Heterotrimeric G protein beta1gamma2 subunits change orientation upon complex formation with G protein-coupled receptor kinase 2 (GRK2) on a model membrane

Role of tungsten disulfide quantum dots in specific protein-protein interactions at air-water interface

The intriguing network of antibody-antigen (Ab-Ag) interactions is highly governed by environmental perturbations and the nature of biomolecular interaction. Protein-protein interactions (PPIs) have potential applications in developing protein-adsorption-based sensors and nano-scale materials. Therefore, characterizing PPIs in the presence of a nanomaterial at the molecular level becomes imperative. The present work involves the investigation of antiferritin-ferritin (Ab-Ag) protein interactions under the influence of tungsten disulfide quantum dots (WS2 QDs). Isothermal calorimetry and contact angle measurements validated the strong influence of WS2 QDs on Ab-Ag interactions. The interfacial signatures of nano-bio-interactions were evaluated using sum frequency generation vibration spectroscopy (SFG-VS) at the air-water interface. Our SFG results reveal a variation in the tilt angle of methyl groups by ∼12° ± 2° for the Ab-Ag system in the presence of WS2 QDs. The results illustrated an enhanced ordering of water molecules in the presence of QDs, which underpins the active role of interfacial water molecules during nano-bio-interactions. We have also witnessed a differential impact of QDs on Ab-Ag by raising the concentration of the Ab-Ag combination, which showcased an increased inter-molecular interaction among the Ab and Ag molecules and a minimal influence on the methyl tilt angle. These findings suggest the formation of stronger and ordered Ab-Ag complexes upon introducing WS2 QDs in the aqueous medium and signify the potentiality of WS2 QDs relevant to protein-based sensing assays.

Hydration behaviors of nonfouling zwitterionic materials

Zwitterionic materials have emerged as highly effective ultralow fouling materials for many applications, however the underlying mechanism of fouling resistance remains unclear. Using ab initio molecular dynamics simulations and surface-sensitive sum frequency generation vibrational spectroscopy, we studied the hydration behaviors of zwitterionic materials, including trimethylamine-N-oxide (TMAO) and carboxybetaines of different charge-separation distances, to understand their fouling-resistant mechanism and provide a design principle for improved performance. Our study reveals that the interplay among hydrogen bonding, net charge, and dipole moment is crucial to the fouling-resistant capabilities of zwitterionic materials. Shortening of the zwitterionic spacing strengthens hydrogen bonding with water against biomolecule attachment due to the increased electrostatic and induction interactions, charge transfer, and improved structural stability. Moreover, the shortened charge separation reduces the dipole moment of zwitterionic materials with an intrinsic near-neutral net charge, decreasing their electrostatic and dipole-dipole interactions with biofoulers, and increasing their resistance to fouling. Compared to carboxybetaine compounds, TMAO has the shortest zwitterionic spacing and exhibits the strongest hydrogen bonding, the smallest net charge, and the minimum dipole moment, making it an excellent nonfouling material.

Conformation and Orientation of Antimicrobial Peptides MSI-594 and MSI-594A in a Lipid Membrane

There is significant interest in the development of antimicrobial compounds to overcome the increasing bacterial resistance to conventional antibiotics. Studies have shown that naturally occurring and de novo-designed antimicrobial peptides could be promising candidates. MSI-594 is a synthetic linear, cationic peptide that has been reported to exhibit a broad spectrum of antimicrobial activities. Investigation into how MSI-594 disrupts the cell membrane is important for better understanding the details of this antimicrobial peptide (AMP)'s action against bacterial cells. In this study, we used two different synthetic lipid bilayers: zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and anionic 7:3 POPC/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho(1'-rac-glycerol) (POPG). Sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) were used to determine the orientations of MSI-594 and its analogue MSI-594A associated with zwitterionic POPC and anionic 7:3 POPC/POPG lipid bilayers. The simulated ATR-FTIR and SFG spectra using nuclear magnetic resonance (NMR)-determined structures were compared with experimental spectra to optimize the bent angle between the N- (1-11) and C- (12-24) termini helices and the membrane orientations of the helices; since the NMR structure of the peptide was determined from lipopolysaccharide (LPS) micelles, the optimization was needed to find the most suitable conformation and orientation in lipid bilayers. The reported experimental results indicate that the optimized MSI-594 helical hairpin structure adopts a complete lipid bilayer surface-bound orientation (denoted "face-on") in both POPC and 7:3 POPC/POPG lipid bilayers. The analogue peptide, MSI-584A, on the other hand, exhibited a larger bent angle between the N- (1-11) and C- (12-24) termini helices with the hydrophobic C-terminal helix inserted into the hydrophobic region of the bilayer (denoted "membrane-inserted") when interacting with both POPC and 7:3 POPC/POPG lipid bilayers. These experimental findings on the membrane orientations suggest that both peptides are likely to disrupt the cell membrane through the carpet mechanism.

Monitoring the Molecular Structure of Fibrinogen during the Adsorption Process at the Buried Silicone Oil Interface In Situ in Real Time

Interfacial proteins play important roles in many research fields and applications, such as biosensors, biomedical implants, nonfouling coatings, etc. Directly probing interfacial protein behavior at buried solid/liquid and liquid/liquid interfaces is challenging. We used sum frequency generation vibrational spectroscopy and a Hamiltonian data analysis method to monitor the molecular structure of fibrinogen on silicone oil during the adsorption process in situ in real time. The results showed that the adsorbed fibrinogen molecules tend to adopt a bent structure throughout the entire adsorption process with the same orientation. This is different from the case of adsorbed fibrinogen on CaF₂ with a linear structure or on polystyrene with a bent structure but a different orientation. The method introduced herein is generally applicable for following time-dependent molecular structures of many other proteins and peptides at interfaces in situ in real time at the molecular level.

