholipid phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] together with the actin cytoskeleton, was encapsulated within W/O droplets. Myosin IC and myosin ID caused gliding of actin filaments on the inner bottom membrane of the hemispherical droplet containing PI(4,5)P2, and myosin-driven actin filament movement on the flat membrane surface was quantified. Fast motor myosin ID was more sensitive than slow motor myosin IC to the geometrical conditions and binding manner to the membrane. Therefore, the in-droplet actin filament gliding assay is a useful tool for elucidating the molecular mechanisms underlying cellular events occurring at the cell membrane, which are achieved through the concerted action of myosin and the actin cytoskeleton.

Systematic Model Peptide Studies: A Crucial Step To Understand the Coordination Chemistry of Mn(II) and Fe(II) in Proteins

Pathogenic bacteria and all other species require Mn(II) and Fe(II) ions for proper growth. Microbes use a variety of assimilation pathways to obtain the necessary metal ions, and their metal homeostasis mechanisms are still not fully uncovered. The knowledge of the poorly discovered complexation chemistry of Mn(II) and Fe(II) ions could help us to understand the basis of those processes better. We have designed six model peptides (L1 - Ac-HHHHHH-NH2, L2 - Ac-HHHHHHHHH-NH2, L3 - Ac-HAHAHAHAH-NH2, L4 - Ac-HHAAAAAAAAAHHHH-NH2, L5 - Ac-HDHDHDHDH-NH2, and L6 - Ac-HEHEHEHEH-NH2) inspired by Mn(II) and Fe(II) binding motifs that are prevalent in nature, in order to clarify their coordination preferences. Spectrometric, spectroscopic, and potentiometric techniques were used to determine the thermodynamic and structural properties of the studied systems. All of the investigated ligands possess efficient Mn(II), Fe(II), and Zn(II) binding sites. Complex stability and metal affinity are significantly influenced by the length of the peptide sequences, as well as the location and quantity of coordinating amino acid residues like His, Asp, and Glu.

Chemical tools for probing histidine modifications

Histidine is a unique amino acid with critical roles in protein structure and function, ranging from metal ion binding to enzyme catalysis. Histidine residues in proteins also undergo diverse posttranslational modifications, including methylation, phosphorylation and hydroxylation, by various enzymes, some of them being only recently identified and characterised. In this review, we describe the development of chemical tools for understanding the role of histidine residues in chemical and biological systems. We spotlight the application of histidine analogues in probing biomedically important posttranslational modifications of histidine residues in proteins, and we highlight novel bioconjugation methods that enable chemoselective modifications of histidine residues in peptides and proteins.

Expression and characterization of pantothenate energy-coupling factor transporters as an anti-infective drug target

This study investigates the potential of energy-coupling factor (ECF) transporters as promising anti-infective targets to combat antimicrobial resistance (AMR). ECF transporters, a subclass of ATP-binding cassette (ABC) transporters, facilitate the uptake of B-vitamins across bacterial membranes by utilizing ATP as an energy source. Vitamins are essential cofactors for bacterial metabolism and growth, and they can either be synthesized de novo or absorbed from the environment. These transporters are considered promising drug targets, underscoring the need for further research to harness their medicinal potential and develop selective inhibitors that block vitamin uptake in bacteria. Herein, we focused on the ECF transporter for pantothenate (vitamin B5) from Streptococcus pneumoniae and the ECF transporter for folate (vitamin B9) from Lactobacillus delbrueckii as a reference protein. We also included the energizing module for pantothenate along with both full transporter complexes. Initially, we transformed and purified the transporters, followed by an assessment of their thermal stability under various buffer composition, pH, and salt concentrations. Additionally, we monitored the melting temperature over six days to confirm their stability for further assays. We then measured the binding affinities of six ECF inhibitors using surface plasmon resonance (SPR) and evaluated their inhibitory effects through in vitro assays, including bacterial growth assay, whole-cell uptake, and transport-activity assays. After determining cytotoxicity in two human cell lines, we established an in vivo infection model using Galleria mellonella larvae to further validate our findings.

Molecular Dynamics Simulations Show That Short Peptides Can Drive Synthetic Cell Division by Binding to the Inner Membrane Leaflet

An important functionality of lifelike "synthetic cells" is to mimic cell division. Currently, specialized proteins that induce membrane fission in living cells are the primary candidates for dividing synthetic cells. However, interactions between lipid membranes and proteins that are not found in living cells may also be suitable. Here, we discuss the potential of short membrane-anchored peptides to induce cell division. Specifically, we used the coarse-grained MARTINI model to investigate the interaction between short membrane-anchored peptides and a lipid bilayer patch. The simulation revealed that the anchored peptide induces significant spontaneous curvature and suggests that the lipid-peptide complex can be considered as a conically shaped "bulky headgroup" lipid. By systematically increasing the electrostatic charge of the peptide, we find that membrane-anchored peptides may generate sufficiently large constriction forces even at dilute coverages. Finally, we show that when the peptide has an opposite charge to the membrane, the peptide may induce division by binding the inner membrane leaflet of a synthetic cell, that is, cell division from within.

Contrast enhanced photoacoustic detection of fibrillar collagen in the near infrared region-I

Fibrillar collagen accumulation emerges as a promising biomarker in several diseases, such as desmoplastic tumors and unstable atherosclerotic plaque. Gold nanorods (GNRs) hold great potential as contrast agents in high-resolution, biomedically safe, and non-invasive photoacoustic imaging (PAI). This study presents the design and characterization of a specialized imaging tool which exploits GNR assisted targeted photoacoustic imaging that is tailored for the identification of fibrillar collagen. In addition to the photoacoustic characterization of collagen in the NIR 1 and 2 regions, we demonstrate the detailed steps of conjugating a decoy to GNRs. This study serves as a proof of concept, that demonstrates that conjugated collagenase-1 (MMP-1) generates a distinct and collagen-specific photoacoustic signal, facilitating real-time visualization in the wavelength range of 700-970 nm (NIR I). As most of the reported studies utilized the endogenous contrast of collagen in the NIR II wavelength that has major limitations to perform in vivo deep tissue imaging, the approach that we are proposing is unique and it highlights the promise of MMP-1 decoy-functionalized GNRs as novel contrast agents for photoacoustic imaging of collagen in the NIR 1 region. To our knowledge this is the first time functionalized GNRs are optimized for the detection of fibrillar collagen and utilized in the field of non-invasive photoacoustic imaging that can facilitate a better prognosis of desmoplastic tumors and broken atherosclerotic plaques.

