Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations

Peptides or proteins containing small biomolecular aggregates, such as micelles, bicelles, droplets and nanodiscs, are pivotal in many fields ranging from structural biology to pharmaceutics. Monitoring dynamics of such systems has been limited by the lack of experimental methods that could directly detect their fast (picosecond to nanosecond) timescale dynamics. Spin relaxation times from NMR experiments are sensitive to such motions, but their interpretation for biomolecular aggregates is not straightforward. Here we show that the dynamic landscape of peptide-containing molecular assemblies can be determined by a synergistic combination of solution state NMR experiments and molecular dynamics (MD) simulations. Solution state NMR experiments are straightforward to implement without an excessive amount of sample, while direct combination of spin relaxation data to MD simulations enables interpretation of dynamic landscapes of peptides and other aggregated molecules. To demonstrate this, we interpret NMR data from transmembrane, peripheral, and tail anchored peptides embedded in micelles. Our results indicate that peptides and detergent molecules do not rotate together as a rigid body, but peptides rotate in a viscous medium composed of detergent micelle. Spin relaxation times also provide indirect information on peptide conformational ensembles. This work gives new perspectives on peptide dynamics in complex biomolecular assemblies.

Physicochemical characterization of green sodium oleate-based formulations. Part 3. Molecular and collective dynamics in rodlike and wormlike micelles by proton nuclear magnetic resonance relaxation

HYPOTHESIS

Sodium oleate (NaOL) self-aggregates in water forming rodlike micelles with different length depending on NaOL concentration; when KCl is added wormlike micelles form, which entangle giving rise to a viscoelastic dispersion. It is expected that aggregates with different size and shape exhibit different internal and overall molecular motions and collective dynamics.

EXPERIMENTS

Two low viscosity NaOL/water and two viscoelastic NaOL/KCl/water formulations with different NaOL concentration (0.23 and 0.43 M) were investigated by ¹H fast field cycling NMR relaxometry over broad temperature and Larmor frequency ranges, after a first screening by ¹H and ¹³C NMR spectroscopy at high frequency.

FINDINGS

The analysis of the collected data indicated that fast conformational isomerization and rotation of NaOL about its long molecular axis and lateral diffusion of NaOL around the axis of the cylindrical aggregates are slightly affected by the aggregate shape and length. On the other hand, fluctuations of the local order director are quite different in the fluid and viscoelastic systems, reflecting the shape and size of the aggregates. Quantitative information was obtained on activation energy for fast internal and overall motions, correlation times and activation energy for lateral diffusion, and coherence length for collective order fluctuations.

Dynamic Landscape in Self-Assembled Surfactant Aggregates

A process in which a disordered system of pre-existing molecules generates an organized structure through specific, local interactions among the molecules themselves is termed molecular self-assembly. Micelles, microemulsions, and vesicles are examples of such self-assembled systems where amphiphilic molecules are involved. As the functional properties of these systems (such as wetting and emulsification, release of solubilized drugs, etc.) are dictated by the dynamic behavior of the surfactants at the molecular level, it is of immense interest to investigate these systems for the same. The dynamics in soft matter systems is quite complex, involving different time and length scales. We used a combination of neutron scattering and molecular dynamics simulation studies in probing the dynamic landscape in various self-assembled surfactant aggregates. Neutron scattering experiments were carried out using several spectrometers covering a wide dynamic range to probe motions on different time scales. The interaction between the surfactants can be varied by changing the molecular architecture, counterion concentration, temperature, and so forth. It is important to study the effect of these parameters on the dynamics of surfactants in these aggregates. We have carried out experiments on various ionic (anionic as well as cationic) micelles with varied counterion concentrations, vesicles, and lipid bilayers to unravel the complex dynamic features present in these systems. In this feature article, we will discuss some important results of our recent work on dynamics in these self-assembled surfactant aggregates.

Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules.

Effects of Hydrotropic Salt on the Nanoscopic Dynamics of DTAB Micelles

Effects of a hydrotropic salt, sodium salicylate (NaSal), on the dynamic behavior of cationic dodecyltrimethylammonium bromide (DTAB) micelles as studied using dynamic light scattering (DLS) and quasielastic neutron scattering (QENS) techniques are reported here. DLS study showed that the addition of NaSal leads to a decrease in the apparent diffusion coefficient of the whole micelle indicating micellar growth. QENS data analysis suggested that observed dynamics involves two distinct motions, lateral motion of the surfactant over the curved micellar surface and localized segmental motion of the surfactant. It is found that the addition of NaSal slows down the lateral motion of DTAB while the localized segmental motion of the DTAB chain is not affected much. An atomistic molecular dynamics (MD) simulation was performed to gain further insight into the underlying phenomena. MD simulation results are found to be consistent with the experimental observations. MD simulation revealed that location of the salicylate ions on the micellar surface and their strong electrostatic association with their oppositely charged surfactant headgroup are the major factors in slowing down the lateral motion of the DTAB molecule. In the present work, a quantitative description of the effects of NaSal on the nanoscopic dynamics of DTAB micelles and its correlation with the microstructure of the micelle is provided.

