Genetic, Structural, and Functional Evidence Link TMEM175 to Synucleinopathies.

OBJECTIVE: The TMEM175/GAK/DGKQ locus is the 3rd strongest risk locus in genome-wide association studies of Parkinson disease (PD). We aimed to identify the specific disease-associated variants in this locus, and their potential implications. METHODS: Full sequencing of TMEM175/GAK/DGKQ followed by genotyping of specific associated variants was performed in PD (n = 1,575) and rapid eye movement sleep behavior disorder (RBD) patients (n = 533) and in controls (n = 1,583). Adjusted regression models and a meta-analysis were performed. Association between variants and glucocerebrosidase (GCase) activity was analyzed in 715 individuals with available data. Homology modeling, molecular dynamics simulations, and lysosomal localization experiments were performed on TMEM175 variants to determine their potential effects on structure and function. RESULTS: Two coding variants, TMEM175 p.M393T (odds ratio [OR] = 1.37, p = 0.0003) and p.Q65P (OR = 0.72, p = 0.005), were associated with PD, and p.M393T was also associated with RBD (OR = 1.59, p = 0.001). TMEM175 p.M393T was associated with reduced GCase activity. Homology modeling and normal mode analysis demonstrated that TMEM175 p.M393T creates a polar side-chain in the hydrophobic core of the transmembrane, which could destabilize the domain and thus impair either its assembly, maturation, or trafficking. Molecular dynamics simulations demonstrated that the p.Q65P variant may increase stability and ion conductance of the transmembrane protein, and lysosomal localization was not affected by these variants. INTERPRETATION: Coding variants in TMEM175 are likely to be responsible for the association in the TMEM175/GAK/DGKQ locus, which could be mediated by affecting GCase activity. ANN NEUROL 2020;87:139-153.

Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains.

Cation-π interactions play important roles in molecular recognition and in the stability and function of proteins. However, accurate description of the structure and energetics of cation-π interactions presents a challenge to both additive and polarizable force fields, which are rarely designed to account for the complexation of charged groups with aromatic moieties. We calibrate the Drude polarizable force field for complexes of alkali metal ions (Li+ , Na+ , K+ , Rb+ , Cs+ ), ammonium (NH4+ ), tetramethylammonium (TMA+ ), and tetraethylammonium (TEA+ ) with aromatic amino acid side chain model compounds (benzene, toluene, 4-methylphenol, 3-methylindole) using high-level ab initio quantum chemical properties of these complexes. Molecular dynamics simulations reveal that cation-π complexes of the hard and tightly coordinated Li+ and Na+ ions are not stable in water but that larger ions form stable complexes, with binding free energies ranging between -0.8 and -2.9 kcal/mol. Like in gas phase, all complexes at equilibrium adopt an "en-face" complexation mode in water. The optimized Drude polarizable model provides an accurate description of the cation-π interactions involving small ions and proteins. © 2019 Wiley Periodicals, Inc.

Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian.

Polarizable force fields based on classical Drude oscillators offer a practical and computationally efficient avenue to carry out molecular dynamics (MD) simulations of large biomolecular systems. To treat the polarizable electronic degrees of freedom, the Drude model introduces a virtual charged particle that is attached to its parent nucleus via a harmonic spring. Traditionally, the need to relax the electronic degrees of freedom for each fixed set of nuclear coordinates is achieved by performing an iterative self-consistent field (SCF) calculation to satisfy a selected tolerance. This is a computationally demanding procedure that can increase the computational cost of MD simulations by nearly one order of magnitude. To avoid the costly SCF procedure, a small mass is assigned to the Drude particles, which are then propagated as dynamic variables during the simulations via a dual-thermostat extended Lagrangian algorithm. To help clarify the significance of the dual-thermostat extended Lagrangian propagation in the context of the polarizable force field based on classical Drude oscillators, the statistical mechanics of a dual-temperature canonical ensemble is formulated. The conditions for dynamically maintaining the dual-temperature properties in the case of the classical Drude oscillator are analyzed using the generalized Langevin equation.

The Impact of Composition and Morphology on Ionic Conductivity of Silk/Cellulose Bio-Composites Fabricated from Ionic Liquid and Varying Percentages of Coagulation Agents.

