The First in-silico Model of Leg Movement Activity During Sleep

We developed the first model simulator of leg movements activity during sleep. We designed and calibrated a phenomenological model on control subjects not showing significant periodic leg movements (PLM). To test a single generator hypothesis behind PLM—a single pacemaker possibly resulting from two (or more) interacting spinal/supraspinal generators—we added a periodic excitatory input to the control model. We describe the onset of a movement in one leg as the firing of a neuron integrating physiological excitatory and inhibitory inputs from the central nervous system, while the duration of the movement was drawn in accordance with statistical evidence. The period and the intensity of the periodic input were calibrated on a dataset of subjects showing PLM (mainly restless legs syndrome patients). Despite its many simplifying assumptions—the strongest being the stationarity of the neural processes during night sleep—the model simulations are in remarkable agreement with the polysomnographically recorded data

Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics

Abstract Background Molecular phenomena driving pathological aggregation in neurodegenerative diseases are not completely understood yet. Peculiar is the case of Spinocerebellar Ataxia 3 (SCA3) where the conformational properties of the AT-3 N-terminal region, also called Josephin Domain (JD), play a key role in the first step of aggregation, having the JD an amyloidogenic propensity itself. For this reason, unraveling the intimate relationship between JD structural features and aggregation tendency may lead to a step forward in understanding the pathology and rationally design a cure. In this connection, computational modeling has demonstrated to be helpful in exploring the protein molecular dynamics and mechanism of action. Results Conformational dynamics of the JD is here finely investigated by replica exchange molecular dynamics simulations able to sample the microsecond time scale and to provide both a thermodynamic and kinetic description of the protein conformational changes. Accessible structural conformations of the JD have been identified in: open, intermediate and closed like arrangement. Data indicated the closed JD arrangement as the most likely protein arrangement. The protein transition from closed toward intermediate/open states was characterized by a rate constant higher than 700\ua0ns. This result also explains the inability of classical molecular dynamics to explore transitions from closed to open JD configuration on a time scale of hundreds of nanoseconds. Conclusion This work provides the first kinetic estimation of the JD transition pathway from open-like to closed-like arrangement and vice-versa, indicating the closed-like arrangement as the most likely configuration for a JD in water environment. More widely, the importance of our results is also underscored considering that the ability to provide a kinetic description of the protein conformational changes is a scientific challenge for both experimental and theoretical approaches to date. Reviewers This article was reviewed by Oliviero Carugo, Bojan Zagrovic

Conformational dynamics and stability of u-shaped and s-shaped amyloid β assemblies

Alzheimer’s disease is the most fatal neurodegenerative disorder characterized by the aggregation and deposition of Amyloid β (Aβ) oligomers in the brain of patients. Two principal variants of Aβ exist in humans: Aβ1–40 and Aβ1–42. The former is the most abundant in the plaques, while the latter is the most toxic species and forms fibrils more rapidly. Interestingly, fibrils of Aβ1–40 peptides can only assume U-shaped conformations while Aβ1–42 can also arrange as S-shaped three-stranded chains, as recently discovered. As alterations in protein conformational arrangement correlate with cell toxicity and speed of disease progression, it is important to characterize, at molecular level, the conformational dynamics of amyloid fibrils. In this work, Replica Exchange Molecular Dynamics simulations were carried out to compare the conformational dynamics of U-shaped and S-shaped Aβ17–42 small fibrils. Our computational results provide support for the stability of the recently proposed S-shaped model due to the maximized interactions involving the C-terminal residues. On the other hand, the U-shaped motif is characterized by significant distortions resulting in a more disordered assembly. Outcomes of our work suggest that the molecular architecture of the protein aggregates might play a pivotal role in formation and conformational stability of the resulting fibrils

Cell Penetrating Peptide Adsorption on Magnetite and Silica Surfaces: A Computational Investigation

