Structure of pulmonary surfactant membranes and films: The role of proteins and lipid–protein interactions

The pulmonary surfactant system constitutes an excellent example of how dynamic membrane polymorphism governs some biological functions through specific lipid–lipid, lipid–protein and protein–protein interactions assembled in highly differentiated cells. Lipid–protein surfactant complexes are assembled in alveolar pneumocytes in the form of tightly packed membranes, which are stored in specialized organelles called lamellar bodies (LB). Upon secretion of LBs, surfactant develops a membrane-based network that covers rapidly and efficiently the whole respiratory surface. This membrane-based surface layer is organized in a way that permits efficient gas exchange while optimizing the encounter of many different molecules and cells at the epithelial surface, in a cross-talk essential to keep the whole organism safe from potential pathogenic invaders.The present review summarizes what is known about the structure of the different forms of surfactant, with special emphasis on current models of the molecular organization of surfactant membrane components. The architecture and the behaviour shown by surfactant structures in vivo are interpreted, to some extent, from the interactions and the properties exhibited by different surfactant models as they have been studied in vitro, particularly addressing the possible role played by surfactant proteins. However, the limitations in structural complexity and biophysical performance of surfactant preparations reconstituted in vitro will be highlighted in particular, to allow for a proper evaluation of the significance of the experimental model systems used so far to study structure–function relationships in surfactant, and to define future challenges in the design and production of more efficient clinical surfactants.     

Control and role of pH in peptide–lipid interactions in oriented membrane samples

To understand the molecular mechanisms of amphiphilic membrane-active peptides, one needs to study their interactions with lipid bilayers under ambient conditions. However, it is difficult to control the pH of the sample in biophysical experiments that make use of mechanically aligned multilamellar membrane stacks on solid supports. HPLC-purified peptides tend to be acidic and can change the pH in the sample significantly. Here, we have systematically studied the influence of pH on the lipid interactions of the antimicrobial peptide PGLa embedded in oriented DMPC/DMPG bilayers. Using solid-state NMR (³¹P, ²H, ¹⁹F), both the lipid and peptide components were characterized independently, though in the same oriented samples under typical conditions of maximum hydration. The observed changes in lipid polymorphism were supported by DSC on multilamellar liposome suspensions. On this basis, we can present an optimized sample preparation protocol and discuss the challenges of performing solid-state NMR experiments under controlled pH. DMPC/DMPG bilayers show a significant up-field shift and broadening of the main lipid phase transition temperature when lowering the pH from 10.0 to 2.6. Both, strongly acidic and basic pH, cause a significant degree of lipid hydrolysis, which is exacerbated by the presence of PGLa. The characteristic re-alignment of PGLa from a surface-bound to a tilted state is not affected between pH of 7 to 4 in fluid bilayers. On the other hand, in gel-phase bilayers the peptide remains isotropically mobile under acidic conditions, displays various co-existing orientational states at pH 7, and adopts an unknown structural state at basic pH.     

Electrostatic and hydrophobic interactions of lipid-associated α-synuclein: The role of a water-limited interfaces in amyloid fibrillation

Human α‑synuclein (αSyn) is an intrinsically disordered protein (IDP) whose biological and pathological functions in brain neuronal cells have not yet been fully elucidated. αSyn intrinsically participates in aiding neurotransmitter trafficking through αSyn the association with lipid membranes. However, lipid-associated states of αSyn also induce amyloid self-assembly that is linked to the pathogenesis of various synucleinopathies. These contradicting actions arise from the limited water content near lipid-water interfaces that controls αSyn electrostatic and hydrophobic interactions. Thus, understanding the molecular interactions between αSyn and lipid membranes in the presence of water molecules is critical in elucidating the pivotal role of lipid-associated αSyn in amyloid self-assembly. In this review, we describe how the membrane interface controls electrostatic and hydrophobic interactions of lipid-associated αSyn. Moreover, membrane amyloid self-assembly of αSyn will be further discussed with regards to the structural dynamics of lipid-associated αSyn and water molecules near the interface.     

Detection of lipid–protein microdomains (rafts) and investigation of their functional role in the chloroplast membranes of halophytes

To study the characteristics of the structure and the functional role of chloroplast membranes of halophytes with different salt tolerance strategy, raft structures were isolated. Lipid analysis data provided evidence for the presence of rafts in the chloroplast membranes. The discovered significant differences in the content of raft-forming lipids in different halophytes suggest a relationship between the functions of rafts and the mechanisms of salt tolerance in plants.     

