Two Receptor Binding Strategy of SARS-CoV-2 Is Mediated by Both the N-Terminal and Receptor-Binding Spike Domain.

It is not well understood why severe acute respiratory syndrome (SARS)-CoV-2 spreads much faster than other ß-coronaviruses such as SARS-CoV and Middle East respiratory syndrome (MERS)-CoV. In a previous publication, we predicted the binding of the N-terminal domain (NTD) of SARS-CoV-2 spike to sialic acids (SAs). Here, we experimentally validate this interaction and present simulations that reveal a second possible interaction between SAs and the spike protein via a binding site located in the receptor-binding domain (RBD). The predictions from molecular-dynamics simulations and the previously-published 2D-Zernike binding-site recognition approach were validated through flow-induced dispersion analysis (FIDA)─which reveals the capability of the SARS-CoV-2 spike to bind to SA-containing (glyco)lipid vesicles, and flow-cytometry measurements─which show that spike binding is strongly decreased upon inhibition of SA expression on the membranes of angiotensin converting enzyme-2 (ACE2)-expressing HEK cells. Our analyses reveal that the SA binding of the NTD and RBD strongly enhances the infection-inducing ACE2 binding. Altogether, our work provides in silico, in vitro, and cellular evidence that the SARS-CoV-2 virus utilizes a two-receptor (SA and ACE2) strategy. This allows the SARS-CoV-2 spike to use SA moieties on the cell membrane as a binding anchor, which increases the residence time of the virus on the cell surface and aids in the binding of the main receptor, ACE2, via 2D diffusion.

Umbrella-like Helical Structure of α-Synuclein at the Air-Water Interface Observed with Experimental and Theoretical Sum Frequency Generation Spectroscopy.

The misfolding of α-synuclein (αS) into amyloid aggregates is catalyzed by hydrophobic surfaces and associated with severe brain disorders, such as Parkinson's disease. Despite the important role of interfaces, the three-dimensional structure of αS at the interfaces is still not clear. We report interface-specific sum frequency generation (SFG) experiments of monomeric αS binding to the air-water interface, a model system for the important hydrophobic surfaces. We combine the SFG spectra with calculations of theoretical spectra based on molecular dynamics simulations to show that αS, which is an intrinsically disordered protein in solution, folds into a defined, mostly helical secondary structure at the air-water interface. The binding pose resembles an umbrella shape, where the C-terminus protrudes into the water phase, while the N-terminus and the NAC region span the canopy at the interface. In this binding pose, αS is prone to aggregate, which could explain the catalytic effect of hydrophobic interfaces and air bubbles on αS fibrillation.

Peptide Orientation Strongly Affected by the Nanoparticle Size as Revealed by Sum Frequency Scattering Spectroscopy.

The orientation of proteins at interfaces has a profound effect on the function of proteins. For nanoparticles (NPs) in a biological environment, protein orientation determines the toxicity, function, and identity of the NP. Thus, understanding how proteins orientate at NP surfaces is a critical parameter in controlling NP biochemistry. While planar surfaces are often used to model NP interfaces for protein orientation studies, it has been shown recently that proteins can orient very differently on NP surfaces. This study uses sum frequency scattering vibrational spectroscopy of the model helical leucine-lysine (LK) peptide on NPs of different sizes to determine the cause for the orientation effects. The data show that, for low dielectric constant materials, the orientation of the helical LK peptide is a function of the coulombic forces between peptides across different particle volumes. This finding strongly suggests that flat model systems are only of limited use for determining protein orientation at NP interfaces and that charge interactions should be considered when designing medical NPs or assessing NP biocompatibility.

"Nonlinear" pursuit of understanding pollutant accumulation and chemistry at environmental and biological interfaces.