Dynamics in anionic micelles: effect of phenyl ring

Micellar dynamics in sodium dodecyl benzene sulfonate (SDBS) is studied using quasi-elastic neutron scattering (QENS) technique. Results are compared with sodium dodecyl sulfate (SDS), a very similar surfactant except for the presence of a phenyl ring in SDBS. SDBS is a very important system for various industrial usages and variety of other applications. The aim here is to investigate the effect of molecular architecture of the surfactant molecule on micellar dynamics. Analysis of the QENS data showed that there exists two distinct motions in both of the micellar systems: whole micellar motion or global motion and the internal motion of the monomer within the micelles. The global diffusion associated with the whole micelle is found to be Fickian in nature. The diffusion coefficient corresponding to the global motion is found to be significantly lower for SDBS than SDS micelles. As far as internal motion is concerned, the structure factor indicates that the alkyl chains are more flexible in SDS compared with SDBS. Similar behavior is also reported in a recent molecular-dynamics simulation study. Detailed analysis showed that a localized translational diffusion model in which the hydrogen atoms undergo diffusion within a sphere could describe the internal motions in both the micelles. Diffusion coefficients corresponding to internal motions is found to be lower in the case of SDBS micelles compared with SDS micelles, implying that internal motions in SDBS micelles are relatively hindered vis-a-vis SDS micelles. This could be understood in terms of denser packing in SDBS micelles due to the presence of π-stacking.

Dynamical features in cationic micelles of varied chain length

Chain length is one of the parameters controlling the structural arrangement of micelle monomers, such that one can tailor the monomers for different applications, but the effect of chain length on the dynamical behavior of micelles is unknown. In this article, we report a study on the effect of varying chain length on the dynamical behavior of alkyltrimethylammonium bromide (C(n)TAB) micelles (n = 10, 12, 14, and 16) using incoherent quasielastic neutron scattering (QENS). The data analysis clearly shows the presence of two distinct motions: global motion of whole micelles and faster internal motions of the C(n)TAB monomers. The global diffusion is Fickian in nature, whereas the internal motions can be described with a model that considers the motions of the headgroup and the hydrophobic alkyl chain separately. Methyl groups in the headgroup undergo 3-fold jump rotations, and the hydrogen atoms belonging to the alkyl chain undergo localized translational diffusion. The hydrogen atoms belonging to the alkyl chain are confined within spherical volumes that increase linearly along the C(n)TAB chain: the hydrogen atoms closer to the headgroup move within smaller spheres with lower diffusion coefficients than those farther from the headgroup. The main result is that, with increasing chain length, the dynamics of the C(n)TAB monomer is greatly affected: diffusion is reduced and occurs in smaller spheres, and residence times are increased. Global motion is also hindered with increased chain length.

Internal dynamics in SDS micelles: neutron scattering study

The molecular dynamics of sodium dodecyl sulfate (SDS) micelle has been investigated using high-resolution incoherent quasielastic neutron scattering technique. Data analysis clearly shows presence of two distinct motions: whole micellar motion or global diffusion and faster internal motion of the SDS monomer. The global diffusion associated with the whole micelle is found to be Fickian in nature, and the corresponding diffusion coefficients are found to be consistent with those obtained from dynamic light scattering measurements. The internal motion is described with a model consistent with the structure of the micelle and which accounts for the flexibility of the chains. The SDS monomer consists of a head group, which lies on the surface of the globular micelle, and a tail that hangs from the head toward the center of the globule. Considering various factors like conformational changes of the SDS chains, bending, stretching of the chemical bonds, etc., the dynamics of the SDS molecules is successfully described by a model in which the hydrogen atoms undergo localized translational motion confined within spherical volumes. This volume increases linearly along the SDS chain such that the hydrogen atoms closer to the head group move within smaller spheres with lower diffusion constant than the hydrogen atoms away from the head group. This model is found to be consistent with the data over the whole temperature and concentration range. Diffusivity and the volume of the spheres are also found to increase with temperature. The effect of lowering the SDS concentration is found to be similar to that of increasing the temperature.

