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.

The influences of E22Q mutant on solvated 3Aß11-40 peptide: A REMD study.

The residue E22 plays a critical role in the aggregation process of Amyloid beta (Aß) peptides. The effect of E22Q mutant on the shapes of the solvated Aß11-40 trimer is clarified using a replica exchange molecular dynamics (REMD) simulation employing ∼20.6 µs of MD simulations with 48 disparate replicas. The increase of intramolecular polar contacts and salt bridge between the residue D23 to residues (24-29) was observed. The residual secondary structure of the mutated trimer is shifted in a similar way to the picture observed in previous investigations of F19W mutant. The free energy surface (FES) of the mutated E22Q system has a fewer number of minima in comparison with the wild-type trimer. The optimized shapes of the mutated E22Q form a significant increase in beta structure (47%) and serious decrease in coil content (46%) compared with the wild-type (of 36 and 56%, respectively). The binding affinity of constituting chains to the rest is of -43.7 ±â€¯6.5 kcal/mol, implying that the representative structure of E22Q is more stable than the wild-type one. Furthermore, the E22Q mutant increases the size of stable structures due to larger collision cross section (CCS) and solvent accessible area (SASA). The observed results may enhance the Aß inhibition throughout the contribution to the knowledge of the Aß oligomerization/aggregation.

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.

Comparative Study of Methanol Activation by Different Small Mixed Silicon Clusters Si2M with M = H, Li, Na, Cu, and Ag.

High-accuracy quantum chemical calculations were carried out to study the mechanisms and catalytic abilities of various mixed silicon species Si2M with M = H, Li, Na, Cu, and Ag toward the first step of methanol activation reaction. Standard heats of formation of these small triatomic Si clusters were determined. Potential-energy profiles were constructed using the coupled-cluster theory with extrapolation to complete basis set CCSD(T)/CBS, and CCSD(T)/aug-cc-pVTZ-PP for Si2Cu and Si2Ag. The most stable complexes generated by the interaction of methanol with the mixed clusters Si2M possess low-spin states and mainly stem from an M-O connection in preference to Si-O interaction, except for the Si2H case. In two competitive pathways including O-H and C-H bond breakings, the cleavage of the O-H bond in the presence of all clusters studied becomes predominant. Of the mixed clusters Si2M considered, the dissociation pathways of both O-H and C-H bonds with Si2Li turns out to have the lowest energy barriers. The most remarkable finding is the absence of the overall energy barrier for the O-H cleavage with the assistance of Si2Li. The breaking of O-H and C-H bonds with the assistance of Si2H, Si2Li, and Si2Na is kinetically preferred with respect to the Si2Cu and Si2Ag cases, apart from the case of Si2Na for O-H cleavage. In comparison with other transition-metal clusters with the same size, such as Cu3, Pt3, and PtAu2, the energy barriers for the O-H bond activation in the presence of small Si species, especially Si2H and Si2Li, are found to be lower. Consequently, these small mixed silicon clusters can be regarded as promising alternatives for the expensive metal-based catalysts currently used for methanol activation particularly and other dehydrogenation processes of organic compounds. The present study also suggests a further extensive search for other doped silicon clusters as efficient and more realistic gas-phase catalysts for important dehydrogenation processes in such a way that they can be experimentally prepared and implemented.

Replica exchange molecular dynamics study of the truncated amyloid beta (11-40) trimer in solution.

Amyloid beta (Aß) oligomers are neurotoxic compounds that destroy the brain of Alzheimer's disease patients. Recent studies indicated that the trimer is one of the most cytotoxic forms of low molecular weight Aß oligomers. As there was limited information about the structure of the Aß trimer, either by experiment or by computation, we determined in this work the structure of the 3Aß11-40 oligomer for the first time using the temperature replica exchange molecular dynamics simulations in the presence of an explicit solvent. More than 20.0 µs of MD simulations were performed. The probability of the ß-content and random coil structure of the solvated trimer amounts to 42 ± 6 and 49 ± 7% which is in good agreement with experiments. Intermolecular interactions in central hydrophobic cores play a key role in stabilizing the oligomer. Intermolecular polar contacts between D23 and residues 24-29 replace the salt bridge D23-K28 to secure the loop region. The hydrophilic region of the N-terminus is maintained by the intermolecular polar crossing contacts H13A-Q15B and H13B-Q15C. The difference in the free energy of binding between the constituting monomers and the others amounts to -36 ± 8 kcal mol-1. The collision cross section of the representative structures of the trimer was computed to be 1330 ± 47 Å2, which is in good agreement with previous experiments.