Over the past few decades, the public recognition of the prevalence of certain classes of pollutants, such as perfluoroalkyl substances and nanoplastics, within the environment, has sparked growing concerns over their potential impact on environmental and human health. Within both environmental and biological systems, the adsorption and structural organization of pollutants at aqueous interfaces can greatly impact the chemical reactivity and transformation. Experimentally probing chemical behavior at interfaces can often pose a problem due to bulk solvated molecules convoluting molecular signatures from interfacial molecules. To solve this problem, there exist interface-specific nonlinear spectroscopy techniques that can directly probe both macroscopic planar interfaces and nanoplastic interfaces in aqueous environments. These techniques can provide essential information such as chemical adsorption, structure, and reactivity at interfaces. In this perspective, these techniques are presented with obvious advantages for studying the chemical properties of pollutants adsorbed to environmental and biological interfaces.

Elevated concentrations cause upright alpha-synuclein conformation at lipid interfaces.

The amyloid aggregation of α-synuclein (αS), related to Parkinson's disease, can be catalyzed by lipid membranes. Despite the importance of lipid surfaces, the 3D-structure and orientation of lipid-bound αS is still not known in detail. Here, we report interface-specific vibrational sum-frequency generation (VSFG) experiments that reveal how monomeric αS binds to an anionic lipid interface over a large range of αS-lipid ratios. To interpret the experimental data, we present a frame-selection method ("ViscaSelect") in which out-of-equilibrium molecular dynamics simulations are used to generate structural hypotheses that are compared to experimental amide-I spectra via excitonic spectral calculations. At low and physiological αS concentrations, we derive flat-lying helical structures as previously reported. However, at elevated and potentially disease-related concentrations, a transition to interface-protruding αS structures occurs. Such an upright conformation promotes lateral interactions between αS monomers and may explain how lipid membranes catalyze the formation of αS amyloids at elevated protein concentrations.

Lysozyme Interaction with Phospholipid Nanodroplets Probed by Sum Frequency Scattering Vibrational Spectroscopy.

When a nanoparticle (NP) is introduced into a biological environment, its identity and interactions are immediately attributed to the dense layer of proteins that quickly covers the particle. The formation of this layer, dubbed the protein corona, is in general a combination of proteins interacting with the surface of the NP and a contest between other proteins for binding sites either at the surface of the NP or upon the dense layer. Despite the importance for surface engineering and drug development, the molecular mechanisms and structure behind interfacial biomolecule action have largely remained elusive. We use ultrafast sum frequency scattering (SFS) spectroscopy to determine the structure and the mode of action by which these biomolecules interact with and manipulate interfaces. The majority of work in the field of sum frequency generation has been done on flat model interfaces. This limits some important membrane properties such as membrane fluidity and dimensionality─important factors in biomolecule-membrane interactions. To move toward three-dimensional (3D) nanoscopic interfaces, we utilize SFS spectroscopy to interrogate the surface of 3D lipid monolayers, which can be used as a model lipid-based nanocarrier system. In this study, we have utilized SFS spectroscopy to follow the action of lysozyme. SFS spectra in the amide I region suggest that there is lysozyme at the interface and that the lysozyme induces an increased lipid monolayer order. The binding of lysozyme with the NP is demonstrated by an increase in acyl chain order determined by the ratio of the CH3 symmetric and CH2 symmetric peak amplitudes. Furthermore, the lipid headgroup orientation s-PO2- change strongly supports lysozyme insertion into the lipid layer causing lipid disruption and reorientation. Altogether, with SFS, we have made a huge stride toward understanding the binding and structure change of proteins within the protein corona.

Shape-dependent gold nanoparticle interactions with a model cell membrane.

Customizable gold nanoparticle platforms are motivating innovations in drug discovery with massive therapeutic potential due to their biocompatibility, stability, and imaging capabilities. Further development requires the understanding of how discrete differences in shape, charge, or surface chemistry affect the drug delivery process of the nanoparticle. The nanoparticle shape can have a significant impact on nanoparticle function as this can, for example, drastically change the surface area available for modifications, such as surface ligand density. In order to investigate the effects of nanoparticle shape on the structure of cell membranes, we directly probed nanoparticle-lipid interactions with an interface sensitive technique termed sum frequency generation (SFG) vibrational spectroscopy. Both gold nanostars and gold nanospheres with positively charged ligands were allowed to interact with a model cell membrane and changes in the membrane structure were directly observed by specific SFG vibrational modes related to molecular bonds within the lipids. The SFG results demonstrate that the +Au nanostars both penetrated and impacted the ordering of the lipids that made up the membrane, while very little structural changes to the model membrane were observed by SFG for the +Au nanospheres interacting with the model membrane. This suggests that the +Au nanostars, compared to the +Au nanospheres, are more disruptive to a cell membrane. Our findings indicate the importance of shape in nanomaterial design and provide strong evidence that shape does play a role in defining nanomaterial-biological interactions.

