Quantitative biological surface science: challenges and recent advances

Nanoarchitectonic-Based Material Platforms for Environmental and Bioprocessing Applications

The challenges of pollution, environmental science, and energy consumption have become global issues of broad societal importance. In order to address these challenges, novel functional systems and advanced materials are needed to achieve high efficiency, low emission, and environmentally friendly performance. A promising approach involves nanostructure-level controls of functional material design through a novel concept, nanoarchitectonics. In this account article, we summarize nanoarchitectonic approaches to create nanoscale platform structures that are potentially useful for environmentally green and bioprocessing applications. The introduced platforms are roughly classified into (i) membrane platforms and (ii) nanostructured platforms. The examples are discussed together with the relevant chemical processes, environmental sensing, bio-related interaction analyses, materials for environmental remediation, non-precious metal catalysts, and facile separation for biomedical uses.

Nanoplasmonic sensors for biointerfacial science

In recent years, nanoplasmonic sensors have become widely used for the label-free detection of biomolecules across medical, biotechnology, and environmental science applications. To date, many nanoplasmonic sensing strategies have been developed with outstanding measurement capabilities, enabling detection down to the single-molecule level. One of the most promising directions has been surface-based nanoplasmonic sensors, and the potential of such technologies is still emerging. Going beyond detection, surface-based nanoplasmonic sensors open the door to enhanced, quantitative measurement capabilities across the biointerfacial sciences by taking advantage of high surface sensitivity that pairs well with the size of medically important biomacromolecules and biological particulates such as viruses and exosomes. The goal of this review is to introduce the latest advances in nanoplasmonic sensors for the biointerfacial sciences, including ongoing development of nanoparticle and nanohole arrays for exploring different classes of biomacromolecules interacting at solid-liquid interfaces. The measurement principles for nanoplasmonic sensors based on utilizing the localized surface plasmon resonance (LSPR) and extraordinary optical transmission (EOT) phenomena are first introduced. The following sections are then categorized around different themes within the biointerfacial sciences, specifically protein binding and conformational changes, lipid membrane fabrication, membrane-protein interactions, exosome and virus detection and analysis, and probing nucleic acid conformations and binding interactions. Across these themes, we discuss the growing trend to utilize nanoplasmonic sensors for advanced measurement capabilities, including positional sensing, biomacromolecular conformation analysis, and real-time kinetic monitoring of complex biological interactions. Altogether, these advances highlight the rich potential of nanoplasmonic sensors and the future growth prospects of the community as a whole. With ongoing development of commercial nanoplasmonic sensors and analytical models to interpret corresponding measurement data in the context of biologically relevant interactions, there is significant opportunity to utilize nanoplasmonic sensing strategies for not only fundamental biointerfacial science, but also translational science applications related to clinical medicine and pharmaceutical drug development among countless possibilities.

Grazing-incidence small-angle neutron scattering from structures below an interface

Changes of scattering are observed as the grazing angle of incidence of an incoming beam increases and probes different depths in samples. A model has been developed to describe the observed intensity in grazing-incidence small-angle neutron scattering (GISANS) experiments. This includes the significant effects of instrument resolution, the sample transmission, which depends on both absorption and scattering, and the sample structure. The calculations are tested with self-organized structures of two colloidal samples with different size particles that were measured on two different instruments. The model allows calculations for various instruments with defined resolution and can be used to design future improved experiments. The possibilities and limits of GISANS for different studies are discussed using the model calculations.

Self-assembly of glycine on Cu(001): the effect of temperature and polarity

Glycine on Cu(001) is studied as an example to illustrate the critical role of finite temperature and molecular polarity in the self-assembly of biomolecules at a metal surface.

Electrospun poly-ε-caprolactone scaffold modified with catalytic nitric oxide generation and heparin for small-diameter vascular graft

Vascular grafts are significantly needed in peripheral vascular surgery; however, small diameter grafts are not always available, and synthetic grafts perform poorly because of acute thrombosis and neointimal proliferation after implantation.

