Can local heating and molecular crowders disintegrate amyloid aggregates?

The present study employs a blend of molecular dynamics simulations and a theoretical model to explore the potential disintegration mechanism of a matured Aß octamer, aiming to offer a strategy to combat Alzheimer's disease. We investigate local heating and crowding effects on Aß disintegration by selectively heating key Aß segments and varying the concentration of sodium dodecyl sulphate (SDS), respectively. Despite initiation of disruption, Aß aggregates resist complete disintegration during local heating due to rapid thermal energy distribution to the surrounding water. Conversely, although SDS molecules effectively inhibit Aß aggregation at higher concentration through micelle formation, they fail to completely disintegrate the aggregate due to the exceedingly high energy barrier. To address the sampling challenge posed by the formidable energy barrier, we have performed well-tempered metadynamics simulations. Simulations reveal a multi-step disintegration mechanism for the Aß octamer, suggesting a probable sequence: octamer → pentamer/hexamer ⇌ tetramer → monomer, with a rate-determining step constituting 45 kJ mol-1 barrier during the octamer to pentamer/hexamer transition. Additionally, we have proposed a novel two-state mean-field model based on Ising spins that offers an insight into the kinetics of the Aß growth process and external perturbation effects on disintegration. Thus, the current simulation study, coupled with the newly introduced mean-field model, offers an insight into the detailed mechanisms underlying the Aß aggregation process, guiding potential strategies for effective disintegration of Aß aggregates.

Sequence Dependence in Nucleosome Dynamics.

The basic packaging unit of eukaryotic chromatin is the nucleosome that contains 145-147 base pair duplex DNA wrapped around an octameric histone protein. While the DNA sequence plays a crucial role in controlling the positioning of the nucleosome, the molecular details behind the interplay between DNA sequence and nucleosome dynamics remain relatively unexplored. This study analyzes this interplay in detail by performing all-atom molecular dynamics simulations of nucleosomes, comparing the human α-satellite palindromic (ASP) and the strong positioning "Widom-601" DNA sequence at time scales of 12 µs. The simulations are performed at salt concentrations 10-20 times higher than physiological salt concentrations to screen the electrostatic interactions and promote unwrapping. These microsecond-long simulations give insight into the molecular-level sequence-dependent events that dictate the pathway of DNA unwrapping. We find that the "ASP" sequence forms a loop around SHL ± 5 for three sets of simulations. Coincident with loop formation is a cooperative increase in contacts with the neighboring N-terminal H2B tail and C-terminal H2A tail and the release of neighboring counterions. We find that the Widom-601 sequence exhibits a strong breathing motion of the nucleic acid ends. Coincident with the breathing motion is the collapse of the full N-terminal H3 tail and formation of an α-helix that interacts with the H3 histone core. We postulate that the dynamics of these histone tails and their modification with post-translational modifications (PTMs) may play a key role in governing this dynamics.

Exploration of the Nucleation Pathway for Supramolecular Fibers.

The pathway for supramolecular fiber formation is coupled with the underlying order of the self-assembling molecules. Here, we report on atomistic molecular dynamics simulations to characterize the initial stages of the self-assembly of a model drug amphiphile in an aqueous solution. We perform two-dimensional metadynamics calculations to characterize the assembly space of this model drug amphiphile─Tubustecan, TT1. TT1 is composed of the hydrophobic anticancer drug, Camptothecin (CPT), conjugated to a hydrophilic polyethylene glycol (PEG) chain. We find that the aromatic stacking of CPT drives the formation of a higher-density liquid droplet. This droplet elongates and can form a higher-ordered supramolecular assembly upon reorganizing and forming an interface and additional aromatic stacking of the drugs. We show that novel reaction coordinates tailored to this class of molecules are essential in capturing the underlying degree of molecular order upon assembly. This approach can be refined and extended to characterize the supramolecular assembly pathway of other molecules containing aromatic compounds.

In Silico Studies to Predict the Role of Solvent in Guiding the Conformations of Intrinsically Disordered Peptides and Their Aggregated Protofilaments.

