Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study.

α-Synuclein (α-syn) is a 140 amino acid intrinsically disordered protein (IDP) and the primary component of cytotoxic oligomers implicated in the etiology of Parkinson's disease (PD). While IDPs lack a stable three-dimensional structure, they sample a heterogeneous ensemble of conformations that can, in principle, be assessed through molecular dynamics simulations. However, describing the structure and aggregation of large IDPs is challenging due to force field (FF) accuracy and sampling limitations. To cope with the latter, coarse-grained (CG) FFs emerge as a potential alternative at the expense of atomic detail loss. Whereas CG models can accurately describe the structure of the monomer, less is known about aggregation. The latter is key for assessing aggregation pathways and designing aggregation inhibitor drugs. Herein, we investigate the structure and dynamics of α-syn using different resolution CG (Martini3 and Sirah2) and all-atom (Amber99sb and Charmm36m) FFs to gain insight into the differences and resemblances between these models. The dependence of the magnitude of protein-water interactions and the putative need for enhanced sampling (replica exchange) methods in CG simulations are analyzed to distinguish between force field accuracy and sampling limitations. The stability of the CG models of an α-syn fibril was also investigated. Additionally, α-syn aggregation was studied through umbrella sampling for the CG models and CG/all-atom models for an 11-mer peptide (NACore) from an amyloidogenic domain of α-syn. Our results show that despite the α-syn structures of Martini3 and Sirah2 with enhanced protein-water interactions being similar, major differences exist concerning aggregation. The Martini3 fibril is not stable, and the binding free energy of α-syn and NACore is positive, opposite to Sirah2. Sirah2 peptides in a zwitterionic form, in turn, display termini interactions that are too strong, resulting in end-to-end orientation. Sirah2, with enhanced protein-water interactions and neutral termini, provides, however, a peptide aggregation free energy profile similar to that found with all-atom models. Overall, we find that Sirah2 with enhanced protein-water interactions is suitable for studying protein-protein and protein-drug aggregation.

Essential dynamics of ubiquitin in water and in a natural deep eutectic solvent.

Natural deep eutectic solvents (NADESs) comprised of osmolytes are of interest as potential biomolecular (cryo)protectants. However, the way these solvents influence the structure and dynamics of biomolecules as well as the role of water remains poorly understood. We carried out principal component analysis of various secondary structure elements of ubiquitin in water and a betaine : glycerol : water (1 : 2 : ζ; ζ = 0, 1, 2, 5, 10, 20, 45) NADES, from molecular dynamics trajectories, to gain insight into the protein dynamics as it undergoes a transition from a highly viscous anhydrous to an aqueous environment. A crossover of the protein's essential dynamics at ζ ∼ 5, induced by solvent-shell coupled fluctuations, is observed, indicating that ubiquitin might (re)fold in the NADES upon water addition at ζ > ∼5. Further, in contrast to water, the anhydrous NADES preserves ubiquitin's essential modes at high temperatures explaining the protein's seemingly enhanced thermal stability.

Protein stability in a natural deep eutectic solvent: Preferential hydration or solvent slaving?

Deep eutectic solvents (DESs) emerged as potential alternative solvent media in multiple areas, including biomolecular (cryo)preservation. Herein, we studied the stability of a small protein (ubiquitin) in water and a betaine-glycerol-water (B:G:W) (1:2:ζ; ζ = 0, 1, 2, 5, 10) DES, through molecular dynamics. An AMBER-based model that accurately describes the density and shear viscosity of the DES is proposed. We find that water molecules are largely trapped in the solvent, precluding the formation of a full hydration layer, seemingly opposite to osmolytes' preferential exclusion/preferential hydration mechanism. Although the protein is stable in the DES, structural fluctuations are largely suppressed and only recovered upon sufficient hydration. This is explained by a solvent-slaving mechanism where ß-fluctuations are key, with the non-monotonic hydration of some amino acids with the water content providing an explanation to the non-monotonic folding of some proteins in aqueous DESs. A major thermal stability enhancement in the DES is also observed, caused by a similar slowdown of the backbone torsional dynamics. Our results support a kinetic stabilization of the protein in the DES, whereas a possible thermodynamic stabilization does not follow a preferential hydration or water entrapment mechanism.