Development of stapled short helical peptides capable of inhibiting vitamin D receptor (VDR)–coactivator interactions

We synthesized stapled helical leucine-based peptides (DPI-01-07) containing 2-aminoisobutyric acid and a covalent cross-linked unit as inhibitors of vitamin D receptor (VDR)–coactivator interactions. The effects of these peptides on the human VDR were examined in an inhibition assay based on the receptor cofactor assay system, and one of them, DPI-07, exhibited potent inhibitory activity (IC₅₀: 3.2 μM).     

The interaction of amyloid Aβ(1-40) with lipid bilayers and ganglioside as studied by P solid-state NMR

Amyloid β-peptide (Aβ) is a major component of plaques in Alzheimer's disease, and formation of senile plaques has been suggested to originate from regions of neuronal membrane rich in gangliosides. We analyzed the mode of interaction of Aβ with lipid bilayers by multinuclear NMR using ³¹P nuclei. We found that Aβ (1-40) strongly perturbed the bilayer structure of dimyristoylphosphatidylcholine (DMPC), to form a non-lamellar phase (most likely micellar). The ganglioside GM1 potentiated the effect of Aβ (1-40), as viewed from ³¹P NMR. The difference of the isotropic peak intensity between DMPC/Aβ and DMPC/GM1/Aβ suggests a specific interaction between Aβ and GM1. We show that in the DMPC/GM1/Aβ system there are three lipid phases, namely a lamellar phase, a hexagonal phase and non-oriented lipids. The latter two phases are induced by the presence of the Aβ peptide, and facilitated by GM1.     

Design,synthesis and interaction of BRC4 analogous peptides with RAD51(241–260)

Amino Acids - Breast cancer susceptibility gene 2 (BRCA2) is an important tumor suppressor, which is participated in repair of damaged DNA by its highly conserved BRC repeat motifs regulating RAD51...     

Predator–prey interactions and the cannibalism of larvae of Armigeres subalbatus (Diptera: Culicidae)

Predation and cannibalism can affect the co-existence of mosquito species or the assemblage of mosquito species (i.e., community structure). In this study, predatory feeding patterns and cannibalism of larvae of Armigeres subalbatus mosquitoes were quantified under laboratory conditions using Aedes albopictus and Culex uniformis larvae as prey organisms. Rate of consumption of prey larvae and the rate of cannibalism of 1st to 4th instar larvae of Armigeres subalbatus were reported at 24 h intervals with and without alternative food supplement. Both the 3rd and 4th instar larvae of Ar. subalbatus showed a substantial predation on the larvae of Ae. albopictus (33.6 ± 4.4) and Cx uniformis (47.3 ± 7.6). The cannibalism of the predatory larvae was strongly correlated to the larval density (r = 0.9). The predator and the prey density and the given food type were significant factors that determined the rate of pupation, death and the emergence as adults. A significant relationship was shown for the co-occurrence of predatory larvae and the prey larvae at the 85 natural breeding habitats observed at the field (χ² = 74.4, p < 0.001). Nine breeding sites (10.6%) were positive for both prey and predatory larvae. Our study showed robust information about the predatory and cannibalistic behavior of Ar. subalbatus larvae emphasizing their role in managing the population structure of mosquito communities.     

Hydrophobic matching controls the tilt and stability of the dimeric platelet-derived growth factor receptor (PDGFR) β transmembrane segment

The platelet-derived growth factor receptor β is a member of the cell surface receptor tyrosine kinase family and dimerizes upon activation. We determined the structure of the transmembrane segment in dodecylphosphocholine micelles by liquid-state NMR and found that it forms a stable left-handed helical dimer. Solid-state NMR and oriented circular dichroism were used to measure the tilt angle of the helical segments in macroscopically aligned model membranes with different acyl chain lengths. Both methods showed that decreasing bilayer thickness (DEPC-POPC-DMPC) led to an increase in the helix tilt angle from 10° to 30° with respect to the bilayer normal. At the same time, reconstitution of the comparatively long hydrophobic segment became less effective, eventually resulting in complete protein aggregation in the short-chain lipid DLPC. Unrestrained molecular dynamics simulations of the dimer were carried out in explicit lipid bilayers (DEPC, POPC, DMPC, sphingomyelin), confirming the observed dependence of the helix tilt angle on bilayer thickness. Notably, molecular dynamics revealed that the left-handed dimer gets tilted en bloc, whereas conformational transitions to alternative (e.g. right-handed dimeric) states were not supported. The experimental data along with the simulation results demonstrate a pronounced interplay between the platelet-directed growth factor receptor β transmembrane segment and the bilayer thickness. The effect of hydrophobic mismatch might play a key role in the redistribution and activation of the receptor within different lipid microdomains of the plasma membrane in vivo.     