Platelet Immobilization on Supported Phospholipid Bilayers for Single Platelet Studies

The worldwide cardiovascular disease (CVD) epidemic is of grave concern. A major role in the etiology of CVDs is played by the platelets (thrombocytes). Platelets are anuclear cell fragments circulating in the blood. Their primary function is to catalyze clot formation, limiting traumatic blood loss in the case of injury. The same process leads to thrombosis in the case of CVDs, which are commonly managed with antiplatelet therapy. Platelets also have other, nonhemostatic functions in wound healing, inflammation, and tissue regeneration. They play a role in the early stages of atherosclerosis and the spread of cancer through metastases. Much remains to be learned about the regulation of these diverse platelet functions under physiological and pathological conditions. Breakthroughs in this regard are expected to come from single platelet studies and systems approaches. The immobilization of platelets at surfaces is advantageous for developing such approaches, but platelets are activated when they come in contact with foreign surfaces. In this work, we develop and validate a protocol for immobilizing platelets on supported lipid bilayers without activation due to immobilization. Our protocol can therefore be used for studying platelets with a wide variety of surface-sensitive techniques.

Ionic strength dependent vesicle adsorption and phase behavior of anionic phospholipids on a gold substrate

The authors report on the effect of ionic strength on the formation of supported vesicle layers of anionic phospholipids 1,2-dimyristoyl-sn-glycero-3-phospho-rac-glycerol (DMPG) and dimyristoylphosphatidylserine (DMPS) onto gold. Using quartz crystal microbalance with dissipation monitoring the authors show that vesicle adsorption is mainly governed by NaCl concentration, reflecting the importance of electrostatic interactions in anionic lipids, as compared to zwitterionic 1,2-dimyristoyl-sn-glycero-3-phosphocholine. At low ionic strength, low or no adsorption is observed as a result of vesicle-vesicle electrostatic repulsion. At medium ionic strength, the negative charges of DMPG and DMPS are screened resulting in larger adsorption and a highly dissipative intact vesicle layer. In addition, DMPS exhibits a peculiar behavior at high ionic strength that depends on the temperature of the process.

Influence of Solution Chemistry and Soft Protein Coronas on the Interactions of Silver Nanoparticles with Model Biological Membranes

The influence of solution chemistry and soft protein coronas on the interactions between citrate-coated silver nanoparticles (AgNPs) and model biological membranes was investigated by assembling supported lipid bilayers (SLBs) composed of zwitterionic 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) on silica crystal sensors in a quartz crystal microbalance with dissipation monitoring (QCM-D). Our results show that the deposition rates of AgNPs on unmodified silica surfaces increased with increasing electrolyte concentrations under neutral pH conditions. Similar trends were observed when AgNPs were deposited on SLBs, hence indicating that the deposition of AgNPs on model cell membranes was controlled by electrostatic interactions. In the presence of human serum albumin (HSA) proteins at both pH 7 and pH 2, the colloidal stability of AgNPs was considerably enhanced due to the formation of HSA soft coronas surrounding the nanoparticles. At pH 7, the deposition of AgNPs on SLBs was suppressed in the presence of HSA due to steric repulsion between HSA-modified AgNPs and SLBs. In contrast, pronounced deposition of HSA-modified AgNPs on SLBs was observed at pH 2. This observation was attributed to the reduction of electrostatic repulsion as well as conformation changes of adsorbed HSA under low pH conditions, resulting in the decrease of steric repulsion between AgNPs and SLBs.

Growing Embossed Nanostructures of Polymer Brushes on Wet-Etched Silicon Templated via Block Copolymers

Block copolymer nanolithography has attracted enormous interest in chip technologies, such as integrated silicon chips and biochips, due to its large-scale and mass production of uniform patterns. We further modified this technology to grow embossed nanodots, nanorods, and nanofingerprints of polymer brushes on silicon from their corresponding wet-etched nanostructures covered with pendent SiHx (X = 1–3) species. Atomic force microscopy (AFM) was used to image the topomorphologies, and multiple transmission-reflection infrared spectroscopy (MTR-IR) was used to monitor the surface molecular films in each step for the sequential stepwise reactions. In addition, two layers of polymethacrylic acid (PMAA) brush nanodots were observed, which were attributed to the circumferential convergence growth and the diffusion-limited growth of the polymer brushes. The pH response of PMAA nanodots in the same region was investigated by AFM from pH 3.0 to 9.0.

