Biophysical modeling of the whole-cell dynamics of C. elegans motor and interneurons families.

The nematode Caenorhabditis elegans is a widely used model organism for neuroscience. Although its nervous system has been fully reconstructed, the physiological bases of single-neuron functioning are still poorly explored. Recently, many efforts have been dedicated to measuring signals from C. elegans neurons, revealing a rich repertoire of dynamics, including bistable responses, graded responses, and action potentials. Still, biophysical models able to reproduce such a broad range of electrical responses lack. Realistic electrophysiological descriptions started to be developed only recently, merging gene expression data with electrophysiological recordings, but with a large variety of cells yet to be modeled. In this work, we contribute to filling this gap by providing biophysically accurate models of six classes of C. elegans neurons, the AIY, RIM, and AVA interneurons, and the VA, VB, and VD motor neurons. We test our models by comparing computational and experimental time series and simulate knockout neurons, to identify the biophysical mechanisms at the basis of inter and motor neuron functioning. Our models represent a step forward toward the modeling of C. elegans neuronal networks and virtual experiments on the nematode nervous system.

Modeling of olfactory transduction in AWCON neuron via coupled electrical-calcium dynamics.

Amphid wing "C" (AWC) neurons are among the most important and studied neurons of the nematode Caenorhabditis elegans. In this work, we unify the existing electrical and intracellular calcium dynamics descriptions to obtain a biophysically accurate model of olfactory transduction in AWCON neurons. We study the membrane voltage and the intracellular calcium dynamics at different exposure times and odorant concentrations to grasp a complete picture of AWCON functioning. Moreover, we investigate the complex cascade of biochemical processes that allow AWC activation upon odor removal. We analyze the behavior of the different components of the models and, by suppressing them selectively, we extrapolate their contribution to the overall neuron response and study the resilience of the dynamical system. Our results are all in agreement with the available experimental data. Therefore, we provide an accurate mathematical and biophysical model for studying olfactory signal processing in C. elegans.

Evolution of large Aß16-22 aggregates at atomic details and potential of mean force associated to peptide unbinding and fragmentation events.

Atomic characterization of large nonfibrillar aggregates of amyloid polypeptides cannot be determined by experimental means. Starting from ß-rich aggregates of Y and elongated topologies predicted by coarse-grained simulations and consisting of more than 100 Aß16-22 peptides, we performed atomistic molecular dynamics (MD), replica exchange with solute scaling (REST2), and umbrella sampling simulations using the CHARMM36m force field in explicit solvent. Here, we explored the dynamics within 3 µs, the free energy landscape, and the potential of mean force associated with either the unbinding of one single peptide in different configurations within the aggregate or fragmentation events of a large number of peptides. Within the time scale of MD and REST2, we find that the aggregates experience slow global conformational plasticity, and remain essentially random coil though we observe slow beta-strand structuring with a dominance of antiparallel beta-sheets over parallel beta-sheets. Enhanced REST2 simulation is able to capture fragmentation events, and the free energy of fragmentation of a large block of peptides is found to be similar to the free energy associated with fibril depolymerization by one chain for longer Aß sequences.

Assessment of tools for RNA secondary structure prediction and extraction: a final-user perspective.

The study of RNA structure is fundamental to clarify the RNA molecular functioning. The flexible RNA nature, the huge number of expressed RNAs, and the variety of functions make it challenging to obtain a quantity of structural information comparable to what is already available for proteins. The in silico prediction of RNA 3D structures is of particular relevance, to understand the fundamental features of the structure-function relationship, because the 3D structure drives the molecular interaction with DNA or protein complexes. The quality of the prediction of the RNA 3D structure is determined by the knowledge of a properly predicted or measured secondary structure. In this paper, we comparatively evaluate computational tools to model RNA secondary structure, focusing our investigation, among the dozens of methods in literature, on tools which are freely available and implemented in web-server versions, providing a more direct access to the final users, not necessarily bioinformatics experts. Our focus is on assessing performances for long sequences, with the final aim of selecting best methods for perspective lncRNAs investigation. Indeed, among RNAs, the non-coding and long non-coding RNAs (lncRNAs, with sequence length larger than 200 nts) assume special relevance, due to their function in regulatory mechanisms, which is still largely unexplored in the case of lncRNAs. As lncRNA experimental structures are at present missing, other families of large RNAs are here used as test cases, to establish the reliability of predictive bioinformatics tools and their perspective applicability to the case of lncRNAs.Communicated by Ramaswamy H. Sarma.