Magnetic nanoparticles (MNPs) represent one of the most promising materials as they can act as a versatile platform in the field of bionanotechnology for enhanced imaging, diagnosis, and treatment of various diseases. Silica is the most common compound for preparing coated iron oxide NPs since it improves colloidal stability and the binding affinity for various organic molecules. Biomolecules such as cell penetrating peptides (CPPs) might be employed to decorate MNPs, combining their promising physicochemical properties with a cell penetrating ability. In this work, a computational investigation on adsorption of Antennapedia homeodomain-derived penetrating peptide (pAntp) on silica and magnetite (MAG) surfaces is presented. By employing umbrella sampling molecular dynamics, we provided a quantitative estimation of the pAntp-surface adsorption free energy to highlight the influence of surface hydroxylation state on the adsorption mechanism. The interaction between peptide and surface has shown to be mainly driven by electrostatics. In case of MAG surface, also an important contribution of van der Waals (VdW) attraction was observed. Our data suggest that a competitive mechanism between MNPs and cell membrane might partially inhibit the CPP to carry out its membrane penetrating function

High-density EEG power topography and connectivity during confusional arousal.

Confusional arousal is the milder expression of a family of disorders known as Disorders of Arousal (DOA) from non-REM sleep. These disorders are characterized by recurrent abnormal behaviors that occur in a state of reduced awareness for the external environment. Despite frequent amnesia for the nocturnal events, when actively probed, patients are able to report vivid hallucinatory/dream-like mental imagery. Traditional (low-density) scalp and stereo-electroencephalographic (EEG) recordings previously showed a pathological admixture of slow oscillations typical of NREM sleep and wake-like fast-mixed frequencies during these phenomena. However, our knowledge about the specific neural EEG dynamics over the entire brain is limited. We collected 2 consecutive in-laboratory sleep recordings using high-density (hd)-EEG (256 vertex-referenced geodesic system) coupled with standard video-polysomnography (v-PSG) from a 12-year-old drug-naïve and otherwise healthy child with a long-lasting history of sleepwalking. Source power topography and functional connectivity were computed during 20 selected confusional arousal episodes (from -6 to +18 sec after motor onset), and during baseline slow wave sleep preceding each episode (from - 3 to -2 min before onset). We found a widespread increase in slow wave activity (SWA) theta, alpha, beta, gamma power, associated with a parallel decrease in the sigma range during behavioral episodes compared to baseline sleep. Bilateral Broadman area 7 and right Broadman areas 39 and 40 were relatively spared by the massive increase in SWA power. Functional SWA connectivity analysis revealed a drastic increase in the number and complexity of connections from baseline sleep to full-blown episodes, that mainly involved an increased out-flow from bilateral fronto-medial prefrontal cortex and left temporal lobe to other cortical regions. These effects could be appreciated in the 6 sec window preceding behavioral onset. Overall, our results support the idea that DOA are the expression of peculiar brain states, compatible with a partial re-emergence of consciousness

Percolative properties of hard oblate ellipsoids of revolution with a soft shell

We present an in-depth analysis of the geometrical percolation behavior in the continuum of random assemblies of hard oblate ellipsoids of revolution. Simulations where carried out by considering a broad range of aspect-ratios, from spheres up to aspect-ratio 100 plate-like objects, and with various limiting two particle interaction distances, from 0.05 times the major axis up to 4.0 times the major axis. We confirm the widely reported trend of a consistent lowering of the hard particle critical volume fraction with the increase of the aspect-ratio. Moreover, assimilating the limiting interaction distance to a shell of constant thickness surrounding the ellipsoids, we propose a simple relation based on the total excluded volume of these objects which allows to estimate the critical concentration from a quantity which is quasi-invariant over a large spectrum of limiting interaction distances. Excluded volume and volume quantities are derived explicitly.Comment: 11 pages, 8 figure

The Role of Structural Polymorphism in Driving the Mechanical Performance of the Alzheimer's Beta Amyloid Fibrils

