Monte Carlo simulations of antibody adsorption and orientation on charged surfaces

Paper electrochemical immunosensor for the rapid screening of Galectin-3 patients with heart failure

A paper electrochemical immunosensor for the combined binding and quantification of the heart failure (HF) biomarker Galectin-3 has been developed. The simple design of the new sensor is comprised of paper material that is decorated with gold nanostructures, to maximize its electroactive surface area, and functionalized with target-specific recognition molecules to selectively bind the protein from aqueous solutions. The binding of the protein caused the blockage of the electron flow to the sensor electroactive surface, thus causing its oxidation potential to shift and the corresponding current to reduce quantitatively with the increase in the protein concentration within the working range of 0.5ng/mL-8ng/mL (LOQ-0.5 ng/mL). This novel sensor was able to quantify Galectin-3 concentration in saliva samples from HF patients and healthy controls within 20 min with good reproducibility (RSD = 3.64%), without the need for complex sample processing steps. The electrochemical measurements of the patient samples were cross validated by ELISA where the percent agreement between the two methods was found to be 92.7% (RSD = 7.20%). Therefore, the new paper immunosensor sensor has a strong potential for rapid and cost-effective screening of the Galectin 3 biomarker at points of care, thus supporting the timely diagnosis of heart failure.

All-atom modeling of methacrylate-based multi-modal chromatography resins for Langmuir constant prediction of peptides

In downstream processing, the intricate nature of the interactions between biomolecules and adsorbent materials presents a significant challenge in the prediction of their binding and elution behaviors. This complexity is further heightened in multi-modal chromatography (MMC), which employs two distinct binding mechanisms. To gain a deeper understanding of the involved interactions, simulating the adsorption of biomolecules on resin surfaces is a focal point of ongoing research. However, previous studies often simplified the adsorbent surface, modeling it as a flat or slightly curved plane without including a realistic backbone structure. Here, we introduce and validate two novel workflows aimed at predicting peptide binding behaviors in MMC, specifically targeting methacrylate-based resins. Our first achievement was the development of an all-atom model of a commercial MMC resin surface, incorporating its polymethacrylic backbone. Furthermore, we established and tested a workflow for rapid calculations of binding free energies (ΔG) with 10 linear peptides as target molecules. These ΔG calculations were effectively used to predict Langmuir constants, achieving a high coefficient of determination (R²) of 0.96. In subsequent benchmarking tests, our model outperformed established, simpler resin surface models in terms of predictive capabilities.

Interfacial Interaction between Functionalization of Polysulfone Membrane Materials and Protein Adsorption

This study that modified polysulfone membranes with different end-group chemical functionalities were prepared using chemical synthesis methods and experimentally characterized. The molecular dynamics (MD) method were used to discuss the adsorption mechanism of proteins on functionalized modified polysulfone membrane materials from a molecular perspective, revealing the interactions between different functionalized membrane surfaces and protein adsorption. Theoretical analysis combined with basic experiments and MD simulations were used to explore the orientation and spatial conformational changes of protein adsorption at the molecular level. The results show that BSA exhibits different variability and adsorption characteristics on membranes with different functional group modifications. On hydrophobic membrane surfaces, BSA shows the least stable configuration stability, making it prone to nonspecific structural changes. In addition, surface charge effects lead to electrostatic repulsion for BSA and reduce the protein adsorption sites. These MD simulation results are consistent with experimental findings, providing new design ideas and support for modifying blood-compatible membrane materials.

Electrically Oriented Antibodies on Transistor for Monitoring Several Copies of Methylated DNA

An antibody transistor is a promising biosensing platform for the diagnosis and monitoring of various diseases. Nevertheless, the low concentration and short half-life of biomarkers require biodetection at the trace-molecule level, which remains a challenge for existing antibody transistors. Herein, we demonstrate a graphene field-effect transistor (gFET) with electrically oriented antibody probes (EOA-gFET) for monitoring several copies of methylated DNA. The electric field confines the orientation of antibody probes on graphene and diminishes the distance between graphene and methylated DNAs captured by antibodies, generating more induced charges on graphene and amplifying the electric signal. EOA-gFET realizes a limit of detection (LoD) of ∼0.12 copy μL-1, reaching the lowest LoD reported before. EOA-gFET shows a distinguishable signal for liver cancer clinical serum samples within ∼6 min, which proves its potential as a powerful tool for disease screening and diagnosis.

Electric Field-Assisted Molecularly Imprinted Polymer-Modified QCM Sensor for Enhanced Detection of Immunoglobulin

In this study, an electric-field-assisted molecularly imprinted polymer (EFAMIP) as an enhanced form of MIP was developed to improve the MIP-modified quartz crystal microbalance (QCM) biosensors. While exerting a vertical electric field, polymerization of methacrylic acid in the presence of immunoglobulin G (IgG) as the template was initiated, and later, after the template removal process, the EFAMIPs were obtained. The polymer surface characterization was conducted by using a scanning electron microscope. The impact of electric field direction on IgG binding sites, forming either EFAMIP-Fab or EFAMIP-Fc, was assessed. Next, the static measurement results in liquid for EFAMIP-modified QCM and MIP-modified QCM were compared. While encompassing IgG, EFAMIP-modified QCMs exhibited up to a 113.5% higher frequency shift than typical MIP in time-limited detection. The final frequency shift of EFAMIP, which determines the detection limit of IgG, was improved up to 12.5% compared to typical MIP. Moreover, the EFAMIP-Fab performance was promising for the selective detection of IgG in a solution containing different types of immunoglobulins.