Coupling liquid phases in 3D condensates and 2D membranes: Successes, challenges, and tools

This review describes the major experimental challenges researchers meet when attempting to couple phase separation between membranes and condensates. Although it is well known that phase separation in a 2D membrane could affect molecules capable of forming a 3D condensate (and vice versa), few researchers have quantified the effects to date. The scarcity of these measurements is not due to a lack of intense interest or effort in the field. Rather, it reflects significant experimental challenges in manipulating coupled membranes and condensates to yield quantitative values. These challenges transcend many molecular details, which means they impact a wide range of systems. This review highlights recent exciting successes in the field, and it lays out a comprehensive list of tools that address potential pitfalls for researchers who are considering coupling membranes with condensates.

Heterogeneous and Cooperative Rupture of Histidine-Ni2+ Metal-Coordination Bonds on Rationally Designed Protein Templates

Metal-coordination bonds, a highly tunable class of dynamic noncovalent interactions, are pivotal to the function of a variety of protein-based natural materials and have emerged as binding motifs to produce strong, tough, and self-healing bioinspired materials. While natural proteins use clusters of metal-coordination bonds, synthetic materials frequently employ individual bonds, resulting in mechanically weak materials. To overcome this current limitation, we rationally designed a series of elastin-like polypeptide templates with the capability of forming an increasing number of intermolecular histidine-Ni2+ metal-coordination bonds. Using single-molecule force spectroscopy and steered molecular dynamics simulations, we show that templates with three histidine residues exhibit heterogeneous rupture pathways, including the simultaneous rupture of at least two bonds with more-than-additive rupture forces. The methodology and insights developed improve our understanding of the molecular interactions that stabilize metal-coordinated proteins and provide a general route for the design of new strong, metal-coordinated materials with a broad spectrum of dissipative time scales.

Screening, separation and identification of metal-chelating peptides for nutritional, cosmetics and pharmaceutical applications

Metal-chelating peptides, which form metal-peptide coordination complexes with various metal ions, can be used as biofunctional ingredients notably to enhance human health and prevent diseases. This review aims to discuss recent insights into food-derived metal-chelating peptides, the strategies set up for their discovery, their study, and identification. After understanding the overall properties of metal-chelating peptides, their production from food-derived protein sources and their potential applications will be discussed, particularly in nutritional, cosmetics and pharmaceutical fields. In addition, the review provides an overview of the last decades of progress in discovering food-derived metal-chelating peptides, addressing several screening, separation and identification methodologies. Furthermore, it emphasizes the methods used to assess peptide-metal interaction, allowing for better understanding of chemical and thermodynamic parameters associated with the formation of peptide-metal coordination complexes, as well as the specific amino acid residues that play important roles in the metal ion coordination.

Design of a Biohybrid Materials Circuit with Binary Decoder Functionality

Synthetic biology applies concepts from electrical engineering and information processing to endow cells with computational functionality. Transferring the underlying molecular components into materials and wiring them according to topologies inspired by electronic circuit boards has yielded materials systems that perform selected computational operations. However, the limited functionality of available building blocks is restricting the implementation of advanced information-processing circuits into materials. Here, a set of protease-based biohybrid modules the bioactivity of which can either be induced or inhibited is engineered. Guided by a quantitative mathematical model and following a design-build-test-learn (DBTL) cycle, the modules are wired according to circuit topologies inspired by electronic signal decoders, a fundamental motif in information processing. A 2-input/4-output binary decoder for the detection of two small molecules in a material framework that can perform regulated outputs in form of distinct protease activities is designed. The here demonstrated smart material system is strongly modular and can be used for biomolecular information processing for example in advanced biosensing or drug delivery applications.

Exploring binding preferences: Cu(II), Ni(II), and Zn(II) complexes of mycobacterial GroEL1 His-rich and Glu/His-rich domains

Mycobacterial histidine-rich GroEL1 protein significantly differs from the well-known methionine-glycine-rich GroEL chaperonin and most preferably participates in Cu(II) homeostasis. Some GroEL1 proteins, however, do not possess six but only three histidine residues and more acidic residues that can function as binding sites for metal ions. To evaluate the importance of this difference, we examined and compared the properties of GroEL1 His-rich or Glu/His-rich C-terminal domains as ligands for Cu(II), Ni(II), and Zn(II) ions. We studied the stoichiometry, stability, and binding sites of Cu(II)/Ni(II)/Zn(II) complexes of two model peptides: XEN = Ac-DKPEEEEDGHGHAH (M. xenopi) and ABS = Ac-DKPAEEADHGHGHHGHAH (M. abscessus) in the pH range 2-11. In the case of Cu(II), Ni(II), and Zn(II) complexes of XEN and ABS, ABS always formed more stable complexes. For XEN, there seemed to be no preference for Ni(II) or Zn(II) ions. In contrast, for ABS, Zn(II) formed a complex that was slightly more stable than the one formed by Ni(II). This may be due to the 6 His residues, which preferentially interact with Zn(II) rather than Ni(II). The study identified that an equilibrium of complexes-known as polymorphism-may occur in ABS complexes. Therefore, distinct sets of histidine residues may be involved in metal binding.

Antirepressor specificity is shaped by highly efficient dimerization of the staphylococcal pathogenicity island regulating repressors: Stl repressor dimerization perturbed by dUTPases

The excision and replication, thus the life cycle of pathogenicity islands in staphylococci are regulated by Stl master repressors that form strong dimers. It has been recently shown that SaPIbov1-Stl dimers are separated during the activation of the Staphylococcus aureus pathogenicity island (SaPI) transcription via helper phage proteins. To understand the mechanism of this regulation, a quantitative analysis of the dimerization characteristics is required. Due to the highly efficient dimerization process, such an analysis has to involve specific solutions that permit relevant experiments to be performed. In the present work, we focused on two staphylococcal Stls associated with high biomedical interest, namely Stl proteins of Staphylococcus aureus bov1 and Staphylococcus hominis ShoCI794_SEPI pathogenicity islands. Exploiting the interactions of these two Stl proteins with their antirepressor-mimicking interaction partners allowed precise determination of the Stl dimerization constant in the subnanomolar range.