In Silico Conformational Features of Botulinum Toxins A1 and E1 According to Intraluminal Acidification.

Although botulinum neurotoxins (BoNTs) are among the most toxic compounds found in nature, their molecular mechanism of action is far from being elucidated. A key event is the conformational transition due to acidification of the interior of synaptic vesicles, leading to translocation of the BoNT catalytic domain into the neuronal cytosol. To investigate these conformational variations, homology modeling and atomistic simulations are combined to explore the internal dynamics of the sub-types BoNT/A1 (the most-used sub-type in medical applications) and BoNT/E1 (the most kinetically efficient sub-type). This first simulation study of di-chain BoNTs in closed and open states considers the effects of both neutral and acidic pH. The conformational mobility is driven by domain displacements of the ganglioside-binding site in the receptor binding domain, the translocation domain (HCNT) switch, and the belt α-helix, which present multiple conformations, depending on the primary sequence and the pH. Fluctuations of the belt α-helix are observed for closed conformations of the toxins and at acidic pH, while patches of more solvent-accessible residues appear under the same conditions in the core translocation domain HCNT. These findings suggest that, during translocation, the higher mobility of the belt could be transmitted to HCNT, leading to the favorable interaction of HCNT residues with the non-polar membrane environment.

Inferring Excitatory and Inhibitory Connections in Neuronal Networks.

The comprehension of neuronal network functioning, from most basic mechanisms of signal transmission to complex patterns of memory and decision making, is at the basis of the modern research in experimental and computational neurophysiology. While mechanistic knowledge of neurons and synapses structure increased, the study of functional and effective networks is more complex, involving emergent phenomena, nonlinear responses, collective waves, correlation and causal interactions. Refined data analysis may help in inferring functional/effective interactions and connectivity from neuronal activity. The Transfer Entropy (TE) technique is, among other things, well suited to predict structural interactions between neurons, and to infer both effective and structural connectivity in small- and large-scale networks. To efficiently disentangle the excitatory and inhibitory neural activities, in the article we present a revised version of TE, split in two contributions and characterized by a suited delay time. The method is tested on in silico small neuronal networks, built to simulate the calcium activity as measured via calcium imaging in two-dimensional neuronal cultures. The inhibitory connections are well characterized, still preserving a high accuracy for excitatory connections prediction. The method could be applied to study effective and structural interactions in systems of excitable cells, both in physiological and in pathological conditions.

A Shearless Microfluidic Device Detects a Role in Mechanosensitivity for AWCON Neuron in Caenorhabditis elegans.

AWC olfactory neurons are fundamental for chemotaxis toward volatile attractants in Caenorhabditis elegans. Here, it is shown that AWCON responds not only to chemicals but also to mechanical stimuli caused by fluid flow changes in a microfluidic device. The dynamics of calcium events are correlated with the stimulus amplitude. It is further shown that the mechanosensitivity of AWCON neurons has an intrinsic nature rather than a synaptic origin, and the calcium transient response is mediated by TAX-4 cGMP-gated cation channel, suggesting the involvement of one or more "odorant" receptors in AWCON mechano-transduction. In many cases, the responses show plateau properties resembling bistable calcium dynamics where neurons can switch from one stable state to the other. To investigate the unprecedentedly observed mechanosensitivity of AWCON neurons, a novel microfluidic device is designed to minimize the fluid shear flow in the arena hosting the nematodes. Animals in this device show reduced neuronal activation of AWCON neurons. The results observed indicate that the tangential component of the mechanical stress is the main contributor to the mechanosensitivity of AWCON . Furthermore, the microfluidic platform, integrating shearless perfusion and calcium imaging, provides a novel and more controlled solution for in vivo analysis both in micro-organisms and cultured cells.

Correction: Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD.

[This corrects the article DOI: 10.1371/journal.pone.0218738.].

Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor.