Pathogen–pathogen interactions: a comparative study of Escherichia coli interactions with the clinical and environmental isolates of Acanthamoeba

In this study, we compared the interactions of invasive and non-invasive strains of E. coli with clinical and environmental isolates of Acanthamoeba. The environmental isolate of Acanthamoeba exhibited significantly higher association with E. coli compared with the clinical isolates of Acanthamoeba. The ratio of E. coli per amoebae was more than 8-fold higher in the environmental isolate compared with the clinical isolates of Acanthamoeba. Interestingly, non-pathogenic environmental Acanthamoeba showed uptake and/or survival of the non-invasive E. coli. In contrast, clinical isolates of Acanthamoeba did not support uptake and/or survival of non-invasive E. coli. Using several mutants derived from K1, we demonstrated that outer membrane protein A (OmpA) and lipopolysaccharide (LPS) are crucial bacterial determinants responsible for E. coli K1 interactions and in the intracellular survival of E. coli in Acanthamoeba. The use of Acanthamoeba as a model to study E. coli K1 pathogenesis and to understand bacterial immune evasion strategies is discussed further.     

Habitat complexity modifies ant–parasitoid interactions: implications for community dynamics and the role of disturbance

Species must balance effective competition with avoidance of mortality imposed by predators or parasites to coexist within a local ecological community. Attributes of the habitat in which species interact, such as structural complexity, have the potential to affect how species balance competition and mortality by providing refuge from predators or parasites. Disturbance events such as fire can drastically alter habitat complexity and may be important modifiers of species interactions in communities. This study investigates whether the presence of habitat complexity in the form of leaf litter can alter interactions between the behaviorally dominant host ants Pheidole diversipilosa and Pheidole bicarinata, their respective specialist dipteran parasitoids (Phoridae: Apocephalus sp. 8 and Apocephalus sp. 25) and a single species of ant competitor (Dorymyrmex insanus). We used a factorial design to manipulate competition (presence/absence of competitors), mortality risk (presence/absence of parasitoids) and habitat complexity (presence/absence of leaf litter). Parasitoid presence reduced soldier caste foraging, but refuge from habitat complexity allowed increased soldier foraging in comparison to treatments in which no refuge was available. Variation in soldier foraging behavior correlated strongly with foraging success, a proxy for colony fitness. Habitat complexity allowed both host species to balance competitive success with mortality avoidance. The effect of fire on habitat complexity was also studied, and demonstrated that the immediate negative impact of fire on habitat complexity can persist for multiple years. Our findings indicate that habitat complexity can increase dominant host competitive success even in the presence of parasitoids, which may have consequences for coexistence of subordinate competitors and community diversity in general.     

Differing modes of interaction between monomeric Aβ(1-40) peptides and model lipid membranes: an AFM study

Membrane interactions with β-amyloid peptides are implicated in the pathology of Alzheimer's disease and cholesterol has been shown to be key modulator of this interaction, yet little is known about the mechanism of this interaction. Using atomic force microscopy, we investigated the interaction of monomeric Aβ(1-40) peptides with planar mica-supported bilayers composed of DOPC and DPPC containing varying concentrations of cholesterol. We show that below the bilayer melting temperature, Aβ monomers adsorb to, and assemble on, the surface of DPPC bilayers to form layers that grow laterally and normal to the bilayer plane. Above the bilayer melting temperature, we observe protofibril formation. In contrast, in DOPC bilayers, Aβ monomers exhibit a detergent-like action, forming defects in the bilayer structure. The kinetics of both modes of interaction significantly increases with increasing membrane cholesterol content. We conclude that the mode and rate of the interaction of Aβ monomers with lipid bilayers are strongly dependent on lipid composition, phase state and cholesterol content.     