The formation of amyloids due to the self-assembly of intrinsically disordered proteins or peptides is a hallmark for different neurodegenerative diseases. For example, amyloids formed by the amyloid beta (Aß) peptides are responsible for the most devastating neuropathological disease, namely, Alzheimer's disease, while aggregation of α-synuclein peptides causes the etiology of another neuropathological disease, Parkinson's disease. Characterization of the intermediates and the final amyloid formed during the aggregation process is, therefore, crucial for microscopic understanding of the origin behind such diseases, as well as for the development of proper therapeutics to combat those. However, most of the research activities reported in this area have been directed toward examining the early stages of the aggregation process, including probing the conformational characteristics of the responsible protein/peptide in the monomeric state or in small oligomeric forms. This is because the small soluble oligomers have been found to be more deleterious than the final insoluble amyloids. This review discusses some of the recent findings obtained from our simulation studies on Aß and α-synuclein monomers and small preformed Aß aggregates. A molecular-level insight of the aggregation process with a special emphasis on the role of water in inducing the aggregation process has been provided.

Exploring Heterogeneous Dynamical Environment around an Ensemble of Aß42 Peptide Monomer Conformations.

Exploring the conformational properties of amyloid ß (Aß) peptides and the role of solvent (water) in guiding the dynamical environment at their interfaces is crucial for microscopic understanding of Aß misfolding, which is involved in causing the most common neurodegenerative disorder, i.e., Alzheimer's disease. While numerous studies in the past have emphasized examining the conformational states of Aß peptides, the role of water has not received much attention. Here, we have performed all-atom molecular dynamics simulations of several full-length Aß42 peptide monomers with different initial configurations. Our efforts are directed toward probing the origin of the heterogeneous dynamics of water around various segments of the Aß peptide, identified as the two terminal segments (N-term and C-term) and the two hydrophobic segments (hp1 and hp2), along with the central turn region interconnecting hp1 and hp2. Our results revealed that water hydrating hp1, hp2, and turn (nonterminal segments) and C-term segments exhibit nonuniformly restricted translational as well as rotational motions. The degree of such restriction has been found to be correlated with the hydrogen bond relaxation time scales at the interface. Importantly, it is revealed that the water molecules around hp1 and, to some extent, around hp2, form relatively rigid hydration layers, compared to that around the other segments. Such rigid hydration layers arise due to relatively more solid-like caging motions resulting in relatively lesser hydration entropy. As hp1 and hp2 have been demonstrated to play a central role in Aß aggregation, we believe that distinct water dynamics in the vicinity of these two segments, as outlined in this study, can provide vital information in understanding the early stages of the onset of the aggregation process of such peptides at higher concentration that can further aid toward advances in AD therapeutics.

Effect of Lauric Acid on the Stability of Aß42 Oligomers.

While Alzheimer's disease is correlated with the presence of Aß fibrils in patient brains, the more likely agents are their precursors, soluble oligomers that may form pores or otherwise distort cell membranes. Using all-atom molecular dynamics simulation, we study how the presence of fatty acids such as lauric acid changes the stability of pore-forming oligomers built from three-stranded Aß42 chains. Such a change would alter the distribution of amyloids in the fatty acid-rich brain environment and therefore could explain the lower polymorphism observed in Aß fibrils derived from brains of patients with Alzheimer's disease. We find that lauric acid stabilizes both ring-like and barrel-shaped models, with the effect being stronger for barrel-like models than for ring-like oligomers.

Bifurcated Hydrogen Bonds and the Fold Switching of Lymphotactin.

Lymphotactin (Ltn) exists under physiological conditions in an equilibrium between two interconverting structures with distinct biological functions. Using replica-exchange-with-tunneling, we study the conversion between the 2-folds. Unlike previously proposed, we find that the fold switching does not require unfolding of lymphotactin but proceeds through a series of intermediates that remain partially structured. This process relies on two bifurcated hydrogen bonds that connect the ß2 and ß3 strands and ease the transition between the hydrogen bond pattern by which the central three-stranded ß-sheet in the two forms differs.

Cleavage, Downregulation, and Aggregation of Serum Amyloid A.

