A computational study to assess the pathogenicity of single or combinations of missense variants on respiratory complex I.

Variants found in the respiratory complex I (CI) subunit genes encoded by mitochondrial DNA can cause severe genetic diseases. However, it is difficult to establish a priori whether a single or a combination of CI variants may impact oxidative phosphorylation. Here we propose a computational approach based on coarse-grained molecular dynamics simulations aimed at investigating new CI variants.

One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics.

The supramolecular interaction between lanthanide complexes and proteins is at the heart of numerous chemical and biological studies. Some of these complexes have demonstrated remarkable interaction properties with proteins or peptides in solution and in the crystalline state. Here we have used the paramagnetism of lanthanide ions to characterize the affinity of two lanthanide complexes for ubiquitin.

Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations.

Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines.

Current Overview of CDKL-5 Deficiency Disorder Treatment.

CDKL5 deficiency disorder (CDD) is a complex of clinical symptoms resulting from the presence of non-functional or absent CDKL5 protein, a serine-threonine kinase involved in neural maturation and synaptogenesis [...

Probing the dynamical interaction of the -sulfonato-calix[4]arene with an antifungal protein.

Calixarenes are hallmark molecules in supramolecular chemistry as hosts for small ligands. They have also conversely proved their interest as ligands toward assisted co-crystallization of proteins. These functionalized macrocycles target positively-charged residues, and notably surface-exposed lysines, with a site-selectivity finely characterized experimentally, but that remains to be assessed.

Capturing the Recognition Dynamics of -Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment.

Calix[]arenes' selective recognition of protein surfaces covers a broad range of timely applications, from controlling protein assembly and crystallization to trapping partially disordered proteins. Here, the interaction of -sulfonated calix-[4]-arenes with cytochrome c is investigated through all-atom, explicit water molecular dynamics simulations which allow characterization of two binding sites in quantitative agreement with experimental evidence. Free energy calculations based on the MM-PBSA and the attach-pull-release (APR) methods highlight key residues implicated in the recognition process and provide binding free energy results in quantitative agreement with isothermal titration calorimetry.

Influence of Divalent Cations in the Protein Crystallization Process Assisted by Lanthanide-Based Additives.

The use of lanthanide complexes as powerful auxiliaries for biocrystallography prompted us to systematically analyze the influence of the commercial crystallization kit composition on the efficiency of two lanthanide additives: [Eu(DPA)] and Tb-Xo4. This study reveals that the tris(dipicolinate) complex presents a lower chemical stability and a strong tendency toward false positives, which are detrimental for its use in a high-throughput robotized crystallization platform. In particular, the crystal structures of (Mg(HO))[Eu(DPA)]·7HO (), {(Ca(HO))[Eu(DPA)]}·10HO (), and {Cu(DPA)(HO)} (), resulting from spontaneous crystallization in the presence of a divalent alkaline-earth cation and transmetalation, are reported.

REM Sleep and Total Sleep Time Improvement After Routine Repetitive Transcranial Magnetic Stimulation in Active Duty Service Members With Depression.

Objectives: The prevalence of depression and insomnia in the military are substantial. Several transcranial magnetic stimulation (TMS) studies have used self-report sleep data as secondary research outcomes; however, there are limited studies using the gold standard of polysomnography (PSG) to ascertain actual sleep changes. Here, we provide data from a pilot and feasibility study using PSG to measure sleep changes after repetitive TMS.

Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration.

In the realm of biomolecules, peptides can present a large diversity of structures. Our study sheds new light on the structural interplay between a tris-dipicolinate lanthanide probe and a decapeptide SASYKTLPRG. Although a rather trivial, electrostatically driven interaction was expected, the combination of paramagnetic NMR and molecular dynamics simulations reveals a highly dynamic association process and allows for providing extensive insights into the interaction sites and their occupancy.

Assessing the sequence dependence of pyrimidine-pyrimidone (6-4) photoproduct in a duplex double-stranded DNA: A pitfall for microsecond range simulation.

Sequence dependence of the (6-4) photoproduct conformational landscape when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending, and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing different upstream and downstream flexibilities.

Molecular Dynamics Approach for Capturing Calixarene-Protein Interactions: The Case of Cytochrome C.

Functionalized supramolecular cages are of growing importance in biology and biochemistry. They have recently been proposed as efficient auxiliaries to obtain high-resolution cocrystallized proteins. Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonated calix-[8]-arenes to cytochrome c starting from initially distant proteins and ligands.

Interaction of O2 with CH4, CF4, and CCl4 by Molecular Beam Scattering Experiments and Theoretical Calculations.

Gas phase collisions of O2 by CH4, CF4, and CCl4 have been investigated with the molecular beam technique by measuring both the integral cross section value, Q, and its dependence on the collision velocity, v. The adopted experimental conditions have been appropriate to resolve the oscillating "glory" pattern, a quantum interference effect controlled by the features of the intermolecular interaction, for all the three case studies. The analysis of the Q(v) data, performed by adopting a suitable representation of the intermolecular potential function, provided the basic features of the anisotropic potential energy surfaces at intermediate and large separation distances and information on the relative role of the physically relevant types of contributions to the global interaction.