Sum frequency spectroscopy studies on cell membrane fusion induced by divalent cations

Cell membrane fusion is a fundamental biological process involved in a number of cellular living functions. Regarding this, divalent cations can induce fusion of the lipid bilayers through binding and bridging of divalent cations to the charged lipids, thus leading to the cell membrane fusion. How-ever, the elaborate mechanism of cell membrane fusion induced by divalent cations is still needed to be elucidated. Here, surface/interface sensitive sum frequency generation vibrational spectroscopy (SFG-VS) and dynamic light scattering (DLS) were applied in this research to study the responses of phospholipid monolayer to the exposure of divalent metal ions i.e. Ca2+ and Mg2+. According to the particle size distribution results measured by DLS experiments, it was found that Ca2+ could induce inter-vesicular fusion while Mg2+ could not. An octadecyltrichlorosilane self-assembled monolayer (OTS SAM)-lipid monolayer system was designed to model the cell membrane for the SFG-VS experiment. Ca2+ could interact with the lipid PO2− head groups more strongly, resulting in cell membrane fusion more easily, in comparison with Mg2+. No specific interaction between the two metal cations and the C=O groups was observed. However, the C=O orientations changed more after Ca2+-PO2− binding than Mg2+ mediation on lipid monolayer. Meanwhile, Ca2+ could induce dehydration of the lipids (which should be related to the strong Ca2+-PO2− interaction), leading to the reduced hindrance for cell membrane fusion.

Early sum frequency generation vibrational spectroscopic studies on peptides and proteins at interfaces

This paper summarizes the early research results on studying proteins and peptides at interfaces using sum frequency generation (SFG) vibrational spectroscopy. SFG studies in the C-H stretching frequency region to examine the protein side-chain behavior and in the amide I frequency region to investigate the orientation and conformation of interfacial peptides/proteins are presented. The early chiral SFG research and SFG isotope labeling studies on interfacial peptides/proteins are also discussed. These early SFG studies demonstrate the feasibility of using SFG to elucidate interfacial molecular structures of peptides and proteins in situ, which built a foundation for later SFG investigations on peptides and proteins at interfaces.

Probing protein aggregation at buried interfaces: distinguishing between adsorbed protein monomers, dimers, and a monomer-dimer mixture in situ

Protein adsorption on surfaces greatly impacts many applications such as biomedical materials, anti-biofouling coatings, bio-separation membranes, biosensors, antibody protein drugs etc. For example, protein drug adsorption on the widely used lubricant silicone oil surface may induce protein aggregation and thus affect the protein drug efficacy. It is therefore important to investigate the molecular behavior of proteins at the silicone oil/solution interface. Such an interfacial study is challenging because the targeted interface is buried. By using sum frequency generation vibrational spectroscopy (SFG) with Hamiltonian local mode approximation method analysis, we studied protein adsorption at the silicone oil/protein solution interface in situ in real time, using bovine serum albumin (BSA) as a model. The results showed that the interface was mainly covered by BSA dimers. The deduced BSA dimer orientation on the silicone oil surface from the SFG study can be explained by the surface distribution of certain amino acids. To confirm the BSA dimer adsorption, we treated adsorbed BSA dimer molecules with dithiothreitol (DTT) to dissociate these dimers. SFG studies on adsorbed BSA after the DTT treatment indicated that the silicone oil surface is covered by BSA dimers and BSA monomers in an approximate 6 : 4 ratio. That is to say, about 25% of the adsorbed BSA dimers were converted to monomers after the DTT treatment. Extensive research has been reported in the literature to determine adsorbed protein dimer formation using ex situ experiments, e.g., by washing off the adsorbed proteins from the surface then analyzing the washed-off proteins, which may induce substantial errors in the washing process. Dimerization is a crucial initial step for protein aggregation. This research developed a new methodology to investigate protein aggregation at a solid/liquid (or liquid/liquid) interface in situ in real time using BSA dimer as an example, which will greatly impact many research fields and applications involving interfacial biological molecules.

SGIP1 modulates kinetics and interactions of the cannabinoid receptor 1 and G protein-coupled receptor kinase 3 signalosome

Cannabinoid receptor 1 (CB1R), a G protein‐coupled receptor, plays a fundamental role in synaptic plasticity. Abnormal activity and deregulation of CB1R signaling result in a broad spectrum of pathological conditions. CB1R signaling is regulated by receptor desensitization including phosphorylation of residues within the intracellular C terminus by G protein‐coupled receptor kinases (GRKs) that may lead to endocytosis. Furthermore, CB1R signaling is regulated by the protein Src homology 3‐domain growth factor receptor‐bound 2‐like (SGIP1) that hinders receptor internalization, while enhancing CB1R association with β‐arrestin. It has been postulated that phosphorylation of two clusters of serine/threonine residues, ⁴²⁵SMGDS⁴²⁹ and ⁴⁶⁰TMSVSTDTS⁴⁶⁸, within the CB1R C‐tail controls dynamics of the association between receptor and its interaction partners involved in desensitization. Several molecular determinants of these events are still not well understood. We hypothesized that the dynamics of these interactions are modulated by SGIP1. Using a panel of CB1Rs mutated in the aforementioned serine and threonine residues, together with an array of Bioluminescence energy transfer‐based (BRET) sensors, we discovered that GRK3 forms complexes with Gβγ subunits of G proteins that largely independent of GRK3’s interaction with CB1R. Furthermore, CB1R interacts only with activated GRK3. Interestingly, phosphorylation of two specific residues on CB1R triggers GRK3 dissociation from the desensitized receptor. SGIP1 increases the association of GRK3 with Gβγ subunits of G proteins, and with CB1R. Altogether, our data suggest that the CB1R signalosome complex is dynamically controlled by sequential phosphorylation of the receptor C‐tail and is also modified by SGIP1.

Probing Orientations and Conformations of Peptides and Proteins at Buried Interfaces

Molecular structures of peptides/proteins at interfaces determine their interfacial properties, which play important roles in many applications. It is difficult to probe interfacial peptide/protein structures because of the lack of appropriate tools. Sum frequency generation (SFG) vibrational spectroscopy has been developed into a powerful technique to elucidate molecular structures of peptides/proteins at buried solid/liquid and liquid/liquid interfaces. SFG has been successfully applied to study molecular interactions between model cell membranes and antimicrobial peptides/membrane proteins, surface-immobilized peptides/enzymes, and physically adsorbed peptides/proteins on polymers and 2D materials. A variety of other analytical techniques and computational simulations provide supporting information to SFG studies, leading to more complete understanding of structure-function relationships of interfacial peptides/proteins. With the advance of SFG techniques and data analysis methods, along with newly developed supplemental tools and simulation methodology, SFG research on interfacial peptides/proteins will further impact research in fields like chemistry, biology, biophysics, engineering, and beyond.

Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein

Recently, a super uranyl binding protein (SUP) was developed, which exhibits excellent sensitivity/selectivity to bind uranyl ions. It can be immobilized onto a surface in sensing devices to detect uranyl ions. Here, sum frequency generation (SFG) vibrational spectroscopy was applied to probe the interfacial structures of surface-immobilized SUP. The collected SFG spectra were compared to the calculated orientation-dependent SUP SFG spectra using a one-excitonic Hamiltonian approach based on the SUP crystal structures to deduce the most likely surface-immobilized SUP orientation(s). Furthermore, discrete molecular dynamics (DMD) simulation was applied to refine the surface-immobilized SUP conformations and orientations. The immobilized SUP structures calculated from DMD simulations confirmed the SUP orientations obtained from SFG data analyzed based on the crystal structures and were then used for a new round of SFG orientation analysis to more accurately determine the interfacial orientations and conformations of immobilized SUP before and after uranyl ion binding, providing an in-depth understanding of molecular interactions between SUP and the surface and the effect of uranyl ion binding on the SUP interfacial structures. We believe that the developed method of combining SFG measurements, DMD simulation, and Hamiltonian data analysis approach is widely applicable to study biomolecules at solid/liquid interfaces.

Control of Protein Conformation and Orientation on Graphene

Graphene-based biosensors have attracted considerable attention due to their advantages of label-free detection and high sensitivity. Many such biosensors utilize noncovalent van der Waals force to attach proteins onto graphene surface while preserving graphene's high conductivity. Maintaining the protein structure without denaturation/substantial conformational change and controlling proper protein orientation on the graphene surface are critical for biosensing applications of these biosensors fabricated with proteins on graphene. Based on the knowledge we obtained from our previous experimental study and computer modeling of amino acid residual level interactions between graphene and peptides, here we systemically redesigned an important protein for better conformational stability and desirable orientation on graphene. In this paper, immunoglobulin G (IgG) antibody-binding domain of protein G (protein GB1) was studied to demonstrate how we can preserve the protein native structure and control the protein orientation on graphene surface by redesigning protein mutants. Various experimental tools including sum frequency generation vibrational spectroscopy, attenuated total refection-Fourier transform infrared spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy were used to study the protein GB1 structure on graphene, supplemented by molecular dynamics simulations. By carefully designing the protein GB1 mutant, we can avoid strong unfavorable interactions between protein and graphene to preserve protein conformation and to enable the protein to adopt a preferred orientation. The methodology developed in this study is general and can be applied to study different proteins on graphene and beyond. With the knowledge obtained from this research, one could apply this method to optimize protein function on surfaces (e.g., to enhance biosensor sensitivity).

Probing Surface Hydration and Molecular Structure of Zwitterionic and Polyacrylamide Hydrogels

A hydrogel is a hydrophilic cross-linked polymer network which can contain a large amount of water. Hydrogels with distinguished interfacial physical toughness were analyzed for their potential application as antifouling coating materials, utilizing sum frequency generation (SFG) spectroscopy as the interfacial analytical technique. The surface structures of one sulfobetaine (SBMA) zwitterionic hydrogel (ZWHG) and two polysaccharide hydrogels (PHGs) were probed in air; their interfacial structures with silica were examined using SFG in water and protein solutions, respectively. Both ZWHG and PHGs interfaces in water were dominated by strongly hydrogen-bonded water molecules, but the bonding strength associated with ZWHG was much stronger. Although all hydrogels experienced interfacial change in the presence of protein solutions, after cleaning, the zwitterionic hydrogel interface recovered almost completely while the other two hydrogels were subject to irreversible protein adsorption. Additionally, orientational analysis of ZWHG methyl groups in water was conducted and related to the superior hydrogen-bonding strength of water molecules at the ZWHG interface. The interfacial structures of hydrogel materials probed by SFG can be correlated to their antifouling properties. This research highlighted the critical role that hydrogen-bonding strength of interfacial water molecules play for antifouling applications.

Orientational Analysis of Monolayers at Low Surface Concentrations Due to an Increased Signal-to-Noise Ratio (S/N) Using Broadband Sum Frequency Generation Vibrational Spectroscopy

Sum frequency generation (SFG) * Equal contributors. spectroscopy was used to deduce the orientation of the terminal methyl (CH₃) group of self-assembled monolayers (SAMs) at the air-solid and air-liquid interfaces at surface concentrations as low as 1% protonated molecules in the presence of 99% deuterated molecules. The SFG spectra of octadecanethiol (ODT) and deuterated octadecanethiol (d₃₇ ODT) SAMs on gold were used for analysis at the air-solid interface. However, the eicosanoic acid (EA) and deuterated EA (d₃₉ EA) SAMs on the water were analyzed at the air-liquid interface. The tilt angle of the terminal CH₃ group was estimated to be ∼39 ° for a SAM of 1% ODT : 99% d₃₇ ODT, whereas the tilt angle of the terminal CH₃ group of the 1% EA : 99% d₃₉ EA monolayer was estimated to be ∼32 °. The reliability of the orientational analysis at low concentrations was validated by testing the sensitivity of the SFG spectroscopy. A signal-to-noise (S/N) ratio of ∼60 and ∼45 was obtained for the CH₃ symmetric stretch (SS) of 1% ODT : 99% d₃₇ ODT and 1% EA : 99% d₃₉ EA, respectively. The estimated increase in S/N ratio values, as a measure of the sensitivity of the SFG spectroscopy, verified the capacity to acquire the SFG spectra at low concentrations of interfacial molecules under ambient conditions. Overall, the orientational analysis of CH₃ SS vibrational mode was feasible at low concentrations of protonated molecules due to increased S/N ratio. In support, the improved S/N ratio on varying incident power density of the visible beam was also experimentally demonstrated.