Various diseases cause overexpression of the serum amyloid A (SAA) protein, which in some cases, but not in all cases, leads to amyloidosis as a secondary disease. Response to the overexpression involves dissociation of the SAA hexamer and subsequent cleavage of the released monomers, most commonly yielding fragments SAA1-76 of the full-sized SAA1-104. We report results from molecular dynamic simulations that probe the role of this cleavage for downregulating the activity and concentration of SAA. We propose a mechanism that relies on two elements. First, the probability to assemble into hexamers is lower for the fragments than it is for the full-sized protein. Second, unlike other fragments, SAA1-76 can switch between two distinct configurations. The first kind is easy to proteolyse (allowing a fast reduction of the SAA concentration) but prone to aggregation, whereas the situation is opposite for the second kind. If the time scale for amyloid formation is longer than the one for proteolysis, the aggregation-prone species dominates. However, if environmental conditions such as low pH increases the risk of amyloid formation, the ensemble shifts toward the more protected form. We speculate that SAA amyloidosis is a failure of this switching mechanism leading to accumulation of the aggregation-prone species and subsequent amyloid formation.

Effects of Metal Ions on Aß42 Peptide Conformations from Molecular Simulation Studies.

In this study, we investigate the conformational characteristics of full-length Aß42 peptide monomers in the presence of Na+ and Zn2+ metal ions using atomistic molecular dynamics (MD) simulations with an aim to explore the possible driving forces behind enhanced aggregation rates of the peptides in the presence of salts. The calculations reveal that the presence of metal ions shifts the conformational equilibrium more toward the compact ordered Aß structures. Such compact ordered structures stabilized by distant nonlocal contacts between two crucial hydrophobic segments, hp1 and hp2, primarily through two important hydrophobic aromatic residues, Phe-19 and Phe-20, are expected to trigger the aggregation process at a faster rate by populating and stabilizing the aggregation prone structures. Formation of a significant number of such distant contacts in the presence of Na+ ions has also been found to result in breaking of the N-terminal helix. On the contrary, binding of Zn2+ ion to Aß peptide is highly specific, which stabilizes the N-terminal helix instead of breaking it. This explains why the aggregation rate of Aß peptides is higher in the presence of divalent Zn2+ ions than monovalent Na+ ions. Relatively higher overall stability of the most populated Aß peptide monomers in the presence of Zn2+ ions has been found to be associated with specific Zn2+-Aß binding and significant free energy gain.

Understanding the microscopic origin behind heterogeneous properties of water confined in and around Aß17-42 protofilaments.

Aggregation of amyloid beta (Aß) peptides in the brain is responsible for one of the most devastating neurodegenerative diseases, namely, Alzheimer's disease. In this study, we have carried out atomistic molecular dynamics simulations to explore the effects of non-uniform structural distortions of Aß17-42 pre-fibrillar aggregates of different sizes on the microscopic structure and ordering of water molecules confined within their amphiphilic nanocores. The calculations revealed non-uniform peptide-water interactions resulting in simultaneous existence of both highly ordered and disordered water molecules within the spatially heterogeneous confined environment of the protofilament cores. It is found that the high degree of ordering originates from a sizable fraction of doubly coordinated core water molecules, while the randomly oriented ones are those that are coordinated with three neighbors in their first coordination shells. Furthermore, it is quantitatively demonstrated that relative fractions of these two types of water molecules are correlated with the protofilament core topology and the degree of confinement within that. It is proposed that the ordered core waters are likely to stabilize the Aß protofilaments by screening the residue charges and favoring water-mediated salt bridge formations, while the randomly oriented ones can drive further growth of the protofilaments by being displaced easily during the docking of additional peptides. In that way, both types of core water molecules can play equally important roles in controlling the growth and stability of the Aß-aggregates.

Dynamical crossover of water confined within the amphiphilic nanocores of aggregated amyloid ß peptides.