Atomic force microscopy of red-light photoreceptors using peakforce quantitative nanomechanical property mapping

Atomic force microscopy (AFM) uses a pyramidal tip attached to a cantilever to probe the force response of a surface. The deflections of the tip can be measured to ~10 pN by a laser and sectored detector, which can be converted to image topography. Amplitude modulation or "tapping mode" AFM involves the probe making intermittent contact with the surface while oscillating at its resonant frequency to produce an image. Used in conjunction with a fluid cell, tapping-mode AFM enables the imaging of biological macromolecules such as proteins in physiologically relevant conditions. Tapping-mode AFM requires manual tuning of the probe and frequent adjustments of a multitude of scanning parameters which can be challenging for inexperienced users. To obtain high-quality images, these adjustments are the most time consuming. PeakForce Quantitative Nanomechanical Property Mapping (PF-QNM) produces an image by measuring a force response curve for every point of contact with the sample. With ScanAsyst software, PF-QNM can be automated. This software adjusts the set-point, drive frequency, scan rate, gains, and other important scanning parameters automatically for a given sample. Not only does this process protect both fragile probes and samples, it significantly reduces the time required to obtain high resolution images. PF-QNM is compatible for AFM imaging in fluid; therefore, it has extensive application for imaging biologically relevant materials. The method presented in this paper describes the application of PF-QNM to obtain images of a bacterial red-light photoreceptor, RpBphP3 (P3), from photosynthetic R. palustris in its light-adapted state. Using this method, individual protein dimers of P3 and aggregates of dimers have been observed on a mica surface in the presence of an imaging buffer. With appropriate adjustments to surface and/or solution concentration, this method may be generally applied to other biologically relevant macromolecules and soft materials.

Hybridization of bioelectrochemically functional infinite coordination polymer nanoparticles with carbon nanotubes for highly sensitive and selective in vivo electrochemical monitoring

This study demonstrates the formation of a three-dimensional conducting framework through hybridization of bioelectrochemically active infinite coordination polymer (ICP) nanoparticles with single-walled carbon nanotubes (SWNTs) for highly sensitive and selective in vivo electrochemical monitoring with combination with in vivo microdialysis. The bioelectrochemically active ICP nanoparticles are synthesized through the self-assembly process of NAD(+) and Tb(3+), in which all biosensing elements including an electrocatalyst (i.e., methylene green, MG), cofactor (i.e., β-nicotinamide adenine dinucleotide, NAD(+)), and enzyme (i.e., glucose dehydrogenase, GDH) are adaptively encapsulated. The ICP/SWNT-based biosensors are simply prepared by drop-coating the as-formed ICP/SWNT nanocomposite onto a glassy carbon substrate. Electrochemical studies demonstrate that the simply prepared ICP/SWNT-based biosensors exhibit excellent biosensing properties with a higher sensitivity and stability than the ICP-based biosensors prepared only with ICP nanoparticles (i.e., without hybridization of SWNTs). By using a GDH-based electrochemical biosensor as an example, we demonstrate a technically simple yet effective online electroanalytical platform for continuously monitoring glucose in the brain of guinea pigs with the ICP/SWNT-based biosensor as an online detector in a continuous-flow system combined with in vivo microdialysis. Under the experimental conditions employed here, the dynamic linear range for glucose with the ICP/SWNT-biosensor is from 50 to 1000 μM. Moreover, in vivo selectivity investigations with the biosensors prepared by the GDH-free ICPs reveal that ICP/SWNT-based biosensors are very selective for the measurement of glucose in the cerebral system. The basal level of glucose in the microdialysates from the striatum of guinea pigs is determined to be 0.31 ± 0.03 mM (n = 3). The study offers a simple route to the preparation of electrochemical biosensors, which is envisaged to be particularly useful for probing the chemical events involved in some physiological and pathological processes.

Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study

BACKGROUND

The establishment of spectroscopic analysis techniques for complex, surface-bound biological systems is an important step toward the further application of these powerful experimental tools to new questions in biology and medicine.

METHODS

We use a combination of the complementary spectroscopic techniques of X-ray photoelectron spectroscopy, Infrared reflection-absorption spectroscopy, and near-edge x-ray absorption fine structure spectroscopy to monitor the composition and molecular orientation in adenine/thymine diblock oligonucleotide films and their hybridized brushes on gold.

RESULTS

We demonstrate that the surface-bound probe molecules, consisting of a binding adenine block, d(A), and a sensing thymine block, d(T), deviate from the ideal L-shape model due to the internal intra- and intermolecular hybridization. This effect becomes more pronounced with increasing length of the d(A) block. Nevertheless, these films were found to hybridize well with the complementary target d(A) strands, especially if they were treated in advance to reduce internal interaction between the molecules. In spite of the structural complexity of these films, the hybridization efficiency correlated well with the potential accessibility of the sensing d(T) blocks, defined by their lateral spacing.