Novel His-tag Variants for Insertion Inside Polypeptide Chain

His-tags are protein affinity tags ubiquitously used due to their convenience and effectiveness. However, in some individual cases, the attachment of His-tags to a protein's N- or C-termini resulted in impairment of the protein's structure or function, which led to attempts to include His-tags inside of polypeptide chains. In this work, we describe newly designed internal His-tags, where two triplets of histidine residues are separated by glycine residues to avoid steric hindrances and consequently minimize their impact on the protein structure. The applicability of these His-tags was tested with eGFP, a multifaceted reference protein, and GrAD207, a modified apical domain of GroEL chaperone, designed to stabilize in soluble form initially insoluble proteins. Both proteins are used as fusion partners for different purposes, and providing them with His-tags introduced into their polypeptide chains should conveniently broaden their functionality without involving the termini. We conclude that the insertable tags may be adjusted for the purification of proteins belonging to different structural classes.

His1-tagged DM or DDM detergent micelles are reversibly conjugated by nickel ions

Specific conjugation of decyl β-D-maltoside (DM) or dodecyl β-D-maltoside (DDM) detergent micelles is accomplished between pH 7.0-8.5 in the presence of an amphiphilic analog of the amino acid histidine, bound to a 10-carbon hydrocarbon chain (His1-C10) and Ni2+ ions. Following addition of 10-15 wt% PEG-6000 as precipitant, phase separation in the form of oil-rich globules (30-600 µm) is observed by light microscopy. Other divalent cations: Zn2+, Fe2+, Cu2+ lead to dark precipitates rather than colorless globules; while Mg2+, Ca2+ do not promote any phase separation at all. Even in the absence of precipitant, dynamic light scattering (DLS) measurements demonstrate that DM micelles (hydrodynamic size ~ 6 nm) or DDM micelles (8 nm) self-associate into larger particles (9 nm and 411 nm for DM; 10 nm and 982 nm for DDM) in the presence of His1-C10 and nickel ions. Micellar conjugation is partially reversible in the presence of water soluble 50 mM EDTA, histidine or imidazole chelators. Cryo-transmission electron microscopy (cryo-TEM) imaging revealed the formation of non-uniformly dense detergent aggregates for both DM and DDM micelles in the presence of precipitant. The possible utility of such His1-tagged DM or DDM micelles for promoting crystallization of integral membrane proteins is discussed.

Biosensors Based on the Binding Events of Nitrilotriacetic Acid-Metal Complexes

Molecular immobilization and recognition are two key events for the development of biosensors. The general ways for the immobilization and recognition of biomolecules include covalent coupling reactions and non-covalent interactions of antigen-antibody, aptamer-target, glycan-lectin, avidin-biotin and boronic acid-diol. Tetradentate nitrilotriacetic acid (NTA) is one of the most common commercial ligands for chelating metal ions. The NTA-metal complexes show high and specific affinity toward hexahistidine tags. Such metal complexes have been widely utilized in protein separation and immobilization for diagnostic applications since most of commercialized proteins have been integrated with hexahistidine tags by synthetic or recombinant techniques. This review focused on the development of biosensors with NTA-metal complexes as the binding units, mainly including surface plasmon resonance, electrochemistry, fluorescence, colorimetry, surface-enhanced Raman scattering spectroscopy, chemiluminescence and so on.

Bond clusters control rupture force limit in shear loaded histidine-Ni2+ metal-coordinated proteins

Dynamic noncovalent interactions are pivotal to the structure and function of biological proteins and have been used in bioinspired materials for similar roles. Metal-coordination bonds, in particular, are especially tunable and enable control over static and dynamic properties when incorporated into synthetic materials. Despite growing efforts to engineer metal-coordination bonds to produce strong, tough, and self-healing materials, the systematic characterization of the exact contribution of these bonds towards mechanical strength and the effect of geometric arrangements is missing, limiting the full design potential of these bonds. In this work, we engineer the cooperative rupture of metal-coordination bonds to increase the rupture strength of metal-coordinated peptide dimers. Utilizing all-atom steered molecular dynamics simulations on idealized bidentate histidine-Ni²⁺ coordinated peptides, we show that histidine-Ni²⁺ bonds can rupture cooperatively in groups of two to three bonds. We find that there is a strength limit, where adding additional coordination bonds does not contribute to the additional increase in the protein rupture strength, likely due to the highly heterogeneous rupture behavior exhibited by the coordination bonds. Further, we show that this coordination bond limit is also found natural metal-coordinated biological proteins. Using these insights, we quantitatively suggest how other proteins can be rationally designed with dynamic noncovalent interactions to exhibit cooperative bond breaking behavior. Altogether, this work provides a quantitative analysis of the cooperativity and intrinsic strength limit for metal-coordination bonds with the aim of advancing clear guiding molecular principles for the mechanical design of metal-coordinated materials.

Tuning Targeted Liposome Avidity to Cells via Lipid Phase Separation

The addition of both cell-targeting moieties and polyethylene glycol (PEG) to nanoparticle (NP) drug delivery systems is a standard approach to improve the biodistribution, specificity, and uptake of therapeutic cargo. The spatial presentation of these molecules affects avidity of the NP to target cells in part through an interplay between the local ligand concentration and the steric hindrance imposed by PEG molecules. Here, we show that lipid phase separation in nanoparticles can modulate liposome avidity by changing the proximity of PEG and targeting protein molecules on a nanoparticle surface. Using lipid-anchored nickel-nitrilotriacetic acid (Ni-NTA) as a model ligand, we demonstrate that the attachment of lipid anchored Ni-NTA and PEG molecules to distinct lipid domains in nanoparticles can enhance liposome binding to cancer cells by increasing ligand clustering and reducing steric hindrance. We then use this technique to enhance the binding of RGD-modified liposomes, which can bind to integrins overexpressed on many cancer cells. These results demonstrate the potential of lipid phase separation to modulate the spatial presentation of targeting and shielding molecules on lipid nanocarriers, offering a powerful tool to enhance the efficacy of NP drug delivery systems.