It is believed that the self-assembly of amyloid beta (Aß) peptides in the brain is the cause of Alzheimer's disease. Atomistic molecular dynamics simulations of aqueous solutions of Aß protofilaments of different sizes at room temperature have been carried out to explore the dynamic properties of water confined within the core and at the exterior surface of the protofilaments. Attempts have been made to understand how the non-uniform distortion of the protofilaments associated with their structural crossover influences the diffusivity and the hydrogen bonding environment of the confined water molecules. In contrast to the homogeneous solvent dynamical environment at the exterior surface, the calculations revealed heterogeneously restricted motions of water confined within the distorted cores of the protofilaments. Importantly, it is demonstrated that the structural crossover of the aggregates observed for the decamer is associated with a dynamical transition of water confined within its core. A direct one-to-one correlation between the heterogeneously restricted core water motions and the kinetics of the breaking and formation of hydrogen bonds quantitatively demonstrated that a modified hydrogen bond arrangement within the cores of higher order Aß protofilaments is the origin behind the crossover in core water mobility. A fraction of the water molecules forming short-lived water-water hydrogen bonds within the core of the crossover protofilament decamer are believed to diffuse away easily from the core and thus play a crucial role in further growth of the protofilament by facilitating the binding of new peptide monomers.

Hydration Behavior along the Folding Pathways of Trpzip4, Trpzip5 and Trpzip6.

The microscopic properties of water confined within different segments of Trpzip4 (TZ4), Trpzip5 (TZ5), and Trzpip6 (TZ6) have been compared for all the states characterized along their folding pathways. In particular, structural ordering, energetics, and dynamics of water have been examined as the peptide unfolds along the free energy landscape. It is observed that the structuring of tetrahedral network as well as translational and rotational motions of hydration waters confined within the strands and the turn regions are very different, revealing motional heterogeneity in small 16-residue trpzips. The polar and charged groups present at the peptide surface anchor to water molecules through hydrogen bonds and are responsible for differential hydration among various segments of the peptide, which is found to be correlated to their hydropathy values. The coherent collective dynamics of water is strongly coupled with conformational changes in the peptide since the trends observed in most of the computed quantities are in accordance with the folded and unfolded states classified along the folding pathway for all trpzips. The hydration behavior conform to the heterogeneity observed in the free energy landscape of stable TZ4 with four unfolded states as compared to more flexible TZ5 and TZ6 with two unfolded states each, in addition to the folded state. The hydration waters are observed to regulate the protein dynamics by continuous fluctuations in hydrogen bond network involving lateral side chains that inject conformational motions in the peptide to facilitate its unfolding. The implications of mutations on various aspects of hydration water dynamics including their impact on structural and dynamic organization of hydrogen bonds are also highlighted. Our studies affirm that topology of the free energy landscape is shaped by both spatial organization and dynamic transitions in hydration waters in addition to the conformational fluctuations in the peptide along the folding pathway.

Size-Dependent Conformational Features of Aß17-42 Protofilaments from Molecular Simulation Studies.

Alzheimer's disease is caused due to aggregation of amyloid beta (Aß) peptide into soluble oligomers and insoluble fibrils in the brain. In this study, we have performed room temperature molecular dynamics simulations to probe the size-dependent conformational features and thermodynamic stabilities of five Aß17-42 protofilaments, namely, O5 (pentamer), O8 (octamer), O10 (decamer), O12 (dodecamer), and O14 (tetradecamer). Analysis of the free energy profiles of the aggregates showed that the higher order protofilaments (O10, O12, and O14) undergo conformational transitions between two minimum energy states separated by small energy barriers, while the smaller aggregates (O5 and O8) remain in single deep minima surrounded by high barriers. Importantly, it is demonstrated that O10 is the crossover point for which the twisting of the protofilament is maximum, beyond which the monomers tend to rearrange themselves in an intermediate state and eventually transform into more stable conformations. Our results suggest that the addition of monomers along the axis of an existing protofilament with a critical size (O10 according to the present study) proceeds via an intermediate step with relatively less stable twisted structure that allows the additional monomers to bind and form stable larger protofilaments with minor rearrangements among themselves. More importantly, it is demonstrated that a combination of twist angle and end-to-end distance can be used as a suitable reaction coordinate to describe the growth mechanism of Aß protofilaments in simulation studies.

The sensitivity of folding free energy landscapes of trpzips to mutations in the hydrophobic core.