Peptide Orientation at Emulsion Nanointerfaces Dramatically Different from Flat Surfaces.

The adsorption of protein to nanoparticles plays an important role in toxicity, food science, pharmaceutics, and biomaterial science. Understanding how proteins bind to nanophase surfaces is instrumental for understanding and, ultimately, controlling nanoparticle (NP) biochemistry. Techniques probing the adsorption of proteins at NP interfaces exist; however, these methods have been unable to determine the orientation and folding of proteins at these interfaces. For the first time, we probe in situ with sum frequency scattering vibrational spectroscopy the orientation of model leucine-lysine (LK) peptides adsorbed to NPs. The results show that both α-helical and ß-strand LK peptides bind the particles in an upright orientation, in contrast to the flat orientation of LKs binding to planar surfaces. The different binding geometry is explained by Coulombic forces between peptides across the particle volume.

Measuring Protein Conformation at Aqueous Interfaces with 2D Infrared Spectroscopy of Emulsions.

Determining the secondary and tertiary structures of proteins at aqueous interfaces is crucial for understanding their function, but measuring these structures selectively at the interface is challenging. Here we demonstrate that two-dimensional infrared (2D-IR) spectroscopy of protein stabilized emulsions offers a new route to measuring interfacial protein structure with high levels of detail. We prepared hexadecane/water oil-in-water emulsions stabilized by model LK peptides that are known to fold into either α-helix or ß-sheet conformations at hydrophobic interfaces and measured 2D-IR spectra in a transmission geometry. We saw clear spectral signatures of the peptides folding at the interface, with no detectable residue from remaining bulk peptides. Using 2D spectroscopy gives us access to correlation and dynamics data, which enables structural assignment in cases where linear spectroscopy fails. Using the emulsions allows one to study interfacial spectra with standard transmission geometry spectrometers, bringing the richness of 2D-IR to the interface with no additional optical complexity.

Model Asphaltenes Adsorbed onto Methyl- and COOH-Terminated SAMs on Gold.

Petroleum asphaltenes are surface-active compounds found in crude oils, and their interactions with surfaces and interfaces have huge implications for many facets of reservoir exploitation, including production, transportation, and oil-water separation. The asphaltene fraction in oil, found in the highest boiling-point range, is composed of many different molecules that vary in size, functionality, and polarity. Studies done on asphaltene fractions have suggested that they interact via polyaromatic and heteroaromatic ring structures and functional groups containing nitrogen, sulfur, and oxygen. However, isolating a single pure chemical structure of asphaltene in abundance is challenging and often not possible, which impairs the molecular-level study of asphaltenes of various architectures on surfaces. Thus, to further the molecular fundamental understanding, we chose to use functionalized model asphaltenes (AcChol-Th, AcChol-Ph, and 1,6-DiEtPy[Bu-Carb]) and model self-assembled monolayer (SAM) surfaces with precisely known chemical structures, whereby the hydrophobicity of the model surface is controlled. We applied solutions of asphaltenes to these SAM surfaces and then analyzed them with surface-sensitive techniques of near-edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectroscopy (XPS). We observe no adsorption of asphaltenes to the hydrophobic surface. On the hydrophilic surface, AcChol-Ph penetrates into the SAM with a preferential orientation parallel to the surface; AcChol-Th adsorbs in a similar manner, and 1,6-DiEtPy[Bu-Carb] binds the surface with a bent binding geometry. Overall, this study demonstrates the need for studying pure and fractionated asphaltenes at the molecular level, as even within a family of asphaltene congeners, very different surface interactions can occur.