Molecular studies of human pentameric ligand-gated ion channels (LGICs) expressed in neurons and at neuromuscular junctions are of utmost importance in the development of therapeutic strategies for neurological disorders. We focus here on the nicotinic acetylcholine receptor nAChR-α7, a homopentameric channel widely expressed in the human brain, with a proven role in a wide spectrum of disorders including schizophrenia and Alzheimer's disease. By exploiting an all-atom structural model of the full (transmembrane and extracellular) protein in the open, agonist-bound conformation we recently developed, we evaluate the free energy and the mean first passage time of single-ion permeation using molecular dynamics simulations and the milestoning method with Voronoi tessellation. The results for the wild-type channel provide the first available mapping of the potential of mean force in the full-length α7 nAChR, reveal its expected cationic nature, and are in good agreement with simulation data for other channels of the LGIC family and with experimental data on nAChRs. We then investigate the role of a specific mutation directly related to ion selectivity in LGICs, the E-1' → A-1' substitution at the cytoplasmatic selectivity filter. We find that the mutation strongly affects sodium and chloride permeation in opposite directions, leading to a complete inversion of selectivity, at variance with the limited experimental results available that classify this mutant as cationic. We thus provide structural determinants for the observed cationic-to-anionic inversion, revealing a key role of the protonation state of residue rings far from the mutation, in the proximity of the hydrophobic channel gate.

Improved transition metal surface energies from a generalized gradient approximation developed for quasi two-dimensional systems.

Nonuniform density scaling in the quasi-two-dimensional (quasi-2D) regime is an important and challenging aspect of the density functional theory. Semilocal exchange-correlation energy functionals, developed by solving the dimensional crossover criterion in the quasi-2D regime, have great theoretical and practical importance. However, the only semilocal generalized gradient approximation (GGA) that has been designed to satisfy this criterion is the Q2D-GGA [L. Chiodo et al., Phys. Rev. Lett. 108, 126402 (2012)]. Here, we establish the applicability, broadness, and accuracy of the Q2D-GGA functional by performing an extensive assessment of this functional for transition metal surface energies. The important characteristic of the surface density localization and oscillation due to the rearrangement of the d electrons is also shown for different metal surfaces.

Hepatitis B protein HBx binds the DLEU2 lncRNA to sustain cccDNA and host cancer-related gene transcription.

OBJECTIVE: The HBV HBx regulatory protein is required for transcription from the covalently closed circular DNA (cccDNA) minichromosome and affects the epigenetic control of both viral and host cellular chromatin. DESIGN: We explored, in relevant cellular models of HBV replication, the functional consequences of HBx interaction with DLEU2, a long non-coding RNA (lncRNA) expressed in the liver and increased in human hepatocellular carcinoma (HCC), in the regulation of host target genes and the HBV cccDNA. RESULTS: We show that HBx binds the promoter region, enhances the transcription and induces the accumulation of DLEU2 in infected hepatocytes. We found that nuclear DLEU2 directly binds HBx and the histone methyltransferase enhancer of zeste homolog 2 (EZH2), the catalytic active subunit of the polycomb repressor complex 2 (PRC2) complex. Computational modelling and biochemical evidence suggest that HBx and EZH2 share two preferential binding sites in DLEU2 intron 1. HBx and DLEU2 co-recruitment on the cccDNA displaces EZH2 from the viral chromatin to boost transcription and viral replication. DLEU2-HBx association with target host promoters relieves EZH2 repression and leads to the transcriptional activation of a subset of EZH2/PRC2 target genes in HBV-infected cells and HBV-related HCCs. CONCLUSIONS: Our results highlight the ability of HBx to bind RNA to impact on the epigenetic control of both viral cccDNA and host genes and provide a new key to understand the role of DLEU2 and EZH2 overexpression in HBV-related HCCs and HBx contribution to hepatocytes transformation.

Ab initio accelerated molecular dynamics study of the hydride ligands in the ruthenium complex: Ru(H2)2H2(P(C5H9)3)2.

The dihydrogen complex Ru(H2)2H2(P(C5H9)3)2 has been investigated, via ab initio accelerated molecular dynamics, to elucidate the H ligands dynamics and possible reaction paths for H2/H exchange. We have characterized the free energy landscape associated with the H atoms positional exchange around the Ru centre. From the free energy landscape, we have been able to estimate a barrier of 6 kcal mol-1 for the H2/H exchange process. We have also observed a trihydrogen intermediate as a passing state along some of the possible reaction pathways.

Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD.