On the not so anomalous water-induced structural transformations of choline chloride-urea (reline) deep eutectic system.

The choline chloride-urea binary mixture in the molar ratio (1 : 2), commonly known as reline, is an archetypal solvent among deep eutectic solvents (DES). Neutron diffraction (ND) and empirical potential structure refinement (EPSR) results provided evidence that reline exhibits a peculiar structural transformation upon water addition that manifests in a sudden dewetting of the choline cations at ∼51 wt% water and, therefore, a non-monotonic variation of the choline-water and choline-choline coordination. Here, we study, through molecular dynamics (MD), the influence of water on the structure of a choline chloride : urea : water DES (1 : 2 : ζ; ζ = 0 to 40), to gain additional insight into the molecular source of this peculiar structural transformation. Five different force fields were investigated. Our results show that the ND/EPSR non-monotonic behavior of the choline-choline coordination is qualitatively reproduced by those force fields that describe more accurately the dynamics of the DES, namely, the diffusion and viscosity coefficients. However, the apparent increase of the choline-choline coordination at ζ > 10 (41 wt%) is associated with the drain of a particular first coordination sphere, rather than with a dewetting of the choline cations, as predicted by ND/EPSR. Thus, a monotonic increase of the choline-water coordination is found instead, as well as the emergence of a tetrahedral hydrogen bond network of water, opposite to ND/EPSR. The highest rate of depletion upon initial hydration is found for urea around choline (∼0.9 urea molecules/ζ), whereas choline depicts the highest rate of hydration (∼2.5 water molecules/ζ). These rates decrease with ζ and a structural transition that stabilizes above 41 wt% is observed, consistent with ND/EPSR results. Despite limitations in the force fields, we argue that the experimental and simulation opposite pictures could be related to an underestimation of water's hydrogen bond network portrayed by the EPSR method. Overall, a smoother transition from a DES to an aqueous solution of the DES components is portrayed by MD, compared with ND/EPSR.

Exploring a near-Hartree-Fock-Kohn-Sham approach to study electronic properties of azobenzene in interaction with gold: From clusters to the Au(111) surface.

The electronic properties of azobenzene (AB) in interaction with gold clusters and adsorbed on the Au(111) surface are investigated by adopting a near-Hartree-Fock-Kohn-Sham (HFKS) scheme. This scheme relies on a hybrid Perdew-Burke-Ernzerhof functional, in which the exact non-local HF exchange contribution to the energy is taken as 3/4. Ionization energies and electron affinities for gas phase AB are in very good agreement with experimental data and outer valence Green's function) calculations. The presence of C-H⋯Au interactions in AB-Aun complexes illustrates the role played by weak interactions between molecular systems and Au nanoparticles, which is in line with recent works on Au-H bonding. In AB-Aun complexes, the frontier orbitals are mainly localized on the gold platform when n ≥ 10, which indicates the transition from a molecular to a semiconducting regime. In the latter regime, the electronic density reorganization in AB-Aun clusters is characterized by significant polarization effects on the Au platform. The accuracy of the near-HFKS scheme for predicting adsorption energies of AB on Au(111) and the interest of combining exact non-local HF exchange with a non-local representation of the dispersion energy are discussed. Taking into account the significant computational cost of the exact non-local HF exchange contribution, calculations for the adsorption energies and density of states for AB adsorbed on Au(111) were carried out by using a quantum mechanics/molecular mechanics approach. The results strongly support near-HFKS as a promising methodology for predicting the electronic properties of hybrid organic-metal systems.

Translational and rotational dynamics of high and low density TIP4P/2005 water.

We use molecular dynamics simulations using TIP4P/2005 to investigate the self- and distinct-van Hove functions for different local environments of water, classified using the local structure index as an order parameter. The orientational dynamics were studied through the calculation of the time-correlation functions of different-order Legendre polynomials in the OH-bond unit vector. We found that the translational and orientational dynamics are slower for molecules in a low-density local environment and correspondingly the mobility is enhanced upon increasing the local density, consistent with some previous works, but opposite to a recent study on the van Hove function. From the analysis of the distinct dynamics, we find that the second and fourth peaks of the radial distribution function, previously identified as low density-like arrangements, show long persistence in time. The analysis of the time-dependent interparticle distance between the central molecule and the first coordination shell shows that particle identity persists longer than distinct van Hove correlations. The motion of two first-nearest-neighbor molecules thus remains coupled even when this correlation function has been completely decayed. With respect to the orientational dynamics, we show that correlation functions of molecules in a low-density environment decay exponentially, while molecules in a local high-density environment exhibit bi-exponential decay, indicating that dynamic heterogeneity of water is associated with the heterogeneity among high-density and between high-density and low-density species. This bi-exponential behavior is associated with the existence of interstitial waters and the collapse of the second coordination sphere in high-density arrangements, but not with H-bond strength.

