Specific Ion Interaction Dominates over Hydrophobic Matching Effects in Peptide–Lipid Bilayer Interactions: The Case of Short Peptide

Insertion of short peptides into the cell membrane is energetically unfavorable and challenges the commonly accepted hydrophobic matching principle. Yet there has been evidence that many short peptides can penetrate into the cells to perform the biological functions in salt solution. On the basis of the previous study (J. Phys. Chem. C 2013, 117, 11095−11103), here we further performed a systematic study on the interaction of mastoparan with various neutral lipid bilayers with different lipid chain lengths in situ to examine the hydrophobic matching principle in different aqueous salt environments using sum frequency generation vibrational spectroscopy. It is found that the hydrophobic matching is the dominant driving force for the association of MP with a lipid bilayer in a pure water environment. However, in a kosmotropic ion environment, the hydration of ions can overcome the hydrophobic mismatching effects, leading to the insertion of MP into lipid bilayers with much longer hydrophobic lengths. When the hydrophobic thickness of the bilayer is much longer than MP’s hydrophobic length, MP diffuses on a single monolayer, rather than spanning the bilayer to prevent the exposure of the hydrophilic part of MP to the lipid hydrophobic moiety. Findings from the present study suggest that the interaction between the positively charged choline group of a lipid and kosmotropic ions could be an important step for effective peptide insertion into a cell membrane. Results from our studies will provide an insight into how the short peptides form the ion channel in a thick membrane and offer some ideas for cellular delivery

Phosphate Ions Promoting Association between Peptide and Modeling Cell Membrane Revealed by Sum Frequency Generation Vibrational Spectroscopy

Phosphate ion is one of the most important anions present in the intracellular and extracellular fluid. It can form strongly hydrogen-bonded and salt-bridged complexes with arginine and lysine to activate the voltage gated channel protein. A molecular-level insight into how the phosphate anions mediate the interaction between peptides and cell membrane is critical to understand membrane-bound peptide actions. In this study, sum frequency generation vibrational spectroscopy (SFG-VS) has been applied to characterize interactions between mastoparan (MP, a G-protein-activating peptide) and different charged lipid bilayers in situ. It is found that phosphate ions can greatly promote the association of MP with lipid bilayers and accelerate the conformation transition of membrane-bound MP from aggregation into α-helical structure. In phosphate buffer solution, MP can insert not only into negatively and neutrally charged lipid bilayers but also into positively charged lipid bilayers. In neutrally and negatively charged lipid bilayers, the tilt angle of α-helical structure becomes smaller with increasing buffer concentration, while MP adopts a multiple orientation distribution in the positively charged lipid bilayer. MP interacts with lipid bilayers in the salt solution environment most likely by formation of toroidal pores inside the bilayer matrix. Results from our studies will provide insight into the MP action mechanism and offer some ideas to deliver exogenous protein into the cytosol

Accurate Determination of Interfacial Protein Secondary Structure by Combining Interfacial-Sensitive Amide I and Amide III Spectral Signals

Accurate determination of protein structures at the interface is essential to understand the nature of interfacial protein interactions, but it can only be done with a few, very limited experimental methods. Here, we demonstrate for the first time that sum frequency generation vibrational spectroscopy can unambiguously differentiate the interfacial protein secondary structures by combining surface-sensitive amide I and amide III spectral signals. This combination offers a powerful tool to directly distinguish random-coil (disordered) and α-helical structures in proteins. From a systematic study on the interactions between several antimicrobial peptides (including LKα14, mastoparan X, cecropin P1, melittin, and pardaxin) and lipid bilayers, it is found that the spectral profiles of the random-coil and α-helical structures are well separated in the amide III spectra, appearing below and above 1260 cm^–1, respectively. For the peptides with a straight backbone chain, the strength ratio for the peaks of the random-coil and α-helical structures shows a distinct linear relationship with the fraction of the disordered structure deduced from independent NMR experiments reported in the literature. It is revealed that increasing the fraction of negatively charged lipids can induce a conformational change of pardaxin from random-coil to α-helical structures. This experimental protocol can be employed for determining the interfacial protein secondary structures and dynamics in situ and in real time without extraneous labels

Molecular Binding Sites Are Located Near the Interface of Intrinsic Dynamics Domains (IDDs)

We provide evidence supporting that protein–protein and protein–ligand docking poses are functions of protein shape and intrinsic dynamics. Over sets of 68 protein–protein complexes and 240 nonhomologous enzymes, we recognize common predispositions for binding sites to have minimal vibrations and angular momenta, while two interacting proteins orient so as to maximize the angle between their rotation/bending axes (>65°). The findings are then used to define quantitative criteria to filter out docking decoys less likely to be the near-native poses; hence, the chances to find near-native hits can be doubled. With the novel approach to partition a protein into “domains” of robust but disparate intrinsic dynamics, 90% of catalytic residues in enzymes can be found within the first 50% of the residues closest to the interface of these dynamics domains. The results suggest an anisotropic rather than isotropic distribution of catalytic residues near the mass centers of enzymes

In Situ Molecular-Level Insights into the Interfacial Structure Changes of Membrane-Associated Prion Protein Fragment [118–135] Investigated by Sum Frequency Generation Vibrational Spectroscopy