Synthesis and properties of (2-pyridyl)alkylamine- and (2-pyridyl)alkylamine–amide-coordinated copper(II) complexes: Structures and non-covalent interactions

Reaction of the ligand N-methyl-N-((6-pivaloylamido-2-pyridyl)methyl)-N-(2-pyridylethyl)amine (mpppa) with equimolar amounts of [Cu(H₂O)₆][ClO₄]₂ or CuCl₂ · 2H₂O in MeCN afforded mononuclear copper(II) complexes [Cu(mpppa)][ClO₄]₂ (1) and [Cu(mpppa)Cl₂] (2). Crystal structure analysis reveals CuN₃O (two pyridyl, an aliphatic amine, and an amide oxygen) coordination in 1 and CuN₃Cl₂ (two pyridyl, an aliphatic amine, and two chlorides) coordination in 2. Crystal packing diagram of 1 reveals that one of the perchlorate counteranions provides weak coordination to copper(II) centers and in turn the copper(II) centers assume pseudo-six-coordination, generating 1D chain. Notably, one of the copper(II)-coordinated chloride ions in 2 participates in an intramolecular N–H?Cl interaction. Intermolecular C–H?Cl interactions in the solid state generate helical structure. Spectroscopic (IR, UV–Vis, and EPR) and redox properties of the two complexes have been investigated and compared.     

Combined Hepatocellular–Cholangiocarcinoma with Fever of Unknown Origin: A Case Report and Review of Literature

Combined hepatocellular carcinoma and cholangiocarcinoma (cHCC–CC) is a rare form of primary liver cancer (PLC). It is difficult to make a correct preoperative diagnosis of cHCC–CC because of the lack of special features of the disease. We here present a case of a 68-year-old man who presented with fluctuant fever, chills, and sweating and was eventually diagnosed as cHCC–CC after surgery. The tumor was 6.0 cm in diameter with distinct borders and no satellite lesions or lymph nodes were observed during macroscopic examination of the resection specimen. The fever resolved in the postoperative period till the 28th day after surgery, when the patient developed extensive abdominal metastases and died shortly after. More attention should be paid to the patient with PLC showing abnormal features such as FUO, normal range of tumor markers, atypical imaging, and less cirrhosis. Hepatic resection is the treatment of choice although with short-term outcomes.     

Structural dynamics and interactions of Xeroderma pigmentosum complementation group A (XPA98–210) with damaged DNA

Nucleotide excision repair (NER) in higher organisms repair massive DNA abrasions caused by ultraviolet rays, and various mutagens, where Xeroderma pigmentosum group A (XPA) protein is known to be involved in damage recognition step. Any mutations in XPA cause classical Xeroderma pigmentosum disease. The extent to which XPA is required in the NER is still unclear. Here, we present the comparative study on the structural and conformational changes in globular DNA binding domain of XPA_98–210 in DNA bound and DNA free state. Atomistic molecular dynamics simulation was carried out for both XPA_98–210 systems using AMBER force fields. We observed that XPA_98–210 in presence of damaged DNA exhibited more structural changes compared to XPA_98–210 in its free form. When XPA is in contact with DNA, we found marked stability of the complex due to the formation of characteristic longer antiparallel β-sheets consisting mainly lysine residues.     

Protein–DNA/RNA interactions: Machine intelligence tools and approaches in the era of artificial intelligence and big data

With the development of artificial intelligence (AI) technologies and the availability of large amounts of biological data, computational methods for proteomics have undergone a developmental process from traditional machine learning to deep learning. This review focuses on computational approaches and tools for the prediction of protein – DNA/RNA interactions using machine intelligence techniques. We provide an overview of the development progress of computational methods and summarize the advantages and shortcomings of these methods. We further compiled applications in tasks related to the protein – DNA/RNA interactions, and pointed out possible future application trends. Moreover, biological sequence-digitizing representation strategies used in different types of computational methods are also summarized and discussed.     

Structural stability of soybean (Glycine max) α-amylase: properties of the unfolding transition studied with fluorescence and CD spectroscopy

Stability and unfolding of mammalian and microbial α-amylases have been intensively investigated. However, there is only limited information available on the structural stability of plant α-amylases, namely of the two isoenzymes from barley AMY1 and AMY2, of the α-amylase from mung bean (Vigna radiata), and of the α-amylase from malted sorghum (Sorghum bicolor). We report here the stability of soyabean α-amylase (GMA), against elevated temperatures and chemical denaturants (GndHCl) by employing circular dichroism and fluorescence spectroscopy. Since it is well-known that calcium ions play a crucial role for enzymatic activity and stability of a-amylases, we performed our studies with calcium bound and calcium free GMA. The thermal unfolding transition temperature decreased from 72°C for calcium saturated samples to 57°C for the case of calcium depleted GMA. Similarly, the GndHCl transition concentration was lowered from 0.70 M for calcium bound GMA to 0.41 M in the absence of calcium. Thermal unfolding of GMA irreversible due to aggregation of the unfolded state. GMA unfolded in 6 M GndHCl shows high degree of reversibility after diluting the unfolded enzyme in native buffer containing 7 M glycerol. Furthermore, the refolded enzyme showed 93% of activity.