Structural investigation of human cystine/glutamate antiporter system xc - (Sxc -) using homology modeling and molecular dynamics.

The cystine/glutamate antiporter system xc - (Sxc -) belongs to the SLC7 family of plasma membrane transporters. It exports intracellular glutamate along the latter's concentration gradient as a driving force for cellular uptake of cystine. Once imported, cystine is mainly used for the production of glutathione, a tripeptide thiol crucial in maintenance of redox homeostasis and protection of cells against oxidative stress. Overexpression of Sxc - has been found in several cancer cells, where it is thought to counteract the increased oxidative stress. In addition, Sxc - is important in the central nervous system, playing a complex role in regulating glutamatergic neurotransmission and glutamate toxicity. Accordingly, this transporter is considered a potential target for the treatment of cancer as well as neurodegenerative diseases. Till now, no specific inhibitors are available. We herein present four conformations of Sxc - along its transport pathway, obtained using multi-template homology modeling and refined by means of Molecular Dynamics. Comparison with a very recently released cryo-EM structure revealed an excellent agreement with our inward-open conformation. Intriguingly, our models contain a structured N-terminal domain that is unresolved in the experimental structures and is thought to play a gating role in the transport mechanism of other SLC7 family members. In contrast to the inward-open model, there is no direct experimental counterpart for the other three conformations we obtained, although they are in fair agreement with the other stages of the transport mechanism seen in other SLC7 transporters. Therefore, our models open the prospect for targeting alternative Sxc - conformations in structure-based drug design efforts.

Mechanistic Study on Water Splitting Reactions by Small Silicon Clusters Si3X, X = Si, Be, Mg, Ca.

Interaction, dissociation, and dehydrogenation reactions of water monomer and dimer with pure and mixed tetrameric silicon clusters Si3X with X = Si, Be, Mg, Ca were investigated using high accuracy quantum chemical calculations. While geometries were optimized using the DFT/B3LYP functional with the aug-cc-pVTZ basis set, reaction energy profiles were constructed making use of the coupled-cluster theory with extrapolation to complete basis set, CCSD(T)/CBS. Cleavage of the O-H bond in water dimer is found to be more favored than that of water monomer in the reaction with Si4. The water acceptor monomer in water dimer performs as an internal catalyst facilitating H atom transfer to form H2. Adsorption of water dimer on Si3X clusters mostly takes place upon interaction of the donor water molecule with Si cluster. Water dimer adsorbs more strongly on Si3M than on Si4. The most stable complexes obtained upon interaction of water dimer with Si3M mainly arise from M-O interaction in preference over a Si-O connection. Substitution of a Si atom in Si4 by an earth alkaline metal induces a substantial reduction of the energy barrier for the (rate-limiting) first O-H bond cleavage of water dimer. The most remarkable achievement upon doping is a disappearance of the overall energy barrier for the initial O-H bond cleavage in water dimer. Of the three binary Si3M clusters considered, dehydrogenation of water dimer driven by Si3Be is the most kinetically and thermodynamically favorable pathway. In comparison to another cluster such as Al6 and nanoparticles Ru55, energy barriers for water dimer dissociation on Si3M are much lower. The mixed clusters Si3M turn out to be as efficient alternative reagents for O-H dissociation and hydrogen production from water dimer. This study proposes further searches for other mixed silicon clusters as realistic gas phase reagents for crucial dehydrogenation processes in such a way they can be prepared and conducted in experiment.

Molecular details of spontaneous insertion and interaction of HCV non-structure 3 protease protein domain with PIP2-containing membrane.