Protein aggregation is associated with many “protein deposition diseases”. A precise molecular detail of the conformational transitions of such a membrane-associated protein structure is critical to understand the disease mechanism and develop effective treatments. One potential model peptide for studying the mechanism of protein deposition diseases is prion protein fragment [118–135] (PrP118–135), which shares homology with the C-terminal domain of the Alzheimer’s β-amyloid peptide. In this study, sum frequency generation vibrational spectroscopy (SFG-VS) has been applied to characterize interactions between PrP118–135 and 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phospho-(1′-<i>rac</i>-glycerol) (POPG) lipid bilayer in situ. The conformation change and orientation of PrP118–135 in lipid bilayers have been determined using SFG spectra with different polarization combinations. It is found that low-concentration PrP118–135 predominantly adopts α-helical structure but with tiny β-sheet structure. With the PrP118–135 concentration increasing, the molecular number ratio of parallel β-sheet structure increases and reaches about 44% at a concentration of 0.10 mg/mL, indicating the formation of abnormally folded scrapie isoforms. The α-helical structure inserts into the lipid bilayer with a tilt angle of ∼32° versus the surface normal, while the β-sheet structure lies down on the lipid bilayer with the tilt and twist angle both of 90°. The 3300 cm^–1 N–H stretching signal in psp spectra arises from α-helical structure at low PrP concentration and from the β-sheet structure at high PrP concentration. Results from this study will provide an in-depth insight into the early events in the aggregation of PrP in cell membrane

Effect of Dehydration on the Interfacial Water Structure at a Charged Polymer Surface: Negligible χ⁽³⁾ Contribution to Sum Frequency Generation Signal

Interfacial water structure at charged surfaces plays a key role in many physical, chemical, biological, environmental, and industrial processes. Understanding the release of interfacial water from the charged solid surfaces during dehydration process may provide insights into the mechanism of protein folding and the nature of weak molecular interactions. In this work, sum frequency generation vibrational spectroscopy (SFG-VS), supplemented by quartz crystal microbalance (QCM) measurements, has been applied to study the interfacial water structure at polyelectrolyte covered surfaces. Poly­[2-(dimethylamino)­ethyl methacrylate] (PDMAEMA) chains are grafted on solid surfaces to investigate the change of interfacial water structure with varying surface charge density induced by tuning the solution pH. At pH ≤ 7.1, SFG-VS intensity is linear to the loss of mass of interfacial water caused by the dehydration of PDMAEMA chains, and no reorientation of the strongly bonded water molecules is observed in the light of χ_ppp/χ_ssp ratio. χ⁽³⁾ contribution to SFG signal is deduced based on the combination of SFG and QCM results. It is the first direct experimental evidence to reveal that the χ⁽³⁾ has a negligible contribution to SFG signal of the interfacial water at a charged polymer surface

In Situ and Real-Time SFG Measurements Revealing Organization and Transport of Cholesterol Analogue 6‑Ketocholestanol in a Cell Membrane

Cholesterol organization and transport within a cell membrane are essential for human health and many cellular functions yet remain elusive so far. Using cholesterol analogue 6-ketocholestanol (6-KC) as a model, we have successfully exploited sum frequency generation vibrational spectroscopy (SFG-VS) to track the organization and transport of cholesterol in a membrane by combining achiral-sensitive ssp (ppp) and chiral-sensitive psp polarization measurements. It is found that 6-KC molecules are aligned at the outer leaflet of the DMPC lipid bilayer with a tilt angle of about 10°. 6-KC organizes itself by forming an α–β structure at low 6-KC concentration and most likely a β–β structure at high 6-KC concentration. Among all proposed models, our results favor the so-called umbrella model with formation of a 6-KC cluster. Moreover, we have found that the long anticipated flip-flop motion of 6-KC in the membrane takes time to occur, at least much longer than previously thought. All of these interesting findings indicate that it is critical to explore in situ, real-time, and label-free methodologies to obtain a precise molecular description of cholesterol’s behavior in membranes. This study represents the first application of SFG to reveal the cholesterol–lipid interaction mechanism at the molecular level

Observing a Model Ion Channel Gating Action in Model Cell Membranes in Real Time in Situ: Membrane Potential Change Induced Alamethicin Orientation Change

Ion channels play crucial roles in transport and regulatory functions of living cells. Understanding the gating mechanisms of these channels is important to understanding and treating diseases that have been linked to ion channels. One potential model peptide for studying the mechanism of ion channel gating is alamethicin, which adopts a split α/3₁₀-helix structure and responds to changes in electric potential. In this study, sum frequency generation vibrational spectroscopy (SFG-VS), supplemented by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), has been applied to characterize interactions between alamethicin (a model for larger channel proteins) and 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phosphocholine (POPC) lipid bilayers in the presence of an electric potential across the membrane. The membrane potential difference was controlled by changing the pH of the solution in contact with the bilayer and was measured using fluorescence spectroscopy. The orientation angle of alamethicin in POPC lipid bilayers was then determined at different pH values using polarized SFG amide I spectra. Assuming that all molecules adopt the same orientation (a δ distribution), at pH = 6.7 the α-helix at the N-terminus and the 3₁₀-helix at the C-terminus tilt at about 72° (θ₁) and 50° (θ₂) versus the surface normal, respectively. When pH increases to 11.9, θ₁ and θ₂ decrease to 56.5° and 45°, respectively. The δ distribution assumption was verified using a combination of SFG and ATR-FTIR measurements, which showed a quite narrow distribution in the angle of θ₁ for both pH conditions. This indicates that all alamethicin molecules at the surface adopt a nearly identical orientation in POPC lipid bilayers. The localized pH change in proximity to the bilayer modulates the membrane potential and thus induces a decrease in both the tilt and the bend angles of the two helices in alamethicin. This is the first reported application of SFG to the study of model ion channel gating mechanisms in model cell membranes