Simulation Study of Polyethylene Terephthalate Hydrolase Adsorption on Self-Assembled Monolayers

Polyethylene terephthalate (PET) hydrolase, discovered in Ideonella sakaiensis (IsPETase), is a promising agent for the biodegradation of PET under mild reaction conditions, yet the thermal stability is poor. The efficient immobilization and orientation of IsPETase on different solid substrates are essential for its application. In this work, the combined parallel tempering Monte Carlo simulation with the all-atom molecular dynamics simulation approach was adopted to reveal the adsorption mechanism, orientation, and conformational changes of IsPETase adsorbed on charged self-assembled monolayers (SAMs), including COOH-SAM and NH2-SAM with different surface charge densities (SCDs). The results show that the protein adsorption orientation was determined not only by attraction interactions but also by repulsion interactions. IsPETase is adsorbed on the COOH-SAM surface with an "end-on" orientation, which favors the exposure of the catalyzed triplet to the solution. In addition, the entrance to the catalytic active center is larger on the COOH-SAM surface with a low SCD. This work reveals the controlled orientation and conformational information on IsPETase on charged surfaces at the atomistic level. This study would certainly promote our understanding of the mechanism of IsPETase adsorption and provide theoretical support for the design of substrates for IsPETase immobilization.

APOE Christchurch-mimetic therapeutic antibody reduces APOE-mediated toxicity and tau phosphorylation

INTRODUCTION

We discovered that the APOE3 Christchurch (APOE3Ch) variant may provide resistance to Alzheimer's disease (AD). This resistance may be due to reduced pathological interactions between ApoE3Ch and heparan sulfate proteoglycans (HSPGs).

METHODS

We developed and characterized the binding, structure, and preclinical efficacy of novel antibodies targeting human ApoE-HSPG interactions.

RESULTS

We found that one of these antibodies, called 7C11, preferentially bound ApoE4, a major risk factor for sporadic AD, and disrupts heparin-ApoE4 interactions. We also determined the crystal structure of a Fab fragment of 7C11 and used computer modeling to predict how it would bind to ApoE. When we tested 7C11 in mouse models, we found that it reduced recombinant ApoE-induced tau pathology in the retina of MAPT*P301S mice and curbed pTau S396 phosphorylation in brains of systemically treated APOE4 knock-in mice. Targeting ApoE-HSPG interactions using 7C11 antibody may be a promising approach to developing new therapies for AD.

High throughput screening for rapid and reliable prediction of monovalent antibody binding behavior in flowthrough mode

Flowthrough (FT) anion exchange (AEX) chromatography is a widely used polishing step for the purification of monoclonal antibody (mAb) formats. To accelerate downstream process development, high throughput screening (HTS) tools have proven useful. In this study, the binding behavior of six monovalent mAbs (mvAbs) was investigated by HTS in batch binding mode on different AEX and mixed-mode resins at process-relevant pH and NaCl concentrations. The HTS entailed the evaluation of mvAb partition coefficients (Kp ) and visualization of results in surface-response models. Interestingly, the HTS data grouped the mvAbs into either a strong-binding group or a weak-binding/FT group independent of theoretical Isoelectric point. Mapping the charged and hydrophobic patches by in silico protein surface property analyses revealed that the distribution of patches play a major role in predicting FT behavior. Importantly, the conditions identified by HTS were successfully verified by 1 mL on-column experiments. Finally, employing the optimal FT conditions (7-9 mS/cm and pH 7.0) at a mini-pilot scale (CV = 259 mL) resulted in 99% yield and a 21-23-fold reduction of host cell protein to <100 ppm, depending on the varying host cell protein (HCP) levels in the load. This work opens the possibility of using HTS in FT mode to accelerate downstream process development for mvAb candidates in early research.

A stable physisorbed layer of packed capture antibodies for high-performance sensing applications

Antibody physisorption at a solid interface is a very interesting phenomenon that has important effects on applications such as the development of novel biomaterials and the rational design and fabrication of high-performance biosensors. The strategy selected to immobilize biorecognition elements can determine the performance level of a device and one of the simplest approaches is physical adsorption, which is cost-effective, fast, and compatible with printing techniques as well as with green-chemistry processes. Despite its huge advantages, physisorption is very seldom adopted, as there is an ingrained belief that it does not lead to high performance because of its lack of uniformity and long-term stability, which, however, have never been systematically investigated, particularly for bilayers of capture antibodies. Herein, the homogeneity and stability of an antibody layer against SARS-CoV-2-Spike1 (S1) protein physisorbed onto a gold surface have been investigated by means of multi-parametric surface plasmon resonance (MP-SPR). A surface coverage density of capture antibodies as high as (1.50 ± 0.06) × 10¹² molecules per cm^-2 is measured, corresponding to a thickness of 12 ± 1 nm. This value is compatible with a single monolayer of homogeneously deposited antibodies. The effect of the ionic strength (i_s) of the antibody solution in controlling physisorption of the protein was thoroughly investigated, demonstrating an enhancement in surface coverage at lower ionic strength. An atomic force microscopy (AFM) investigation shows a globular structure attributed to i_s-related aggregations of antibodies. The long-term stability over two weeks of the physisorbed proteins was also assessed. High-performance sensing was proven by evaluating figures of merit, such as the limit of detection (2 nM) and the selectivity ratio between a negative control and the sensing experiment (0.04), which is the best reported performance for an SPR S1 protein assay. These figures of merit outmatch those measured with more sophisticated biofunctionalization procedures involving chemical bonding of the capture antibodies to the gold surface. The present study opens up interesting new pathways toward the achievement of a cost-effective and scalable biofunctionalization protocol, which could guarantee the prolonged stability of the biolayer and easy handling of the biosensing system.

