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

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.

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 β-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.

Theoretical Sum Frequency Generation Spectra of Protein Amide with Surface-Specific Velocity-Velocity Correlation Functions

Vibrational sum frequency generation (vSFG) spectroscopy is widely used to probe the protein structure at interfaces. Because protein vSFG spectra are complex, they can only provide detailed structural information if combined with computer simulations of protein molecular dynamics and spectra calculations. We show how vSFG spectra can be accurately modeled using a surface-specific velocity-velocity scheme based on ab initio normal modes. Our calculated vSFG spectra show excellent agreement with the experimental sum frequency spectrum of LTα14 peptide and provide insight into the origin of the characteristic α-helical amide I peak. Analysis indicates that the peak shape can be explained largely by two effects: (1) the uncoupled response of amide groups located on opposite sides of the α-helix will have different orientations with respect to the interface and therefore different local environments affecting the local mode vibrations and (2) vibrational splitting from nearest neighbor coupling evaluated as inter-residue vibrational correlation. The conclusion is consistent with frequency mapping techniques with an empirically based ensemble of peptide structures, thus showing how time correlation approaches and frequency mapping techniques can give independent yet complementary molecular descriptions of protein vSFG. These models reveal the sensitive relationship between protein structure and their amide I response, allowing exploitation of the complicated molecular vibrations and their interference to derive the structures of proteins under native conditions at interfaces.

Peptide Mimic of the Marine Sponge Protein Silicatein Fabricates Ultrathin Nanosheets of Silicon Dioxide and Titanium Dioxide

Two-dimensional (2D) materials have attracted attention for potential applications in light harvesting, catalysis, and molecular electronics. Mineral proteins involved in hard tissue biogenesis can produce 2D structures with high fidelity by using sustainable production routes. This study shows that a peptide mimic based on the catalytic triad of the marine sponge protein silicatein catalyzes the formation of nanometer thin and stable sheets of silicon dioxide and titanium dioxide.

Choose your own adventure: Picosecond or broadband vibrational sum-frequency generation spectroscopy

Vibrational sum-frequency generation (VSFG) spectroscopy is a method capable of measuring chemical structure and dynamics within the interfacial region between two bulk phases. At the core of every experimental system is a laser source that influences the experimental capabilities of the VSFG spectrometer. In this article, we discuss the differences between VSFG spectrometers built with picosecond and broadband laser sources as it will impact everything from material costs, experimental build time, experimental capabilities, and more. A focus is placed on the accessibility of the two different SFG systems to newcomers in the SFG field and provides a resource for laboratories considering incorporating VSFG spectroscopy into their research programs. This Tutorial provides a model decision tree to aid newcomers when determining whether the picosecond or femtosecond laser system is sufficient for their research program and navigates through it for a few specific scenarios.

Long seed, short pump: converting Yb-doped laser radiation to multi-µJ few-cycle pulses tunable through 2.5-15 µm

We present a setup for generating broadband (up to 1050 cm^-1) and broadly tunable (2.5-15 µm) mid-infrared pulses using an Yb-doped femtosecond laser as the pump source. Our scheme, comprising two parametric amplifiers and a mixing stage, exploits favorable group velocity matching conditions in GaSe pumped at 2 µm to directly produce sub-70 fs pulses throughout the tuning range without any additional dispersion compensation, while 30-50 fs pulse durations are achieved with simple dispersion compensation by propagation through thin bulk media. The generated pulses have sub-1% short- and long-term energy noise, as well as stable spectral parameters, while delivering 0.5-2 W average mid-IR power. We expect the source to be useful for various spectroscopic applications in the mid-IR.

