Adsorption, Folding, and Packing of an Amphiphilic Peptide at the Air/Water Interface

The molecular basis for the increased stability of the FUS-LC fibril at the anionic membrane- and air-water interfaces

Self-organization of biomolecules can lead to the formation of liquid droplets, hydrogels, and irreversible aggregates that bear immense significance in biology and diseases. Despite the considerable number of studies conducted on biomolecular condensation in bulk solution, there is still a lack of understanding of how different surfaces regulate the condensation process. In this context, recent studies showed that, in contrast to zwitterionic lipid membranes, anionic membranes promoted the production of liquid droplets of FUsed in Sarcoma Low Complexity domain (FUS-LC) despite exhibiting no specific protein-lipid interactions. Moreover, the air-water interface led to a solid fibril-like aggregate of FUS-LC. The molecular mechanism of condensation/aggregation of proteins in response to surfaces of various charged states or levels of hydrophobicity remains to be better elucidated. Here, we provide initial insights into this question by investigating the stability of a small β fibril state of FUS-LC in bulk solution vs. membrane- and air-water interfaces. We perform multiple independent molecular dynamics simulations with distinct starting conformations for each system to demonstrate the statistical significance of our findings. Our study demonstrates the stability of the FUS-LC fibril in the presence of anionic membranes on the μs timescale while the fibril falls apart in bulk solution. We observe that a zwitterionic membrane does not enhance the stability of the fibril and 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (DOPS) has a higher propensity to stabilize the fibril than dioleoylphosphatidylglycerol (DOPG), in qualitative agreement with experiments. We further show that the fibril becomes more stable at the air-water interface. We pinpoint interfacial solvation at the membrane- and air-water interfaces as a key factor that contributes to the stabilization of the peptide assembly.

Complex role of chemical nature and tacticity in the adsorption free energy of carboxylic acid polymers at the oil-water interface: molecular dynamics simulations

Scientific understanding of the molecular structure and adsorption of polymers at oil-water liquid interfaces is very limited. In this study the adsorption free energy at the oil (CCl4)-water interface was estimated using umbrella sampling molecular dynamics simulations for six carboxylate type vinyl polymers differing in hydrophobic nature and tacticity: isotactic and syndiotactic poly(acrylic acid) (i-PAA, s-PAA), isotactic and syndiotactic poly(methacrylic acid) (i-PMA, s-PMA), and atactic and syndiotactic poly(ethylacrylic acid) (a-PEA, s-PEA). ΔGads values are in the order i-PMA < a-PEA < s-PEA < s-PAA < i-PAA < s-PMA. The results show the significant and complex influence of the chemical nature as well as tacticity of the polymer on its adsorption free energy as related to hydrogen bonding and orientation of bonds with respect to oil and water phases. The influence of tacticity is found to be the highest for PMA, which is interpreted to occur due to the balance between interactions among side groups and those occurring between side groups and solvent. Interactions between side-groups are crucial for determining the conformation of PAA (most hydrophilic) and the solvation of the side-group in water is crucial for determining the conformation of PEA (most hydrophobic). The adsorption of PMA represents the transition between these two dominating effects. The molecular contributions to the enthalpy of adsorption indicate that adsorption is favored mainly through two interactions: polymer-CCl4 and water-water.

Molecular Dynamics Simulation of Protein Biosurfactants

Surfaces and interfaces are ubiquitous in nature and are involved in many biological processes. Due to this, natural organisms have evolved a number of methods to control interfacial and surface properties. Many of these methods involve the use of specialised protein biosurfactants, which due to the competing demands of high surface activity, biocompatibility, and low solution aggregation may take structures that differ from the traditional head–tail structure of small molecule surfactants. As well as their biological functions, these proteins have also attracted interest for industrial applications, in areas including food technology, surface modification, and drug delivery. To understand the biological functions and technological applications of protein biosurfactants, it is necessary to have a molecular level description of their behaviour, in particular at surfaces and interfaces, for which molecular simulation is well suited to investigate. In this review, we will give an overview of simulation studies of a number of examples of protein biosurfactants (hydrophobins, surfactin, and ranaspumin). We will also outline some of the key challenges and future directions for molecular simulation in the investigation of protein biosurfactants and how this can help guide future developments.