Investigating the Orientation of an Interfacially Adsorbed Monoclonal Antibody and Its Fragments Using Neutron Reflection

Interfacial adsorption is a molecular process occurring during the production, purification, transport, and storage of antibodies, with a direct impact on their structural stability and subsequent implications on their bioactivities. While the average conformational orientation of an adsorbed protein can be readily determined, its associated structures are more complex to characterize. Neutron reflection has been used in this work to investigate the conformational orientations of the monoclonal antibody COE-3 and its Fab and Fc fragments at the oil/water and air/water interfaces. Rigid body rotation modeling was found to be suitable for globular and relatively rigid proteins such as the Fab and Fc fragments but less so for relatively flexible proteins such as full COE-3. Fab and Fc fragments adopted a 'flat-on' orientation at the air/water interface, minimizing the thickness of the protein layer, but they adopted a substantially tilted orientation at the oil/water interface with increased layer thickness. In contrast, COE-3 was found to adsorb in tilted orientations at both interfaces, with one fragment protruding into the solution. This work demonstrates that rigid-body modeling can provide additional insights into protein layers at various interfaces relevant to bioprocess engineering.

Evaluation of preferred binding regions on ubiquitin and IgG1 FC for interacting with multimodal cation exchange resins using DEPC labeling/mass spectrometry

There is significant interest in identifying the preferred binding domains of biological products to various chromatographic materials. In this work, we develop a biophysical technique that uses diethyl pyrocarbonate (DEPC) based covalent labeling in concert with enzymatic digestion and mass spectrometry to identify the binding patches for proteins bound to commercially available multimodal (MM) cation exchange chromatography resins. The technique compares the changes in covalent labeling of the protein in solution and in the bound state and uses the differences in this labeling to identify residues that are sterically shielded upon resin binding and, therefore, potentially involved in the resin binding process. Importantly, this approach enables the labeling of many amino acids and can be carried out over a pH range of 5.5-7.5, thus enabling the protein surface mapping at conditions of interest in MM cation exchange systems. The protocol is first developed using the model protein ubiquitin and the results indicate that lysine residues located on the front face of the protein show dramatic changes in DEPC labeling while residues present on other regions have minimal or no reductions. This indicates that the front face of ubiquitin is likely involved in resin binding. In addition, surface property maps indicate that the hypothesized front face binding region consists of overlapping positively charged and hydrophobic patches. The technique is then employed with an IgG1 F_C and the results indicate that residues on the C_H 2-C_H 3 interface and the hinge are significantly sterically shielded upon binding to the resin. Further, these regions are again associated with significant overlap of positively charged and hydrophobic patches. On the other hand, while, residues on the C_H 2 and the front face of the IgG1 F_C also exhibited some changes in DEPC labeling upon binding, these regions have less distinct charged and hydrophobic patches. Importantly, the hypothesized binding patches identified for both ubiquitin and F_C using this approach are shown to be consistent with previously reported NMR studies. In contrast to NMR, this new approach enables the identification of preferred binding regions without the need for isotopically labeled proteins or chemical shift assignments. The technique developed in this work sets the stage for the evaluation of the binding domains of a wide range of biological products to chromatographic surfaces, with important implications for designing biomolecules with improved biomanufacturability properties.

Graphene Oxide-Magnetic Nanoparticles Loaded Polystyrene-Polydopamine Electrospun Nanofibers Based Nanocomposites for Immunosensing Application of C-Reactive Protein

The large surface area/volume ratio and controllable surface conformation of electrospun nanofibers (ENFs) make them highly attractive in applications where a large surface area is desired, such as sensors and affinity membranes. In this study, nanocomposite-based ENFs were produced and immobilization of Anti-CRP was carried out for the non-invasive detection of C-reactive protein (CRP). Initially, the synthesis of graphene oxide (GO) was carried out and it was modified with magnetic nanoparticles (MNP, Fe₃O₄) and polydopamine (PDA). Catechol-containing and quinone-containing functional groups were created on the nanocomposite surface for the immobilization of Anti-CRP. Polystyrene (PS) solution was mixed with rGO-MNP-PDA nanocomposite and PS/rGO-MNP-PDA ENFs were produced with bead-free, smooth, and uniform. The surface of the screen-printed carbon electrode (SPCE) was covered with PS/rGO-MNP-PDA ENFs by using the electrospinning technique under the determined optimum conditions. Next, Anti-CRP immobilization was carried out and the biofunctional surface was created on the PS/rGO-MNP-PDA ENFs coated SPCE. Moreover, PS/rGO-PDA/Anti-CRP and PS/MNP-PDA/Anti-CRP immunosensors were also prepared and the effect of each component in the nanocomposite-based electrospun nanofiber (MNP, rGO) on the sensor response was investigated. The analytic performance of the developed PS/rGO-MNP-PDA/Anti-CRP, PS/rGO-PDA/Anti-CRP, and PS/MNP-PDA/Anti-CRP immunosensors were examined by performing electrochemical measurements in the presence of CRP. The linear detection range of PS/rGO-MNP-PDA/Anti-CRP immunosensor was found to be from 0.5 to 60 ng/mL and the limit of detection (LOD) was calculated as 0.33 ng/mL for CRP. The PS/rGO-MNP-PDA/Anti-CRP immunosensor also exhibited good repeatability with a low coefficient of variation.

pH-Regulated Strategy and Mechanism of Antibody Orientation on Magnetic Beads for Improving Capture Performance of Staphylococcus Species

Immunomagnetic beads (IMBs) have been widely used to capture and isolate target pathogens from complex food samples. The orientation of the antibody immobilized on the surface of magnetic beads (MBs) is closely related to the effective recognition with an antigen. We put forward an available strategy to orient the antibody on the surface of MBs by changing the charged amino group ratio of the reactive amino groups at optimal pH value. Quantum dots labeling antigen assay, antigen-binding fragment (Fab) accessibility assay and lysine mimicking were used for the first time to skillfully illustrate the antibody orientation mechanism. This revealed that the positively charged ε-NH₂ group of lysine on the Fc relative to the uncharged amino terminus on Fab was preferentially adsorbed on the surface of MBs with a negatively charged group at pH 8.0, resulting in antigen binding sites of antibody fully exposed. This study contributes to the understanding of the antibody orientation on the surface of MBs and the potential application of IMBs in the separation and detection of pathogenic bacteria in food samples.