Membrane Structure of Aquaporin Observed with Combined Experimental and Theoretical Sum Frequency Generation Spectroscopy

High-resolution structural information on membrane proteins is essential for understanding cell biology and for the structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide angstrom-level information about the structure of membrane proteins, yet for XRD experiments, proteins are removed from their native membrane environment, chemically stabilized, and crystallized, all of which can compromise the conformation. Here, we describe how a combination of surface-sensitive vibrational spectroscopy and molecular dynamics simulations can account for the native membrane environment. We observe the structure of a glycerol facilitator channel (GlpF), an aquaporin membrane channel finely tuned to selectively transport water and glycerol molecules across the membrane barrier. We find subtle but significant differences between the XRD structure and the inferred in situ structure of GlpF.

Developments and Ongoing Challenges for Analysis of Surface-Bound Proteins

Proteins at surfaces and interfaces play important roles in the function and performance of materials in applications ranging from diagnostic assays to biomedical devices. To improve the performance of these materials, detailed molecular structure (conformation and orientation) along with the identity and concentrations of the surface-bound proteins on those materials must be determined. This article describes radiolabeling, surface plasmon resonance, quartz crystal microbalance with dissipation, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, sum frequency generation spectroscopy, and computational techniques along with the information each technique provides for characterizing protein films. A multitechnique approach using both experimental and computation methods is required for these investigations. Although it is now possible to gain much insight into the structure of surface-bound proteins, it is still not possible to obtain the same level of structural detail about proteins on surfaces as can be obtained about proteins in crystals and solutions, especially for large, complex proteins. However, recent results have shown it is possible to obtain detailed structural information (e.g., backbone and side chain orientation) about small peptides (5-20 amino sequences) on surfaces. Current studies are extending these investigations to small proteins such as protein G B1 (∼6 kDa). Approaches for furthering the capabilities for characterizing the molecular structure of surface-bound proteins are proposed.

A Unified Mathematical Formalism for First to Third Order Dielectric Response of Matter: Application to Surface-Specific Two-Colour Vibrational Optical Spectroscopy

To take advantage of the singular properties of matter, as well as to characterize it, we need to interact with it. The role of optical spectroscopies is to enable us to demonstrate the existence of physical objects by observing their response to light excitation. The ability of spectroscopy to reveal the structure and properties of matter then relies on mathematical functions called optical (or dielectric) response functions. Technically, these are tensor Green’s functions, and not scalar functions. The complexity of this tensor formalism sometimes leads to confusion within some articles and books. Here, we do clarify this formalism by introducing the physical foundations of linear and non-linear spectroscopies as simple and rigorous as possible. We dwell on both the mathematical and experimental aspects, examining extinction, infrared, Raman and sum-frequency generation spectroscopies. In this review, we thus give a personal presentation with the aim of offering the reader a coherent vision of linear and non-linear optics, and to remove the ambiguities that we have encountered in reference books and articles.

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.

Location and Conformation of the LKα14 Peptide in Water/Ethanol Mixtures

It is widely recognized that solvation is one of the major factors determining structure and functionality of proteins and long peptides, however it is a formidable challenge to address it both experimentally and computationally. For this reason, simple peptides are used to study fundamental aspects of solvation. It is well established that alcohols can change the peptide conformation and tuning of the alcohol content in solution can dramatically affect folding and, as a consequence, the function of the peptide. In this work, we focus on the leucine and lysine based LKα14 peptide designed to adopt an α-helical conformation at an apolar-polar interface. We investigate LKα14 peptide's bulk and interfacial behavior in water/ethanol mixtures combining a suite of experimental techniques (namely, circular dichroism and nuclear magnetic resonance spectroscopy for the bulk solution, surface pressure measurements and vibrational sum frequency generation spectroscopy for the air-solution interface) with molecular dynamics simulations. We observe that ethanol highly affects both the peptide location and conformation. At low ethanol content LKα14 lacks a clear secondary structure in bulk and shows a clear preference to reside at the air-solution interface. When the ethanol content in solution increases, the peptide's interfacial affinity is markedly reduced and the peptide approaches a stable α-helical conformation in bulk facilitated by the amphiphilic nature of the ethanol molecules.

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.

