Probing the orientation of electrostatically immobilized cytochrome C by time of flight secondary ion mass spectrometry and sum frequency generation spectroscopy

Protein Adsorption on Mixed Self-Assembled Monolayers: Influence of Chain Length and Terminal Group

Mixed self-assembled monolayers (SAMs) are often used as highly tunable substrates for biomedical and biosensing applications. It is well documented, however, that mixed SAMs can be highly disordered at the molecular level and do not pack as closely or homogeneously as single-component SAMs, particularly when the chain lengths and head groups of the SAM thiol components are significantly different. In this study, we explore the impact of SAM structure and mixing ratio (-OH and -CH3 termini) on the weak physisorption behavior of bovine serum albumin (BSA), which adsorbs more readily to hydrophobic, methyl-terminated SAMs. Our results suggest that once the mixture includes 50% or more of the methyl terminus, the mixing ratio alone is a relatively good predictor of adsorption, regardless of the relative chain lengths of the thiols used in the mixture. This trend persists at any mixing ratio for SAMs where methyl- and hydroxyl-terminated groups are the same length or where the hydroxyl-terminated thiol is longer. The only variance observed is at low mixing ratios (<50% methyl-terminated) for a mixed SAM where the methyl-terminated component has a longer chain length. Relative protein adsorption increases on these mixtures, perhaps due to the disordered exposure of the excess alkane backbone. Taken together, however, we do not find significant evidence that varying chain lengths for mixed SAMs prepared on polycrystalline substrates and analyzed in air have an outsized influence on nanoscopic adsorption behavior, despite molecular-level disorder in the SAM itself.

Back to the basics of time-of-flight secondary ion mass spectrometry data analysis of bio-related samples. II. Data processing and display

This is the second half of a two-part Tutorial on the basics of the time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis of bio-related samples. Part I of this Tutorial series covers planning for a ToF-SIMS experiment, preparing and shipping samples, and collecting ToF-SIMS data. This Tutorial aims at helping the ToF-SIMS user to process, display, and interpret ToF-SIMS data. ToF-SIMS provides detailed chemical information about surfaces but comes with a steep learning. The purpose of this Tutorial is to provide the reader with a solid foundation in the ToF-SIMS data analysis.

Molecularly imprinted electrochemical sensor for the ultrasensitive detection of cytochrome c

Cytochrome c (Cyt c) is an important biomarker for the early stage of apoptosis that plays a role in the diagnosis and therapy of several diseases including cancer. Here, an electrochemical sensor based on molecularly imprinted polymer (MIP) for the ultrasensitive detection of Cyt c is studied. It is prepared by electropolymerization of o-phenylenediamine in the presence of Cyt c as template, followed by solvent extraction, resulting in the formation of Cyt c recognition sites. The MIP is characterised by cyclic voltammetry and differential pulse voltammetry, using ferrocenecarboxylic acid as redox probe. Voltammetric data indicates that the MIP-sensor behaves as an electrode with partially blocked surface. The partition isotherm obtained fits the Langmuir model, indicating a high affinity for Cyt c, with an association constant K_a = 5 × 10 ¹¹ M^-1. DPV measurements allow to achieve extremely high analytical sensitivity and low detection limit, in the femtomolar range, with negligible unspecific adsorption. Satisfactory analytical recovery tests performed in the presence of possible interfering proteins and in diluted human serum confirmed the selectivity of the MIP-sensor as well as its potential applicability for real samples analysis.

