Overlay databank unlocks data-driven analyses of biomolecules for all.

Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank-a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution.

Rocking motion in solid proteins studied by the 15N proton-decoupled R1ρ relaxometry.

Recently it has been revealed that proteins in solid samples undergo slow overall rocking. The parameters of this motion depend on intermolecular interactions. Therefore, the characterization of the rocking motion enables one to investigate protein-protein interactions. NMR R1ρ relaxometry is the most suitable tool to study slow molecular motions. However, the time scale of the rocking motion is on the edge of the dynamics window of the standard R1ρ experiment, precluding the R1ρ data analysis from being precise and reliable. In this work, we apply a modified R1ρ relaxation method to characterize the slow motion in solids with much higher precision and reliability. The modification is the simultaneous use of a strong 1H-CW pulse and a weak/moderate 15N spin-lock pulse. We demonstrate theoretically and experimentally that under this condition, R1ρ decays have a significantly better signal-to-noise ratio and a much shorter "dead time" caused by the initial oscillations compared to the conventional R1ρ experiment. Moreover, the proton-decoupled R1ρ's can be measured at a much smaller difference between the spin-lock and MAS frequencies; thus, much slower molecular motions can be sampled. The proton decoupling during the 15N spin-lock pulse also suppresses the interfering coherent spin-spin relaxation pathway at low spin-lock fields, which overlaps the Bloch-McConnell (chemical exchange) range of R1ρ dispersions. The proton-decoupled and standard R1ρ experiments were used to study the rocking motion of 15N,2H-enriched protein GB1 in two solid forms, microcrystals and lyophilized amorphous powder. The most striking finding is that the correlation function of this motion consists of two components with very different correlation times, 2-20 µs and a few hundred µs. The rocking motion parameters in microcrystals and powder are quite different, revealing the distinct nature of inter-protein interactions in these two samples.

Cholesterol-like effects of a fluorotelomer alcohol incorporated in phospholipid membranes.

Fluorocarbon amphiphiles are anthropogenic substances widely used in diverse applications such as food packaging, clothing or cookware. Due to their widespread use and non-biodegradability, these chemicals are now ubiquitous in the natural world with high propensity to bioaccumulate in biological membranes, wherein they may affect microscopic properties. Here, we test the hypothesis that a typical fluorocarbon amphiphile can affect lipid membranes similarly to cholesterol by investigating the effect of 1H,1H,2H,2H-perfluoro-1-decanol (8:2 FTOH) on 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes. Using solid-state nuclear magnetic resonance spectroscopy, differential scanning calorimetry and confocal microscopy, we present a consistent set of independent experimental evidences supporting this hypothesis, namely that upon incorporation of 8:2 FTOH, (i) a condensing effect on the acyl chains occurs in the fluid phase, (ii) coexistence of two membrane phases is observed below melting, and (iii) the melting temperature of DPPC varies no more than approximately ±1 °C up to a concentration of 40 mol% of 8:2 FTOH. The condensing effect is quantified by means of advanced dipolar recoupling solid-state NMR experiments and is found to be of approximately half the magnitude of the cholesterol effect at the same concentration.

Effect of cholesterol on the molecular structure and transitions in a clinical-grade lung surfactant extract.

The lipid-protein film covering the interface of the lung alveolar in mammals is vital for proper lung function and its deficiency is related to a range of diseases. Here we present a molecular-level characterization of a clinical-grade porcine lung surfactant extract using a multitechnique approach consisting of [Formula: see text]-[Formula: see text] solid-state nuclear magnetic spectroscopy, small- and wide-angle X-ray scattering, and mass spectrometry. The detailed characterization presented for reconstituted membranes of a lung extract demonstrates that the molecular structure of lung surfactant strongly depends on the concentration of cholesterol. If cholesterol makes up about 11% of the total dry weight of lung surfactant, the surfactant extract adopts a single liquid-ordered lamellar phase, [Formula: see text], at physiological temperatures. This [Formula: see text] phase gradually changes into a liquid-disordered lamellar phase, [Formula: see text], when the temperature is increased by a few degrees. In the absence of cholesterol the system segregates into one lamellar gel phase and one [Formula: see text] phase. Remarkably, it was possible to measure a large set of order parameter magnitudes [Formula: see text] from the liquid-disordered and -ordered lamellar phases and assign them to specific C-H bonds of the phospholipids in the biological extract with no use of isotopic labeling. These findings with molecular details on lung surfactant mixtures together with the presented NMR methodology may guide further development of pulmonary surfactant pharmaceuticals that better mimic the physiological self-assembly compositions for treatment of pathological states such as respiratory distress syndrome.

Applications of Solid-State NMR Spectroscopy for the Study of Lipid Membranes with Polyphilic Guest (Macro)Molecules.

The incorporation of polymers or smaller complex molecules into lipid membranes allows for property modifications or the introduction of new functional elements. The corresponding molecular-scale details, such as changes in dynamics or features of potential supramolecular structures, can be studied by a variety of solid-state NMR techniques. Here, we review various approaches to characterizing the structure and dynamics of the guest molecules as well as the lipid phase structure and dynamics by different high-resolution magic-angle spinning proton and 13C NMR experiments as well as static 31P NMR experiments. Special emphasis is placed upon the incorporation of novel synthetic polyphilic molecules such as shape-persistent T- and X-shaped molecules as well as di- and tri-block copolymers. Most of the systems studied feature dynamic heterogeneities, for instance those arising from the coexistence of different phases; possibilities for a quantitative assessment are of particular concern.