Electric-Field-Mediated In-Sensor Alignment of Antibody's Orientation to Enhance the Antibody-Antigen Binding for Ultrahigh Sensitivity Sensors

Applying an electric-field (E-field) during antibody immobilization aligns the orientation of the antibody on the biosensor surface, thereby enhancing the binding probability between the antibody and antigen and maximizing the sensitivity of the biosensor. In this study, a biosensor with enhanced antibody-antigen binding probability was developed using the alignment of polar antibodies (immunoglobulin G [IgG]) under an E-field applied inside the interdigitated electrodes. The optimal alignment condition was first theoretically calculated and then experimentally confirmed by comparing the impedance change before and after the alignment of IgG (a purified anti-β-amyloid antibody). With the optimized condition, the impedance change of the biosensor was maximized because of the alignment of IgG orientation on the sensor surface; the detection sensitivity of the antigen amyloid-beta 1-42 was also maximized. The E-field-based in-sensor alignment of antibodies is an easy and effective method for enhancing biosensor sensitivity.

Comparison of Physical Adsorption and Covalent Coupling Methods for Surface Density-Dependent Orientation of Antibody on Silicon

The orientation of antibodies, employed as capture molecules on biosensors, determines biorecognition efficiency and bioassay performance. In a previous publication we demonstrated for antibodies attached covalently to silicon that an increase in their surface amount Γ, evaluated with ellipsometry, induces changes in their orientation, which is traced directly using Time-of-Flight Secondary Ion Mass Spectroscopy combined with Principal Component Analysis. Here, we extend the above studies to antibodies adsorbed physically on a 3-aminopropyltriethoxysilane (APTES) monolayer. Antibodies physisorbed on APTES (0 ≤ Γ ≤ 3.5 mg/m²) reveal the Γ ranges for flat-on, side-on, and vertical orientation consistent with random molecular packing. The relation between orientation and Γ is juxtaposed for silicon functionalized with APTES, APTES modified with glutaraldehyde (APTES/GA) and N-hydroxysuccinimide-silane (NHS-silane). Antibody reorientation occurs at lower Γ values when physisorption (APTES) is involved rather than chemisorption (APTES/GA, NHS-silane). At high Γ values, comparable proportions of molecules adapting head-on and tail-on vertical alignment are concluded for APTES and the NHS-silane monolayer, and they are related to intermolecular dipole–dipole interactions. Intermolecular forces seem to be less decisive than covalent binding for antibodies on the APTES/GA surface, with dominant head-on orientation. Independently, the impact of glutaraldehyde activation of APTES on vertical orientation is confirmed by separate TOF-SIMS measurements.

Developing G value as an indicator for assessing the molecular status of immobilized antibody

Antibody-functionalized nanoparticles (Ab-NPs) are widely used in bioassays due to their excellent affinity, specificity toward antigen, and ease of operation. However, the uncontrollable molecular status of antibodies on NPs severely limits their applications. This work aims at developing a simple method to evaluate the antigen-binding activity of Ab-NPs using two parameters, i.e., antibody adsorption amount and antigen-binding strength. Herein, we proposed a mathematical expression, G, to quantitively describe the amount and strength of Ab-NPs. G value could be used to assess the antigen-binding performance of NPs influenced by surface and solution factors. Seven types of polymers with different surface properties, including four positively and three negatively charged polymer brushes, were grown from silica NPs via surface-initiated atom transfer radical polymerization (SI-ATRP). A pair of antigen and antibody, human chorionic gonadotropin (hCG) and anti-hCG, were selected to screen the antibody immobilization property of polymer brushes. Among them, the G values of 2 polymer-NPs with opposite charges reached maximum, resulting in low detection limits for hCG, where pDMAEA-NP and pMMA-NP represent Poly[N,N-(dimethylamino)ethyl acrylate]-NP and poly(methyl methacrylate)-NP, respectively. The G value of Ab-NPs makes it feasible to estimate the molecular status of the adsorbed antibodies on surfaces, thus showing great potential for in vitro biosensing and bioseparation.

Antibody coated conductive polymer for the electrochemical immunosensing of Human Cardiac Troponin I in blood plasma

Cardiac troponin I (cTnI) is a sensitive biomarker for cardiovascular disease (CVD). Rapid determination of cTnI concentration in blood can greatly reduce the potential of significant heart damage and heart failure. Herein, we demonstrate a new electrochemical immunosensor for selective affinity binding and rapid detection of cTnI in blood plasma by an electrochemical method. A conductive film of "poly 2,5-bis(2-thienyl)3,4-diamine-terthiophene (PDATT)" was deposited onto an Indium Tin Oxide (ITO) electrode using chronoamperometry. Anti-cardiac troponin I antibody was then attached to the two amine (NH₂) groups substituted on the central thiophene of terthiophene repeating unit of the polymer chain via amide bond formation. The gaps on the surface of the antibody coated immunosensor were backfilled with bovine serum albumin (BSA) to prevent nonspecific binding of interfering molecules. Differential pulse voltammetry (DPV) was used to determine cTnI upon the formation of cTnI immunocomplex on the sensing surface, appearing a peak at 0.27 V. The response range was 0.01-100 ng mL^-1 with limit of quantification down to 0.01 ng mL^-1. The developed immunosensor was used to determine cTnI in spiked blood plasma without interference from cardiac troponin T (cTnT). Therefore, this new sensor can be utilised for the detection of cTnI biomarker in pathological laboratories and points of care in less than 15 min.