Predicting the Orientation of Adsorbed Proteins Steered with Electric Fields Using a Simple Electrostatic Model

Under the most common experimental conditions, the adsorption of proteins to solid surfaces is a spontaneous process that leads to a rather compact layer of randomly oriented molecules. However, controlling such orientation is critically important for the development of catalytic surfaces. In this regard, the use of electric fields is one of the most promising alternatives. Our work is motivated by experimental observations that show important differences in catalytic activity of a trypsin-covered surface, which depended on the applied potential during the adsorption. Even though adsorption results from the combination of several processes, we were able to determine that (under the selected conditions) mean-field electrostatics play a dominant role, determining the orientation and yielding a difference in catalytic activity. We simulated the electrostatic potential numerically, using an implicit-solvent model based on the linearized Poisson-Boltzmann equation. This was implemented in an extension of the code PyGBe that included an external electric field, and rendered the electrostatic component of the solvation free energy. Our model (extensions available at the Github repository) allowed estimating the overall affinity of the protein with the surface, and their most likely orientation as a function of the potential applied. Our results show that the active sites of trypsin are, on average, more exposed when the electric field is negative, which agrees with the experimental results of catalytic activity, and confirm the premise that electrostatic interactions can be used to control the orientation of adsorbed proteins.

Direct Evidence That Mutations within Dysferlin's C2A Domain Inhibit Lipid Clustering

Mechanical stress on sarcolemma can create small tears in the muscle cell membrane. Within the sarcolemma resides the multidomain dysferlin protein. Mutations in this protein render it unable to repair the sarcolemma and have been linked to muscular dystrophy. A key step in dysferlin-regulated repair is the binding of the C2A domain to the lipid membrane upon increased intracellular calcium. Mutations mapped to this domain cause loss of binding ability of the C2A domain. There is a crucial need to understand the geometry of dysferlin C2A at a membrane interface as well as cell membrane lipid reorientation when compared to that of a mutant. Here, we describe a comparison between the wild-type dysferlin C2A and a mutation to the conserved aspartic acids in the domain binding loops. To identify both the geometry and the cell membrane lipid reorientation, we applied sum frequency generation (SFG) vibrational spectroscopy and coupled it with simulated SFG spectra to observe and quantify the interaction with a model cell membrane composed of phosphotidylserine and phosphotidylcholine. Observed changes in surface pressure demonstrate that calcium-bridged electrostatic interactions govern the initial interaction of the C2A domains docking with a lipid membrane. SFG spectra taken from the amide-I region for the wild type and variant contain features near 1642, 1663, and 1675 cm^-1 related to the C2A domain β-sandwich secondary structure, indicating that the domain binds in a specific orientation. Mapping simulated SFG spectra to the experimentally collected spectra indicated that both wild-type and variant domains have nearly the same orientation to the membrane surface. However, examining the ordering of the lipids that make up a model membrane using SFG, we find that the wild type clusters the lipids as seen by the increase in the ratio of the CD₃ and CD₂ symmetric intensities by 170% for the wild type and by 120% for the variant. This study highlights the capabilities of SFG to probe with great detail biological mutations in proteins at cell membrane interfaces.

Modulating the biological function of protein by tailoring the adsorption orientation on nanoparticles

Protein orientation in nanoparticle-protein conjugates plays a crucial role in binding to cell receptors and ultimately, defines their targeting efficiency. Therefore, understanding fundamental aspects of the role of protein orientation upon adsorption on the surface of nanoparticles (NPs) is vital for the development of clinically important protein-based nanomedicines. In this work, new insights on the effect of the different orientation of cytochrome c (cyt c) bound to gold nanoparticles (GNPs) using various ligands on its apoptotic activity is reported. Time-of-Flight Secondary-Ion Mass Spectrometry (ToF-SIMS), electrochemical and circular dichroism (CD) analyses are used to investigate the characteristics of cyt c orientation and structure on functionalized GNPs. These studies indicate that the orientation and position of the heme ring inside the cyt c structure can be altered by changing the surface chemistry on the GNPs. A difference in the apoptosis inducing capability because of different orientation of cyt c bound to the GNPs is observed. These findings indicate that the biological activity of a protein can be modulated on the surface of NPs by varying its adsorption orientation. This study will impact on the rational design of new nanoscale biosensors, bioelectronics, and nanoparticle-protein based drugs.