Model-free estimation of the effective correlation time for C-H bond reorientation in amphiphilic bilayers: (1)H-(13)C solid-state NMR and MD simulations.

Molecular dynamics (MD) simulations give atomically detailed information on structure and dynamics in amphiphilic bilayer systems on timescales up to about 1 µs. The reorientational dynamics of the C-H bonds is conventionally verified by measurements of (13)C or (2)H nuclear magnetic resonance (NMR) longitudinal relaxation rates R1, which are more sensitive to motional processes with correlation times close to the inverse Larmor frequency, typically around 1-10 ns on standard NMR instrumentation, and are thus less sensitive to the 10-1000 ns timescale motion that can be observed in the MD simulations. We propose an experimental procedure for atomically resolved model-free estimation of the C-H bond effective reorientational correlation time τe, which includes contributions from the entire range of all-atom MD timescales and that can be calculated directly from the MD trajectories. The approach is based on measurements of (13)C R1 and R1ρ relaxation rates, as well as (1)H-(13)C dipolar couplings, and is applicable to anisotropic liquid crystalline lipid or surfactant systems using a conventional solid-state NMR spectrometer and samples with natural isotopic composition. The procedure is demonstrated on a fully hydrated lamellar phase of 1-palmitoyl-2-oleoyl-phosphatidylcholine, yielding values of τe from 0.1 ns for the methyl groups in the choline moiety and at the end of the acyl chains to 3 ns for the g1 methylene group of the glycerol backbone. MD simulations performed with a widely used united-atom force-field reproduce the τe-profile of the major part of the acyl chains but underestimate the dynamics of the glycerol backbone and adjacent molecular segments. The measurement of experimental τe-profiles can be used to study subtle effects on C-H bond reorientational motions in anisotropic liquid crystals, as well as to validate the C-H bond reorientation dynamics predicted in MD simulations of amphiphilic bilayers such as lipid membranes.

Cholesterol and POPC segmental order parameters in lipid membranes: solid state 1H-13C NMR and MD simulation studies.

The concentration of cholesterol in cell membranes affects membrane fluidity and thickness, and might regulate different processes such as the formation of lipid rafts. Since interpreting experimental data from biological membranes is rather intricate, investigations on simple models with biological relevance are necessary to understand the natural systems. We study the effect of cholesterol on the molecular structure of multi-lamellar vesicles (MLVs) composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a phospholipid ubiquitous in cell membranes, with compositions in the range 0-60 mol% cholesterol. Order parameters, |S(CH)|, are experimentally determined by using (1)H-(13)C solid-state nuclear magnetic resonance (NMR) spectroscopy with segmental detail for all parts of both the cholesterol and POPC molecules, namely the ring system and alkyl chain of the sterol, as well as the glycerol backbone, choline headgroup and the sn-1 and sn-2 acyl chains of POPC. With increasing cholesterol concentration the acyl chains gradually adopt a more extended conformation while the orientation and dynamics of the polar groups are rather unaffected. Additionally, we perform classical molecular dynamics simulations on virtual bilayers mimicking the POPC-cholesterol MLVs investigated by NMR. Good agreement between experiments and simulations is found for the cholesterol alignment in the bilayer and for the |S(CH)| profiles of acyl chains below 15 mol% cholesterol. Deviations occur for the choline headgroup and glycerol backbone parts of POPC, as well as for the phospholipid and cholesterol alkyl chains at higher cholesterol concentrations. The unprecedented detail of the NMR data enables a more complete comparison between simulations and experiments on POPC-cholesterol bilayers and may aid in developing more realistic model descriptions of biological membranes.

Segmental order parameters in a nonionic surfactant lamellar phase studied with 1H-13C solid-state NMR.

A lyotropic nonionic lamellar system composed of pentaethyleneglycol mono n-dodecyl ether and D(2)O was studied using natural abundance (13)C NMR under magic-angle spinning. Applying a two-dimensional recoupling method proposed by Dvinskikh (R-PDLF), (1)H-(13)C dipolar couplings were estimated over a range of temperatures (300-335 K), thus enabling analysis of structural changes in the liquid crystalline system. The results obtained are used to correlate the conformation and mobility of local sites in the surfactant molecule with overall changes in the lamellar structure.

Hyperspherical nuclear motion of H3 + and D3 + in the electronic triplet state, a 3Sigmau +.

The potential energy surface of H(3) (+) in the lowest electronic triplet state, a (3)Sigma(u) (+), shows three equivalent minima at linear nuclear configurations. The vibrational levels of H(3) (+) and D(3) (+) on this surface can therefore be described as superimposed linear molecule states. Owing to such a superposition, each vibrational state characterized by quantum numbers of an isolated linear molecule obtains a one- and a two-dimensional component. The energy splittings between the two components have now been rationalized within a hyperspherical picture. It is shown that nuclear motion along the hyperangle phi mainly accounts for the splittings and provides upper bounds. This hyperspherical motion can be considered an extension of the antisymmetric stretching motion of the individual linear molecule.