On the Structural and Dynamical Properties of DOPC Reverse Micelles.

The structure and dynamics of phospholipid reverse micelles are studied by molecular dynamics. We report all-atom unconstrained simulations of 1,2-dioleoyl-sn-phosphatidylcholine (DOPC) reverse micelles in benzene of increasing sizes, with water-to-surfactant number ratios ranging from W0 = 1 to 16. The aggregation number, i.e., the number of DOPC molecules per reverse micelle, is determined to fit experimental light-scattering measurements of the reverse micelle diameter. The simulated reverse micelles are found to be approximately spherical. Larger reverse micelles (W0 > 4) exhibit a layered structure with a water core and the hydration structure of DOPC phosphate head groups is similar to that found in phospholipid membranes. In contrast, the structure of smaller reverse micelles (W0 ≤ 4) cannot be described as a series of concentric layers successively containing water, surfactant head groups, and surfactant tails, and the head groups are only partly hydrated and frequently present in the core. The dynamics of water molecules within the phospholipid reverse micelles slow down as the reverse micelle size decreases, in agreement with prior studies on AOT and Igepal reverse micelles. However, the average water reorientation dynamics in DOPC reverse micelles is found to be much slower than in AOT and Igepal reverse micelles with the same W0 ratio. This is explained by the smaller water pool and by the stronger interactions between water and the charged head groups, as confirmed by the red-shift of the computed infrared line shape with decreasing W0.

Ab initio calculation of the electronic absorption spectrum of liquid water.

The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O-H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.

Cyclic Peptides as Aggregation Inhibitors for Sickle Cell Disease.

Sickle cell disease is a missense genetic disorder characterized by the aggregation of deoxy-HbS into helical fibers that distort erythrocytes into a sickle-like shape. Herein, we investigate, through molecular dynamics, the effect of nine 5-mer cyclic peptides (CPs), tailor-designed to block key lateral contacts of the fibers. Our results show that the CPs bind orthogonally to the main HbS pocket involved in the latter contacts, with some revealing exceedingly long residence times. These CPs display moderate to high specificity, exhibiting molecular recognition events even at a HbS/CP (1:1) ratio. A much lower HbS-CP binding free energy, longer residence times, and higher specificity are also found relative to a previously reported CP with modest in vitro antisickling activity. These results indicate that some of these CPs have the potential to reduce the concentration of aggregation-competent deoxy-HbS, precluding or delaying the formation of lateral contact at the homogeneous nucleation stage.

Study of specific ion-amino acid interactions through the use of local correlation methods.

Specific ion effects, related to the hydration of ions and ion-solute interactions, play a fundamental part in many processes in chemistry and biology. Although intensively studied since the seminal studies of Franz Hofmeister and co-workers, their molecular origin has only recently started to be unveiled. In this work, we have investigated the interaction between halide anions and a selected set of amino acid residues in an attempt to identify the forces behind ion specificity. Two-dimensional potential energy surfaces have been calculated with the use of local second order Møller-Plesset perturbation theory (LMP2), coupled with the COSMO model to describe solvent effects. The results show in great detail the impact of dispersion interactions, in particular for the heavier anions (Br(-) and I(-)). The obtained potential energy surfaces also hint at a greater mobility of iodide in the vicinity of a residue, which correlates well with its placing in the Hofmeister series.

Structure and electronic properties of a benzene-water solution.