CONCLUSIONS

These findings are a good demonstration of the strength of multi-technique spectroscopic analysis when applied to assemblies of biological molecules intrinsically prone to complex interactions.

Model membrane platforms for biomedicine: case study on antiviral drug development

As one of the most important interfaces in cellular systems, biological membranes have essential functions in many activities such as cellular protection and signaling. Beyond their direct functions, they also serve as scaffolds to support the association of proteins involved in structural support, adhesion, and transport. Unfortunately, biological processes sometimes malfunction and require therapeutic intervention. For those processes which occur within or upon membranes, it is oftentimes difficult to study the mechanism in a biologically relevant, membranous environment. Therefore, the identification of direct therapeutic targets is challenging. In order to overcome this barrier, engineering strategies offer a new approach to interrogate biological activities at membrane interfaces by analyzing them through the principles of the interfacial sciences. Since membranes are complex biological interfaces, the development of simplified model systems which mimic important properties of membranes can enable fundamental characterization of interaction parameters for such processes. We have selected the hepatitis C virus (HCV) as a model viral pathogen to demonstrate how model membrane platforms can aid antiviral drug discovery and development. Responsible for generating the genomic diversity that makes treating HCV infection so difficult, viral replication represents an ideal step in the virus life cycle for therapeutic intervention. To target HCV genome replication, the interaction of viral proteins with model membrane platforms has served as a useful strategy for target identification and characterization. In this review article, we demonstrate how engineering approaches have led to the discovery of a new functional activity encoded within the HCV nonstructural 5A protein. Specifically, its N-terminal amphipathic, α-helix (AH) can rupture lipid vesicles in a size-dependent manner. While this activity has a number of exciting biotechnology and biomedical applications, arguably the most promising one is in antiviral medicine. Based on the similarities between lipid vesicles and the lipid envelopes of virus particles, experimental findings from model membrane platforms led to the prediction that a range of medically important viruses might be susceptible to rupturing treatment with synthetic AH peptide. This hypothesis was tested and validated by molecular virology studies. Broad-spectrum antiviral activity of the AH peptide has been identified against HCV, HIV, herpes simplex virus, and dengue virus, and many more deadly pathogens. As a result, the AH peptide is the first in class of broad-spectrum, lipid envelope-rupturing antiviral agents, and has entered the drug pipeline. In summary, engineering strategies break down complex biological systems into simplified biomimetic models that recapitulate the most important parameters. This approach is particularly advantageous for membrane-associated biological processes because model membrane platforms provide more direct characterization of target interactions than is possible with other methods. Consequently, model membrane platforms hold great promise for solving important biomedical problems and speeding up the translation of biological knowledge into clinical applications.

Orientation-dependent electron transport in a single redox protein

The redox-active protein cytochrome b(562) has been engineered to introduce pairs of thiol groups in the form of cysteine residues at specified sites. Successful STM imaging of the molecules adsorbed on a gold surface indicated that one thiol group controls the orientation of the molecule and that the protein maintains its native form under the experimental conditions. Stable protein-gold STM tip electrical contact was directly observed to form via the second free thiol group in current-voltage and current-distance measurements. Proteins with thiol contacts positioned across the protein's short axis displayed a conductance of (3.48 ± 0.05) × 10(-5)G(0). However proteins with thiol groups placed along the long axis reproducibly yielded two distinct values of (1.95 ± 0.03) × 10(-5)G(0) and (3.57 ± 0.11) × 10(-5)G(0), suggesting that the placement of the asymmetrically located haem within the protein influences electron transfer. In contrast, the unengineered wild-type cytochrome b(562) had conductance values at least 1 order of magnitude less. Here we show that an electron transfer protein engineered to bind gold surfaces can be controllably oriented and electrically contacted to metallic electrodes, a prerequisite for potential integration into electronic circuits.