Metal-chelating activity of soy and pea protein hydrolysates obtained after different enzymatic treatments from protein isolates

Soy and pea proteins are two rich sources of essential amino acids. The hydrolysis of these proteins reveals functional and bioactive properties of the produced small peptide mixtures. In our study, we employed the hydrolysis of soy and pea protein isolates with the endopeptidases Alcalase® and Protamex®, used alone or followed by the exopeptidase Flavourzyme®. The sequential enzyme treatments were the most efficient regarding the degree of hydrolysis. Then, soy and pea protein hydrolysates (SPHs and PPHs, respectively) were ultrafiltrated in order to select peptides of molecular weight ≤ 1 kDa. Whatever the protein source or the hydrolysis treatment, the hydrolysates showed similar molecular weight distributions and amino acid compositions. In addition, all the ultrafiltrated hydrolysates possess metal-chelating activities, as determined by UV-spectrophotometry and Surface Plasmon Resonance (SPR). However, the SPR data revealed better chelating affinities in SPHs and PPHs when produced by sequential enzymatic treatment.

Residue-specific binding of Ni(II) ions influences the structure and aggregation of amyloid beta (Aβ) peptides

Alzheimer's disease (AD) is the most common cause of dementia worldwide. AD brains display deposits of insoluble amyloid plaques consisting mainly of aggregated amyloid-β (Aβ) peptides, and Aβ oligomers are likely a toxic species in AD pathology. AD patients display altered metal homeostasis, and AD plaques show elevated concentrations of metals such as Cu, Fe, and Zn. Yet, the metal chemistry in AD pathology remains unclear. Ni(II) ions are known to interact with Aβ peptides, but the nature and effects of such interactions are unknown. Here, we use numerous biophysical methods-mainly spectroscopy and imaging techniques-to characterize Aβ/Ni(II) interactions in vitro, for different Aβ variants: Aβ(1-40), Aβ(1-40)(H6A, H13A, H14A), Aβ(4-40), and Aβ(1-42). We show for the first time that Ni(II) ions display specific binding to the N-terminal segment of full-length Aβ monomers. Equimolar amounts of Ni(II) ions retard Aβ aggregation and direct it towards non-structured aggregates. The His6, His13, and His14 residues are implicated as binding ligands, and the Ni(II)·Aβ binding affinity is in the low µM range. The redox-active Ni(II) ions induce formation of dityrosine cross-links via redox chemistry, thereby creating covalent Aβ dimers. In aqueous buffer Ni(II) ions promote formation of beta sheet structure in Aβ monomers, while in a membrane-mimicking environment (SDS micelles) coil-coil helix interactions appear to be induced. For SDS-stabilized Aβ oligomers, Ni(II) ions direct the oligomers towards larger sizes and more diverse (heterogeneous) populations. All of these structural rearrangements may be relevant for the Aβ aggregation processes that are involved in AD brain pathology.

Development of a Modular NTA:His Tag Viral Vaccine for Co-delivery of Antigen and Adjuvant

The SARS-CoV-2 pandemic has highlighted the need for vaccines that are effective, but quickly produced. Of note, vaccines with plug-and-play capabilities that co-deliver antigen and adjuvant to the same cell have shown remarkable success. Our approach of utilizing a nitrilotriacetic acid (NTA) histidine (His)-tag chemistry with viral adjuvants incorporates both of these characteristics: plug-and-play and co-delivery. We specifically utilize the cowpea mosaic virus (CPMV) and the virus-like particles from bacteriophage Qβ as adjuvants and bind the model antigen ovalbumin (OVA). Successful binding of the antigen to the adjuvant/carrier was verified by SDS-PAGE, western blot, and ELISA. Immunization in C57BL/6J mice demonstrates that with Qβ - but not CPMV - there is an improved antibody response against the target antigen using the Qβ-NiNTA:His-OVA versus a simple admixture of antigen and adjuvant. Antibody isotyping also shows that formulation of the vaccines can alter T helper biases; while the Qβ-NiNTA:His-OVA particle produces a balanced Th1/Th2 bias the admixture was strongly Th2. In a mouse model of B16F10-OVA, we further demonstrate improved survival and slower tumor growth in the vaccine groups compared to controls. The NiNTA:His chemistry demonstrates potential for rapid development of future generation vaccines enabling plug-and-play capabilities with effectiveness boosted by co-delivery to the same cell.

Metal-Chelating Peptides Separation Using Immobilized Metal Ion Affinity Chromatography: Experimental Methodology and Simulation

Metal-Chelating Peptides (MCPs), obtained from protein hydrolysates, present various applications in the field of nutrition, pharmacy, cosmetic etc. The separation of MCPs from hydrolysates mixture is challenging, yet, techniques based on peptide-metal ion interactions such as Immobilized Metal Ion Affinity Chromatography (IMAC) seem to be efficient. However, separation processes are time consuming and expensive, therefore separation prediction using chromatography modelling and simulation should be necessary. Meanwhile, the obtention of sorption isotherm for chromatography modelling is a crucial step. Thus, Surface Plasmon Resonance (SPR), a biosensor method efficient to screen MCPs in hydrolysates and with similarities to IMAC might be a good option to acquire sorption isotherm. This review highlights IMAC experimental methodology to separate MCPs and how, IMAC chromatography can be modelled using transport dispersive model and input data obtained from SPR for peptides separation simulation.

Synthesis of 2,5-Dialkyl-1,3,4-oxadiazoles Bearing Carboxymethylamino Groups

A series of new symmetrical 2,5-dialkyl-1,3,4-oxadiazoles containing substituted alkyl groups at the terminal positions with substituents, such as bromine, isopropyloxycarbonylmethylamino, and carboxymethylamino, were successfully synthesized. The developed multistep method employed commercially available acid chlorides differing in alkyl chain length and terminal substituent, hydrazine hydrate, and phosphorus oxychloride. The intermediate bromine-containing 2,5-dialkyl-1,3,4-oxadiazoles were easily substituted with diisopropyl iminodiacetate, followed by hydrolysis in aqueous methanol solution giving the corresponding 1,3,4-oxadiazoles bearing carboxymethylamino substituents. The structure of all products was confirmed by conventional spectroscopic methods including ¹H NMR, ¹³C NMR, and HRMS.