Surface chemistry of the ladybird beetle adhesive foot fluid across various substrates.

Nature has coevolved highly adaptive and reliable bioadhesives across a multitude of animal species. Much attention has been paid in recent years to selectively mimic these adhesives for the improvement of a variety of technologies. However, very few of the chemical mechanisms that drive these natural adhesives are well understood. Many insects combine hairy feet with a secreted adhesive fluid, allowing for adhesion to considerably rough and slippery surfaces. Insect adhesive fluids have evolved highly specific compositions which are consistent across most surfaces and optimize both foot adhesion and release in natural environments. For example, beetles are thought to have adhesive fluids made up of a complex molecular mixture containing both hydrophobic and hydrophilic parts. We hypothesize that this causes the adhesive interface to be dynamic, with molecules in the fluid selectively organizing and ordering at surfaces with complimentary hydrophobicity to maximize adhesion. In this study, we examine the adhesive fluid of a seven-spotted ladybird beetle with a surface-sensitive analytical technique, sum frequency generation spectroscopy, as the fluid interacts with three substrates of varied wettabilities. The resulting spectra present no evidence of unique molecular environments between hydrophilic and hydrophobic surfaces but exhibit significant differences in the ordering of hydrocarbons. This change in surface interactions across different substrates correlates well with traction forces measured from beetles interacting with substrates of increasing hydrophobicities. We conclude that insect adhesion is dependent upon a dynamic molecular-interfacial response to an environmental surface.

In-Silico Evidence for a Two Receptor Based Strategy of SARS-CoV-2.

We propose a computational investigation on the interaction mechanisms between SARS-CoV-2 spike protein and possible human cell receptors. In particular, we make use of our newly developed numerical method able to determine efficiently and effectively the relationship of complementarity between portions of protein surfaces. This innovative and general procedure, based on the representation of the molecular isoelectronic density surface in terms of 2D Zernike polynomials, allows the rapid and quantitative assessment of the geometrical shape complementarity between interacting proteins, which was unfeasible with previous methods. Our results indicate that SARS-CoV-2 uses a dual strategy: in addition to the known interaction with angiotensin-converting enzyme 2, the viral spike protein can also interact with sialic-acid receptors of the cells in the upper airways.

Windowless detection geometry for sum frequency scattering spectroscopy in the C-D and amide I regions.

Understanding the structure and chemistry of nanoscopic surfaces is an important challenge for biointerface sciences. Sum frequency scattering (SFS) spectroscopy can specifically probe the surfaces of nanoparticles, vesicles, liposomes, and other materials relevant to biomaterial research, and, as a vibrational spectroscopy method, it can provide molecular level information about the surface chemistry. SFS is particularly promising to probe the structure of proteins, and other biological molecules, at nanoparticle surfaces. Here, amide I spectra can provide information about protein folding and orientation, while spectra in the C-D and C-H stretching regions allow experiments to determine the mode of interaction between particle surfaces and proteins. Methods used currently employ a closed liquid cell or cuvette, which works extremely well for C-H and phosphate regions but is often impeded in the amide I and C-D regions by a strong background signal that originates from the window material of the sample cells. Here, we discuss a windowless geometry for collecting background-free and high-fidelity SFS spectra in the amide I and C-D regions. We demonstrate the improvement in spectra quality by comparing SFS spectra of unextruded, multilamellar vesicles in a sample cuvette with those recorded using the windowless geometry. The sample geometry we propose will enable new experiments using SFS as a probe for protein-particle interactions.

Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water.