Chirality discrimination at the carvone air/liquid interfaces detected by heterodyne-detected sum frequency generation

The chiral signal of the carvone air/liquid interface is probed by heterodyne-detected sum frequency generation (HD-SFG) without the electronic resonance. The chiral SFG spectra exhibit two distinguishable spectral signatures. Four chiral vibrational peaks of the R- and S-carvone molecules are with opposite signs, which can directly determine the surface molecular chirality. Two achiral vibrational peaks are also observed with the same sign. The different spectral signatures can provide a detailed chirality characterization at the molecular interface.

The Surface Science of Microarray Generation-A Critical Inventory

Microarrays are powerful tools in biomedical research and have become indispensable for high-throughput multiplex analysis, especially for DNA and protein analysis. The basis for all microarray processing and fabrication is surface modification of a chip substrate and many different strategies to couple probe molecules to such substrates have been developed. We present here a critical assessment of typical biochip generation processes from a surface science point of view. While great progress has been made from a molecular biology point of view on the development of qualitative assays and impressive results have been obtained on the detection of rather low concentrations of DNA or proteins, quantitative chip-based assays are still comparably rare. We argue that lack of stable and reliable deposition chemistries has led in many cases to suboptimal quantitative reproducibility, impeded further progress in microarray development and prevented a more significant penetration of microarray technology into the diagnostic market. We suggest that surface-attached hydrogel networks might be a promising strategy to achieve highly sensitive and quantitatively reproducible microarrays.

Both Poly(ethylene glycol) and Poly(methyl ethylene phosphate) Guide Oriented Adsorption of Specific Proteins

Developing new functional biomaterials requires the ability to simultaneously repel unwanted and guide wanted protein adsorption. Here, we systematically interrogate the factors determining the protein adsorption by comparing the behaviors of different polymeric surfaces, poly(ethylene glycol) and a poly(phosphoester), and five different natural proteins. Interestingly we observe that, at densities comparable to those used in nanocarrier functionalization, the same proteins are either adsorbed (fibrinogen, human serum albumin, and transferrin) or repelled (immunoglobulin G and lysozyme) by both polymers. However, when adsorption takes place, the specific surface dictates the amount and orientation of each protein.

Otoferlin C2F Domain-Induced Changes in Membrane Structure Observed by Sum Frequency Generation

Proteins that contain C2 domains are involved in a variety of biological processes, including encoding of sound, cell signaling, and cell membrane repair. Of particular importance is the interface activity of the C-terminal C2F domain of otoferlin due to the pathological mutations known to significantly disrupt the protein's lipid membrane interface binding activity, resulting in hearing loss. Therefore, there is a critical need to define the geometry and positions of functionally important sites and structures at the otoferlin-lipid membrane interface. Here, we describe the first in situ probe of the protein orientation of otoferlin's C2F domain interacting with a cell membrane surface. To identify this protein's orientation at the lipid interface, we applied sum frequency generation (SFG) vibrational spectroscopy and coupled it with simulated SFG spectra to observe and quantify the otoferlin C2F domain interacting with model lipid membranes. A model cell membrane was built with equal amounts of phosphatidylserine and phosphatidylcholine. SFG measurements of the lipids that make up the model membrane indicate a 62% increase in amplitude from the SFG signal near 2075 cm^-1 upon protein interaction, suggesting domain-induced changes in the orientation of the lipids and possible membrane curvature. This increase is related to lipid ordering caused by the docking interaction of the otoferlin C2F domain. SFG spectra taken from the amide-I region contain features near 1630 and 1670 cm^-1 related to the C2F domains beta-sandwich secondary structure, thus indicating that the domain binds in a specific orientation. By mapping the simulated SFG spectra to the experimentally collected SFG spectra, we found the C2F domain of otoferlin orients 22° normal to the lipid surface. This information allows us to map what portion of the domain directly interacts with the lipid membrane.