High-efficiency recombinant protein purification using mCherry and YFP nanobody affinity matrices

Mammalian cell lines are important expression systems for large proteins and protein complexes, particularly when the acquisition of post-translational modifications in the protein's native environment is desired. However, low or variable transfection efficiencies are challenges that must be overcome to use such an expression system. Expression of recombinant proteins as a fluorescent protein fusion enables real-time monitoring of protein expression, and also provides an affinity handle for one-step protein purification using a suitable affinity reagent. Here, we describe a panel of anti-GFP and anti-mCherry nanobody affinity matrices and their efficacy for purification of GFP/YFP or mCherry fusion proteins. We define the molecular basis by which they bind their target proteins using X-ray crystallography. From these analyses, we define an optimal pair of nanobodies for purification of recombinant protein tagged with GFP/YFP or mCherry, and demonstrate these nanobody-sepharose supports are stable to many rounds of cleaning and extended incubation in denaturing conditions. Finally, we demonstrate the utility of the mCherry-tag system by using it to purify recombinant human topoisomerase 2α expressed in HEK293F cells. The mCherry-tag and GFP/YFP-tag expression systems can be utilized for recombinant protein expression individually or in tandem for mammalian protein expression systems where real-time monitoring of protein expression levels and a high-efficiency purification step is needed.

Binding of His-tagged fluorophores to lipid bilayers of giant vesicles

His-tagged molecules can be attached to lipid bilayers via certain anchor lipids, a method that has been widely used for the biofunctionalization of membranes and vesicles. To observe the membrane-bound molecules, it is useful to consider His-tagged molecules that are fluorescent as well. Here, we study two such molecules, green fluorescence protein (GFP) and green-fluorescent fluorescein isothiocyanate (FITC), both of which are tagged with a chain of six histidines (6H) that bind to the anchor lipids within the bilayers. The His-tag 6H is much smaller than the GFP molecule but somewhat larger than the FITC dye. The lipid bilayers form giant unilamellar vesicles (GUVs), the behavior of which can be directly observed in the optical microscope. We apply and compare three well-established preparation methods for GUVs: electroformation on platinum wire, polyvinyl alcohol (PVA) hydrogel swelling, and electroformation on indium tin oxide (ITO) glass. Microfluidics is used to expose the GUVs to a constant fluorophore concentration in the exterior solution. The brightness of membrane-bound 6H-GFP exceeds the brightness of membrane-bound 6H-FITC, in contrast to the quantum yields of the two fluorophores in solution. In fact, 6H-FITC is observed to be strongly quenched by the anchor lipids which bind the fluorophores via Ni²⁺ ions. For both 6H-GFP and 6H-FITC, the membrane fluorescence is measured as a function of the fluorophores' molar concentration. The theoretical analysis of these data leads to the equilibrium dissociation constants K_d = 37.5 nM for 6H-GFP and K_d = 18.5 nM for 6H-FITC. We also observe a strong pH-dependence of the membrane fluorescence.

Poly-Gly Region Regulates the Accessibility of Metal Binding Sites in Snake Venom Peptides

It is supposed that the presence of poly-His regions in close proximity to poly-Gly domains in snake venoms is related to their biological activity; poly-His/poly-Gly (pHpG) peptides inhibit the activity of metalloproteinases during venom storage via the chelation metal ions, necessary for their proper functioning. This work shows that only the histidyl residues from the N-terminal VDHDHDH motif (but not from the poly-His tag) were the primary Zn(II) binding sites and that the poly-Gly domain situated in the proximity of a central proline residue may play a regulatory role in venom gland protection. The proline induces a kink of the peptide, resulting in steric hindrance, which may modulate the accessibility of potential metal binding sites in the poly-His domain and may, in turn, be one of the regulators of Zn(II) accessibility in the venom gland and therefore a modulator of metalloproteinase activity during venom storage.

The proline induces a kink of the peptide, resulting in a steric hindrance, which may modulate the accessibility of potential metal binding sites in the poly-His domain and may, in turn, be one of the regulators of Zn(II) accessibility in the venom gland and therefore a modulator of metalloproteinase activity during venom storage.

Lignin-containing hydrogels with anti-freezing, excellent water retention and super-flexibility for sensor and supercapacitor applications

We developed a highly conductive and flexible, anti-freezing sulfonated lignin (SL)-containing polyacrylic acid (PAA) (SL-g-PAA-Ni) hydrogel, with a high concentration of NiCl₂. Ni²⁺ contributes multi-functions to the preparation of the hydrogel and its final properties, such as fast polymerization reaction as a result of the presence of redox pairs of Ni³⁺/Ni²⁺ and hydroquinone/quinone, and anti-freezing properties of the hydrogel due to the salt effects of NiCl₂ so that at -20 °C the hydrogel shows similar properties to those at the room temperature. Thanks to the effective coordinations of Ni²⁺ with catecholic groups and carboxylic groups, as well as the rich hydrogen bonding capacity, the resultant hydrogel possesses excellent mechanical properties. High ionic conductivity (6.85 S·m^-1) of the hydrogel is obtained due to the supply of high concentration of Ni²⁺. Moreover, the ionic solvation effect of NiCl₂ in the hydrogel imparts excellent water retention ability, with water retention of ~93 % after 21-day storage. The SL-g-PAA-Ni hydrogel can accurately detect various human motions at -20 °C. The supercapacitor assembled from SL-g-PAA-Al hydrogel at -20 °C manifests a high specific capacitance of 252 F·g^-1, with maximum energy density of 26.97 Wh·kg^-1, power density of 2667 W·kg^-1, and capacitance retention of 96.7 % after 3000 consecutive charge-discharge cycles.