The sensitivity of the stability of folded states and free energy landscapes to the differences in the hydrophobic content of the core residues has been studied for the set of 16-residue trpzips, namely, Trpzip4, Trpzip5 and Trpzip6. The combination of principal component analysis and different secondary structure order metrics as reaction coordinates has been used to characterize and identify all the underlying attractive basins corresponding to the folded and the unfolded states for each trpzip at 300 K. Our results reveal that even a single mutation in the hydrophobic core perturbs the stability of the folded peptide and the conformational preferences for the partially folded and unfolded states significantly, leading to concomitant alterations in the free energy landscape of trpzips. Trpzip4 is observed to have the most rugged and variegated free energy landscape with occurrence of four metastable unfolded states in addition to the folded native state. In contrast, Trpzip5 and Trpzip6 are characterized by two such metastable states. The order metrics pertaining to the rigidity of the turn residues and the distances between the side chains of the hydrophobic core residues have been found to be most revealing to understand the degree of discrimination among the folded states of different peptides in addition to the unfolded states. Our results suggest that both turn propensity and hydrophobic interactions influence the thermodynamics of the folding pathways of trpzips. The implications of the sequence dependent response of amino acids, effect of aromatic stacking interactions and packing of protein's interior for shaping the free energy landscape of the peptides have been highlighted.

Conformational features of the Aß42 peptide monomer and its interaction with the surrounding solvent.

Accumulation of the amyloid beta (Aß) peptide in the brain is responsible for debilitating neurodegenerative diseases, such as Alzheimer's disease (AD). We have carried out atomistic molecular dynamics simulations of the full-length Aß42 peptide monomer with a wide range of conformations at room temperature. Efforts have been made to probe the conformational features of different segments of the peptide, namely the two terminal segments (N-term and C-term), the central hydrophobic regions (hp1 and hp2) and the central turn region joining hp1 and hp2, and their nonuniform influence on the spatial arrangements and binding energies of the surrounding water molecules. Our calculations reveal fluctuating conformations of the monomers with the formation and breaking of different secondary structural elements. In particular, it is noticed that the Aß monomers exhibit a propensity to either retain or transform into a helical form toward the N-term region and a ß-strand-like form near the C-term segment. Besides, heterogeneous conformational flexibility of the Aß monomers has been found to be correlated with the corresponding nonuniform entropy gains. Additionally, our calculation further reveals a heterogeneous hydration environment around the peptide. It is found that irrespective of the Aß peptide conformations and their nonuniform fluctuations, water molecules around the hydrophobic hp1 and hp2 segments are relatively weakly bound. This is an important observation, as in the presence of other monomers such weakly bound water molecules around hp1 and hp2 are expected to be easily displaced during the hydrophobic collapse that leads to Aß aggregation.

Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies.

One crucial issue in DNA hydration is the effect of salts on its conformational features. This has relevance in biology as cations present in the cellular environment shield the negative charges on the DNA backbone, thereby reducing the repulsive force between them. By screening the negative charges along the backbone, cations stabilize the folded structure of DNA. To study the effect of the added salt on single-stranded DNA (ss-DNA) conformations, we have performed room temperature molecular dynamics simulations of an aqueous solution containing the ss-DNA dodecamer with the 5'-CGCGAATTCGCG-3' sequence in the presence of 0.2, 0.5, and 0.8 M NaCl. Our calculations reveal that in the presence of the salt, the DNA molecule forms more collapsed coil-like conformations due to the screening of negative charges along the backbone. Additionally, we demonstrated that the formation of an octahedral inner-sphere complex by the strongly bound ion plays an important role in the stabilization of such folded conformation of DNA. Importantly, it is found that ion-DNA interactions can also explain the formation of non-sequential base stackings with longer lifetimes. Such non-sequential base stackings further stabilize the collapsed coil-like folded form of the DNA oligomer.

Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids.