Chiral Inversion of Amino Acids in Antiparallel β-Sheets at Interfaces Probed by Vibrational Sum Frequency Generation Spectroscopy

A parallel study of protein variants with all (l-), all (d-), or mixed (l-)/(d-) amino acids can be used to assess how backbone architecture versus side chain identity determines protein structure. Here, we investigate the secondary structure and side chain orientation dynamics of the antiparallel β-sheet peptide LK7β (Ac-Leu-Lys-Leu-Lys-Leu-Lys-Leu-NH2) composed of all (l-), all (d-), or alternating (l-Leu)/(d-Lys) amino acids. Using interface-selective vibrational sum frequency generation spectroscopy (VSFG), we observe that the alternating (l-)/(d-) peptide lacks a resonant C-H stretching mode compared to the (l-) and (d-) variants and does not form antiparallel β-sheets. We rationalize our observations on the basis of density functional theory calculations and molecular dynamics (MD) simulations of LK7β at the air-water interface. Irrespective of the handedness of the amino acids, leucine side chains prefer to orient toward the hydrophobic air phase while lysine side chains prefer the hydrophilic water phase. These preferences dictate the backbone configuration of LK7β and thereby the folding of the peptide. Our MD simulations show that the preferred side chain orientations can force the backbone of a single strand of (l-) LK7β at the air-water interface to adopt β-sheet Ramachandran angles. However, denaturation of the β-sheets at pH = 2 results in a negligible chiral VSFG amide I response. The combined computational and experimental results lend critical support to the theory that a chiral VSFG response requires macroscopic chirality, such as in β-sheets. Our results can guide expectations about the VSFG optical responses of proteins and should improve understanding of how amino acid chirality modulates the structure and function of natural and de novo proteins at biological interfaces.

Interfacial Conformation of Hydrophilic Polyphosphoesters Affects Blood Protein Adsorption

Synthetic polymers are commonly used as protein repelling materials for a variety of biomedical applications. Despite their widespread use, the fundamental mechanism underlying protein repellence is often elusive. Such insights are essential for improving existing and developing new materials. Here, we investigate how subtle differences in the chemistry of hydrophilic polyphosphoesters influence the adsorption of the human blood proteins serum albumin and fibrinogen. Using thermodynamic measurements, surface-specific vibrational spectroscopy, and Brewster angle microscopy, we investigate protein adsorption, hydration, and steric repulsion properties of the polyphosphoester polymers. Whereas both surface hydration and polymer conformation of the polymers vary substantially as a consequence of the chemical differences in the polymer structure, the protein repellency ability of these hydrophilic materials appears to be dominated by steric repulsion.

Structure of von Willebrand factor A1 on polystyrene determined from experimental and calculated sum frequency generation spectra

The blood-clotting protein von Willebrand factor (vWF) can be activated by small molecules, high shear stress, and interactions with interfaces. It subsequently binds platelet receptor glycoprotein Ibα (GPIbα) at the surface of platelets, thereby playing a crucial role in blood clotting due to platelet activation, which is an important process to consider in the design of cardiovascular implants and biomaterials used in blood-contacting applications. The influence of surfaces on the activation and the molecular-level structure of surface-bound vWF is largely unknown. Recent studies have indicated that when bound to hydrophobic polystyrene (PS), the A1 domain of vWF remains accessible for GPIbα binding. However, the detailed secondary structure and exact orientation of vWF A1 at the PS surface is still unresolved. Here, the authors resolve these features by studying the system with sum-frequency generation (SFG) spectroscopy. The data are consistent with a scenario where vWF A1 maintains a native secondary structure when bound to PS. Comparison of experimental and calculated SFG spectra combined with previously reported time-of-flight secondary ion mass spectrometry data suggests that A1 assumes an orientation with the GPIbα binding domain oriented away from the solid surface and exposed to the solution phase. This structural information will benefit future in vitro experiments with surface-adsorbed A1 domain and may have relevance for the design of novel blood-contacting biomaterials and wound-healing applications.