Modeling the impact of amino acid substitution in a monoclonal antibody on cation exchange chromatography

A vital part of biopharmaceutical research is decision making around which lead candidate should be progressed in early-phase development. When multiple antibody candidates show similar biological activity, developability aspects are taken into account to ease the challenges of manufacturing the potential drug candidate. While current strategies for developability assessment mainly focus on drug product stability, only limited information is available on how antibody candidates with minimal differences in their primary structure behave during downstream processing. With increasing time-to-market pressure and an abundance of monoclonal antibodies (mAbs) in development pipelines, developability assessments should also consider the ability of mAbs to integrate into the downstream platform. This study investigates the influence of amino acid substitutions in the complementarity-determining region (CDR) of a full-length IgG1 mAb on the elution behavior in preparative cation exchange chromatography. Single amino acid substitutions within the investigated mAb resulted in an additional positive charge in the light chain (L) and heavy chain (H) CDR, respectively. The mAb variants showed an increased retention volume in linear gradient elution compared with the wild-type antibody. Furthermore, the substitution of tryptophan with lysine in the H-CDR3 increased charge heterogeneity of the product. A multiscale in silico analysis, consisting of homology modeling, protein surface analysis, and mechanistic chromatography modeling increased understanding of the adsorption mechanism. The results reveal the potential effects of lead optimization during antibody drug discovery on downstream processing.

Lysozyme Adsorption on Different Functionalized MXenes: A Multiscale Simulation Study

Recently, MXenes, due to their abundant advantages, have been widely applied in energy storage, separation, catalysis, biosensing, et al. In this study, parallel tempering Monte Carlo and molecular dynamics methods were performed to investigate lysozyme adsorption on different functionalized Ti₃C₂T_x (-O, -OH, and -F). The simulation results show that lysozyme can adsorb effectively on Ti₃C₂T_x surfaces, and the order of interaction strength is Ti₃C₂O₂ > Ti₃C₂F₂ > Ti₃C₂(OH)₂. Electrostatics together with van der Waals interactions control protein adsorption. The orientation distributions of lysozyme adsorbed on the Ti₃C₂O₂ and Ti₃C₂F₂ surfaces are more concentrated than that on the Ti₃C₂(OH)₂ surface. During adsorption, the conformation of lysozyme remains stable, suggesting the good biocompatibility of Ti₃C₂T_x. Besides, the distribution of the interfacial water layer on the Ti₃C₂T_x surface has a certain impact on protein adsorption. This study provides theoretical insights for understanding the biocompatibility of 2D Ti₃C₂T_x materials and may help us evaluate the engineering of their surfaces for future biorelated applications.

Recent Advances in Studying Interfacial Adsorption of Bioengineered Monoclonal Antibodies

Monoclonal antibodies (mAbs) are an important class of biotherapeutics; as of 2020, dozens are commercialized medicines, over a hundred are in clinical trials, and many more are in preclinical developmental stages. Therapeutic mAbs are sequence modified from the wild type IgG isoforms to varying extents and can have different intrinsic structural stability. For chronic treatments in particular, high concentration (≥ 100 mg/mL) aqueous formulations are often preferred for at-home administration with a syringe-based device. MAbs, like any globular protein, are amphiphilic and readily adsorb to interfaces, potentially causing structural deformation and even unfolding. Desorption of structurally perturbed mAbs is often hypothesized to promote aggregation, potentially leading to the formation of subvisible particles and visible precipitates. Since mAbs are exposed to numerous interfaces during biomanufacturing, storage and administration, many studies have examined mAb adsorption to different interfaces under various mitigation strategies. This review examines recent published literature focusing on adsorption of bioengineered mAbs under well-defined solution and surface conditions. The focus of this review is on understanding adsorption features driven by distinct antibody domains and on recent advances in establishing model interfaces suitable for high resolution surface measurements. Our summary highlights the need to further understand the relationship between mAb interfacial adsorption and desorption, solution aggregation, and product instability during fill-finish, transport, storage and administration.

Fundamental Principles of the Thermodynamics and Kinetics of Protein Adsorption to Material Surfaces

Protein adsorption is important for essentially any process that involves the contact of a protein-containing solution and a material surface, with the resulting formation of the adsorbed layer of protein determined by the thermodynamics and kinetics of the system involved. This paper presents an overview of the fundamentals of these processes. First, the hierarchical structure of proteins and the types of bonding that stabilize a protein's native-state structure are presented. This section is then followed by a section presenting the thermodynamic driving forces that influence the way that proteins adsorb and conformationally change for three characteristically different types of surface chemistries: nonpolar (hydrophobic) surfaces, neutral hydrophilic surfaces, and charged surfaces. The final section of this paper addresses how kinetics and thermodynamics combine together to influence protein adsorption behavior, followed by concluding remarks.

Antibody-Oriented Strategy and Mechanism for the Preparation of Fluorescent Nanoprobes for Fast and Sensitive Immunodetection

Nanoprobes have been widely used in biomedical engineering. However, antibodies are generally conjugated onto nanoparticles disorderly, which reduces their antigen recognition ability. The existing antibody orientation approaches are usually complex. Here, we developed and demonstrated a simple antibody-oriented strategy for the lateral flow immunoassay of cardiac troponin I by conjugating antibodies onto polystyrene nanospheres at the optimal pH. The binding amount and orientation of antibodies as well as the detection sensitivity were significantly improved. Although pH regulation is commonly used to optimize antibody conjugation, this paper illustrates the mechanism of its antibody orientation enhancement ability for the first time and reveals the important influences of the density, the charge distribution and hydrophilicity of the antibody, the control of the velocities of physical adsorption and chemical coupling, and other factors on antibody orientation. It is of great significance to understand and regulate antibody conjugation on the surface of micro- or nanospheres to construct high-performance probes for in vitro diagnosis applications.