Molecular Mechanisms of Interactions between Monolayered Transition Metal Dichalcogenides and Biological Molecules

Single layered two-dimensional (2D) materials such as transition metal dichalcogenides (TMDs) show great potential in many microelectronic or nanoelectronic applications. For example, because of extremely high sensitivity, TMD-based biosensors have become promising candidates for next-generation label-free detection. However, very few studies have been conducted on understanding the fundamental interactions between TMDs and other molecules including biological molecules, making the rational design of TMD-based sensors (including biosensors) difficult. This study focuses on the investigations of the fundamental interactions between proteins and two widely researched single-layered TMDs, MoS₂, and WS₂ using a combined study with linear vibrational spectroscopy attenuated total reflectance FTIR and nonlinear vibrational spectroscopy sum frequency generation vibrational spectroscopy, supplemented by molecular dynamics simulations. It was concluded that a large surface hydrophobic region in a relatively flat location on the protein surface is required for the protein to adsorb onto a monolayered MoS₂ or WS₂ surface with preferred orientation. No disulfide bond formation between cysteine groups on the protein and MoS₂ or WS₂ was found. The conclusions are general and can be used as guiding principles to engineer proteins to attach to TMDs. The approach adopted here is also applicable to study interactions between other 2D materials and biomolecules.

Chemically Immobilized Antimicrobial Peptide on Polymer and Self-Assembled Monolayer Substrates

Surfaces with chemically immobilized antimicrobial peptides have been shown to have great potential in various applications such as biosensors and antimicrobial coatings. This research investigated the chemical immobilization of a cecropin-melittin hybrid antimicrobial peptide on two different surfaces, a polymer surface prepared by chemical vapor deposition (CVD) polymerization and a self-assembled monolayer surface. We probed the structure of immobilized peptides using spectroscopic methods and correlated such structural information to the measured antimicrobial activity. We found that the hybrid peptide adopts an α-helical structure after immobilization onto both surfaces. As we have shown previously for another α-helical peptide, MSI-78, immobilized on a SAM, we found that the α-helical hybrid peptide lies down when it contacts bacteria. This study shows that the antimicrobial activity of the surface-immobilized peptides on the two substrates can be well explained by the spectroscopically measured peptide structural data. In addition, it was found that the polymer-based antimicrobial peptide coating is more stable. This is likely due to the fact that the SAM prepared using silane may be degraded after several days whereas the polymer prepared by CVD polymerization is more stable than the SAM, leading to a more stable antimicrobial coating.

Structures and Adhesion Properties at Polyethylene/Silica and Polyethylene/Nylon Interfaces

The molecular structures of buried interfaces of maleic anhydride grafted and ungrafted polyethylene films with silica and nylon surfaces were studied in situ using sum-frequency generation (SFG) vibrational spectroscopy. Grafting maleic anhydride to polyethylene altered the molecular structures at buried interfaces, including changing the orientation of polymer methylene groups and resulting in the presence of C═O groups at silica interfaces. These molecular level changes are correlated with enhanced adhesion properties, with ordered C═O groups and in-plane orientation of the methylene groups associated with higher levels of adhesion. While improved adhesion was observed for grafted polyethylene at the nylon interface, no C═O groups were detected at the interface using SFG, for films thermally treated at 185 °C. In this case, either no C═O groups are present at the interface or they are disordered; the latter explanation is more likely, considering the observed improvement in adhesion.

Regulation of G Protein βγ Signaling

Heterotrimeric guanine nucleotide-binding proteins (G proteins) deliver external signals to the cell interior, upon activation by the external signal stimulated G protein-coupled receptors (GPCRs).While the activated GPCRs control several pathways independently, activated G proteins control the vast majority of cellular and physiological functions, ranging from vision to cardiovascular homeostasis. Activated GPCRs dissociate GαGDPβγ heterotrimer into GαGTP and free Gβγ. Earlier, GαGTP was recognized as the primary signal transducer of the pathway and Gβγ as a passive signaling modality that facilitates the activity of Gα. However, Gβγ later found to regulate more number of pathways than GαGTP does. Once liberated from the heterotrimer, free Gβγ interacts and activates a diverse range of signaling regulators including kinases, lipases, GTPases, and ion channels, and it does not require any posttranslation modifications. Gβγ family consists of 48 members, which show cell- and tissue-specific expressions, and recent reports show that cells employ the subtype diversity in Gβγ to achieve desired signaling outcomes. In addition to activated GPCRs, which induce free Gβγ generation and the rate of GTP hydrolysis in Gα, which sequester Gβγ in the heterotrimer, terminating Gβγ signaling, additional regulatory mechanisms exist to regulate Gβγ activity. In this chapter, we discuss structure and function, subtype diversity and its significance in signaling regulation, effector activation, regulatory mechanisms as well as the disease relevance of Gβγ in eukaryotes.

Interactions between Surface-Immobilized Antimicrobial Peptides and Model Bacterial Cell Membranes

Sum frequency generation (SFG) vibrational spectroscopy was used to study surface immobilization effects on the interactions between antimicrobial peptide cecropin P1 (CP1) and model cell membranes. While free CP1 in solution interacted with a model cell membrane composed of a phosphatidylglycerol (PG) bilayer, electrostatic interaction led to the attachment of CP1 molecules onto the PG surface and the hydrophobic domain in the lipid bilayer enabled the peptides to insert into the bilayer and form α-helices from random coil structures. While CP1 molecules immobilized on a self-assembled monolayer interacted with PG lipid vesicles, the intensity of the SFG peak for the peptide α-helix decreased as the PG vesicle concentration increased. It was believed that when surface-immobilized CP1 molecules interacted with lipid vesicles, they lay down on the surface or became random coils. When the immobilized CP1 interacted with a PG lipid monolayer on water, the strong interaction led to the lying-down orientation of all of the surface-immobilized peptides as well. Differently, no significant interactions between surface-immobilized CP1 with the mammalian cell membrane model 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer were observed. Our results suggest that, instead of membrane insertion, the electrostatic interactions between the surface cationic charges of CP1 and anionic bacterial membranes may play an important role in the antimicrobial activity of the surface-immobilized CP1 peptide.