Hepatitis C virus (HCV), known as the leading cause of liver cirrhosis, viral hepatitis, and hepatocellular carcinoma, has been affecting more than 150 million people globally. The HCV non-structure 3 (NS3) protease protein domain plays a key role in HCV replication and pathogenesis; and is currently a primary target for HCV antiviral therapy. Through unbiased molecular dynamics simulations which take advantage of the novel highly mobile membrane mimetic model, we constructed the membrane-bound state of the protein domain at the atomic level. Our results indicated that protease domain of HCV NS3 protein can spontaneously bind and penetrate to an endoplasmic reticulum complex membrane containing phosphatidylinositol 4,5-bisphosphate (PIP2). An amphipathic helix α0 and loop S1 show their anchoring role to keep the protein on the membrane surface. Proper orientation of the protein domain at membrane surface was identified through measuring tilt angles of two specific vectors, wherein residue R161 plays a crucial role in its final orientation. Remarkably, PIP2 molecules were observed to bind to three main sites of the protease domain via specific electrostatic contacts and hydrogen bonds. PIP2-interaction determines the protein orientation at the membrane while both hydrophobic interplay and PIP2-interaction can stabilize the NS3 - membrane complex. Simulated results provide us with a detailed characterization of insertion, orientation and PIP2-interaction of NS3 protease domain at membrane environment, thus enhancing our understanding of structural functions and mechanism for the association of HCV non-structure 3 protein with respect to ER membranes.

Theoretical Study of Silicon Monoxide Reactions with Ammonia and Methane.

High-accuracy calculations were performed to study the mechanisms of the reactions between the diatomic silicon monoxide (SiO) with NH3 and CH4. These reactions are relevant to the SiO-related astrochemistry and atmospheric chemistry as well as the activation of the N-H and C-H bonds by the SiO triple bond. Energetic data used in the construction of potential energy surfaces describing the SiO + NH3/CH4 reactions were obtained at the coupled-cluster theory with extrapolation to the complete basis set limit (CCSD(T)/CBS) using DFT/B3LYP/aug-cc-pVTZ optimized geometries. Standard heats of formation of a series of small Si-molecules were predicted. Insertion of SiO into the N-H bond is exothermic with a small energy barrier of ∼8 kcal/mol with respect to the SiO + NH3 reactants, whereas the C-H bond activation by SiO involves a higher energy barrier of 45 kcal/mol. Eight product channels are opened in the SiO + NH3 reaction including dehydrations giving HNSi/HSiN and dehydrogenations. These reactions are endothermic by 16-119 kcal/mol (calculated at 298.15 K) with the CCSD(T)/CBS energy barriers of 21-128 kcal/mol. The most stable set of products, HNSi + H2O, was also the product of the reaction pathway having lowest energy barrier of 21 kcal/mol. Ten product channels of the SiO + CH4 reaction including decarbonylation, dehydration, dehydrogenation, and formation of Si + CH3OH are endothermic by 19-118 kcal/mol with the energy barriers in the range of 71-126 kcal/mol. The formation of H2CSiO + H2O has the lowest energy barrier of 71 kcal/mol, whereas the most stable set of products, SiH4 + CO, is formed via a higher energy barrier of 90 kcal/mol. Accordingly, while SiO can break the N-H bond of ammonia without the assistance of other molecules, it is not able to break the C-H bond of methane.

Structural assignment, and electronic and magnetic properties of lanthanide metal doped silicon heptamers Si7M0/- with M = Pr, Gd and Ho.

The ground state geometries of neutral and anionic lanthanide-metal-doped silicon clusters Si7M0/- with M = Pr, Gd and Ho were determined by quantum chemical (DFT) computations and the previous experimental photoelectron spectra were assigned. The hybrid B3LYP functional is suitable for predicting the ground electronic states of these Si clusters and reproducing well their photoelectron spectra. All the most stable isomers are substitutive derivatives of the bicapped octahedral pure Si80/- clusters. The bicapped octahedral Si7M is generated by substituting one Si atom on a plane of the D4h octahedron by one M atom. Replacement of a Si atom on the C2 axis of another bicapped octahedron by a lanthanide metal atom, where two capping Si atoms are situated in front of opposite triangular face on the side of the central square, gives rise to the anionic Si7M-. The limited participation of f-electrons of the lanthanide metal atoms on the valence electronic structure and thereby in the bonding of Si7M0/- induces high magnetic moments of the doped clusters. As a consequence, not only Si7M0/- but also SinLn0/- clusters can be regarded as suitable building blocks for assembling silicon-based cluster magnetic materials.