Hearing what you cannot see and visualizing what you hear: interpreting quartz crystal microbalance data from solvated interfaces

Over the last 2 decades, the quartz crystal microbalance (QCM or QCM-D) has emerged as a versatile tool for investigating soft and solvated interfaces between solid surfaces and bulk liquids because it can provide a wealth of information about key structural and functional parameters of these interfaces. In this Feature, we offer QCM users a set of guidelines for interpretation and quantitative analysis of QCM data based on a synthesis of well-established concepts rooted in rheological research of the last century and of new results obtained in the last several years.

pH-driven assembly of various supported lipid platforms: a comparative study on silicon oxide and titanium oxide

Supported lipid platforms are versatile cell membrane mimics whose structural properties can be tailored to suit the application of interest. By identifying parameters that control the self-assembly of these platforms, there is potential to develop advanced biomimetic systems that overcome the surface specificity of lipid vesicle interactions under physiological conditions. In this work, we investigated the adsorption kinetics of vesicles onto silicon and titanium oxides as a function of pH. On each substrate, a planar bilayer and a layer of intact vesicles could be self-assembled in a pH-dependent manner, demonstrating the role of surface charge density in the self-assembly process. Under acidic pH conditions where both zwitterionic lipid vesicles and the oxide films possess near-neutral electric surface charges, vesicle rupture could occur, demonstrating that the process is driven by nonelectrostatic interactions. However, we observed that the initial rupturing process is insufficient for propagating bilayer formation. The role of electrostatic interactions for propagating bilayer formation differs for the two substrates; electrostatic attraction between vesicles and the substrate is necessary for complete bilayer formation on titanium oxide but is not necessary on silicon oxide. Conversely, in the high pH regime, repulsive electrostatic interactions can result in the irreversible adsorption of intact vesicles on silicon oxide and even a reversibly adsorbed vesicle layer on titanium oxide. Together, the results show that pH is an effective tool to modulate vesicle-substrate interactions in order to create various self-assembled lipid platforms on hydrophilic substrates.

Understanding protein adsorption phenomena at solid surfaces

Protein adsorption at solid surfaces plays a key role in many natural processes and has therefore promoted a widespread interest in many research areas. Despite considerable progress in this field there are still widely differing and even contradictive opinions on how to explain the frequently observed phenomena such as structural rearrangements, cooperative adsorption, overshooting adsorption kinetics, or protein aggregation. In this review recent achievements and new perspectives on protein adsorption processes are comprehensively discussed. The main focus is put on commonly postulated mechanistic aspects and their translation into mathematical concepts and model descriptions. Relevant experimental and computational strategies to practically approach the field of protein adsorption mechanisms and their impact on current successes are outlined.

Fabrication of a planar zwitterionic lipid bilayer on titanium oxide

There is great demand to fabricate planar phospholipid bilayers on biocompatible materials. The preferred method of forming bilayers on these substrates is the spontaneous adsorption and rupture of phospholipid vesicles. However, in the case of titanium oxide, model vesicles composed solely of zwitterionic phospholipids do not follow this self-assembly pathway under physiological conditions, prompting the use of complex bilayer materials and less-facile methods. Herein, we report a novel pH-based strategy for fabricating zwitterionic bilayers on titanium oxide in a simple and robust manner. Depending on the pH conditions under which lipid vesicles adsorb onto titanium oxide, quartz crystal microbalance-dissipation (QCM-D) monitoring demonstrated that the self-assembly pathway can in fact result in planar bilayer formation. The pH of the solution could then be adjusted to physiological levels with no effect on the mass and viscoelastic properties of the bilayer. Moreover, fluorescence recovery after photobleaching (FRAP) measurements indicated a high degree of lateral lipid diffusivity within the bilayer at physiological pH, commensurate with its role as a cell membrane mimic. Compared to existing protocols, this strategy permits the fabrication of a more diverse array of planar bilayers on titanium oxide by tuning the self-assembly pathway of lipid vesicle adsorption onto solid substrates.

Quartz crystal microbalance with dissipation monitoring of supported lipid bilayers on various substrates

Supported lipid bilayers (SLBs) mimic biological membranes and are a versatile platform for a wide range of biophysical research fields including lipid-protein interactions, protein-protein interactions and membrane-based biosensors. The quartz crystal microbalance with dissipation monitoring (QCM-D) has had a pivotal role in understanding SLB formation on various substrates. As shown by its real-time kinetic monitoring of SLB formation, QCM-D can probe the dynamics of biomacromolecular interactions. We present a protocol for constructing zwitterionic SLBs supported on silicon oxide and titanium oxide, and discuss technical issues that need to be considered when working with charged lipid compositions. Furthermore, we explain a recently developed strategy that uses an amphipathic, alpha-helical (AH) peptide to form SLBs on gold and titanium oxide substrates. The protocols can be completed in less than 3 h.