Search

Diacylglycerol kinases (DGKs) are important enzymes in molecular membrane biology, as they can lower the concentration of diacylglycerol through phosphorylation while at the same time producing phosphatidic acid. Dysfunction of DGK is linked with multiple diseases including cancer and autoimmune disorders. Currently, the high-resolution structures have not been determined for any of the 10 human DGK paralogs, which has made it difficult to gain a more complete understanding of the enzyme's mechanism of action and regulation. In the present study, we have taken advantage of the significant developments in protein structural prediction technology by artificial intelligence (i.e., Alphafold 2.0), to conduct a comprehensive investigation on the properties of all 10 human DGK paralogs. Structural alignment of the predictions reveals that the C1, catalytic, and accessory domains are conserved in their spatial arrangement relative to each other, across all paralogs. This suggests a critical role played by this domain architecture in DGK function. Moreover, docking studies corroborate the existence of a conserved ATP-binding site between the catalytic and accessory domains. Interestingly, the ATP bound to the interdomain cleft was also found to be in proximity of the conserved glycine-rich motif, which in protein kinases has been suggested to function in ATP binding. Lastly, the spatial arrangement of DGK, with respect to the membrane, reveals that most paralogs possess a more energetically favorable interaction with curved membranes. In conclusion, AlphaFold predictions of human DGKs provide novel insights into the enzyme's structural and functional properties while also paving the way for future experimentation.

We consider the impact of phosphatidic acid (namely, 1,2-dioleoyl-sn-glycero-3-phosphate, DOPA) on the properties of a zwitterionic (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC) bilayer used as a model system for protein-free cell membranes. For this purpose, experimental measurements were performed using differential scanning calorimetry and the Langmuir monolayer technique at physiological pH. Moreover, atomistic-scale molecular dynamics (MD) simulations were performed to gain information on the mixed bilayer's molecular organization. The results of the monolayer studies clearly showed that the DPPC/DOPA mixtures are nonideal and the interactions between lipid species change from attractive, at low contents of DOPA, to repulsive, at higher contents of that component. In accordance with these results, the MD simulations demonstrated that both monoanionic and dianionic forms of DOPA have an ordering and condensing effect on the mixed bilayer at low concentrations. For the DOPA monoanions, this is the result of both (i) strong electrostatic interactions between the negatively charged oxygen of DOPA and the positively charged choline groups of DPPC and (ii) conformational changes of the lipid acyl chains, leading to their tight packing according to the so-called "umbrella model", in which large headgroups of DPPC shield the hydrophobic part of DOPA (the conical shape lipid) from contact with water. In the case of the DOPA dianions, cation-mediated clustering was observed. Our results provide a detailed molecular-level description of the lipid organization inside the mixed zwitterionic/PA membranes, which is fully supported by the experimental data.

The Raman scattering and pulsed electron paramagnetic resonance (EPR) of spin-labeled saturated 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and monounsaturated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) phospholipid bilayers in a wide temperature range were studied. Raman spectra in the frequency range of CH2 and C-C stretching vibrations were obtained between 25 and 320 K. The modes sensitive to phospholipid interchain packing, interaction, and intrachain torsional motions (asymmetric CH2 stretching mode at 2880 cm(-1)) as well as conformational states (C-C stretching mode at 1130 cm(-1)) were analyzed. The Raman intensities of these modes significantly depend on the temperature in the gel phase. In the saturated phospholipid DPPC, changes in the temperature dependence of Raman intensities occur near the same temperature for the CH2 and C-C stretching modes, which is approximately 200-230 K. However, in monounsaturated POPC lipids, the temperature dependence for the C-C stretching mode at 1130 cm(-1) reveals a transition near 170 K, and the temperature dependence for the asymmetric CH2 stretching mode transition was near 120 K. For spin-labeled 5-DOXYL- and 16-DOXYL-stearic acids embedded into lipid bilayers, the anisotropic contribution to the electron spin-echo signal decays was interpreted as a result of nanosecond stochastic librations. The decay rates increased remarkably at temperatures above 200 K for DPPC and POPC, which is consistent with the Raman scattering data. A noticeable increase in the libration-induced relaxation rate was observed in POPC lipids above 120 K, and libration-induced relaxation was nearly temperature-independent in DPPC lipids up to 200 K. In the framework of the suggested interpretation, the bilayer structure of monounsaturated lipids contains defective, free volume-like places that provide freedom for phospholipid acyl-tail motions at low temperatures.