Detection of Histidine-Tagged Protein in Escherichia coli by Single-Cell Inductively Coupled Plasma-Mass Spectrometry

We have developed a rapid and precise quantification method for a histidine (His)-tagged recombinant protein produced in Escherichia coli (E. coli) by single-cell inductively coupled plasma-mass spectrometry (SC-ICP-MS). Plasmid vector containing enhanced green fluorescent protein (EGFP) or red fluorescent protein (mCherry) gene fused with His-tag was transformed into E. coli. The transformed E. coli was exposed to nickel (Ni) chloride or cobalt (Co) chloride for labeling His-tag with the Ni or Co ion. Then, E. coli was analyzed by SC-ICP-MS to determine the amount of EGFP or mCherry protein on the basis of the signal of Ni or Co bound to His-tag. By comparing Ni and Co contents in E. coli expressing His-tagged mCherry with those in nontagged mCherry, the specific binding of Co to His-tag was more clearly detected than that of Ni. The Co contents were increased until 6 h after the protein induction, and this observation was coincident with the increases in fluorescence intensity of EGFP or mCherry measured by a flow cytometer. However, the Co contents were decreased for EGFP and kept at a constant level for mCherry from 6 to 24 h despite the continuous increase in the fluorescence intensity through incubation. The fluorescent proteins were mainly recovered in the insoluble fraction 24 h after the induction. This can be explained by the fact that the overexpressed fluorescent proteins with His-tag are transferred into inclusion bodies, which hampers the binding of the fluorescent proteins to the Co ion. SC-ICP-MS can be a useful technique to precisely quantify soluble recombinant proteins in E. coli without the extraction and purification process.

Can DyeCycling break the photobleaching limit in single-molecule FRET?

Biomolecular systems, such as proteins, crucially rely on dynamic processes at the nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that control biomolecular systems. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique to observe in real-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural states. Currently, this technique is fundamentally limited by irreversible photobleaching, causing the untimely end of the experiment and thus, a narrow temporal bandwidth of ≤ 3 orders of magnitude. Here, we introduce "DyeCycling", a measurement scheme with which we aim to break the photobleaching limit in smFRET. We introduce the concept of spontaneous dye replacement by simulations, and as an experimental proof-of-concept, we demonstrate the intermittent observation of a single biomolecule for one hour with a time resolution of milliseconds. Theoretically, DyeCycling can provide > 100-fold more information per single molecule than conventional smFRET. We discuss the experimental implementation of DyeCycling, its current and fundamental limitations, and specific biological use cases. Given its general simplicity and versatility, DyeCycling has the potential to revolutionize the field of time-resolved smFRET, where it may serve to unravel a wealth of biomolecular dynamics by bridging from milliseconds to the hour range.

Electronic Supplementary Material

Supplementary material is available for this article at 10.1007/s12274-022-4420-5 and is accessible for authorized users.

Data-rich process development of immobilized biocatalysts in flow

The authors describe an automated, data-rich screening and process development method for rapid discovery, development, and optimization of immobilized enzymes, critical to many biocatalytic processes.

Two-point immobilization of a conformation-specific beta2-adrenoceptor for recognizing the receptor agonists or antagonists inspired by binding-induced DNA assembly

Immobilized protein has advanced in many areas like drug discovery. While this field evolved rapidly over the last three decades, the immobilization platform for the G-protein-coupled receptor (GPCR) remains unpromising due to its instability under the relatively harsh conditions of current methodologies. Taking beta₂-adrenoceptor (β₂-AR) as an example, we presented here a general strategy for immobilization of GPCRs by combining the His₆-tag trap system, conformation-specific aptamer, and target binding induced DNA hybridization. Morphology characterization by diverse assays confirmed a monolayer of β₂-AR on the microsphere surface. The radio-ligand binding assay and immuno-transmission electron microscopy showed desirable ligand- and antibody-binding activities. A case study of chromatography using the immobilized receptor as a stationary phase exhibited a demonstrable conformation specificity that enables the selective recognition of the receptor agonists or antagonists. Owing to the competitive strand displacement during the immobilization, the method proved to be capable of sensitively and directly determining the receptor density on the surface which enormously challenges most of the reported assays. This method is possible to turn into a general strategy for the immobilization of GPCRs with a defined orientation, conformation, function, and density, thus paving the way for precisely realizing the receptor-ligand binding interaction and screening the receptor agonist or antagonist with high efficiency.

Biofabrication of functional protein nanoparticles through simple His-tag engineering

We have developed a simple, robust, and fully transversal approach for the a-la-carte fabrication of functional multimeric nanoparticles with potential biomedical applications, validated here by a set of diverse and unrelated polypeptides. The proposed concept is based on the controlled coordination between Zn2+ ions and His residues in His-tagged proteins. This approach results in a spontaneous and reproducible protein assembly as nanoscale oligomers that keep the original functionalities of the protein building blocks. The assembly of these materials is not linked to particular polypeptide features, and it is based on an environmentally friendly and sustainable approach. The resulting nanoparticles, with dimensions ranging between 10 and 15 nm, are regular in size, are architecturally stable, are fully functional, and serve as intermediates in a more complex assembly process, resulting in the formation of microscale protein materials. Since most of the recombinant proteins produced by biochemical and biotechnological industries and intended for biomedical research are His-tagged, the green biofabrication procedure proposed here can be straightforwardly applied to a huge spectrum of protein species for their conversion into their respective nanostructured formats.

Tyrosine-Based Cross-Linking of Peptide Antigens to Generate Nanoclusters with Enhanced Immunogenicity: Demonstration Using the Conserved M2e Peptide of Influenza A

A method of creating nanoclusters (NCs) from soluble peptide molecules is described utilizing an approach based on a tyrosine-tyrosine cross-linking reaction. A reactive tag comprising histidine and tyrosine residues was introduced at the termini of the peptide molecules. The cross-linking reaction led to the creation of dityrosine bonds within the tag, which allowed for the generation of peptide NCs. We show that it is essential for the reactive tag to be present at both the "N" and "C" termini of the peptide for cluster formation to occur. Additionally, the cross-linking reaction was systematically characterized to show the importance of reaction conditions on final cluster diameter, allowing us to generate NCs of various sizes. To demonstrate the immunogenic potential of the peptide clusters, we chose to study the conserved influenza peptide, M2e, as the antigen. M2e NCs were formulated using the cross-linking reaction. We show the ability of the clusters to generate protective immunity in a dose, size, and frequency dependent manner against a lethal influenza A challenge in BALB/c mice. Taken together, the data presented suggest this new cluster formation technique can generate highly immunogenic peptide NCs in a simple and controllable manner.