Multiscale simulations on conformational dynamics and membrane interactions of the non-structural 2 (NS2) transmembrane domain.

Hepatitis C virus (HCV) is one of the most crucial global health issues, in which the HCV non-structural protein 2 (NS2), particularly its three transmembrane segments, plays a crucial role in HCV assembly. In this context, multiscale MD simulations have been applied to investigate the preferred orientation of transmembrane domain of NS2 protein (TNS2) in a POPC bilayer, structural stability and characteristic of intramembrane protein-lipid and protein-protein interaction. Our study indicates that NS2 protein adopts three trans-membrane segments with highly stable α-helix structure in a POPC bilayer and a short helical luminal segment. While the first and second TM segment involved in continuous helical domain, the third TM segment is however cleaved into two sub-segments with different tilt angles via a kink at L87G88. Salt bridges K81-E45, R32-PO4 and R43-PO4 are determined as the key factor to stabilize the structure of TM2 and TM3 which consist of charged residues located in the hydrophobic region of the membrane.

Structures, Thermochemical Properties, and Bonding of Mixed Alkaline-Earth-Metal Silicon Trimers Si3M(+/0/-) with M = Be, Mg, Ca.

The ground state geometries, electronic structures, and thermochemical properties of binary alkaline-earth-metal silicon clusters Si3M with M = Be, Mg, Ca in neutral, cationic, and anionic states were investigated using quantum chemical computations. Lowest-lying isomers of the clusters were determined on the basis of the composite G4 energies. Along with total atomization energies, thermochemical parameters were determined for the first time by means of the G4 and coupled-cluster theory with complete basis set CCSD(T)/CBS approaches. The most favored equilibrium formation sequences for Si3M clusters emerge as follows: all Si3M(+/0/-) clusters are formed by attaching the M atom into the corresponding cation, neutral and anion silicon trimer Si3(+/0/-), except for the Si3Mg(+) and Si3Ca(+) where the metal cations are bound to the neutral Si3. The resulting mixed tetramers exhibit geometrical and electronic features similar to those of the pure silicon tetramer Si4(+/0/-). Electron localization function (ELF) and ring current analyses point out that the σ-aromatic character of silicon tetramer remains unchanged upon substituting one Si atom by one alkaline-earth-metal atom.

Bonding and singlet-triplet gap of silicon trimer: effects of protonation and attachment of alkali metal cations.

We revisit the singlet-triplet energy gap (ΔE(ST)) of silicon trimer and evaluate the gaps of its derivatives by attachment of a cation (H(+), Li(+), Na(+), and K(+)) using the wavefunction-based methods including the composite G4, coupled-cluster theory CCSD(T)/CBS, CCSDT and CCSDTQ, and CASSCF/CASPT2 (for Si3) computations. Both (1)A1 and (3)A2' states of Si3 are determined to be degenerate. An intersystem crossing between both states appears to be possible at a point having an apex bond angle of around α = 68 ± 2° which is 16 ± 4 kJ/mol above the ground state. The proton, Li(+) and Na(+) cations tend to favor the low-spin state, whereas the K(+) cation favors the high-spin state. However, they do not modify significantly the ΔE(ST). The proton affinity of silicon trimer is determined as PA(Si3) = 830 ± 4 kJ/mol at 298 K. The metal cation affinities are also predicted to be LiCA(Si3) = 108 ± 8 kJ/mol, NaCA(Si3) = 79 ± 8 kJ/mol and KCA(Si3) = 44 ± 8 kJ/mol. The chemical bonding is probed using the electron localization function, and ring current analyses show that the singlet three-membered ring Si3 is, at most, nonaromatic. Attachment of the proton and Li(+) cation renders it anti-aromatic.