Molecular dynamics simulation of interactions between a sodium dodecyl sulfate micelle and a poly(ethylene oxide) polymer

We have performed atomistic molecular dynamics simulations of an anionic sodium dodecyl sulfate (SDS) micelle and a nonionic poly(ethylene oxide) (PEO) polymer in aqueous solution. The micelle consisted of 60 surfactant molecules, and the polymer chain lengths varied from 20 to 40 monomers. The force field parameters for PEO were adjusted by using 1,2-dimethoxymethane (DME) as a model compound and matching its hydration enthalpy and conformational behavior to experiment. Excellent agreement with previous experimental and simulation work was obtained through these modifications. The simulated scaling behavior of the PEO radius of gyration was also in close agreement with experimental results. The SDS-PEO simulations show that the polymer resides on the micelle surface and at the hydrocarbon-water interface, leading to a selective reduction in the hydrophobic contribution to the solvent-accessible surface area of the micelle. The association is mainly driven by hydrophobic interactions between the polymer and surfactant tails, while the interaction between the polymer and sulfate headgroups on the micelle surface is weak. The 40-monomer chain is mostly wrapped around the micelle, and nearly 90% of the monomers are adsorbed at low PEO concentration. Simulations were also performed with multiple 20-monomer chains, and gradual addition of polymer indicates that about 120 monomers are required to saturate the micelle surface. The stoichiometry of the resulting complex is in close agreement with experimental results, and the commonly accepted "beaded necklace" structure of the SDS-PEO complex is recovered by our simulations.

Hydrogen-bonding propensities of sphingomyelin in solution and in a bilayer assembly: a molecular dynamics study

Sphingomyelin is enriched within lipid microdomains of the cell membrane termed lipid rafts. These microdomains play a part in regulating a variety of cellular events. Computer simulations of the hydrogen-bonding properties of sphingolipids, believed to be central to the organization of these domains, can delineate the possible molecular interactions that underlie this lipid structure. We have therefore used molecular dynamics simulations to unravel the hydrogen-bonding behavior of palmitoylsphingomyelin (PSM). A series of eight simulations of 3 ns each of a single PSM molecule in water showed that the sphingosine OH and NH groups can form hydrogen bonds with the phosphate oxygens of their own polar head, in agreement with NMR data. Simulations of PSM in a bilayer assembly were carried out for 8 ns with three different force field parameterizations. The major physico-chemical parameters of the simulated bilayer agree with those established experimentally. The sphingosine OH group was mainly involved in intramolecular hydrogen bonds, in contrast to the almost exclusive intermolecular hydrogen bonds formed by the amide NH moiety. During the bilayer simulations the intermolecular hydrogen bonds among lipids formed a dynamic network characterized by the presence of hydrogen-bonded lipid clusters of up to nine PSM molecules.

The structure and dynamics of ACTH (1-10) on the surface of a sodium dodecylsulfate (SDS) micelle: a molecular dynamics simulation study

ACTH (1-10), an adrenocorticotropin hormone fragment, was studied by molecular dynamics (MD) simulation in the NPT ensemble in an explicit sodium dodecylsulfate (SDS) micelle. Initially, distance restraints derived from NMR nuclear Overhauser enhancements were incorporated during the equilibration stage of the simulation. The analyses of the trajectories from the subsequent unrestrained MD showed that ACTH (1-10) does not conform to a helical structure at the micelle-water interface; however, the structure is amphipathic. The loss of the helical structure is due to decreased intramolecular hydrogen bonding accompanied by an increase of hydrogen bonding between the amide hydrogens of the peptide and the micelle head-groups. ACTH (1-10) was found to lie on the surface of the SDS micelle. Most of the hydrophobic interactions came from the side-chains of Met-4, Phe-7 and Trp-9. The peptide bonds were either hydrated or involved in intramolecular hydrogen bonding. Decreased hydration for the backbone of His-6 and Phe-7 was due to intermolecular hydrogen bonding with the SDS head-groups. The time correlation functions of the N-H bonds of the peptide in water and in the micelle showed that the motions of the peptide, except for the N- and C-termini, are significantly reduced when partitioned in the micelle.