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.

Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work.

The fast pulling ligand (FPL) out of binding cavity using non-equilibrium molecular dynamics (MD) simulations was demonstrated to be a rapid, accurate and low CPU demand method for the determination of the relative binding affinities of a large number of HIV-1 protease (PR) inhibitors. In this approach, the ligand is pulled out of the binding cavity of the protein using external harmonic forces, and the work of pulling force corresponds to the relative binding affinity of HIV-1 PR inhibitor. The correlation coefficient between the pulling work and the experimental binding free energy of R=-0.95 shows that FPL results are in good agreement with experiment. It is thus easier to rank the binding affinities of HIV-1 PR inhibitors, that have similar binding affinities because the mean error bar of pulling work amounts to δW=7%. The nature of binding is discovered using the FPL approach. © 2016 Wiley Periodicals, Inc.

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.

Theoretical study of the interactions between the first transmembrane segment of NS2 protein and a POPC lipid bilayer.

Non-structural protein 2 (NS2) plays a crucial role in the hepatitis C virus (HCV) assembly. NS2 was predicted to be composed of three transmembrane (TM) segments. However, the mechanism of interactions between TM segments of NS2 and surrounding lipid environment remains unclear. Molecular dynamics simulations were applied to investigate the conformation and orientation of the first transmembrane segment (TM1) as well as the interactions of TM1 with a zwitterionic POPC lipid bilayer which identifies several key residues that stabilize the position of TM1 within the membrane. Along with the charged residues R3 and K27, the S23 and H25 were found to be the key elements in establishing the conformation of TM1 inside the membrane. The peptide forms a stable α-helix (the sequence 12-21) connected to N-terminal haft in POPC bilayer. The results also reveal that TM1 induces the ordering of lipid and does not destabilize the lipid bilayer system. The hydrophobic mismatch in which the segment tilts an angle along the membrane normal was observed in this system. The binding free energy profile of TM1 to the membrane was also estimated using umbrella sampling.

Radical Pathways for the Prebiotic Formation of Pyrimidine Bases from Formamide.

The prebiotic formation of nucleobases, the building blocks of RNA/DNA, is of current interest. Highly reactive radical species present in the atmosphere under irradiation have been suggested to be involved in the prebiotic synthesis of nucleobases from formamide (FM). We studied several free radical reaction pathways for the synthesis of pyrimidine bases (cytosine, uracil, and thymine) from FM under cold conditions. These pathways are theoretically determined using density functional theory (DFT) computations to examine their kinetic and thermodynamic feasibilities. These free radical reaction pathways share some common reaction types such as H-rearrangement, (•)H/(•)OH/(•)NH2 radical loss, and intramolecular radical cyclization. The rate-determining steps in these pathways are characterized with low energy barriers. The energy barriers of the ring formation steps are in the range of 3-7 kcal/mol. Although DFT methods are known to significantly underestimate the barriers for addition of (•)H radical to neutral species, many of these reactions are highly exergonic with energy release of -15 to -52 kcal/mol and are thus favorable. Among the suggested pathways for formation of cytosine (main route, routes 7a and 1a), uracil (main route, routes 7b and 1b), and thymine (main route and route 26a), the main routes are in general thermodynamically more exergonic and more kinetically favored than other alternative routes with lower overall energy barriers. The reaction energies released following formation of cytosine, uracil, and thymine from FM via the main radical routes amount to -59, -81, and -104 kcal/mol, respectively. Increasing temperature induces unfavorable changes in both kinetic and thermodynamic aspects of the suggested routes. However, the main routes are still more favored than the alternative pathways at the temperature up to the boiling point of FM.

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.