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

Understanding the structure of proteins at surfaces is key in fields such as biomaterials research, biosensor design, membrane biophysics, and drug design. A particularly important factor is the orientation of proteins when bound to a particular surface. The orientation of the active site of enzymes or protein sensors and the availability of binding pockets within membrane proteins are important design parameters for engineers developing new sensors, surfaces, and drugs. Recently developed methods to probe protein orientation, including immunoessays and mass spectrometry, either lack structural resolution or require harsh experimental conditions. We here report a new method to track the absolute orientation of interfacial proteins using phase-resolved sum frequency generation spectroscopy in combination with molecular dynamics simulations and theoretical spectral calculations. As a model system we have determined the orientation of a helical lysine-leucine peptide at the air-water interface. The data show that the absolute orientation of the helix can be reliably determined even for orientations almost parallel to the surface.

Structure Formation in Langmuir Peptide Films As Revealed from Coarse-Grained Molecular Dynamics Simulations

Molecular dynamics simulations in conjunction with the Martini coarse-grained model have been used to investigate the (nonequilibrium) behavior of helical 22-residue poly(γ-benzyl-l-glutamate) (PBLG) peptides at the water/vapor interface. Preformed PBLG mono- or bilayers homogeneously covering the water surface laterally collapse in tens of nanoseconds, exposing significant proportions of empty water surface. This behavior was also observed in recent AFM experiments at similar areas per monomer, where a complete coverage had been assumed in earlier work. In the simulations, depending on the area per monomer, either elongated clusters or fibrils form, whose heights (together with the portion of empty water surface) increase over time. Peptides tend to align with respect to the fiber axis or with the major principal axis of the cluster, respectively. The aspect ratio of the cluster observed is 1.7 and, hence, comparable to though somewhat smaller than the aspect ratio of the peptides in α-helical conformation, which is 2.2. The heights of the fibrils is 3 nm after 20 ns and increases to 4.5 nm if the relaxation time is increased by 2 orders of magnitude, in agreement with the experiment. Aggregates with heights of about 3 or 4.5 nm are found to correspond to local bi- or trilayer structures, respectively.

Assembly of Huntingtin headpiece into α-helical bundles

Protein aggregation is a hallmark of neurodegenerative disorders. In this group of brain-related disorders, a disease-specific "host" protein or fragment misfolds and adopts a metastatic, aggregate-prone conformation. Often, this misfolded conformation is structurally and thermodynamically different from its native state. Intermolecular contacts, which arise in this non-native state, promote aggregation. In this regard, understanding the molecular principles and mechanisms that lead to the formation of such a non-native state and further promote the formation of the critical nucleus for fiber growth is essential. In this study, the authors analyze the aggregation propensity of Huntingtin headpiece (htt^NT), which is known to facilitate the polyQ aggregation, in relation to the helix mediated aggregation mechanism proposed by the Wetzel group. The authors demonstrate that even though htt^NT displays a degenerate conformational spectrum on its own, interfaces of macroscopic or molecular origin can promote the α-helix conformation, eliminating all other alternatives in the conformational phase space. Our findings indicate that htt^NT molecules do not have a strong orientational preference for parallel or antiparallel orientation of the helices within the aggregate. However, a parallel packed bundle of helices would support the idea of increased polyglutamine concentration, to pave the way for cross-β structures.

Peptide self-assembly: thermodynamics and kinetics

Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.

Conformation and Aggregation of LKα14 Peptide in Bulk Water and at the Air/Water Interface

Historically, the protein folding problem has mainly been associated with understanding the relationship between amino acid sequence and structure. However, it is known that both the conformation of individual molecules and their aggregation strongly depend on the environmental conditions. Here, we study the aggregation behavior of the model peptide LKα14 (with amino acid sequence LKKLLKLLKKLLKL) in bulk water and at the air/water interface. We start by a quantitative analysis of the conformational space of a single LKα14 in bulk water. Next, in order to analyze the aggregation tendency of LKα14, by using the umbrella sampling technique we calculate the potential of mean force for pulling a single peptide from an n-molecule aggregate. In agreement with the experimental results, our calculations yield the optimal aggregate size as four. This equilibrium state is achieved by two opposing forces: Coulomb repulsion between the lysine side chains and the reduction of solvent accessible hydrophobic surface area upon aggregation. At the vacuum/water interface, however, even dimers of LKα14 become marginally stable, and any larger aggregate falls apart instantaneously. Our results indicate that even though the interface is highly influential in stabilizing the α-helix conformation for a single molecule, it significantly reduces the attraction between two LKα14 peptides, along with their aggregation tendency.