C. elegans neuronal system constitutes the ideal framework for studying simple, yet realistic, neuronal activity, since the whole nervous system is fully characterized with respect to the exact number of neurons and the neuronal connections. Most recent efforts are devoted to investigate and clarify the signal processing and functional connectivity, which are at the basis of sensing mechanisms, signal transmission, and motor control. In this framework, a refined modelof whole neuron dynamics constitutes a key ingredient to describe the electrophysiological processes, both at thecellular and at the network scale. In this work, we present Hodgkin-Huxley-based models of ion channels dynamics black, built on data available both from C. elegans and from other organisms, expressing homologous channels. We combine these channel models to simulate the electrical activity oftwo among the most studied neurons in C. elegans, which display prototypical dynamics of neuronal activation, the chemosensory AWCON and the motor neuron RMD. Our model properly describes the regenerative responses of the two cells. We analyze in detail the role of ion currents, both in wild type and in in silico knockout neurons. Moreover, we specifically investigate the behavior of RMD, identifying a heterogeneous dynamical response which includes bistable regimes and sustained oscillations. We are able to assess the critical role of T-type calcium currents, carried by CCA-1 channels, and leakage currents in the regulation of RMD response. Overall, our results provide new insights in the activity of key C. elegans neurons. The developed mathematical framework constitute a basis for single-cell and neuronal networks analyses, opening new scenarios in the in silico modeling of C. elegans neuronal system.

Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study.

Nicotinic acetylcholine receptors, belonging to the Cys-loop superfamily of ligand-gated ion channels (LGICs), are membrane proteins present in neurons and at neuromuscular junctions. They are responsible for signal transmission, and their function is regulated by neurotransmitters, agonists, and antagonists drugs. A detailed knowledge of their conformational transition in response to ligand binding is critical to understanding the basis of ligand-receptor interaction, in view of new pharmacological approaches to control receptor activity. However, the scarcity of experimentally derived structures of human channels makes this perspective extremely challenging. To contribute overcoming this issue, we have recently reported structural models for the open and the desensitized states of the human α7 nicotinic receptor. Here, we provide all-atom structural models of the same receptor in two different nonconductive states. The first structure, built via homology modeling and relaxed with extensive Molecular Dynamics simulations, represents the receptor bound to the natural antagonist α-conotoxin ImI. After comparison with available experimental data and computational models of other eukaryotic LGICs, we deem it consistent with the "closed-locked" state. The second model, obtained with simulations from the spontaneous relaxation of the open, agonist-bound α7 structure after ligand removal, recapitulates the characteristics of the apo-resting state of the receptor. These results add to our previous work on the active and desensitized state conformations, contributing to the structural characterization of the conformational landscape of the human α7 receptor and suggesting benchmarks to discriminate among conformations found in experiments or in simulations of LGICs. In particular key interactions at the interface between the extracellular domain and the transmembrane domain are identified, that could be critical to the α7 receptor function.

A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation.

Nicotinic acetylcholine receptors (nAchRs) are ligand-gated ion channels that regulate chemical transmission at the neuromuscular junction. Structural information is available at low resolution from open and closed forms of an eukaryotic receptor, and at high resolution from other members of the same structural family, two prokaryotic orthologs and an eukaryotic GluCl channel. Structures of human channels however are still lacking. Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far. This is due to different problems with the template structures: on one side the homology with prokaryotic species is too low, while on the other the open eukaryotic GluCl proved itself unstable in several MD studies and collapsed to a dehydrated, non-conductive conformation, even when bound to an agonist. Aim of this work is to obtain, by a mixing of state-of-the-art homology and simulation techniques, a plausible prediction of the structure (still unknown) of the open state of human α7 nAChR complexed with epibatidine, from which it is possible to start structural and functional test studies. To prevent channel closure we employ a restraint that keeps the transmembrane pore open, and obtain in this way a stable, hydrated conformation. To further validate this conformation, we run four long, unbiased simulations starting from configurations chosen at random along the restrained trajectory. The channel remains stable and hydrated over the whole runs. This allows to assess the stability of the putative open conformation over a cumulative time of 1 µs, 800 ns of which are of unbiased simulation. Mostly based on the analysis of pore hydration and size, we suggest that the obtained structure has reasonable chances to be (at least one of the possible) structures of the channel in the open conformation.