Although a minor component of the lipidome, phosphatidic acid (PA) plays a crucial role in nearly all signaling pathways involving cell membranes, in part because of its variable electrical charge in response to environmental conditions. To investigate how charge is regulated in domains of PA, we applied surface-sensitive X-ray reflectivity and fluorescence near-total-reflection techniques to determine the binding of divalent ions (Ca(2+) at various pH values) to 1,2-dimyristoyl-sn-glycero-3-phosphate (DMPA) and to the simpler lipid dihexadecyl phosphate (DHDP) spread as monolayers at the air/water interface. We found that the protonation state of PA is controlled not only by the pK(a) and local pH but also by the strong affinity to PA driven by electrostatic correlations from divalent ions and the cooperative effect of the two dissociable protons, which dramatically enhance the surface charge. A precise theoretical model is presented providing a general framework to predict the protonation state of PA. Implications for recent experiments on charge regulation by hydrogen bonding and the role of pH in PA signaling are discussed in detail.

In this work we have investigated the influence of NaCl on the adsorption of the antimicrobial cationic peptide bactenecin in the monolayer of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) at the air-water interface, as a function of NaCl concentrations in the subphase. We show that the effect of the salt concentration on DPPC monolayers is a monotonic decrease of the liquid-condensed-liquid-expanded (LC-LE) coexistence region. By contrast, the effect of the bactenecin adsorption at the DPPC monolayer not only removed the LC-LE coexistence region plateau, but also shifted the DPPC isotherms to higher pressures and increased the compressibility of the DPPC/bactenecin monolayers with respect to the pure DPPC monolayer around the LC phase. Analysis of the domain structure, obtained by Brewster angle and atomic force microscopes, indicates that the salt concentration in the subphase builds an electrostatic barrier, increasing the rigidity of DPPC monolayers and limiting the bactenecin adsorption at the LC-LE phase coexistence.

We report on mixing an anionic diacyl phospholipid (1,2-dipalmitoyl-sn-glycero-3-phosphate monosodium salt, DPPA) with either monoacyl and diacyl arginine-based surfactants. These mixtures are part of the rich family of pseudo-triple-chain and pseudo-tetra-chain catanionic mixtures, respectively. Vesicle size and zeta-potential were measured at several mixing ratios. Additional information on counterion binding, vesicle size, and integrity was obtained from ion selective electrode and Cryo-TEM measurements. Addition of positively charged surfactants to DPPA results in an increase of vesicle size. However, zeta-potential shows different trends, depending on whether water or acid media are used as solvent. In the latter, zeta-potential values progressively approach 0 upon addition of amino acid based surfactants. In water, surprisingly, zeta-potential values become more negative. The results are discussed in terms of modifications in counterion binding and vesicle size.

The phase behavior of anionic/zwitterionic mixtures can be controlled by tuning the charge state of the anionic lipid. In the case of dioleoylphosphatidic acid (DOPA)/dioleoylphosphatidylcholine (DOPC) mixtures, demixing occurs either when DOPA is protonated or when DOPA(2-):Ca(2+) complexes form. Herein it will be shown that the final end point, a three-phase or two-phase system, depends on the order in which the charge state is manipulated. The facile accessibility of different end points is a clear demonstration of the inherent flexibility of biological systems.