Corn Oil-Water Separation: Interactions of Proteins and Surfactants at Corn Oil/Water Interfaces

Purification and collection of industrial products from oil-water mixtures are commonly implemented processes. However, the efficiencies of such processes can be severely influenced by the presence of emulsifiers that induce the formation of small oil droplets dispersed in the mixtures. Understanding of this emulsifying effect and its counteractions which occur at the oil/water interface is therefore necessary for the improvement of designs of these processes. In this paper, we investigated the interfacial mechanisms of protein-induced emulsification and the opposing surfactant-induced demulsification related to corn oil refinement. At corn oil/water interfaces, the pH-dependent emulsifying function of zein protein, which is the major storage protein of corn, was elucidated by the surface/interface-sensitive sum frequency generation (SFG) vibrational spectroscopy technique. The effective stabilization of corn oil droplets by zein protein was illustrated and correlated to its ordered amide I group at the oil/water interface. Substantial decrease of this ordering with the addition of three industrial surfactants to corn oil-zein solution mixtures was also observed using SFG, which explains the surfactant-induced destabilization and coalescence of small oil droplets. Surfactant-protein interaction was then demonstrated to be the driving force for the disordering of interfacial proteins, either by disrupting protein layers or partially excluding protein molecules from the interface. The ordered zein proteins at the interface were therefore revealed to be the critical factor for the formation of corn oil-water emulsion.

Cysteine-Modified Self-Assembling Peptides on Gold: The Role of the Head and Tail

Molecular self-assembly consists of the spontaneous aggregation of molecules into a well-defined structure guided by noncovalent bonds. The self-assembly strategy is ubiquitous in nature and recently has been proposed as a nature-mimetic strategy in polymer science and biomaterial engineering. In this context, we aim at designing and testing innovative but simple chemical strategies to efficiently modify surfaces by exploiting minor modifications in the bioactive molecule functionalities, for example, introducing cysteine (Cys) as a terminal residue in self-assembling peptides (SAPs). In this work, we report the attenuated total reflection-Fourier transform infrared spectroscopy, synchrotron radiation-induced X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and time-of-flight secondary ion mass spectrometry investigation of self-assembled layers of oligopeptides anchored onto gold surfaces through cysteine residues, opportunely inserted in an SAP (EAK16-II) main chain in three different positions: at the amine end group, at the carboxyl end group, and at both terminal groups (i.e., a bidentate SAP). This study, which allowed us to individuate in the bidentate SAP the best candidate for the controlled production of ordered SAP layers on the gold substrate surface, is envisaged to open wide perspectives for efficient chemical modification of surfaces with biomolecules, leading to obtaining innovative bioactive materials for applications in the field of tissue engineering.

Probing the Interfacial Interactions of Monoclonal and Bispecific Antibodies at the Silicone Oil-Aqueous Solution Interface by Using Sum Frequency Generation Vibrational Spectroscopy

Silicone oil has been widely utilized in the pharmaceutical industry especially as a lubricant coating commonly used in syringes for the smooth delivery of drugs. Protein structure perturbation and aggregation have been reported upon protein contacting silicone oil by using indirect methods and ex-situ techniques. The conclusions derived from such indirect and ex-situ methods may not truly reflect the exact nature of the protein-silicone oil interfacial interactions. Recently, we have successfully demonstrated that sum frequency generation (SFG) vibrational spectroscopy can be used as a powerful and direct method of studying the fusion protein-silicone oil interfacial interactions in situ and in real time. In this article, we studied monoclonal and bispecific antibody interactions with the silicone oil surface by using SFG spectroscopy. Being structurally and functionally different in the nature of fusion proteins and antibodies, this study is important in enhancing our current understanding of protein-silicone oil interfacial interactions. Both types of antibodies investigated here readily and strongly adsorb onto the silicone oil surface and remain stable at least for 10 h. SFG spectra in the amide I region for monoclonal and bispecific antibodies centered at 1660 and 1665 cm^-1, respectively, suggest the difference in their molecular structures. The absence of the antibody signals in the amide I region of time-dependent and static SFG spectra obtained for preadsorbed antibodies onto silicone oil after contacting polysorbate 80 (PS-80) surfactant suggests that PS-80 can effectively remove both types of antibodies from the silicone oil surface. This study demonstrated the feasibility of using SFG spectroscopy as a powerful tool for probing the antibody-interfacial interactions in situ and in real time.