Ice-nucleation active (INA) bacteria can promote the growth of ice more effectively than any other known material. Using specialized ice-nucleating proteins (INPs), they obtain nutrients from plants by inducing frost damage and, when airborne in the atmosphere, they drive ice nucleation within clouds, which may affect global precipitation patterns. Despite their evident environmental importance, the molecular mechanisms behind INP-induced freezing have remained largely elusive. We investigate the structural basis for the interactions between water and the ice-nucleating protein InaZ from the INA bacterium Pseudomonas syringae. Using vibrational sum-frequency generation (SFG) and two-dimensional infrared spectroscopy, we demonstrate that the ice-active repeats of InaZ adopt a ß-helical structure in solution and at water surfaces. In this configuration, interaction between INPs and water molecules imposes structural ordering on the adjacent water network. The observed order of water increases as the interface is cooled to temperatures close to the melting point of water. Experimental SFG data combined with molecular-dynamics simulations and spectral calculations show that InaZ reorients at lower temperatures. This reorientation can enhance water interactions, and thereby the effectiveness of ice nucleation.

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 ß-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.

Assembly of iron oxide nanosheets at the air-water interface by leucine-histidine peptides.

The fabrication of inorganic nanomaterials is important for a wide range of disciplines. While many purely inorganic synthetic routes have enabled a manifold of nanostructures under well-controlled conditions, organisms have the ability to synthesize structures under ambient conditions. For example, magnetotactic bacteria, can synthesize tiny 'compass needles' of magnetite (Fe3O4). Here, we demonstrate the bio-inspired synthesis of extended, self-supporting, nanometer-thin sheets of iron oxide at the water-air interface through self-assembly using small histidine-rich peptides.

Synthetic Artificial Apoptosis-Inducing Receptor for On-Demand Deactivation of Engineered Cells.

The design of a fully synthetic, chemical "apoptosis-inducing receptor" (AIR) molecule is reported that is anchored into the lipid bilayer of cells, is activated by the incoming biological input, and responds with the release of a secondary messenger-a highly potent toxin for cell killing. The AIR molecule has four elements, namely, an exofacial trigger group, a bilayer anchor, a toxin as a secondary messenger, and a self-immolative scaffold as a mechanism for signal transduction. Receptor installation into cells is established via a robust protocol with minimal cell handling. The synthetic receptor remains dormant in the engineered cells, but is effectively triggered externally by the addition of an activating biomolecule (enzyme) or in a mixed cell population through interaction with the surrounding cells. In 3D cell culture (spheroids), receptor activation is accessible for at least 5 days, which compares favorably with other state of the art receptor designs.

Orientation and Conformation of Proteins at the Air-Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy.

Understanding the assembly of proteins at the air-water interface (AWI) informs the formation of protein films, emulsion properties, and protein aggregation. Determination of protein conformation and orientation at an interface is difficult to resolve with a single experimental or simulation technique alone. To date, the interfacial structure of even one of the most widely studied proteins, lysozyme, at the AWI remains unresolved. In this study, molecular dynamics (MD) simulations are used to determine if the protein adopts a side-on, head-on, or axial orientation at the AWI with two different forcefields, GROMOS-53a6 + SPC/E and a99SB-disp + TIP4P-D. Vibrational sum frequency generation (SFG) spectroscopy experiments and spectral SFG calculations validate consistency between the structure determined from MD and experiments. Overall, we show with strong agreement that lysozyme adopts an axial conformation at pH 7. Further, we provide molecular-level insight as to how pH influences the binding domains of lysozyme resulting in side-on adsorption near the isoelectric point of the lysozyme.

How Universal Is the Wetting Aging in 2D Materials.

Previous studies indicate that 2D materials such as graphene, WS2, and MoS2 deposited on oxidized silicon substrate are susceptible to aging due to the adsorption of airborne contamination. As a result, their surfaces become more hydrophobic. However, it is not clear how ubiquitous such a hydrophobization is, and the interplay between the specific adsorbed species and resultant wetting aging remains elusive. Here, we report a pronounced and general hydrophilic-to-hydrophobic wetting aging on 2D InSe films, which is independent of the substrates to synthesize these films (silicon, glass, nickel, copper, aluminum oxide), though the extent of wetting aging is sensitive to the layer of films. Our findings are ascribed to the occurrence and enrichment of airborne contamination that contains alkyl chains. Our results also suggest that the wetting aging effect might be universal to a wide range of 2D materials.