Molecular dynamics study of substance P peptides partitioned in a sodium dodecylsulfate micelle

Two neuropeptides, substance P (SP) and SP-tyrosine-8 (SP-Y8), have been studied by molecular dynamics (MD) simulation in an explicit sodium dodecylsulfate (SDS) micelle. Initially, distance restraints derived from NMR nuclear Overhauser enhancements (NOE) were incorporated in the restrained MD (RMD) during the equilibration stage of the simulation. It was shown that when SP-Y8 was initially placed in an insertion (perpendicular) configuration, the peptide equilibrated to a surface-bound (parallel) configuration in approximately 450 ps. After equilibration, the conformation and orientation of the peptides, the solvation of both the backbone and the side chain of the residues, hydrogen bonding, and the dynamics of the peptides were analyzed from trajectories obtained from the RMD or the subsequent free MD (where the NOE restraints were removed). These analyses showed that the peptide backbones of all residues are either solvated by water or are hydrogen-bonded. This is seen to be an important factor against the insertion mode of interaction. Most of the interactions come from the hydrophobic interaction between the side chains of Lys-3, Pro-4, Phe-7, Phe-8, Leu-10, and Met-11 for SP, from Lys-3, Phe-7, Leu-10, and Met-11 in SP-Y8, and the micellar interior. Significant interactions, electrostatic and hydrogen bonding, between the N-terminal residues, Arg-Pro-Lys, and the micellar headgroups were observed. These latter interactions served to affect both the structure and, especially, the flexibility, of the N-terminus. The results from simulation of the same peptides in a water/CCl4 biphasic cell were compared with the results of the present study, and the validity of using the biphasic system as an approximation for peptide-micelle or peptide-bilayer systems is discussed.

Studies of the binding and structure of adrenocorticotropin peptides in membrane mimics by NMR spectroscopy and pulsed-field gradient diffusion

The partition and structure of three adrenocorticotropic hormone peptides ACTH(1-10), ACTH(1-24), and ACTH(11-24) in water and in sodium dodecylsulfate (SDS) and dodecylphosphocholine (DPC) micelles were studied by 2D NMR and NMR gradient diffusion measurements. The diffusion rates, the NH chemical shifts, and the nuclear Overhauser effect patterns provided a coherent picture of binding of these peptides. All three peptides are significantly partitioned in the negatively charged SDS micelles and possess definite secondary structure, as opposed to random structures in water. For ACTH (1-24), the hydrophobic 1-10 segment is partitioned in DPC micelles, but the charged 11-24 segment prefers to remain in the aqueous region. ACTH(11-24) does not bind significantly to the DPC micelles. The binding of the ACTH peptides in these two widely used "membrane mimics" are substantially different from that in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers obtained by attenuated total reflection infrared spectroscopy and from our preliminary diffusion studies of the same peptides in POPC vesicles. This study showed that, in a given micellar medium, all corresponding segments of these peptides are located in the same membrane environment in the system, regardless of whether these segments exist by themselves or are attached to other segments. This result may contradict the membrane-compartments concept of Schwyzer, which suggests that ACTH(1-10) and ACTH(1-24) are located in different membrane compartments because they have different address segments, and consequently, bind to different receptors. The present results also suggest that the assumption that micelles are good membrane mimics should be carefully examined.

Magnetic alignment and orientational order of dipalmitoylphosphatidylcholine bilayers containing palmitoyllysophosphatidylcholine

Mixed bilayers of 1-palmitoyl-sn-glycero-3-phosphocholine (palmitoyllysophosphatidylcholine; PaLPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (dipalmitoyl phosphatidylcholine; DPPC) have been investigated by 2H-NMR and 31P-NMR spectroscopy. Binary phospholipid mixtures were studied in which the acyl chains of one or the other component were perdeuterated. At temperatures below the main order-disorder phase transition, the mixed PaLPC/DPPC bilayers appear to coexist with PaLPC micelles. The micelles disappear at temperatures above the phase transition, where mixed bilayers in the liquid-crystalline state are formed. The orientational order of the alkyl chains of the PaLPC component is essentially identical to that of the DPPC component in the mixed bilayers, both in the low temperature and liquid-crystalline phases. However, the presence of PaLPC perturbs the segmental ordering of DPPC as compared to the pure system. The order is increased in the low-temperature phase, where effective diffusion of the chains about their long axes occurs, but is decreased in the liquid-crystalline phase compared to pure DPPC bilayers. The mixed liquid-crystalline bilayers orient preferentially with their director axes perpendicular to the magnetic field. This alignment is easily observed in 31P- and 2H-NMR spectra, where the intensity of the perpendicular edges of the lineshapes is pronounced. One possible explanation of the magnetic alignment involves alteration of the curvature free energy of the DPPC bilayer due to incorporation of PaLPC in the mixed membranes.