Structural Properties of gp41 Fusion Peptide at a Model Membrane Interface

Probing the Molecular Structure and Dynamics of Membrane-Bound Proteins during Misfolding Processes by Sum-Frequency Generation Vibrational Spectroscopy

Protein misfolding and amyloid formation are implicated in the protein dysfunction, but the underlying mechanism remains to be clarified due to the lack of effective tools for detecting the transient intermediates. Sum frequency generation vibrational spectroscopy (SFG-VS) has emerged as a powerful tool for identifying the structure and dynamics of proteins at the interfaces. In this review, we summarize recent SFG-VS studies on the structure and dynamics of membrane-bound proteins during misfolding processes. This paper first introduces the methods for determining the secondary structure of interfacial proteins: combining chiral and achiral spectra of amide A and amide I bands and combining amide I, amide II, and amide III spectral features. To demonstrate the ability of SFG-VS in investigating the interfacial protein misfolding and amyloid formation, studies on the interactions between different peptides/proteins (islet amyloid polypeptide, amyloid β, prion protein, fused in sarcoma protein, hen egg-white lysozyme, fusing fusion peptide, class I hydrophobin SC3 and class II hydrophobin HFBI) and surfaces such as lipid membranes are discussed. These molecular-level studies revealed that SFG-VS can provide a unique understanding of the mechanism of interfacial protein misfolding and amyloid formation in real time, in situ and without any exogenous labeling.

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.

The role of fusion peptides in depth-dependent membrane organization and dynamics in promoting membrane fusion

Membrane fusion is an important event in the life of eukaryotes; occurs in several processes such as endocytosis, exocytosis, cellular trafficking, compartmentalization, import of nutrients and export of waste, vesiculation, inter cellular communication, and fertilization. The enveloped viruses as well utilize fusion between the viral envelope and host cell membrane for infection. The stretch of 20-25 amino acids located at the N-terminus of the fusion protein, known as fusion peptide, plays a decisive role in the fusion process. The stalk model of membrane fusion postulated a common route of bilayer transformation for stalk, transmembrane contact, and pore formation; and fusion peptide is believed to facilitate bilayer transformation to promote membrane fusion. The peptide-induced change in depth-dependent organization and dynamics could provide important information in understanding the role of fusion peptide in membrane fusion. In this review, we have discussed about three depth-dependent properties of the membrane such as rigidity, polarity and heterogeneity, and the impact of fusion peptide on these three membrane properties.

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

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

Quantifying Surfactant Alkyl Chain Orientation and Conformational Order from Sum Frequency Generation Spectra of CH Modes at the Surfactant-Water Interface

We combine second-order nonlinear vibrational spectroscopy and quantum-chemical calculations to quantify the molecular tilt angle and the structural variation of a decanoic acid surfactant monolayer on water. We demonstrate that there is a remarkable degree of delocalization of the vibrational modes along the backbone of the amphiphilic molecule. A simulation-based on modeled sum frequency generation (SFG) spectra offers quantitative insights into the disorder of surfactant monolayers at the water-air interface. It is shown that an average of one gauche defect in the alkyl chain suffices to give rise to the methylene stretch intensity similar in magnitude to the methyl stretch.

Sum frequency generation image reconstruction: aliphatic membrane under spherical cap geometry

The article explores an opportunity to approach structural properties of phospholipid membranes using Sum Frequency Generation microscopy. To establish the principles of sum frequency generation image reconstruction in such systems, at first approach, we may adopt an idealistic spherical cap uniform assembly of hydrocarbon molecules. Quantum mechanical studies for decanoic acid (used here as a representative molecular system) provide necessary information on transition dipole moments and Raman tensors of the normal modes specific to methyl terminal - a typical moiety in aliphatic (and phospholipid) membranes. Relative degree of localization and frequencies of the normal modes of methyl terminals make nonlinearities of this moiety to be promising in structural analysis using Sum Frequency Generation imaging. Accordingly, the article describes derivations of relevant macroscopic nonlinearities and suggests a mapping procedure to translate amplitudes of the nonlinearities onto microscopy image plane according to geometry of spherical assembly, local molecular orientation, and optical geometry. Reconstructed images indicate a possibility to extract local curvature of bilayer envelopes of spherical character. This may have practical implications for structural extractions in membrane systems of practical relevance.

Metadynamics simulation study on the conformational transformation of HhaI methyltransferase: an induced-fit base-flipping hypothesis

DNA methyltransferases play crucial roles in establishing and maintenance of DNA methylation, which is an important epigenetic mark. Flipping the target cytosine out of the DNA helical stack and into the active site of protein provides DNA methyltransferases with an opportunity to access and modify the genetic information hidden in DNA. To investigate the conversion process of base flipping in the HhaI methyltransferase (M.HhaI), we performed different molecular simulation approaches on M.HhaI-DNA-S-adenosylhomocysteine ternary complex. The results demonstrate that the nonspecific binding of DNA to M.HhaI is initially induced by electrostatic interactions. Differences in chemical environment between the major and minor grooves determine the orientation of DNA. Gln237 at the target recognition loop recognizes the GCGC base pair from the major groove side by hydrogen bonds. In addition, catalytic loop motion is a key factor during this process. Our study indicates that base flipping is likely to be an “induced-fit” process. This study provides a solid foundation for future studies on the discovery and development of mechanism-based DNA methyltransferases regulators.

Comparison between the behavior of different hydrophobic peptides allowing membrane anchoring of proteins

Membrane binding of proteins such as short chain dehydrogenase reductases or tail-anchored proteins relies on their N- and/or C-terminal hydrophobic transmembrane segment. In this review, we propose guidelines to characterize such hydrophobic peptide segments using spectroscopic and biophysical measurements. The secondary structure content of the C-terminal peptides of retinol dehydrogenase 8, RGS9-1 anchor protein, lecithin retinol acyl transferase, and of the N-terminal peptide of retinol dehydrogenase 11 has been deduced by prediction tools from their primary sequence as well as by using infrared or circular dichroism analyses. Depending on the solvent and the solubilization method, significant structural differences were observed, often involving α-helices. The helical structure of these peptides was found to be consistent with their presumed membrane binding. Langmuir monolayers have been used as membrane models to study lipid-peptide interactions. The values of maximum insertion pressure obtained for all peptides using a monolayer of 1,2-dioleoyl-sn-glycero-3-phospho-ethanolamine (DOPE) are larger than the estimated lateral pressure of membranes, thus suggesting that they bind membranes. Polarization modulation infrared reflection absorption spectroscopy has been used to determine the structure and orientation of these peptides in the absence and in the presence of a DOPE monolayer. This lipid induced an increase or a decrease in the organization of the peptide secondary structure. Further measurements are necessary using other lipids to better understand the membrane interactions of these peptides.

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.