Insights on the emerging biotechnology of histidine-rich peptides

In the late 70's, the discovery of the restriction enzymes made possible the biological production of functional proteins by recombinant DNA technologies, a fact that largely empowered both biotechnological and pharmaceutical industries. Short peptides or small protein domains, with specific molecular affinities, were developed as purification tags in downstream processes to separate the target protein from the culture media or cell debris, upon breaking the producing cells. Among these tags, and by exploiting the interactivity of the imidazole ring of histidine residues, the hexahistidine peptide (H6) became a gold standard. Although initially used almost exclusively in protein production, H6 and related His-rich peptides are progressively proving a broad applicability in novel utilities including enzymatic processes, advanced drug delivery systems and diagnosis, through a so far unsuspected adaptation of their binding capabilities. In this context, the coordination of histidine residues and metals confers intriguing functionalities to His-rich sequences useable in the forward-thinking design of protein-based nano- and micro-materials and devices, through strategies that are comprehensively presented here.

Electrically Switchable Nanolever Technology for the Screening of Metal-Chelating Peptides in Hydrolysates

Metal-chelating peptides (MCP) are considered as indirect antioxidants due to their capacity to inhibit radical chain reaction and oxidation. Here, we propose a new proof of concept for the screening of MCPs present in protein hydrolysates for valorizing their antioxidant properties by using the emerging time-resolved molecular dynamics technology, switchSENSE. This method unveils possible interactions between MCPs and immobilized nickel ions using fluorescence and electro-switchable DNA chips. The switchSENSE method was first set up on synthetic peptides known for their metal-chelating properties. Then, it was applied to soy and tilapia viscera protein hydrolysates. Their Cu²⁺-chelation capacity was, in addition, determined by UV-visible spectrophotometry as a reference method. The switchSENSE method has displayed a high sensitivity to evidence the presence of MCPs in both hydrolysates. Hence, we demonstrate for the first time that this newly introduced technology is a convenient methodology to screen protein hydrolysates in order to determine the presence of MCPs before launching time-consuming separations.

Recent Advancements in Receptor Layer Engineering for Applications in SPR-Based Immunodiagnostics

The rapid progress in the development of surface plasmon resonance-based immunosensing platforms offers wide application possibilities in medical diagnostics as a label-free alternative to enzyme immunoassays. The early diagnosis of diseases or metabolic changes through the detection of biomarkers in body fluids requires methods characterized by a very good sensitivity and selectivity. In the case of the SPR technique, as well as other surface-sensitive detection strategies, the quality of the transducer-immunoreceptor interphase is crucial for maintaining the analytical reliability of an assay. In this work, an overview of general approaches to the design of functional SPR-immunoassays is presented. It covers both immunosensors, the design of which utilizes well-known and often commercially available substrates, as well as the latest solutions developed in-house. Various approaches employing chemical and passive binding, affinity-based antibody immobilization, and the introduction of nanomaterial-based surfaces are discussed. The essence of their influence on the improvement of the main analytical parameters of a given immunosensor is explained. Particular attention is paid to solutions compatible with the latest trends in the development of label-free immunosensors, such as platforms dedicated to real-time monitoring in a quasi-continuous mode, the use of in situ-generated receptor layers (elimination of the regeneration step), and biosensors using recombinant and labelled protein receptors.

Design and Development of Antibody Functionalized Gold Nanoparticles for Biomedical Applications

Antibody-functionalized gold nanoparticle constitutes a powerful interface biosystem for biomedical applications where the properties of gold nanoparticles and the specificity of antibody-antigen interactions are combined. This study provides insight into the key factors for the development of antibody functionalized gold nanoparticles focusing on the immobilization of the antibody. Here, we address an oriented antibody immobilization procedure on gold nanoparticles. It comprises chelatemodified gold nanoparticles that are designed for oriented immobilization of IgG antibodies (end on spatial orientation) through the metal-chelation to histidine-rich metal binding site in the heavy chain (Fc) of the antibody.

Taking Advantage of the Morpheein Behavior of Peroxiredoxin in Bionanotechnology

Morpheeins are proteins that reversibly assemble into different oligomers, whose architectures are governed by conformational changes of the subunits. This property could be utilized in bionanotechnology where the building of nanometric and new high-ordered structures is required. By capitalizing on the adaptability of morpheeins to create patterned structures and exploiting their inborn affinity toward inorganic and living matter, “bottom-up” creation of nanostructures could be achieved using a single protein building block, which may be useful as such or as scaffolds for more complex materials. Peroxiredoxins represent the paradigm of a morpheein that can be applied to bionanotechnology. This review describes the structural and functional transitions that peroxiredoxins undergo to form high-order oligomers, e.g., rings, tubes, particles, and catenanes, and reports on the chemical and genetic engineering approaches to employ them in the generation of responsive nanostructures and nanodevices. The usefulness of the morpheeins’ behavior is emphasized, supporting their use in future applications.

A disulfide-stabilised helical hairpin fold in acrorhagin I: An emerging structural motif in peptide toxins

Acrorhagin I (U-AITX-Aeq5a) is a disulfide-rich peptide identified in the aggressive organs (acrorhagi) of the sea anemone Actinia equina. Previous studies (Toxicon 2005, 46:768-74) found that the peptide is toxic in crabs, although the structural and functional properties of acrorhagin I have not been reported. In this work, an Escherichia coli (BL21 strain) expression system was established for the preparation of ¹³C,¹⁵N-labelled acrorhagin I, and the solution structure was determined using NMR spectroscopy. Structurally, acrorhagin I is similar to B-IV toxin from the marine worm Cerebratulus lacteus (PDB id 1VIB), with a well-defined helical hairpin structure stabilised by four intramolecular disulfide bonds. The recombinant peptide was tested in patch-clamp electrophysiology assays against voltage-gated potassium and sodium channels, and in bacterial and fungal growth inhibitory assays and haemolytic assays. Acrorhagin I was not active against any of the ion channels tested and showed no activity in functional assays, indicating that this peptide may possess a different biological function. Metal ion interaction studies using NMR spectroscopy showed that acrorhagin I bound zinc and nickel, suggesting that its function might be modulated by metal ions or that it may be involved in regulating metal ion levels and their transport. The similarity between the structure of acrorhagin I and that of B-IV toxin from a marine worm suggests that this fold may prove to be a recurring motif in disulfide-rich peptides from marine organisms.