Effect of immobilization site on the orientation and activity of surface-tethered enzymes

Tethering peptides and proteins to abiotic surfaces has the potential to create biomolecule-functionalized surfaces with useful properties.

Immobilized enzymes: understanding enzyme – surface interactions at the molecular level

Interactions between immobilized enzymes and supporting surfaces are complex and context-dependent and can significantly alter enzyme structure, stability and activity.

Engineering and Characterization of Peptides and Proteins at Surfaces and Interfaces: A Case Study in Surface-Sensitive Vibrational Spectroscopy

Understanding molecular structures of interfacial peptides and proteins impacts many research fields by guiding the advancement of biocompatible materials, new and improved marine antifouling coatings, ultrasensitive and highly specific biosensors and biochips, therapies for diseases related to protein amyloid formation, and knowledge on mechanisms for various membrane proteins and their interactions with ligands. Developing methods for measuring such unique systems, as well as elucidating the structure and function relationship of such biomolecules, has been the goal of our lab at the University of Michigan. We have made substantial progress to develop sum frequency generation (SFG) vibrational spectroscopy into a powerful technique to study interfacial peptides and proteins, which lays a foundation to obtain unique and valuable insights when using SFG to probe various biologically relevant systems at the solid/liquid interface in situ in real time. One highlighting feature of this Account is the demonstration of the power of combining SFG with other techniques and methods such as ATR-FTIR, surface engineering, MD simulation, liquid crystal sensing, and isotope labeling in order to study peptides and proteins at interfaces. It is necessary to emphasize that SFG plays a major role in these studies, while other techniques and methods are supplemental. The central role of SFG is to provide critical information on interfacial peptide and protein structure (e.g., conformation and orientation) in order to elucidate how surface engineering (e.g., to vary the structure) can ultimately affect surface function (e.g., to optimize the activity). This Account focuses on the most significant recent progress in research on interfacial peptides and proteins carried out by our group including (1) the development of SFG analysis methods to determine orientations of regular as well as disrupted secondary structures, and the successful demonstration and application of an isotope labeling method with SFG to probe the detailed local structure and microenvironment of peptides at buried interfaces, (2) systematic research on cell membrane associated peptides and proteins including antimicrobial peptides, cell penetrating peptides, G proteins, and other membrane proteins, discussing the factors that influence interfacial peptide and protein structures such as lipid charge, membrane fluidity, and biomolecule solution concentration, and (3) in-depth discussion on solid surface immobilized antimicrobial peptides and enzymes. The effects of immobilization method, substrate surface, immobilization site on the peptide or protein, and surrounding environment are presented. Several examples leading to high impact new research are also briefly introduced: The orientation change of alamethicin detected while varying the model cell membrane potential demonstrates the feasibility to apply SFG to study ion channel protein gating mechanisms. The elucidation of peptide secondary structures at liquid crystal interfaces shows promising results that liquid crystal can detect and recognize different peptides and proteins. The method of retaining the native structure of surface immobilized peptides or proteins in air demonstrates the feasibility to protect and preserve such structures via the use of hydromimetic functionalities when there is no bulk water. We hope that readers in many different disciplines will benefit from the research progress reported in this Account on SFG studies of interfacial structure-function relationships of peptides and proteins and apply this powerful technique to study interfacial biomolecules in the future.

Effect of Lipid Composition on the Membrane Orientation of the G Protein-Coupled Receptor Kinase 2-Gβ1γ2 Complex

Interactions between proteins and cell membranes are critical for biological processes such as transmembrane signaling, and specific components of the membrane may play roles in helping to organize or mandate particular conformations of both integral and peripheral membrane proteins. One example of a signaling enzyme whose function is dependent on membrane binding and whose activity is affected by specific lipid components is G protein-coupled receptor (GPCR) kinase 2 (GRK2). Efficient GRK2-mediated phosphorylation of activated GPCRs is dependent not only on its recruitment to the membrane by heterotrimeric Gβγ subunits but also on the presence of highly negatively charged lipids, in particular phosphatidylinositol 4',5'-bisphosphate (PIP2). We hypothesized that PIP2 may favor a distinct orientation of the GRK2-Gβγ complex on the membrane that is more optimal for function. In this study, we compared the possible orientations of the GRK2-Gβγ complex and Gβγ alone on model cell membranes prepared with various anionic phospholipids as deduced from sum frequency generation vibrational and attenuated total reflectance Fourier transform infrared spectroscopic methods. Our results indicate that PIP2 affects the membrane orientation of the GRK2-Gβ1γ2 complex but not that of complexes formed with anionic phospholipid binding deficient mutations in the GRK2 pleckstrin homology (PH) domain. Gβ1γ2 exhibits a similar orientation on the lipid bilayer regardless of its lipid composition. The PIP2-induced orientation of the GRK2-Gβ1γ2 complex is therefore most likely caused by specific interactions between PIP2 and the GRK2 PH domain. Thus, PIP2 not only helps recruit GRK2 to the membrane but also "fine tunes" the orientation of the GRK2-Gβγ complex so that it is better positioned to phosphorylate activated GPCRs.

Organ-on-a-Chip Systems: Microengineering to Biomimic Living Systems

"Organ-on-a-chip" systems integrate microengineering, microfluidic technologies, and biomimetic principles to create key aspects of living organs faithfully, including critical microarchitecture, spatiotemporal cell-cell interactions, and extracellular microenvironments. This creative platform and its multiorgan integration recapitulating organ-level structures and functions can bring unprecedented benefits to a diversity of applications, such as developing human in vitro models for healthy or diseased organs, enabling the investigation of fundamental mechanisms in disease etiology and organogenesis, benefiting drug development in toxicity screening and target discovery, and potentially serving as replacements for animal testing. Recent advances in novel designs and examples for developing organ-on-a-chip platforms are reviewed. The potential for using this emerging technology in understanding human physiology including mechanical, chemical, and electrical signals with precise spatiotemporal controls are discussed. The current challenges and future directions that need to be pursued for these proof-of-concept studies are also be highlighted.