Blended biocomposites created from the electrostatic and hydrophobic interactions between polysaccharides and structural proteins exhibit useful and unique properties. However, engineering these biopolymers into applicable forms is challenging due to the coupling of the material's physicochemical properties to its morphology, and the undertaking that comes with controlling this. In this particular study, numerous properties of the Bombyx mori silk and microcrystalline cellulose biocomposites blended using ionic liquid and regenerated with various coagulation agents were investigated. Specifically, the relationship between the composition of polysaccharide-protein bio-electrolyte membranes and the resulting morphology and ionic conductivity is explored using numerous characterization techniques, including scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray scattering, atomic force microscopy (AFM) based nanoindentation, and dielectric relaxation spectroscopy (DRS). The results revealed that when silk is the dominating component in the biocomposite, the ionic conductivity is higher, which also correlates with higher ß-sheet content. However, when cellulose becomes the dominating component in the biocomposite, this relationship is not observed; instead, cellulose semicrystallinity and mechanical properties dominate the ionic conduction.

Gold nanoparticles in ophthalmology.

Many research projects are underway to improve the diagnosis and therapy in ophthalmology. Indeed, visual acuity deficits affect 285 million people worldwide and different strategies are being developed to strengthen patient care. One of these strategies is the use of gold nanoparticles (GNP) for their multiple properties and their ability to be used as both diagnosis and therapy tools. This review exhaustively details research developing GNPs for use in ophthalmology. The toxicity of GNPs and their distribution in the eye are described through in vitro and in vivo studies. All publications addressing the pharmacokinetics of GNPs administered in the eye are extensively reviewed. In addition, their use as biosensors or for imaging with optical coherence tomography is illustrated. The future of GNPs for ophthalmic therapy is also discussed. GNPs can be used to deliver genes or drugs through different administration routes. Their antiangiogenic and anti-inflammatory properties are of great interest for different ocular pathologies. Finally, GNPs can be used to improve stereotactic radiosurgery, brachytherapy, and photothermal therapy because of their many properties.

Deep convolutional networks for quality assessment of protein folds.

Motivation: The computational prediction of a protein structure from its sequence generally relies on a method to assess the quality of protein models. Most assessment methods rank candidate models using heavily engineered structural features, defined as complex functions of the atomic coordinates. However, very few methods have attempted to learn these features directly from the data. Results: We show that deep convolutional networks can be used to predict the ranking of model structures solely on the basis of their raw three-dimensional atomic densities, without any feature tuning. We develop a deep neural network that performs on par with state-of-the-art algorithms from the literature. The network is trained on decoys from the CASP7 to CASP10 datasets and its performance is tested on the CASP11 dataset. Additional testing on decoys from the CASP12, CAMEO and 3DRobot datasets confirms that the network performs consistently well across a variety of protein structures. While the network learns to assess structural decoys globally and does not rely on any predefined features, it can be analyzed to show that it implicitly identifies regions that deviate from the native structure. Availability and implementation: The code and the datasets are available at https://github.com/lamoureux-lab/3DCNN_MQA. Supplementary information: Supplementary data are available at Bioinformatics online.

Dual Role of the C-Terminal Domain in Osmosensing by Bacterial Osmolyte Transporter ProP.

ProP is a member of the major facilitator superfamily, a proton-osmolyte symporter, and an osmosensing transporter. ProP proteins share extended cytoplasmic carboxyl terminal domains (CTDs) implicated in osmosensing. The CTDs of the best characterized, group A ProP orthologs, terminate in sequences that form intermolecular, antiparallel α-helical coiled coils (e.g., ProPEc, from Escherichia coli). Group B orthologs lack that feature (e.g., ProPXc, from Xanthomonas campestris). ProPXc was expressed and characterized in E. coli to further elucidate the role of the coiled coil in osmosensing. The activity of ProPXc was a sigmoid function of the osmolality in cells and proteoliposomes. ProPEc and ProPXc attained similar activities at the same expression level in E. coli. ProPEc transports proline and glycine betaine with comparable high affinities at low osmolality. In contrast, proline weakly inhibited high-affinity glycine-betaine uptake via ProPXc. The KM for proline uptake via ProPEc increases dramatically with the osmolality. The KM for glycine-betaine uptake via ProPXc did not. Thus, ProPXc is an osmosensing transporter, and the C-terminal coiled coil is not essential for osmosensing. The role of CTD-membrane interaction in osmosensing was examined further. As for ProPEc, the ProPXc CTD co-sedimented with liposomes comprising E. coli phospholipid. Molecular dynamics simulations illustrated association of the monomeric ProPEc CTD with the membrane surface. Comparison with the available NMR structure for the homodimeric coiled coil formed by the ProPEc-CTD suggested that membrane association and homodimeric coiled-coil formation by that peptide are mutually exclusive. The membrane fluidity in liposomes comprising E. coli phospholipid decreased with increasing osmolality in the range relevant for ProP activation. These data support the proposal that ProP activates as cellular dehydration increases cytoplasmic cation concentration, releasing the CTD from the membrane surface. For group A orthologs, this also favors α-helical coiled-coil formation that stabilizes the transporter in an active form.