Engineering Proteins at Interfaces: From Complementary Characterization to Material Surfaces with Designed Functions

Once materials come into contact with a biological fluid containing proteins, proteins are generally—whether desired or not—attracted by the material's surface and adsorb onto it. The aim of this Review is to give an overview of the most commonly used characterization methods employed to gain a better understanding of the adsorption processes on either planar or curved surfaces. We continue to illustrate the benefit of combining different methods to different surface geometries of the material. The thus obtained insight ideally paves the way for engineering functional materials that interact with proteins in a predetermined manner.

Nonlinear Optical Methods for Characterization of Molecular Structure and Surface Chemistry

The principles, strengths and limitations of several nonlinear optical (NLO) methods for characterizing biological systems are reviewed. NLO methods encompass a wide range of approaches that can be used for real-time, in-situ characterization of biological systems, typically in a label-free mode. Multiphoton excitation fluorescence (MPEF) is widely used for high-quality imaging based on electronic transitions, but lacks interface specificity. Second harmonic generation (SHG) is a parametric process that has all the virtues of the two-photon version of MPEF, yielding a signal at twice the frequency of the excitation light, which provides interface specificity. Both SHG and MPEF can provide images with high structural contrast, but they typically lack molecular or chemical specificity. Other NLO methods such as coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) can provide high-sensitivity imaging with chemical information since Raman active vibrations are probed. However, CARS and SRS lack interface and surface specificity. A NLO method that provides both interface/surface specificity as well as molecular specificity is vibrational sum frequency generation (SFG) spectroscopy. Vibration modes that are both Raman and IR active are probed in the SFG process, providing the molecular specificity. SFG, like SHG, is a parametric process, which provides the interface and surface specificity. SFG is typically done in the reflection mode from planar samples. This has yielded rich and detailed information about the molecular structure of biomaterial interfaces and biomolecules interacting with their surfaces. However, 2-D systems have limitations for understanding the interactions of biomolecules and interfaces in the 3-D biological environment. The recent advances made in instrumentation and analysis methods for sum frequency scattering (SFS) now present the opportunity for SFS to be used to directly study biological solutions. By detecting the scattering at angles away from the phase-matched direction even centrosymmetric structures that are isotropic (e.g., spherical nanoparticles functionalized with self-assembled monolayers or biomolecules) can be probed. Often a combination of multiple NLO methods or a combination of a NLO method with other spectroscopic methods is required to obtain a full understanding of the molecular structure and surface chemistry of biomaterials and the biomolecules that interact with them. Using the right combination methods provides a powerful approach for characterizing biological materials.

Ice-binding site of surface-bound type III antifreeze protein partially decoupled from water

Combined SFG/MD analysis together with spectral calculations revealed that type III antifreeze proteins adsorbed at the air–water interface maintains a native state and adopts an orientation that leads to a partial decoupling of its ice-binding site from water.

Molecular interactions between single layered MoS2 and biological molecules

In this research, molecular interactions between several de novo designed alpha-helical peptides and monolayer MoS₂ have been studied.

Two-dimensional (2D) materials such as graphene, molybdenum disulfide (MoS₂), tungsten diselenide (WSe₂), and black phosphorous are being developed for sensing applications with excellent selectivity and high sensitivity. In such applications, 2D materials extensively interact with various analytes including biological molecules. Understanding the interfacial molecular interactions of 2D materials with various targets becomes increasingly important for the progression of better-performing 2D-material based sensors. In this research, molecular interactions between several de novo designed alpha-helical peptides and monolayer MoS₂ have been studied. Molecular dynamics simulations were used to validate experimental data. The results suggest that, in contrast to peptide–graphene interactions, peptide aromatic residues do not interact strongly with the MoS₂ surface. It is also found that charged amino acids are important for ensuring a standing-up pose for peptides interacting with MoS₂. By performing site-specific mutations on the peptide, we could mediate the peptide–MoS₂ interactions to control the peptide orientation on MoS₂.