Differential orientation and conformation of surface-bound keratinocyte growth factor on (hydroxyethyl)methacrylate, (hydroxyethyl)methacrylate/methyl methacrylate, and (hydroxyethyl)methacrylate/methacrylic acid hydrogel copolymers

The development of hydrogels for protein delivery requires protein-hydrogel interactions that cause minimal disruption of the protein's biological activity. Biological activity can be influenced by factors such as orientational accessibility for receptor binding and conformational changes, and these factors can be influenced by the hydrogel surface chemistry. (Hydroxyethyl)methacrylate (HEMA) hydrogels are of interest as drug delivery vehicles for keratinocyte growth factor (KGF) which is known to promote re-epithelialization in wound healing. The authors report here the surface characterization of three different HEMA hydrogel copolymers and their effects on the orientation and conformation of surface-bound KGF. In this work, they characterize two copolymers in addition to HEMA alone and report how protein orientation and conformation is affected. The first copolymer incorporates methyl methacrylate (MMA), which is known to promote the adsorption of protein to its surface due to its hydrophobicity. The second copolymer incorporates methacrylic acid (MAA), which is known to promote the diffusion of protein into its surface due to its hydrophilicity. They find that KGF at the surface of the HEMA/MMA copolymer appears to be more orientationally accessible and conformationally active than KGF at the surface of the HEMA/MAA copolymer. They also report that KGF at the surface of the HEMA/MAA copolymer becomes conformationally unfolded, likely due to hydrogen bonding. KGF at the surface of these copolymers can be differentiated by Fourier-transform infrared-attenuated total reflectance spectroscopy and time-of-flight secondary ion mass spectrometry in conjunction with principal component analysis. The differences in KGF orientation and conformation between these copolymers may result in different biological responses in future cell-based experiments.

Sum Frequency Generation Vibrational Spectroscopy for Characterization of Buried Polymer Interfaces

Sum frequency generation vibrational spectroscopy (SFG-VS) has become one of the most appealing technologies to characterize molecular structures at interfaces. In this focal point review, we focus on SFG-VS studies at buried polymer interfaces and review many of the recent publications in the field. We also cover the essential theoretical background of SFG-VS and discuss the experimental implementation of SFG-VS.

Determination of Absolute Orientation of Protein α-Helices at Interfaces Using Phase-Resolved Sum Frequency Generation Spectroscopy

Understanding the structure of proteins at surfaces is key in fields such as biomaterials research, biosensor design, membrane biophysics, and drug design. A particularly important factor is the orientation of proteins when bound to a particular surface. The orientation of the active site of enzymes or protein sensors and the availability of binding pockets within membrane proteins are important design parameters for engineers developing new sensors, surfaces, and drugs. Recently developed methods to probe protein orientation, including immunoessays and mass spectrometry, either lack structural resolution or require harsh experimental conditions. We here report a new method to track the absolute orientation of interfacial proteins using phase-resolved sum frequency generation spectroscopy in combination with molecular dynamics simulations and theoretical spectral calculations. As a model system we have determined the orientation of a helical lysine-leucine peptide at the air-water interface. The data show that the absolute orientation of the helix can be reliably determined even for orientations almost parallel to the surface.