Orbital dependent Rashba splitting and electron-phonon coupling of 2D Bi phase on Cu(100) surface.

A monolayer of bismuth deposited on the Cu(100) surface forms a highly ordered c(2×2) reconstructed phase. The low energy single particle excitations of the c(2×2) Bi/Cu(100) present Bi-induced states with a parabolic dispersion in the energy region close to the Fermi level, as observed by angle-resolved photoemission spectroscopy. The electronic state dispersion, the charge density localization, and the spin-orbit coupling have been investigated combining photoemission spectroscopy and density functional theory, unraveling a two-dimensional Bi phase with charge density well localized at the interface. The Bi-induced states present a Rashba splitting, when the charge density is strongly localized in the Bi plane. Furthermore, the temperature dependence of the spectral density close to the Fermi level has been evaluated. Dispersive electronic states offer a large number of decay channels for transitions coupled to phonons and the strength of the electron-phonon coupling for the Bi/Cu(100) system is shown to be stronger than for Bi surfaces and to depend on the electronic state symmetry and localization.

Nonuniform scaling applied to surface energies of transition metals.

We construct a generalized gradient approximation of the exchange-correlation energy that satisfies the nonuniform scaling in one dimension and is accurate in the whole quasi-two-dimensional (Q2D) regime. Using spatial and energetic analyses of metal (111) surfaces, we show that the Q2D behavior is important at the surface of most transition metals, and that the here proposed Q2D-generalized gradient approximation functional predicts for these metals accurate surface energies as well as bulk properties.

Structure, electronic, and optical properties of TiO2 atomic clusters: an ab initio study.

Atomic clusters of TiO(2) are modeled by means of state-of-the-art techniques to characterize their structural, electronic and optical properties. We combine ab initio molecular dynamics, static density functional theory, time-dependent density functional theory, and many body techniques, to provide a deep and comprehensive characterization of these systems. TiO(2) clusters can be considered as the starting seeds for the synthesis of larger nanostructures, which are of technological interest in photocatalysis and photovoltaics. In this work, we prove that clusters with anatase symmetry are energetically stable and can be considered as the starting seeds to growth much larger and complex nanostructures. The electronic gap of these inorganic molecules is investigated, and shown to be larger than the optical gap by almost 4 eV. Therefore, strong excitonic effects appear in these systems, much more than in the corresponding bulk phase. Moreover, the use of various levels of theory demonstrates that charge transfer effects play an important role under photon absorption, and therefore the use of adiabatic functionals in time dependent density functional theory has to be carefully evaluated.

Experimental and theoretical investigation of the pyrrole/Al(100) interface.

The electronic properties of the pyrrole/Al(100) interface have been investigated from both a theoretical and experimental point of view. Electron energy loss spectroscopy (EELS) in specular reflection geometry does not reveal modification of the electronic structure of the molecule when adsorbed on the Al surface. EELS results and the low desorption temperature of pyrrole indicate a weak molecule/metal interaction. Ab initio calculations in the framework of the single-particle density functional theory within the local density approximation was used to investigate the adsorption energy and geometry. The low adsorption energy, -0.51 eV per molecule, and the high N-Al distance, 1.98 A, confirm the weak interaction of pyrrole adsorbed on the Al surface.

An ab initio study of the magnetic-metallic CoPt(3)-Au interfaces.

The new challenging field of fabrication and interconnection of inorganic nanostructures is giving new impetus to the study of solid-solid interfacial properties. In nanocrystals made of two domains of different chemical composition and sharing an interface, the interfacial behavior is indeed critical for the stability of such an interface, and also in determining the mutual interactions of the two domains. Following a recent study by our group on the growth of colloidal nanocrystal heterodimers made of a domain of Au and a domain of CoPt(3), we report here an ab initio density functional theory study of the structural and electronic properties of Au/CoPt(3) interfaces. We have investigated the structure of different bulk CoPt(3) facets and of Au atoms adsorbed on CoPt(3). We calculated CoPt(3) and Au surface energies, Au/CoPt(3) interfacial energies as well as adsorption energies of Au atoms on CoPt(3) and Au, and we can draw some important conclusions about the growth mechanism of gold on the magnetic alloy. Furthermore, we give here a detailed description of surface and interfacial electronic properties, which in turn determine the possibility of tuning conductivity and magnetic properties in the nanostructure.