Molecular dynamics simulations are used to contrast the supercooling and crystallization behaviour of monatomic liquids that exemplify the transition from simple to anomalous, tetrahedral liquids. As examples of simple fluids, we use the Lennard-Jones (LJ) liquid and a pair-dominated Stillinger-Weber liquid (SW16). As examples of tetrahedral, water-like fluids, we use the Stillinger-Weber model with variable tetrahedrality parameterized for germanium (SW20), silicon (SW21), and water (SW(23.15) or mW model). The thermodynamic response functions show clear qualitative differences between simple and water-like liquids. For simple liquids, the compressibility and the heat capacity remain small on isobaric cooling. The tetrahedral liquids in contrast show a very sharp rise in these two response functions as the lower limit of liquid-phase stability is reached. While the thermal expansivity decreases with temperature but never crosses zero in simple liquids, in all three tetrahedral liquids at the studied pressure, there is a temperature of maximum density below which thermal expansivity is negative. In contrast to the thermodynamic response functions, the excess entropy on isobaric cooling does not show qualitatively different features for simple and water-like liquids; however, the slope and curvature of the entropy-temperature plots reflect the heat capacity trends. Two trajectory-based computational estimation methods for the entropy and the heat capacity are compared for possible structural insights into supercooling, with the entropy obtained from thermodynamic integration. The two-phase thermodynamic estimator for the excess entropy proves to be fairly accurate in comparison to the excess entropy values obtained by thermodynamic integration, for all five Lennard-Jones and Stillinger-Weber liquids. The entropy estimator based on the multiparticle correlation expansion that accounts for both pair and triplet correlations, denoted by S(trip), is also studied. S(trip) is a good entropy estimator for liquids where pair and triplet correlations are important such as Ge and Si, but loses accuracy for purely pair-dominated liquids, like LJ fluid, or near the crystallization temperature (T(thr)). Since local tetrahedral order is compatible with both liquid and crystalline states, the reorganisation of tetrahedral liquids is accompanied by a clear rise in the pair, triplet, and thermodynamic contributions to the heat capacity, resulting in the heat capacity anomaly. In contrast, the pair-dominated liquids show increasing dominance of triplet correlations on approaching crystallization but no sharp rise in either the pair or thermodynamic heat capacities.

Microscopic dynamics of water around unfolded structures of barstar at room temperature.

The breaking of the native structure of a protein and its influences on the dynamic response of the surrounding solvent is an important issue in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to unfold the protein barstar at two different temperatures (400 K and 450 K). The two unfolded forms obtained at such high temperatures are further studied at room temperature to explore the effects of nonuniform unfolding of the protein secondary structures along two different pathways on the microscopic dynamical properties of the surface water molecules. It is demonstrated that though the structural transition of the protein in general results in less restricted water motions around its segments, but there are evidences of formation of new conformational motifs upon unfolding with increasingly confined environment around them, thereby resulting in further restricted water mobility in their hydration layers. Moreover, it is noticed that the effects of nonuniform unfolding of the protein segments on the relaxation times of the protein-water (PW) and the water-water (WW) hydrogen bonds are correlated with hindered hydration water motions. However, the kinetics of breaking and reformation of such hydrogen bonds are found to be influenced differently at the interface. It is observed that while the effects of unfolding on the PW hydrogen bond kinetics seem to be minimum, but the kinetics involving the WW hydrogen bonds around the protein segments exhibit noticeably heterogeneous characteristics. We believe that this is an important observation, which can provide valuable insights on the origin of heterogeneous influence of unfolding of a protein on the microscopic properties of its hydration water.

Microscopic hydration properties of the aß1-42 Peptide monomer and the globular protein ubiquitin: a comparative molecular dynamics study.

Atomistic molecular dynamics simulations of eight selected conformations of a disordered protein, amyloid beta (1-42) (Aß), and a globular protein, ubiquitin (UBQ), have been carried out in aqueous media at 310 K. Detailed analyses were carried out to compare the microscopic properties of water molecules present in the hydration layers of these systems. It is noticed that irrespective of the conformational heterogeneity among the Aß monomers, water molecules hydrating their surfaces exhibit relatively faster dynamics as compared to water molecules hydrating UBQ. Importantly, the conformational heterogeneity of the Aß monomers has been found to affect the translational and rotational motions of hydration water molecules in a nonuniform manner. Detailed investigation of the timescale of hydrogen bond relaxations at the surface and their energetics revealed the possibility of heterogeneous confinement around different Aß conformations. The distribution of water density fluctuation around Aß conformations are broader compared to UBQ because of its predominant hydrophobic nature. Significant heterogeneity in the density fluctuation among the Aß monomers suggests that the structural propensities could affect the peptide's effective surface hydrophobicity.