ReaxFF MD Simulations of Peptide-Grafted Gold Nanoparticles

Functionalized gold nanoparticles have critical applications in biodetection with surface-enhanced Raman spectrum and drug delivery. In this study, reactive force field molecular dynamics simulations were performed to study gold nanoparticles, which are modified with different short-chain peptides consisting of amino acid residues of cysteine and glycine in different grafting densities in the aqueous environment. Our study showed slight facet-dependent peptide adsorption on a gold nanoparticle with the 3 nm core diameter. Peptide chains prefer to adsorb on the Au(111) facet compared to those on other facets of Au(100) and Au(110). In addition to the stable thiol interaction with gold nanoparticle surfaces, polarizable oxygen and nitrogen atoms show strong interactions with the gold surface and polarize the gold nanoparticle surfaces with an overall positive charge. Charges of gold atoms vary according to their contacts with peptide atoms and lattice positions. However, at the outmost peptide layer, the whole functionalized Au nanoparticles exhibit overall negative electrostatic potential due to the grafted peptides. Moreover, simulations show that thiol groups can be deprotonated and subsequently protons can be transferred to water molecules and carboxyl groups.

Adsorption-associated orientational changes of immunoglobulin G and regulated phagocytosis of Staphylococcus epidermidis

Understanding the adsorption of immunoglobulin G (IgG) on biomaterials surfaces is crucial for design and modification of the surfaces to alleviate inflammatory responses after implantation. Here, we report direct visualization and two-dimensional (2D) image interpretation of the IgG molecule adsorbed on simplified surfaces by single particle electron microscopy and atomic force microscopy. Influence of the orientational changes in adsorbed IgG on phagocytosis of macrophages against Staphylococcus epidermidis is further examined. Untreated amorphous carbon film and -COOH and -NH₂ grafted carbon films are employed as the model surfaces for the adsorption testing. Results show that IgG displays flat orientation lying on the untreated surface, while forms vertical orientations standing on the functionalized surfaces. These specific spatial alignments are associated with altered unfolding extent and structure rearrangement of IgG domains, which are influenced synergistically by surface charge and wettability of the substrata. The changes in interdomain distance of IgG molecules subsequently regulate immune behaviors of macrophages and phagocytosis of S. epidermidis. The results would give insight into appropriate design of biomaterial surfaces in nanoscales for desired inflammatory responses. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 2838-2849, 2018.

Single-molecule detection with a millimetre-sized transistor

Label-free single-molecule detection has been achieved so far by funnelling a large number of ligands into a sequence of single-binding events with few recognition elements host on nanometric transducers. Such approaches are inherently unable to sense a cue in a bulk milieu. Conceptualizing cells' ability to sense at the physical limit by means of highly-packed recognition elements, a millimetric sized field-effect-transistor is used to detect a single molecule. To this end, the gate is bio-functionalized with a self-assembled-monolayer of 1012 capturing anti-Immunoglobulin-G and is endowed with a hydrogen-bonding network enabling cooperative interactions. The selective and label-free single molecule IgG detection is strikingly demonstrated in diluted saliva while 15 IgGs are assayed in whole serum. The suggested sensing mechanism, triggered by the affinity binding event, involves a work-function change that is assumed to propagate in the gating-field through the electrostatic hydrogen-bonding network. The proposed immunoassay platform is general and can revolutionize the current approach to protein detection.

Orienting proteins by nanostructured surfaces: evidence of a curvature-driven geometrical resonance

Experimental and theoretical reports have shown that nanostructured surfaces have a dramatic effect on the amount of protein adsorbed and the conformational state and, in turn, on the performances of the related devices in tissue engineering strategies. Here we report an innovative method to prepare silica-based nanostructured surfaces with a reproducible, well-defined local curvature, consisting of ordered hexagonally packed arrays of curved hemispheres, from nanoparticles of different diameters (respectively 147 nm, 235 nm and 403 nm). The nanostructured surfaces have been made chemically homogeneous by partially embedding silica nanoparticles in poly(hydroxymethylsiloxane) films, further modified by means of UV-O3 treatments. This paper has been focused on the experimental and theoretical study of laminin, taken as a model protein, to study the nanocurvature effects on the protein configuration at nanostructured surfaces. A simple model, based on the interplay of electrostatic interactions between the charged terminal domains of laminin and the nanocurved charged surfaces, closely reproduces the experimental findings. In particular, the model suggests that nanocurvature drives the orientation of rigid proteins by means of a "geometrical resonance" effect, involving the matching of dimensions, charge distribution and spatial arrangement of both adsorbed molecules and adsorbent nanostructures. Overall, the results pave the way to unravel the nanostructured surface effects on the intra- and inter-molecular organization processes of proteins.

Hamiltonian replica exchange simulations of glucose oxidase adsorption on charged surfaces

Hamiltonian replica exchange Monte Carlo simulations efficiently identify the lowest-energy orientations of proteins on charged surfaces at variable ionic strengths.