Electronic properties of benzene in water were investigated by a sequential quantum mechanical/molecular dynamics approach. Emphasis was placed on the analysis of the structure, polarization effects, and ionization spectrum. By adopting a polarizable model for both benzene and water the structure of the benzene-water solution is in good agreement with data from first principles molecular dynamics. Further, strong evidence that water molecules acquire enhanced orientational order near the benzene molecule is found. Upon hydration, the quadrupole moment of benzene is not significantly changed in comparison with the gas-phase value. We are also reporting results for the dynamic polarizability of benzene in water. Our results indicate that the low energy behaviour of the dynamic polarizability of gas-phase and hydrated benzene is quite similar. Outer valence Green's function calculations for benzene in liquid water show a splitting of the gas-phase energy levels associated with the 1e(1g)(π), 2e(2g), and 2e(1u) orbitals upon hydration. Lifting of the orbitals degeneracy and redshift of the outer valence bands is related to symmetry breaking of the benzene structure in solution and polarization effects from the surrounding water molecules.

Structure and Dynamic Properties of a Glycerol-Betaine Deep Eutectic Solvent: When Does a DES Become an Aqueous Solution?

Deep eutectic solvents (DESs) are an emerging class of green solvents with a wide spectrum of potential applications whose properties may be further tailored through the addition of water. Here, we study, through molecular dynamics, the influence of water on the properties of a betaine-glycerol-water (B:G:W) DES (1:2:ζ; ζ = 0 to 100), aiming at getting insight into the structural and dynamic crossover between a DES and an aqueous solution. The density, shear viscosity, and diffusion coefficients are found to exhibit a non-linear dependence of ζ, similar to that observed for the solvation layers' composition. Each Gly and Bet are replaced, respectively, by ∼3 and ∼5 water molecules, with the highest rates of depletion being found for Gly around Bet and Gly around Gly. Above ζ = 7 (70 mol %; 29.5 wt %), a major structural transformation occurs, with the complete disruption of the second Bet-Gly solvation layer and the formation of a new second layer at a shorter distance, accompanied by a sudden change in the rate of increase of the components' diffusion. Nonetheless, opposite to other DES, our results indicate a smooth crossover between a DES and an aqueous solution.

Protein Denaturation, Zero Entropy Temperature, and the Structure of Water around Hydrophobic and Amphiphilic Solutes.

The hydrophobic effect plays a key role in many chemical and biological processes, including protein folding. Nonetheless, a comprehensive picture of the effect of temperature on hydrophobic hydration and protein denaturation remains elusive. Here, we study the effect of temperature on the hydration of model hydrophobic and amphiphilic solutes, through molecular dynamics, aiming at getting insight on the singular behavior of water, concerning the zero-entropy temperature, TS, and entropy convergence, TS*, also observed for some proteins, upon denaturation. We show that, similar to hydrocarbons, polar amphiphilic solutes exhibit a TS, although strongly dependent on solute-water interactions, opposite to hydrocarbons. Further, the temperature dependence of the hydration entropy, normalized by the solvent accessible surface area, is shown to be nearly solute size independent for hydrophobic but not for amphiphilic solutes, for similar reasons. These results are further discussed in the light of information theory (IT) and the structure of water around hydrophobic groups. The latter shows that the tetrahedral enhancement of some water molecules around hydrophobic groups, associated with the reduction of water defects, leads to the strengthening of the weakest hydrogen bonds, relative to bulk water. In addition, a larger tetrahedrality is found in low density water populations, demonstrating that pure water has encoded structural information, similar to that associated with hydrophobic hydration. The reversal of the hydration entropy dependence on the solute size, above TS*, is also analyzed and shown to be associated with a greater loss of water molecules exhibiting enhanced orientational order, in the coordination sphere of large solutes. Finally, the source of the differences between Kauzmann's "hydrocarbon model" on protein denaturation and hydrophobic hydration is discussed, with relatively large amphiphilic hydrocarbons seemingly displaying a more similar behavior to some globular proteins than aliphatic hydrocarbons.

Electronic excitation of Cl- in liquid water and at the surface of a cluster: a sequential Born-Oppenheimer molecular dynamics/quantum mechanics approach.