Alzheimer's Disease (AD) is related with the abnormal aggregation of amyloid β-peptides Aβ1−40 and Aβ1−42, the latter having a polymorphic character which gives rise to U- or S-shaped fibrils. Elucidating the role played by the nanoscale-material architecture on the amyloid fibril stability is a crucial breakthrough to better understand the pathological nature of amyloid structures and to support the rational design of bio-inspired materials. The computational study here presented highlights the superior mechanical behavior of the S-architecture, characterized by a Young's modulus markedly higher than the U-shaped architecture. The S-architecture showed a higher mechanical resistance to the enforced deformation along the fibril axis, consequence of a better interchain hydrogen bonds' distribution. In conclusion, this study, focusing the attention on the pivotal multiscale relationship between molecular phenomena and material properties, suggests the S-shaped Aβ1−42 species as a target of election in computational screen/design/optimization of effective aggregation modulators

Modelling protein-protein interactions to elucidate molecular mechanisms behind neurodegenerative diseases

The worldwide significant increase in life expectancy has recently drawn the attention of the scientific community to neurodegenerative pathologies of the elderly population. These neurodegenerative disorders arise from the abnormal protein aggregation in the nervous tissue leading to intracellular inclusions or extracellular aggregates in specific brain areas. A feasible strategy to prevent the resulting neurodegeneration is based on the development of anti-amyloid molecules, i.e., those capable of preventing the generation of toxic aggregates. To address this issue, it’s extremely important to shed light on the molecular interactions responsible for protein aggregation. Despite substantial research efforts in this field, the fundamental mechanisms of protein misfolding and aggregation mechanisms remain somewhat unrevealed. In this context, computational molecular modelling represents a powerful tool in connecting macroscopic experimental findings to nanoscale molecular events. The present PhD thesis focuses on the application of computational methodologies to investigate molecular features of protein-protein interactions responsible for two different pathologies: Spinocerebellar Ataxia Type-1 (SCA1) and Alzheimer’s Disease (AD). To address this goal, molecular dynamics simulations have been employed to elucidate the early stages of protein aggregation mechanism at molecular level. From the computational point of view, insufficient sampling often limits the ability of computer simulations to investigate the conformational properties of biomacromolecules. The limitation mainly results from proteins’ rough energy landscapes, with many local minima separated by high-energy barriers. Within this framework, one of the main challenges of MD simulations is the ability to sample experimentally relevant millisecond to second timescales. However, the time-scale of the classical MD simulations with atomic resolution is today limited to few μs. In this regard, enhanced sampling methods represent a powerful tool to improve the sampling efficiency of classical MD, including those that artificially add an external driving force to guide the protein from one structure to another. The present PhD work benefits from the application of enhanced sampling techniques and dimensionality reduction methodologies to elucidate the aggregation pathway of the Ataxin-1 and Amyloid Beta assembly, responsible for SCA1 and AD, respectively. Outcome of the present research represents an important piece of knowledge to design small molecules able to inhibit the protein-protein interactions leading to aggregation. On the other hand, fine tuning of the interatomic forces responsible for the intriguing mechanical properties of the amyloid fibrils is a crucial breakthrough to support the rational design of amyloid-inspired nanostructures as novel biomaterials

Effect of lactose pseudopolymorphic transition on the aerosolization performance of drug/carrier mixtures

Physico-chemical properties of lactose are key factors in adhesive mixtures used as dry powder inhaler (DPI). Despite the abundant literature on this topic, the effect of the polymorphism and pseudo-polymorphism of lactose has been seldom investigated and discussed although often lactose used in DPI is subjected to unit operations, which may alter its solid-state properties. Here, we studied the aerosolization performance of salbutamol sulphate (SS) or budesonide (BUD) formulations by investigating the effect of lactose pseudopolymorphism in ternary (coarse lactose/fine lactose/drug) and binary (coarse lactose/drug) mixtures. An improvement of the aerosolization performance of SS formulations with the increase of the amount of fine micronized lactose up to 30% (fine particle fraction (FPF) = 57%) was observed. Micronized lactose contained hygroscopic anhydrous α-lactose, which converted to α-lactose monohydrate at ambient conditions. This implied that the positive effect of fines on the aerosolization performance decreased and eventually disappeared with the formulation aging. Positive effect on SS deposition was observed also with binary mixtures with anhydrous lactose, whereas the opposite occurred with budesonide-containing formulations. The collected data demonstrated the crucial role of the carrier crystal form on the positive effect of fines on the deposition