The interaction with gold suppresses fiber-like conformations of the amyloid β (16-22) peptide

Inorganic surfaces and nanoparticles can accelerate or inhibit the fibrillation process of proteins and peptides, including the biomedically relevant amyloid β peptide. However, the microscopic mechanisms that determine such an effect are still poorly understood. By means of large-scale, state-of-the-art enhanced sampling molecular dynamics simulations, here we identify an interaction mechanism between the segments 16-22 of the amyloid β peptide, known to be fibrillogenic by itself, and the Au(111) surface in water that leads to the suppression of fiber-like conformations from the peptide conformational ensemble. Moreover, thanks to advanced simulation analysis techniques, we characterize the conformational selection vs. induced fit nature of the gold effect. Our results disclose an inhibition mechanism that is rooted in the details of the microscopic peptide-surface interaction rather than in general phenomena such as peptide sequestration from the solution.

Probing Site-Specific Structural Information of Peptides at Model Membrane Interface In Situ

Isotope labeling is a powerful technique to probe detailed structures of biological molecules with a variety of analytical methods such as NMR and vibrational spectroscopies. It is important to obtain molecular structural information on biological molecules at interfaces such as cell membranes, but it is challenging to use the isotope labeling method to study interfacial biomolecules. Here, by individually (13)C═(16)O labeling ten residues of a peptide, Ovispirin-1, we have demonstrated for the first time that a site-specific environment of membrane associated peptide can be probed by the submonolayer surface sensitive sum frequency generation (SFG) vibrational spectroscopy in situ. With the peptide associated with a single lipid bilayer, the sinusoidal trend of the SFG line width and peak-center frequency suggests that the peptide is located at the interface beneath the lipid headgroup region. The constructive interferences between the isotope labeled peaks and the main peptide amide I peak contributed by the unlabeled components were used to determine the membrane orientation of the peptide. From the SFG spectral peak-center frequency, line width, and polarization dependence of the isotope labeled units, we deduced structural information on individual units of the peptide associated with a model cell membrane. We also performed molecular dynamics (MD) simulations to understand peptide-membrane interactions. The physical pictures described by simulation agree well with the SFG experimental result. This research demonstrates the feasibility and power of using isotope labeling SFG to probe molecular structures of interfacial biological molecules in situ in real time.

Molecular-Level Insights into Orientation-Dependent Changes in the Thermal Stability of Enzymes Covalently Immobilized on Surfaces

Surface-immobilized enzymes are important for a wide range of technological applications, including industrial catalysis, drug delivery, medical diagnosis, and biosensors; however, our understanding of how enzymes and proteins interact with abiological surfaces on the molecular level remains extremely limited. We have compared the structure, activity, and thermal stability of two variants of a β-galactosidase attached to a chemically well-defined maleimide-terminated self-assembled monolayer surface through a unique cysteinyl residue. In one case the enzyme is attached through an α helix and in the other case through an adjacent loop. Both enzymes exhibit similar specific activities and adopt similar orientations with respect to the surface normal, as determined by sum-frequency generation and attenuated total reflectance FT-IR spectroscopies. Surprisingly, however, the loop-tethered enzyme exhibits a thermal stability 10 °C lower than the helix-tethered enzyme and 13 °C lower than the enzyme in free solution. Using coarse-grain models, molecular dynamics simulations of the thermal unfolding of the surface-tethered enzymes were able to reproduce these differences in stability. Thus, revealing that tethering through the more flexible loop position provides more opportunity for surface residues on the protein to interact with the surface and undergo surface-induced unfolding. These observations point to the importance of the location of the attachment point in determining the performance of surface-supported biocatalysts and suggest strategies for optimizing their activity and thermal stability through molecular simulations.

Surface orientation control of site-specifically immobilized nitro-reductase (NfsB)

We demonstrate the control of enzyme orientation for enzymes chemically immobilized on surfaces. Nitro-reductase (NfsB) has the ability to reduce a broad range of nitro-containing compounds and has potential applications in a broad range of areas including the detection and decomposition of explosives. The enzyme was tethered through unique surface cysteine residues to a self-assembled monolayer (SAM) terminated with maleimide groups. One cysteine was introduced close to the active site (V424C), and the other, at a remote site (H360C). The surface-tethered NfsB variants were interrogated by a combination of surface-sensitive sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) to determine how the mode of attachment altered the enzyme's orientation. The activities of the two immobilized NfsB variants were measured and can be well correlated to the deduced orientations. The relationships among enzyme engineering, surface immobilization, enzyme orientation, and enzyme activity were revealed.

Unveiling the membrane-binding properties of N-terminal and C-terminal regions of G protein-coupled receptor kinase 5 by combined optical spectroscopies

G protein-coupled receptor kinase 5 (GRK5) is thought to associate with membranes in part via N- and C-terminal segments that are typically disordered in available high-resolution crystal structures. Herein we investigate the interactions of these regions with model cell membrane using combined sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. It was found that both regions associate with POPC lipid bilayers but adopt different structures when doing so: GRK5 residues 2-31 (GRK5(2-31)) was in random coil whereas GRK5(546-565) was partially helical. When the subphase for the GRK5(2-31) peptide was changed to 40% TFE/60% 10 mM phosphate pH 7.4 buffer, a large change in the SFG amide I signal indicated that GRK5(2-31) became partially helical. By inspecting the membrane behavior of two different segments of GRK5(2-31), namely, GRK5(2-24) and GRK5(25-31), we found that residues 25-31 are responsible for membrane binding, whereas the helical character is imparted by residues 2-24. With SFG, we deduced that the orientation angle of the helical segment of GRK5(2-31) is 46 ± 1° relative to the surface normal in 40% TFE/60% 10 mM phosphate pH = 7.4 buffer but increases to 78 ± 11° with higher ionic strength. We also investigated the effect of PIP2 in the model membrane and concluded that the POPC:PIP2 (9:1) lipid bilayer did not change the behavior of either peptide compared to a pure POPC lipid bilayer. With ATR-FTIR, we also found that Ca(2+)·calmodulin is able to extract both peptides from the POPC lipid bilayer, consistent with the role of this protein in disrupting GRK5 interactions with the plasma membrane in cells.