The kinetics and the thermodynamics of melanin concentrating hormone (MCH) adsorption, penetration, and mixing with membrane components are reported. MCH behaved as a surface active peptide, forming stable monolayers at a lipid-free air-water interface, with an equilibrium spreading pressure, a collapse pressure, and a minimal molecular area of 11 mN/m, 13 mN/m, and 140 A (2), respectively. Additional peptide interfacial stabilization was achieved in the presence of lipids, as evidenced by the expansion observed at pi > pi sp in monolayers containing premixtures of MCH with zwitterionic or charged lipids. The MCH-monolayer association and dissociation rate constants were 9.52 x 10 (-4) microM (-1) min (-1) and 8.83 x 10 (-4) min (-1), respectively. The binding of MCH to the dpPC-water interface had a K d = 930 nM at 10 mN/m. MCH penetration in lipid monolayers occurred even up to pi cutoff = 29-32 mN/m. The interaction stability, binding orientation, and miscibility of MCH in monolayers depended on the lipid type, the MCH molar fraction in the mixture, and the molecular packing of the monolayer. This predicted its heterogeneous distribution between different self-separated membrane domains. Our results demonstrated the ability of MCH to incorporate itself into biomembranes and supports the possibility that MCH affects the activity of mechanosensitive membrane proteins through mechanisms unrelated with binding to specific receptors.

A ternary mixture of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl phosphatidic acid (POPA), and cholesterol (CHOL) works effectively for a functional conformation of nicotinic acetylcholine receptor (nAChR) that can undergo agonist-induced conformation changes, but POPC alone can stabilize only a desensitized state of nAChR. To gain insights into the lipid mixture that has strong impact to nAChR functions, we performed more than 50 ns all atom molecular dynamic (MD) simulations at 303 K on a fully hydrated bilayer consisting of 240 POPC, 80 POPA, and 80 CHOL (3:1:1). The MD simulation revealed various interactions between different types of molecular pairs that ultimately regulated lipid organization. The heterogeneous interactions among three different constituents resulted in a broad spectrum of lipid properties, including extensive distributions of average area per lipid and varied lipid ordering as a function of lipid closeness to CHOL. Higher percentage of POPA than POPC had close association with CHOL, which coincided with relatively higher ordering of POPA molecules in their acyl chains near lipid head groups. Lower fraction of gauche dihedrals was also found in the same region of POPA. Although the CHOL molecules had the effects on the enhancement of surrounding lipid order, relatively low lipid order parameters and high fraction of gauche bonds were observed in the ternary mixture. Collectively, these results suggest that the dynamical structure of the ternary system could be determinant for a functional nAChR.

It is shown that the organization of lipid bilayers containing phosphatidic acid (PA) and phosphatidlycholine (PC) can be controlled by altering the monovalent and divalent ion concentrations. At high pH and/or calcium concentration, 1:1 Ca(2+)-PA(2-) complexes form; these complexes demix, and PA-rich and PC-rich regions are observable with epifluorescence microscopy. The results are compared with predictions from electrostatic theory. It is noted that the complex formation correlates in a roughly linear fashion with the monovalent/divalent ion ratio, a parameter that cells adjust.

Phosphatidyl-nucleosides are a class of functional amphiphiles, where a nucleic acid monomer is conjugated to a lipid skeleton. These derivatives self-organize in aqueous solution as assemblies of various size, shape, and interfacial curvature. This paper presents a comparison of the aggregation behavior of different 1-R,2-R-sn-glycero-3-phosphatidyl-nucleosides, where R = 8 (DiC8PN) or R = 12 (DLPN) and N is either adenosine (a purine) or uridine (a pyrimidine), a complementary pair in RNA. Surface tension, small angle neutron scattering, cryo-TEM, and circular dichroism are used to highlight and distinguish the impact of the hydrophobic assembler and of the base substitution on the solution phase behavior. Our main conclusion is that the nucleic functionalization provides an additional parameter to control self-assembly through specific interactions among the polar heads. Further nonideal effects are induced by mixing nucleolipids with complementary base substitution. We show that these contributions alter the aggregation thresholds and modulate properties of the aggregates on the mesoscale.