A sequential molecular dynamics/quantum mechanics approach is applied to investigate the electronic excitation of Cl(-) in liquid water and in a water cluster. Time-dependent density functional theory (TDDFT) and equation-of-motion coupled-cluster with single and double excitations (EOM-CCSD) are used to calculate the excitation energies from Born-Oppenheimer molecular dynamics configurations. The selected configurations include a quantum system with the Cl(-) anion and a number of explicit water molecules (n(w)) as well as an embedding background defined by fractional point charges on the remaining water molecules. Our results indicate that for both the liquid and the cluster environments the excited electron is delocalized on the hydrogen atoms of the first hydration shell and in a nearby cavity. Convergence of the charge-transfer-to-solvent (CTTS) energy with the number of water molecules is observed for a quantum system embedded in the polarizing charge background for n(w) > or = 3. Furthermore, we find that the CTTS energy of Cl(-) in both solution and cluster environments is very similar. The predicted CTTS energy threshold for the ionic solution (approximately 6.6 +/- 0.3 eV) is in good agreement with experiment (6.8 and 7.1 eV).

Solubility of Polar and Nonpolar Aromatic Molecules in Subcritical Water: The Role of the Dielectric Constant.

Liquid water at temperatures above the boiling point and high pressures, also known as pressurized hot water, or subcritical water (SBCW), is an effective solvent for both polar and nonpolar organic solutes. This is often associated with the decrease of water's dielectric constant at high temperatures, apparently allowing water to behave like an organic solvent. The decrease of the solubility at high pressures, in turn, is explained by a mild increase of the dielectric constant of water. Nevertheless, the relationship among the dielectric constant of water, hydration, and the solubilities of polar and nonpolar molecules in SBCW remains poorly understood. Here, we study, through molecular dynamics, the hydration thermodynamic parameters and the solubility of nonpolar and polar aromatic model systems, for which a solubility increase in SBCW is observed. We show that the temperature dependence of the hydration free energy of the model nonpolar aromatic solutes is nonmonotonic, exhibiting a solute size independent maximum at ∼475 K, above which hydration becomes entropically favorable and enthalpically unfavorable. The monotonic increase of the solubility, separated here in hydration and vaporization or sublimation components of the pure liquid or solid solute, respectively, is, in turn, related to the temperature increase of the latter, and only to a minor extent with the decrease of the hydration free energy above ∼475 K, via the hydration entropy. A solubility increase or decrease is also found at high pressures for different solutes, explained by the relative magnitude of the hydration and the vaporization or sublimation components of the solubility. For the model solid polar system studied, the hydration free energy increases monotonically with the temperature, instead, and the solubility increase is caused by the decrease of the sublimation component of the solubility. Thus, despite the observed increase of the hydration free energy with pressure, related to the entropic component decrease, our results indicate that the dielectric constant plays no significant role on the solubility increase of nonpolar and polar solutes in SBCW, opposite to the dielectric constant picture. The structure of water next to the solutes is also investigated, and a structural enhancement at room temperature is observed, resulting in significantly stronger pair interactions between a water molecule and its third and fourth nearest water neighbors. This structural and energetic enhancement nearly vanishes, however, at high temperatures, contributing to a positive hydration entropy.

Directing self-assembly in solution towards improved cooperativity in Fe(iii) complexes with amphiphilic tridentate ligands.

An amphiphilic iron(iii) complex with a tridentate Schiff-base ligand was prepared by condensation of a hexadecyloxy functionalised salycylaldehyde with a diamine followed by complexation with FeCl2 and anion methathesis with NaClO4. The complex shows spin crossover both in the solid state and solution. However in solution self-assembly and consequently aggregation of individual molecules form concentration dependent particles with sizes of 300 nm for higher concentrations, or 5 nm for lower concentrations. Aggregate formation was confirmed by NANO-flex 180° DLS Size, scan-rate dependent cyclic voltammetry and scanning electron microscopy. Molecular simulations were used to investigate the self-assembly of the complex in solution, including the role of residual water molecules. The simulations showed the self-assembly of reverse micelle-like structures when a small water cluster is inserted in solution, whereas no large aggregates formed in dehydrated environments. The perchlorate anions were found near the metal centres, stabilizing the aggregates around the water pool. Simulations of pre-assembled structures further showed the lack of stability of large aggregates in the absence of water. The larger aggregates promoted efficient communication between the iron(iii) centres and the compound displayed spin crossover in solution at around 220 K with a 10 K hysteresis window, as measured by NMR and SQUID magnetometry.