Characterization of Monoclonal Antibody-Protein Antigen Complexes Using Small-Angle Scattering and Molecular Modeling

The determination of monoclonal antibody interactions with protein antigens in solution can lead to important insights guiding physical characterization and molecular engineering of therapeutic targets. We used small-angle scattering (SAS) combined with size-exclusion multi-angle light scattering high-performance liquid chromatography to obtain monodisperse samples with defined stoichiometry to study an anti-streptavidin monoclonal antibody interacting with tetrameric streptavidin. Ensembles of structures with both monodentate and bidentate antibody-antigen complexes were generated using molecular docking protocols and molecular simulations. By comparing theoretical SAS profiles to the experimental data it was determined that the primary component(s) were compact monodentate and/or bidentate complexes. SAS profiles of extended monodentate complexes were not consistent with the experimental data. These results highlight the capability for determining the shape of monoclonal antibody-antigen complexes in solution using SAS data and physics-based molecular modeling.

Single Molecule Force Spectroscopy and Molecular Dynamics Simulations as a Combined Platform for Probing Protein Face-Specific Binding

Biomolecular interactions frequently occur in orientation-specific manner. For example, prior nuclear magnetic resonance spectroscopy experiments in our lab have suggested the presence of a group of strongly binding residues on a particular face of the protein ubiquitin for interactions with Capto MMC multimodal ligands ("Capto" ligands) (Srinivasan, K.; et al. Langmuir 2014, 30 (44), 13205-13216). We present a clear confirmation of those studies by performing single-molecule force spectroscopy (SMFS) measurements of unbinding complemented with molecular dynamics (MD) calculations of the adsorption free energy of ubiquitin in two distinct orientations with self-assembled monolayers (SAMs) functionalized with "Capto" ligands. These orientations were maintained in the SMFS experiments by tethering ubiquitin mutants to SAM surfaces through strategically located cysteines, thus exposing the desired faces of the protein. Analogous orientations were maintained in MD simulations using suitable constraining methods. Remarkably, despite differences between the finer details of experimental and simulation methodologies, they confirm a clear preference for the previously hypothesized binding face of ubiquitin. Furthermore, MD simulations provided significant insights into the mechanism of protein binding onto this multimodal surface. Because SMFS and MD simulations both directly probe protein-surface interactions, this work establishes a key link between experiments and simulations at molecular scale through the determination of protein face-specific binding energetics. Our approach may have direct applications in biophysical systems where face- or orientation-specific interactions are important, such as biomaterials, sensors, and biomanufacturing.

Site-selective orientated immobilization of antibodies and conjugates for immunodiagnostics development

Immobilized antibody systems are the key to develop efficient diagnostics and separations tools. In the last decade, developments in the field of biomolecular engineering and crosslinker chemistry have greatly influenced the development of this field. With all these new approaches at our disposal, several new immobilization methods have been created to address the main challenges associated with immobilized antibodies. Few of these challenges that we have discussed in this review are mainly associated to the site-specific immobilization, appropriate orientation, and activity retention. We have discussed the effect of antibody immobilization approaches on the parameters on the performance of an immunoassay.

Allosteric effects of gold nanoparticles on human serum albumin

The ability of nanoparticles to alter protein structure and dynamics plays an important role in their medical and biological applications. We investigate allosteric effects of gold nanoparticles on human serum albumin protein using molecular simulations. The extent to which bound nanoparticles influence the structure and dynamics of residues distant from the binding site is analyzed. The root mean square deviation, root mean square fluctuation and variation in the secondary structure of individual residues on a human serum albumin protein are calculated for four protein-gold nanoparticle binding complexes. The complexes are identified in a brute-force search process using an implicit-solvent coarse-grained model for proteins and nanoparticles. They are then converted to atomic resolution and their structural and dynamic properties are investigated using explicit-solvent atomistic molecular dynamics simulations. The results show that even though the albumin protein remains in a folded structure, the presence of a gold nanoparticle can cause more than 50% of the residues to decrease their flexibility significantly, and approximately 10% of the residues to change their secondary structure. These affected residues are distributed on the whole protein, even on regions that are distant from the nanoparticle. We analyze the changes in structure and flexibility of amino acid residues on a variety of binding sites on albumin and confirm that nanoparticles could allosterically affect the ability of albumin to bind fatty acids, thyroxin and metals. Our simulations suggest that allosteric effects must be considered when designing and deploying nanoparticles in medical and biological applications that depend on protein-nanoparticle interactions.

Probing protein orientation near charged nanosurfaces for simulation-assisted biosensor design

Protein-surface interactions are ubiquitous in biological processes and bioengineering, yet are not fully understood. In biosensors, a key factor determining the sensitivity and thus the performance of the device is the orientation of the ligand molecules on the bioactive device surface. Adsorption studies thus seek to determine how orientation can be influenced by surface preparation, varying surface charge, and ambient salt concentration. In this work, protein orientation near charged nanosurfaces is obtained under electrostatic effects using the Poisson-Boltzmann equation, in an implicit-solvent model. Sampling the free energy for protein G B1 D4' at a range of tilt and rotation angles with respect to the charged surface, we calculated the probability of the protein orientations and observed a dipolar behavior. This result is consistent with published experimental studies and combined Monte Carlo and molecular dynamics simulations using this small protein, validating our method. More relevant to biosensor technology, antibodies such as immunoglobulin G are still a formidable challenge to molecular simulation, due to their large size. With the Poisson-Boltzmann model, we obtained the probability distribution of orientations for the iso-type IgG2a at varying surface charge and salt concentration. This iso-type was not found to have a preferred orientation in previous studies, unlike the iso-type IgG1 whose larger dipole moment was assumed to make it easier to control. Our results show that the preferred orientation of IgG2a can be favorable for biosensing with positive charge on the surface of 0.05 C/m(2) or higher and 37 mM salt concentration. The results also show that local interactions dominate over dipole moment for this protein. Improving immunoassay sensitivity may thus be assisted by numerical studies using our method (and open-source code), guiding changes to fabrication protocols or protein engineering of ligand molecules to obtain more favorable orientations.