Strike a pose: Gαq complexes at the membrane

The heterotrimeric G protein Gαq is a central player in signal transduction, relaying signals from activated G-protein-coupled receptors (GPCRs) to effectors and other proteins to elicit changes in intracellular Ca(2+), the actin cytoskeleton, and gene transcription. Gαq functions at the intracellular surface of the plasma membrane, as do its best-characterized targets, phospholipase C-β, p63RhoGEF, and GPCR kinase 2 (GRK2). Recent insights into the structure and function of these signaling complexes reveal several recurring themes, including complex multivalent interactions between Gαq, its protein target, and the membrane, that are likely essential for allosteric control and maximum efficiency in signal transduction. Thus, the plasma membrane is not only a source of substrates but also a key player in the scaffolding of Gαq-dependent signaling pathways.

Structural insights into G protein-coupled receptor kinase function

The atomic structure of a protein can greatly advance our understanding of molecular recognition and catalysis, properties of fundamental importance in signal transduction. However, a single structure is incapable of fully describing how a protein functions, particularly when allostery is involved. Recent advances in the structure and function of G protein-coupled receptor (GPCR) kinases (GRKs) have concentrated on the mechanism of their inhibition by small and large molecules. These studies have generated a wealth of new information on the conformational flexibility of these enzymes, which opens new avenues for the development of selective chemical probes and provides deeper insights into the molecular basis for activation of these enzymes by GPCRs and phospholipids.

Membrane orientation and binding determinants of G protein-coupled receptor kinase 5 as assessed by combined vibrational spectroscopic studies

G-protein coupled receptors (GPCRs) are integral membrane proteins involved in a wide variety of biological processes in eukaryotic cells, and are targeted by a large fraction of marketed drugs. GPCR kinases (GRKs) play important roles in feedback regulation of GPCRs, such as of β-adrenergic receptors in the heart, where GRK2 and GRK5 are the major isoforms expressed. Membrane targeting is essential for GRK function in cells. Whereas GRK2 is recruited to the membrane by heterotrimeric Gβγ subunits, the mechanism of membrane binding by GRK5 is not fully understood. It has been proposed that GRK5 is constitutively associated with membranes through elements located at its N-terminus, its C-terminus, or both. The membrane orientation of GRK5 is also a matter of speculation. In this work, we combined sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) to help determine the membrane orientation of GRK5 and a C-terminally truncated mutant (GRK51-531) on membrane lipid bilayers. It was found that GRK5 and GRK51-531 adopt a similar orientation on model cell membranes in the presence of PIP2 that is similar to that predicted for GRK2 in prior studies. Mutation of the N-terminal membrane binding site of GRK5 did not eliminate membrane binding, but prevented observation of this discrete orientation. The C-terminus of GRK5 does not have substantial impact on either membrane binding or orientation in this model system. Thus, the C-terminus of GRK5 may drive membrane binding in cells via interactions with other proteins at the plasma membrane or bind in an unstructured manner to negatively charged membranes.

Site-specific orientation of an α-helical peptide ovispirin-1 from isotope-labeled SFG spectroscopy

Sum-frequency generation (SFG) vibrational spectroscopy is often used to probe the backbone structures and orientations of polypeptides at surfaces. Using the ovispirin-1 polypeptide at the solid/liquid interface of polystyrene, we demonstrate for the first time that SFG can probe the polarization response of a single-isotope-labeled residue. To interpret the spectral intensities, we simulated the spectra using an excitonic Hamiltonian approach. We show that the polarization dependence of either the label or the unlabeled amide I band alone does not provide sufficient structural constraints to obtain both the tilt and the twist of the ovispirin helix at a solid/liquid interface, but that both can be determined from the polarization dependence of the complete spectrum. For ovispirin, the detailed analysis of the polarized SFG experimental data shows that the helix axis is tilted at roughly 138° from the surface normal, and the transition dipole of the isotope-labeled C═O group is tilted at 23° from the surface normal, with the hydrophobic region facing the polystyrene surface. We further demonstrate that the Hamiltonian approach is able to address the coupling effect and the structural disorder. For comparison, we also collected the FTIR spectrum of ovispirin under similar conditions, which reveals the enhanced sensitivity of SFG for structural studies of single monolayer peptide surfaces. Our study provides insight into how structural and environmental effects appear in SFG spectra of the amide I band and establishes that SFG of isotope-labeled peptides will be a powerful technique for elucidating secondary structures with residue-by-residue resolution.

Lipid Fluid-Gel Phase Transition Induced Alamethicin Orientational Change Probed by Sum Frequency Generation Vibrational Spectroscopy

Alamethicin has been extensively studied as an antimicrobial peptide (AMP) and is widely used as a simple model for ion channel proteins. It has been shown that the antimicrobial activity of AMPs is related to their cell membrane orientation, which may be influenced by the phase of the lipid molecules in the cell membrane. The "healthy" cell membranes contain fluid phase lipids, while gel phase lipids can be found in injured or aged cells or in some phase separated membrane regions. Thus, investigations on how the phase of the lipids influences the membrane orientation of AMPs are important to understand more details regarding the AMP's action on cell membranes. In this study, we determined the orientational changes of alamethicin molecules associated with planar substrate supported single lipid bilayers (serving as model cell membranes) with different phases (fluid or gel) as a function of peptide concentration using sum frequency generation (SFG) vibrational spectroscopy. The phase changes of the lipid bilayers were realized by varying the sample temperature. Our SFG results indicated that alamethicin lies down on the surface of fluid and gel phase 1,2-dimyristoyl(d54)-sn-glycero-3-phosphocholine (d-DMPC) lipid bilayers when the lipid bilayers are in contact with a peptide solution with a low concentration of 0.84 μM. However, at a medium peptide concentration of 10.80 μM, alamethicin inserts into the fluid phase lipid bilayer. Its orientation switches from a transmembrane to an in-plane (or lying down) orientation when the phase of the lipid bilayer changes from a fluid state to a gel state. At a high peptide concentration of 21.60 μM, alamethicin adopts a transmembrane orientation while associated with both fluid and gel phase lipid bilayers. We also studied the structural changes of the fluid and gel phase lipid bilayers upon their interactions with alamethicin molecules at different peptide concentrations.