Molecular model of hemoglobin N from Mycobacterium tuberculosis bound to lipid bilayers: a combined spectroscopic and computational study.

A singular aspect of the 2-on-2 hemoglobin structures of groups I and II is the presence of tunnels linking the protein surface to the distal heme pocket, supporting the storage and the diffusion of small apolar ligands to/from the buried active site. As the solubility of apolar ligands is greater in biological membranes than in solution, the association of these proteins with biological membranes may improve the efficiency of ligand capture. As very little is known on this subject, we have investigated the interactions between hemoglobin N (HbN), a group I 2-on-2 hemoglobin from the pathogenic Mycobacterium tuberculosis (Mtb), and biological membranes using both experimental techniques and MD simulations. HbN has a potent nitric oxide dioxygenase activity (HbN-Fe²âº-O2 + •NO + H2O → HbN-Fe³âº-OH2 + NO3⁻) that is thought to protect the aerobic respiration of Mtb from inhibition by •NO. Three different membrane compositions were chosen for the studies, representative of the mycobacterial plasma membrane and the mammalian cell membranes. Both the experimental and the modeling results agreed with each other and allow for a detailed molecular description of HbN in association with membranes of different compositions. The results indicated that HbN is a peripheral protein, and the association with the membranes occurred via the pre-A, G, and H helices. In addition, HbN would be allowed to modulate the binding to the membranes via electrostatic interactions between the lipid membranes and the Asp100 residue. In its membrane-bound form the short tunnel of HbN is oriented toward the membrane interior and the other tunnels point toward the solvent. Such protein orientation would facilitate the uptake of nonpolar substrates from the membrane and the release of products to the solvent. It is interesting to note that the pre-A, G, and H helices are conserved among HbN from a few other Mycobacteria.

Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2.

BACKGROUND: RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA ligase 2, a workhorse in molecular biology. Here we report the identification of a divergent RNA ligase 2 (DpRNL) from Diplonema papillatum (Diplonemea), a member of the kinetoplastids' sister group. METHODS: We identified DpRNL with methods based on sensitive hidden Markov Model. Then, using homology modeling and molecular dynamics simulations, we established a three dimensional structure model of DpRNL complexed with ATP and Mg2+. RESULTS: The 3D model of Diplonema was compared with available crystal structures from Trypanosoma brucei, bacteriophage T4, and two archaeans. Interaction of DpRNL with ATP is predicted to involve double π-stacking, which has not been reported before in RNA ligases. This particular contact would shift the orientation of ATP and have considerable consequences on the interaction network of amino acids in the catalytic pocket. We postulate that certain canonical amino acids assume different functional roles in DpRNL compared to structurally homologous residues in other RNA ligases 2, a reassignment indicative of constructive neutral evolution. Finally, both structure comparison and phylogenetic analysis show that DpRNL is not specifically related to RNA ligases from trypanosomes, suggesting a unique adaptation of the latter for RNA editing, after the split of diplonemids and kinetoplastids. CONCLUSION: Homology modeling and molecular dynamics simulations strongly suggest that DpRNL is an RNA ligase 2. The predicted innovative reshaping of DpRNL's catalytic pocket is worthwhile to be tested experimentally.

Identification of a cholesterol-binding pocket in inward rectifier K(+) (Kir) channels.