Molecular simulation study of feruloyl esterase adsorption on charged surfaces: effects of surface charge density and ionic strength

The surrounding conditions, such as surface charge density and ionic strength, play an important role in enzyme adsorption. The adsorption of a nonmodular type-A feruloyl esterase from Aspergillus niger (AnFaeA) on charged surfaces was investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics (AAMD) simulations at different surface charge densities (±0.05 and ±0.16 C·m(-2)) and ionic strengths (0.007 and 0.154 M). The adsorption energy, orientation, and conformational changes were analyzed. Simulation results show that whether AnFaeA can adsorb onto a charged surface is mainly controlled by electrostatic interactions between AnFaeA and the charged surface. The electrostatic interactions between AnFaeA and charged surfaces are weakened when the ionic strength increases. The positively charged surface at low surface charge density and high ionic strength conditions can maximize the utilization of the immobilized AnFaeA. The counterion layer plays a key role in the adsorption of AnFaeA on the negatively charged COOH-SAM. The native conformation of AnFaeA is well preserved under all of these conditions. The results of this work can be used for the controlled immobilization of AnFaeA.

High specific detection of osteopontin using a three-dimensional copolymer layer support based on electrochemical impedance spectroscopy

Tumor marker detection is essential for the therapy efficiency of early stage tumors and the evaluation of disease progression. Osteopontin (OPN) is supposed to be closely related to several kinds of tumors. In the present study, we describe a label-free electrochemical detection of OPN based on a specific reaction between OPN and its relevant antibody. An artificial three-dimensional (3D) scaffold structure consisting of 11-mercaptoundecanoic acid/6-mercapto-1-hexanol, dextran amino and synthetic peptides was designed as a substrate for the immobilization of the antibody. This substrate was characterized using cyclic voltammetry, atomic force microscopy and Fourier transform infrared reflection spectroscopy. Antibody immobilization and OPN detection were conducted using electrochemical impedance spectroscopy (EIS). The low limit of detection was 0.17 nM. The concentration of cancer risk (5.77 nM) can be selectively detected with a high EIS signal. The fabricated 3D OPN sensor is proposed for application in clinical analysis.

Tunable control of antibody immobilization using electric field

The controlled immobilization of proteins on solid-state surfaces can play an important role in enhancing the sensitivity of both affinity-based biosensors and probe-free sensing platforms. Typical methods of controlling the orientation of probe proteins on a sensor surface involve surface chemistry-based techniques. Here, we present a method of tunably controlling the immobilization of proteins on a solid-state surface using electric field. We study the ability to orient molecules by immobilizing IgG molecules in microchannels while applying lateral fields. We use atomic force microscopy to both qualitatively and quantitatively study the orientation of antibodies on glass surfaces. We apply this ability for controlled orientation to enhance the performance of affinity-based assays. As a proof of concept, we use fluorescence detection to indirectly verify the modulation of the orientation of proteins bound to the surface. We studied the interaction of fluorescently tagged anti-IgG with surface immobilized IgG controlled by electric field. Our study demonstrates that the use of electric field can result in more than 100% enhancement in signal-to-noise ratio compared with normal physical adsorption.

Fabrication of calix[4]arene derivative monolayers to control orientation of antibody immobilization

Three calix[4]arene (Cal-4) derivatives which separately contain ethylester (1), carboxylic acid (2), and crownether (3) at the lower rim with a common reactive thiol at the upper rim were synthesized and constructed to self-assembled monolayers (SAMs) on Au films. After spectroscopic characterization of the monolayers, surface coverage and orientation of antibody immobilized on the Cal-4 derivative SAMs were studied by surface plasmon resonance (SPR) technique. Experimental results revealed that the antibody could be immobilized on the Cal-4 derivatives spontaneously. The orientation of absorbed antibody on the Cal-4 derivative SAMs is related to the SAM’s dipole moment. The possible orientations of the antibody immobilized on the Cal-4 derivative 1 SAM are lying-on or side-on, while on the Cal-4 derivative 2 and Cal-4 derivative 3 head-on and end-on respectively. These experimental results demonstrate the surface dipole moment of Cal-4 derivative appears to be an important factor to antibody orientation. Cal-4 derivatives are useful in developing site direct protein chips.

Mesoscopic coarse-grained simulations of lysozyme adsorption

Coarse-grained simulations are adopted to study the adsorption behavior of lysozyme on different (hydrophobic, neutral hydrophilic, zwitterionic, negatively charged, and positively charged) surfaces at the mesoscopic microsecond time scale (1.2 μs). Simulation results indicate the following: (i) the conformation change of lysozyme on the hydrophobic surface is bigger than any other studied surfaces; (ii) the active sites of lysozyme are faced to the hydrophobic surface with a "top end-on" orientation, while they are exposed to the liquid phase on the hydrophilic surface with a "back-on" orientation; (iii) the neutral hydrophilic surface can induce the adsorption of lysozyme, while the nonspecific protein adsorption can be resisted by the zwitterionic surface; (iv) when the solution ionic strength is low, lysozyme can anchor on the negatively charged surface easily but cannot adsorb on the positively charged surface; (v) when the solution ionic strength is high, the positively charged lysozyme can also adsorb on the like-charged surface; (vi) the major positive potential center of lysozyme, especially the residue ARG128, plays a vital role in leading the adsorption of lysozyme on charged surfaces; (vii) when the ionic strength is high, a counterion layer is formed above the positively charged surface, which is the key factor why lysozyme can adsorb on a like-charged surface. The coarse-grained method based on the MARTINI force field for proteins and the BMW water model could provide an efficient way to understand protein interfacial adsorption behavior at a greater length scale and time scale.