Orientation and conformation of osteocalcin adsorbed onto calcium phosphate and silica surfaces

Adsorption isotherms, circular dichroism (CD) spectroscopy, x-ray photoelectron spectroscopy (XPS), and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used to investigate the adsorption of human osteocalcin (hOC) and decarboxylated (i.e., Gla converted back to Glu) hOC (dhOC) onto various calcium phosphate surfaces as well as silica surfaces. The adsorption isotherms and XPS nitrogen signals were used to track the amount of adsorbed hOC and dhOC. The intensities of key ToF-SIMS amino acid fragments were used to assess changes in the structure of adsorbed hOC and dhOC. CD spectra were used to investigate the secondary structure of OC. The largest differences were observed when the proteins were adsorbed onto silica versus calcium phosphate surfaces. Similar amounts (3-4 at. % N) of hOC and dhOC were adsorbed onto the silica surface. Higher amounts of hOC and dhOC were adsorbed on all the calcium phosphate surfaces. The ToF-SIMS data showed that the intensity of the Cys amino acid fragment, normalized to intensity of all amino acid fragments, was significantly higher (∼×10) when the proteins were adsorbed onto silica. Since in the native OC structure the cysteines are located in the center of three α-helices, this indicates both hOC and dhOC are more denatured on the silica surface. As hOC and dhOC denature upon adsorption to the silica surface, the cysteines become more exposed and are more readily detected by ToF-SIMS. No significant differences were detected between hOC and dhOC adsorbed onto the silica surface, but small differences were observed between hOC and dhOC adsorbed onto the calcium phosphate surfaces. In the OC structure, the α-3 helix is located above the α-1 and α-2 helices. Small differences in the ToF-SIMS intensities from amino acid fragments characteristic of each helical unit (Asn for α-1; His for α-2; and Phe for α-3) suggests either slight changes in the orientation or a slight uncovering of the α-1 and α-2 for adsorbed dhOC. XPS showed that similar amounts of hOC and dhOC were absorbed onto hydroxyapaptite and octacalcium phosphate surfaces, but ToF-SIMS detected some small differences in the amino acid fragment intensities on these surfaces for adsorbed hOC and dhOC.

Identifying the selectivity of antimicrobial peptides to cell membranes by sum frequency generation spectroscopy

Cationic amphiphilic peptides have been engineered to target both Gram-positive and Gram-negative bacteria while avoiding damage to other cell types. However, the exact mechanism of how these peptides target, bind, and disrupt bacterial cell membranes is not understood. One specific peptide that has been engineered to selectively capture bacteria is WLBU2 (sequence: RRWVRRVRRWVRRVVRVVRRWVRR). It has been suggested that WLBU2 activity stems from the fact that when interacting with bacterial cell membranes the peptide assumes an α-helical structure and inserts itself into the membrane. Alternatively, in the presence of mammalian cell membranes, the peptide assumes an inert β-sheet structure. To test this hypothesis, the authors applied sum frequency generation (SFG) spectroscopy and surface tensiometry to identify the structure of WLBU2 as it interacts with model lipid monolayers that mimic mammalian and bacterial cell membranes. Model mammalian cell membranes were built upon zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine lipids while bacterial cell membranes were constructed with negatively charged 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) lipids. Observed changes in surface pressure at the peptide-lipid-air interface demonstrate that the peptide has a clear binding preference toward negatively charged bacteria-like lipids. The structure of both the lipids and peptides were characterized by SFG spectra collected at the monolayer interface. Changes in monolayer structure as the peptide binds were observed by tracking the intensities of SFG vibrational modes related to the acyl chains within the lipids. Peptide structures when bound to both types of lipids were determined by SFG spectra collected within the amide I vibrational band. The SFG spectra of WLBU2 interacting with the model mammalian lipid monolayer contain two peaks near 1642 and 1678 cm^-1 indicative of an inactive β-sheet structure. SFG spectra collected from the peptide bound to a bacteria-like lipid monolayer contains just a single peak near 1651 cm^-1 which corresponds to an active α-helix structure. Combined, the tensiometry and SFG results demonstrate that WLBU2 both possesses a higher binding affinity toward and is in an active α-helix structure when bound to bacterial cell membranes.