Stereodynamics in the Collisional Autoionization of Water, Ammonia, and Hydrogen Sulfide with Metastable Rare Gas Atoms: Competition Between Intermolecular Halogen and Hydrogen Bonds.

Recent experiments on the title subject, performed with a high-resolution crossed-beam apparatus, have provided the total ionization cross sections as a function of the collision energy between noble gas atoms, electronically excited in their metastable states (Ng*), and H2 O, H2 S, and NH3 reagents, as well as the emitted electron energy spectra. This paper presents a rationalization of all the experimental findings in a unifying picture to cast light on the basic chemical properties of Ng* under conditions of great relevance both from a fundamental and from an applied point of view. The importance of this investigation is that it isolates the selective role of the intermolecular halogen and hydrogen bonds, to assess their anisotropic effects on the stereodynamics of the promoted ionization reactions, and to model energy transfer and reactivity in systems of applied interest, such as planetary atmospheres, plasmas, lasers, and flames.

MYOCLONIC ASTATIC EPILEPSY IN A PATIENT WITH A DE NOVO 4q21.22q21.23 MICRODUPLICATION.

Myoclonicastatic epilepsy (MAE) is a rare form of symptomatic generalized epilepsy of uncertain etiology. To search the possible genetic basis of the disorder, here we investigate a 15 year-old patient with MAE, who is the only person presenting epilepsy in the family. High resolution array-CGH analysis was conducted on DNA extracted from peripheral blood of the patient and the parents.

H2O-CH4 and H2S-CH4 complexes: a direct comparison through molecular beam experiments and ab initio calculations.

New molecular beam scattering experiments have been performed to measure the total (elastic plus inelastic) cross sections as a function of the velocity in collisions between water and hydrogen sulfide projectile molecules and the methane target. Measured data have been exploited to characterize the range and strength of the intermolecular interaction in such systems, which are of relevance as they drive the gas phase molecular dynamics and the clathrate formation. Complementary information has been obtained by rotational spectra, recorded for the hydrogen sulfide-methane complex, with a pulsed nozzle Fourier transform microwave spectrometer.

Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases.

The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl4 and CF4. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems.

Experimental evidence of chemical components in the bonding of helium and neon with neutral molecules.

The complexes of helium and neon with gaseous neutral molecules are generally perceived to be van der Waals adducts held together by physical (non-covalent) forces, owing to the combination of size (exchange) repulsion with dispersion/induction attraction. Molecular beam experiments confirm that this is the case for He-CF4 , Ne-CF4 adducts, but revealed that the interaction of He and Ne with CCl4 features an appreciable contribution of chemical components that arise from the anisotropy of the electron density of CCl4 that enhances a charge transfer from Ng (Ng=He, Ne). These findings furnish a novel assay of the bonding capabilities of helium and neon, and invite to revisit the neutral complexes of these elements as systems of chemical relevance.

Lacosamide in children with refractory status epilepticus. A multicenter Italian experience.

Objective: Status epilepticus (SE) is considered a life-threatening medical emergency. First-line treatment with antiepileptic drugs (AEDs) consists of intravenous benzodiazepines followed by phenytoin. SE is considered refractory (RSE) when unresponsive to standard doses of the first two AEDs.

Intermolecular interaction in the H2S-H2 complex: molecular beam scattering experiments and ab-inito calculations.

New molecular beam scattering experiments are reported for the H2S-H2 system recording, under high angular and velocity resolution conditions, the "glory" quantum interference in the velocity dependence of the total cross section. The analysis of the experimental data permits the determination, for the first time, of a spherically averaged intermolecular potential for this system. An evaluation of significant cuts of the potential energy surface, obtained by accurate ab initio CCSD(T) calculations using large basis sets, combined with the analysis of the electronic charge displacement accompanying the formation of H2S-H2, has been also performed in order to rationalize the experimental findings.

Aicardi syndrome associated with autosomal genomic imbalance: coincidence or evidence for autosomal inheritance with sex-limited expression?

Aicardi syndrome (AIS), a rare neurodevelopmental disorder thought to be caused by an X-linked dominant mutation, is characterized by 3 main features: agenesis of corpus callosum, infantile spams and chorioretinal lacunae. A genome-wide study of a girl with AIS lead us to identify a 6q deletion;12q duplication, derived from a maternal 6q;12q translocation. The two intellectually impaired brothers of the proband showed the same genomic anomalies, but not the constellation of features characterizing the AIS.

The Influence of Dietary Characteristics on the Milk Quantity and Quality of Riverine Buffaloes: Estimate of the Energy/Protein Requirements, for a Medium-high Production, in the First Ninety Days of Lactation.

The data used came from two trials undertaken under the same climatic conditions (spring-summer). In both trials pluriparious buffaloes were utilized similar in weight, body condition score, and milk production from the previous year. From the first trial the data used was from the sub-period 23-88 DIM provided by seven animals fed ad libitum with diet A (6.