Cholesterol is the major sterol component of all mammalian plasma membranes. Recent studies have shown that cholesterol inhibits both bacterial (KirBac1.1 and KirBac3.1) and eukaryotic (Kir2.1) inward rectifier K(+) (Kir) channels. Lipid-sterol interactions are not enantioselective, and the enantiomer of cholesterol (ent-cholesterol) does not inhibit Kir channel activity, suggesting that inhibition results from direct enantiospecific binding to the channel, and not indirect effects of changes to the bilayer. Furthermore, conservation of the effect of cholesterol among prokaryotic and eukaryotic Kir channels suggests an evolutionary conserved cholesterol-binding pocket, which we aimed to identify. Computational experiments were performed by docking cholesterol to the atomic structures of Kir2.2 (PDB: 3SPI) and KirBac1.1 (PDB: 2WLL) using Autodock 4.2. Poses were assessed to ensure biologically relevant orientation and then clustered according to location and orientation. The stability of cholesterol in each of these poses was then confirmed by molecular dynamics simulations. Finally, mutation of key residues (S95H and I171L) in this putative binding pocket found within the transmembrane domain of Kir2.1 channels were shown to lead to a loss of inhibition by cholesterol. Together, these data provide support for this location as a biologically relevant pocket.

Dock2D: Synthetic data for the molecular recognition problem.

Predicting the physical interaction of proteins is a cornerstone problem in computational biology. New classes of learning-based algorithms are actively being developed, and are typically trained end-to-end on protein complex structures extracted from the Protein Data Bank. These training datasets tend to be large and difficult to use for prototyping and, unlike image or natural language datasets, they are not easily interpretable by non-experts. We present Dock2D-IP and Dock2DIF, two "toy" datasets that can be used to select algorithms predicting protein-protein interactions-or any other type of molecular interactions. Using two-dimensional shapes as input, each example from Dock2D-IP ("interaction pose") describe the interaction pose of two shapes known to interact and each example from Dock2D-IF ("interaction fact") describes whether two shapes form a stable complex or not, regardless of how they bind. We propose a number of baseline solutions to the problem and show that the same underlying energy function can be learned either by solving the interaction pose task (formulated as an energy-minimization "docking" problem) or the fact-ofinteraction task (formulated as a binding free energy estimation problem).

Different hydration patterns in the pores of AmtB and RhCG could determine their transport mechanisms.

The ammonium transporters of the Amt/Rh family facilitate the diffusion of ammonium across cellular membranes. Functional data suggest that Amt proteins, notably found in plants, transport the ammonium ion (NH4(+)), whereas human Rhesus (Rh) proteins transport ammonia (NH3). Comparison between the X-ray structures of the prokaryotic AmtB, assumed to be representative of Amt proteins, and the human RhCG reveals important differences at the level of their pore. Despite these important functional and structural differences between Amt and Rh proteins, studies of the AmtB transporter have led to the suggestion that proteins of both subfamilies work according to the same mechanism and transport ammonia. We performed molecular dynamics simulations of the AmtB and RhCG proteins under different water and ammonia occupancy states of their pore. Free energy calculations suggest that the probability of finding NH3 molecules in the pore of AmtB is negligible in comparison to finding water. The presence of water in the pore of AmtB could support the transport of proton. The pore lumen of RhCG is found to be more hydrophobic due to the presence of a phenylalanine conserved among Rh proteins. Simulations of RhCG also reveal that the signature histidine dyad is occasionally exposed to the extracellular bulk, which is never observed in AmtB. These different hydration patterns are consistent with the idea that Amt and Rh proteins are not functionally equivalent and that permeation takes place according to two distinct mechanisms.

Ammonium transporters achieve charge transfer by fragmenting their substrate.

Proteins of the Amt/MEP family facilitate ammonium transport across the membranes of plants, fungi, and bacteria and are essential for growth in nitrogen-poor environments. Some are known to facilitate the diffusion of the neutral NH(3), while others, notably in plants, transport the positively charged NH(4)(+). On the basis of the structural data for AmtB from Escherichia coli , we illustrate the mechanism by which proteins from the Amt family can sustain electrogenic transport. Free energy calculations show that NH(4)(+) is stable in the AmtB pore, reaching a binding site from which it can spontaneously transfer a proton to a pore-lining histidine residue (His168). The substrate diffuses down the pore in the form of NH(3), while the excess proton is cotransported through a highly conserved hydrogen-bonded His168-His318 pair. This constitutes a novel permeation mechanism that confers to the histidine dyad an essential mechanistic role that was so far unknown.