Effects of Film Morphology and Surface Chemistry on the Direct Electrochemistry of Cytochrome c at Boron-Doped Diamond Electrodes

The effects of film morphology and surface termination on the direct electron transfer of horse heart cytochrome c on boron-doped ultrananocrystalline (B-UNCD) and microcrystalline (B-MCD) diamond thin-film electrodes were investigated. Quasi-reversible, diffusion-controlled cyclic voltammetric responses were observed on oxygen-terminated (atomic O/C ~0.015), but not hydrogen-terminated (atomic O/C ~0.02) diamond thin films. The effect of the surface termination was the same for both the nanostructured B-UNCD film with sp2-bonded carbon atoms in the grain boundaries and the well faceted B-MCD film with micron-sized grains and largely devoid of sp2 carbon. Stable cyclic voltammetric i-E curves were recorded with cycling for both oxygen-terminated films indicating the absence of protein denaturation and electrode fouling. The peak currents increased linearly with the square root of the scan rate and the protein concentration; both indicative of a reaction rate limited by semi-infinite linear diffusion of the protein. Similar heterogeneous electron-transfer rate constants were observed for oxygen-terminated B-UNCD (3.48 (± 1.25) × 10-3 cm/s) and B-MCD films (2.38 (± 0.72) × 10-3 cm/s). The results clearly reveal that the oxygen-terminated surface is more active for electron-transfer with this soluble redox protein than is the hydrogen-terminated surface. The film morphology does not influence the diffusion-controlled response of the redox protein.

In Situ Investigation of Peptide-Lipid Interaction Between PAP248-286 and Model Cell Membranes

Sum frequency generation vibrational spectroscopy (SFG) was utilized to investigate the interaction between PAP248-286 and the two lipid bilayer systems. The present study also provides spectroscopic evidence to confirm that, although PAP248-286 is unable to penetrate into the hydrophobic core of the lipid bilayers, it is capable of interacting more intimately with the fluid-phase POPG/POPC than with the gel-phase DPPG/DPPC lipid bilayer. The helical structure content of lipid-bound PAP248-286 was also observed to be high, in contrast to the results previously reported using nuclear magnetic resonance (NMR). Collectively, our SFG data suggest that lipid-bound PAP248-286 actually resembles its structure in 50 % 2,2,2-trifluoroethanol better than the structure when the peptide binds to SDS micelles. This present study questions the use of SDS micelles as the model membrane for NMR studies of PAP248-286 due to its protein denaturing activity.

Molecular simulations of cytochrome c adsorption on positively charged surfaces: the influence of anion type and concentration

The influence of anion type and concentration on the adsorption of cytochrome c onto the positively charged NH₂-SAM surface.

Full membrane spanning self-assembled monolayers as model systems for UHV-based studies of cell-penetrating peptides

Biophysical studies of the interaction of peptides with model membranes provide a simple yet effective approach to understand the transport of peptides and peptide based drug carriers across the cell membrane. Herein, the authors discuss the use of self-assembled monolayers fabricated from the full membrane-spanning thiol (FMST) 3-((14-((4'-((5-methyl-1-phenyl-35-(phytanyl)oxy-6,9,12,15,18,21,24,27,30,33,37-undecaoxa-2,3-dithiahenpentacontan-51-yl)oxy)-[1,1'-biphenyl]-4-yl)oxy)tetradecyl)oxy)-2-(phytanyl)oxy glycerol for ultrahigh vacuum (UHV) based experiments. UHV-based methods such as electron spectroscopy and mass spectrometry can provide important information about how peptides bind and interact with membranes, especially with the hydrophobic core of a lipid bilayer. Near-edge x-ray absorption fine structure spectra and x-ray photoelectron spectroscopy (XPS) data showed that FMST forms UHV-stable and ordered films on gold. XPS and time of flight secondary ion mass spectrometry depth profiles indicated that a proline-rich amphipathic cell-penetrating peptide, known as sweet arrow peptide is located at the outer perimeter of the model membrane.