SFG analysis of surface bound proteins: a route towards structure determination

The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge X-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface.

From atomic structures to neuronal functions of g protein-coupled receptors

G protein-coupled receptors (GPCRs) are essential mediators of signal transduction, neurotransmission, ion channel regulation, and other cellular events. GPCRs are activated by diverse stimuli, including light, enzymatic processing of their N-termini, and binding of proteins, peptides, or small molecules such as neurotransmitters. GPCR dysfunction caused by receptor mutations and environmental challenges contributes to many neurological diseases. Moreover, modern genetic technology has helped identify a rich array of mono- and multigenic defects in humans and animal models that connect such receptor dysfunction with disease affecting neuronal function. The visual system is especially suited to investigate GPCR structure and function because advanced imaging techniques permit structural studies of photoreceptor neurons at both macro and molecular levels that, together with biochemical and physiological assessment in animal models, provide a more complete understanding of GPCR signaling.

Membrane orientation of Gα(i)β(1)γ(2) and Gβ(1)γ(2) determined via combined vibrational spectroscopic studies

The manner in which the heterotrimeric G protein complexes Gβ1γ2 and Gαiβ1γ2 interact with membranes is likely related to their biological function. We combined complementary measurements from sum frequency generation (SFG) vibrational and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to determine the possible membrane orientations of Gβ1γ2 and the Gαiβ1γ2 heterotrimer more precisely than could be achieved using SFG alone. The most likely orientations of Gβ1γ2 and the Gαiβ1γ2 heterotrimer were both determined to fall within a similar narrow range of twist and tilt angles, suggesting that Gβ1γ2 may bind to Gαi without a significant change in orientation. This "basal" orientation seems to depend primarily on the geranylgeranylated C-terminus of Gγ2 along with basic residues at the N-terminus of Gαi, and suggests that activated G protein-coupled receptors (GPCRs) must reorient G protein heterotrimers at lipid bilayers to catalyze nucleotide exchange. The innovative methodologies developed in this paper can be widely applied to study the membrane orientation of other proteins in situ.

Dependence of Alamethicin Membrane Orientation on the Solution Concentration

Alamethicin has been extensively studied as an antimicrobial peptide and is widely used as a simple model for ion channel proteins. It has been shown that the antimicrobial activity of peptides is related to their membrane orientation. In this study, we determined the relationship between the solution concentration of alamethicin and its membrane orientation in lipid bilayers using sum frequency generation (SFG) vibrational spectroscopy. Our SFG results indicated that the alamethicin molecules more or less lay down on the surface of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayers at a low peptide concentration of 0.84 μM; the α-helix segment tilts at about 88°, and 3₁₀-helix segment tilts at about 58° versus the surface normal. However, when the peptide concentration was increased to 15.6 μM, we observed that alamethicin molecules further inserted into the lipid bilayers: the α-helical component changes its orientation to make a 37° tilt from the lipid bilayer normal, and the 3₁₀-helical component tilts at about 50° versus the surface normal. This is in agreement with the barrel-stave mode for the alamethicin-cell membrane interaction as reported previously. Additionally, we have also studied membrane orientation of alamethicin as a function of peptide concentration with SFG. Our results showed that the membrane orientation of the alamethicin α-helical component changed substantially with the increase of the alamethicin concentration, while the membrane orientation of the 3₁₀-helical component remained more or less the same.

Quantitative molecular level understanding of ethoxysilane at poly(dimethylsiloxane)/polymer interfaces

Because of the wide applications of silicone adhesives, it is important to study adhesion mechanisms of silicone elastomers to polymers. Adhesion properties are believed to be directly related to the molecular structures at the adhesive/substrate interfaces. To improve adhesion, adhesion promoters such as silanes are commonly used to modify the interfacial structures. It is difficult to study buried interfacial molecular structures between two materials in situ using conventional analytical techniques. In this study, sum frequency generation (SFG) vibrational spectroscopy was used to investigate molecular structures at buried silicone/poly(ethylene terephthalate) (PET) interfaces. Environmental-friendly epoxysilanes including (3-glycidoxypropyl)triethoxysilane (γ-GPES), (3-glycidoxypropyl)methyldiethoxysilane (γ-GPDES), and (3-glycidoxypropyl)dimethylethoxysilane (γ-GPDMES) and their mixtures with methylvinylsiloxanol (MVS) were used as adhesion promoters to modify silicone adhesion properties to PET. Various PET/silane, PET/uncured silicone, and PET/cured silicone interfaces were examined. The interfacial structures deduced from SFG spectra were correlated to adhesion testing results. It was found that silane headgroup order at the polymer interfaces is an important factor for improving adhesion. The decrease of silane headgroup order due to chemical reaction and disordering of such groups at the polymer interfaces can be associated with improved adhesion. The molecular level understanding on polymer/adhesive interfacial structures helps to design and develop adhesion promoters and polymer adhesives with improved performance.

Elucidation of molecular structures at buried polymer interfaces and biological interfaces using sum frequency generation vibrational spectroscopy

Sum frequency generation (SFG) vibrational spectroscopy has been developed into an important technique to study surfaces and interfaces. It can probe buried interfaces in situ and provide molecular level structural information such as the presence of various chemical moieties, quantitative molecular functional group orientation, and time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the recent progress in SFG studies on interfaces related to polymer materials and biomolecules. The results discussed here demonstrate that SFG can provide important molecular structural information of buried interfaces in situ and in real time, which is difficult to obtain by other surface sensitive analytical techniques.