Kinesin-Recruiting Microtubules Exhibit Collective Gliding Motion while Forming Motor Trails

Microtubules gliding on surfaces coated with kinesin motors are minimalist experimental systems for studying collective behavior. Collective behavior in these systems arises from interactions between filaments, for example, from steric interactions, depletion forces, or cross-links. To maximize the utilization of system components and the production of work, it is desirable to achieve mutualistic interactions leading to the congregations of both types of agents, that is, cytoskeletal filaments and molecular motors. To this end, we used a microtubule-kinesin system, where motors reversibly bind to the surface via an interaction between a hexahistidine (His₆) tag on the motor and a Ni(II)-nitrilotriacetic acid (Ni-NTA) moiety on the surface. The surface density of binding sites for kinesin motors was increased relative to our earlier work, driving the motors from the solution to the surface. Characterization of the motor-surface interactions in the absence of microtubules yielded kinetic parameters consistent with previous data and revealed the capacity of the surface to support two-dimensional motor diffusion. The motor density gradually fell over 2 h, presumably due to the stripping of Ni(II) from the NTA moieties on the surface. Microtubules gliding on these reversibly bound motors were unable to cross each other and at high enough densities began to align and form long, dense bundles. The kinesin motors accumulated in trails surrounding the microtubule bundles and participated in microtubule transport.

Regenerable Biosensors for Small-Molecule Kinetic Characterization Using SPR

A key activity in small-molecule drug discovery is the characterization of compound-target interactions. Surface plasmon resonance (SPR) is a flexible technique for this purpose, with a wide affinity range (micromoles to picomoles), low protein requirements, and the ability to characterize the kinetics of compound binding. However, a key requirement of SPR is the immobilization of the target protein to the surface of the sensor chip. The most commonly used immobilization techniques (covalent immobilization, streptavidin-biotin) are irreversible in nature, which can afford excellent baseline stability but impose limitations throughput for slowly dissociating compounds or unstable targets. Reversible immobilization (e.g., His-tag-Ni-NTA) is possible but typically precludes accurate quantification of slow dissociation kinetics due to baseline drift.Here we present our investigation of three immobilization strategies (dual-His-tagged target protein, His-tagged streptavidin, and switchavidin) that combine the robustness of irreversible immobilization with the flexibility of reversible immobilization. Each has its own advantages and limitations, and while a universal immobilization procedure remains to be found, these strategies add to the immobilization toolbox that enables previously out-of-scope applications. Such applications are highlighted in two examples that greatly increased throughput for the kinetic characterization of potent kinase inhibitors and kinetic profiling of covalent inhibitors.

Dynamic spatial and structural organization in artificial cells regulates signal processing by protein scaffolding

Structural and spatial organization are fundamental properties of biological systems that allow cells to regulate a wide range of biochemical processes. This organization is often transient and governed by external cues that initiate dynamic self-assembly processes. The construction of synthetic cell-like materials with similar properties requires the hierarchical and reversible organization of selected functional components on molecular scaffolds to dynamically regulate signaling pathways. The realization of such transient molecular programs in synthetic cells, however, remains underexplored due to the associated complexity of such hierarchical platforms. In this contribution, we effectuate dynamic spatial organization of effector protein subunits in a synthetic biomimetic compartment, a giant unilamellar vesicle (GUV), by associating in a reversible manner two fragments of a split luciferase to the membrane. This induces their structural dimerization, which consequently leads to the activation of enzymatic signaling. Importantly, such organization and activation are dynamic processes, and can be autonomously regulated - thus opening up avenues toward continuous spatiotemporal control over supramolecular organization and signaling in an artificial cell.

Asymmetric flow field-flow fractionation coupled to surface plasmon resonance detection for analysis of therapeutic proteins in blood serum

Coupling of surface plasmon resonance (SPR) detection to asymmetric flow field-flow fractionation (AF4) offers the possibility to study active fractions of bio-separations on real samples, such as serum and saliva, including the assessment of activity of possibly aggregated species. The coupling of SPR with AF4 requires the possibility to select fractions from a fractogram and redirect them to the SPR. The combination of SPR with chromatography-like methods also requires a mechanism for regeneration of the receptor immobilised onto the SPR sensor surface. In recent work, the combination of size exclusion chromatography (SEC) with SPR was pioneered as a successful methodology for identification, characterisation and quantification of active biocomponents in biological samples. In this study, the approach using AF4 is evaluated for the antibody trastuzumab in buffer and serum. The particular object of this study was to test the feasibility of using AF4 in combination with SPR to detect and quantify proteins and aggregates in complex samples such as blood serum. Also, in the investigation, three different immobilisation methods for the receptor HER-2 were compared, which involved (1) direct binding via EDC/NHS, the standard approach; (2) immobilisation via NTA-Ni-Histag complexation; and (3) biotin/avidin-linked chemistry using a regenerable form of avidin. The highest specific activity was obtained for the biotin-avidin method, while the lowest specific activity was observed for the NTA-Ni-Histag linkage. The data show that AF4 can separate trastuzumab monomers and aggregates in blood serum and that SPR has the ability to selectively monitor the elution. This is an encouraging result for automated analysis of complex biological samples using AF4-SPR.

Development of a Novel SPR Assay to Study CXCR4-Ligand Interactions

G protein-coupled receptors (GPCRs) are involved in a plethora of different diseases. Consequently, these proteins are considered as an important class of drug targets. Measuring detailed kinetic information on these types of proteins has been challenging. Surface plasmon resonance (SPR) can provide this information, however, the use of SPR on GPCRs remains a complex issue. Here, we report an SPR assay to investigate the interactions between the full-length chemokine receptor CXCR4 and nanobody-Fc (Nb-Fc) ligands. Nb-Fcs consist of two monovalent VHH domains fused with an Fc domain of a human IgG molecule. The CXCR4 protein used in this assay was produced with a C-terminal 10x-histidine tag and was immobilized on a nitrilotriacetic acid chip. In order to verify the sensitivity and effectiveness of this assay, the results were compared to data obtained from cellular assays as well as from another SPR assay using CXCR4 virus-like particles (VLPs). CXCR4 remained intact and stable for at least 12 h, and the kinetic results correlated well with both the cellular assays and the VLP SPR assay results. Apart from determining the binding kinetics of Nb-Fc with CXCR4, our results contributed to understanding CXCR4 interaction dynamics. In conclusion, this assay provides a viable experimental platform that has high potential to be expanded for studying other molecules as well as other histidine-tagged GPCRs.