Salt-Dependent Interactions between the C-Terminal Domain of Osmoregulatory Transporter ProP of Escherichia coli and the Lipid Membrane.

Osmosensing transporter ProP detects the increase in cytoplasmic cation concentration associated with osmotically induced cell dehydration and mediates osmolyte uptake into bacteria. ProP is a 12-transmembrane helix protein with an α-helical, cytoplasmic C-terminal domain (CTD) linked to transmembrane helix XII (TM XII). It has been proposed that the CTD helix associates with the anionic membrane surface to lock ProP in an inactive conformation and that the release of the CTD may activate ProP. To investigate this possible activation mechanism, we have built and simulated a structural model in which the CTD was anchored to the membrane by TM XII and the CTD helix was associated with the membrane surface. Molecular dynamics simulations showed specific intrapeptide salt bridges forming when the CTD associated with the membrane. Experiments supported the presence of the salt bridge Lys447-Asp455 and suggested a role for these residues in osmosensing. Simulations performed at different salt concentrations showed weakened CTD-lipid interactions at 0.25 M KCl and gradual stiffening of the membrane with increasing salinity. These results suggest that salt cations may affect CTD release and activate ProP by increasing the order of membrane phospholipids.

Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.

The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the nitrogen-containing heteroaromatic compounds pyridine, pyrimidine, pyrrole, imidazole, indole, and purine. Initial parameters for the six-membered rings were based on benzene with nonbond parameter optimization focused on the nitrogen atoms and adjacent carbons and attached hydrogens. In the case of five-member rings, parameters were first developed for imidazole and transferred to pyrrole. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data were used for the determination of initial electrostatic parameters, the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones (LJ) parameters, through computations of the interactions of dimers of model compounds, model compound-water interactions, and interactions of rare gases with model compounds. The absolute values of the LJ parameters were determined targeting experimental heats of vaporization, molecular volumes, heats of sublimation, crystal lattice parameters, and free energies of hydration. Final scaling of the polarizabilities from the gas-phase values by 0.85 was determined by reproduction of the dielectric constants of pyridine and pyrrole. The developed parameter set was extensively validated against additional experimental data such as diffusion constants, heat capacities, and isothermal compressibilities, including data as a function of temperature.

Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution.

Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH3+ and RN(CH3)3+) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA+) and tetraethylammonium (TEA+). Polarizable molecular models are calibrated for NH4+, TMA+, and TEA+ interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes. Whereas the gas-phase affinity of the ions with a given aromatic follows the trend NH4+ > TMA+ > TEA+, molecular dynamics simulations using the polarizable models show a reverse trend in water, likely due to a contribution from the hydrophobic effect. This reversed trend follows the solubility of aromatic hydrocarbons in quaternary ammonium salt solutions, which suggests a role for cation-π interactions in the salting-in of aromatic compounds in solution. Simulations in water show that the complexes possess binding free energies ranging from -1.3 to -3.3 kcal/mol (compared to gas-phase binding energies between -8.5 and -25.0 kcal/mol). Interestingly, whereas the most stable complexes involve TEA+ (the largest ion), the most stable solvent-separated complexes involve TMA+ (the intermediate-size ion).

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator.

The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the aromatic compounds benzene and toluene. Parameters were optimized for benzene and then transferred directly to toluene, with parameters for the methyl moiety of toluene taken from the previously published work on the alkanes. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data was used for determination of the electrostatic parameters, for the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones parameters. The absolute values of the Lennard-Jones parameters were determined by comparing computed and experimental heats of vaporization, molecular volumes, free energies of hydration, and dielectric constants. The newly developed parameter set was extensively tested against additional experimental data such as diffusion constants, heat capacities at constant pressure, and isothermal compressibilities including data as a function of temperature. Moreover, the structures of liquid benzene, liquid toluene, and solutions of each in water were studied. In the case of benzene, the computed and experimental total distribution function were compared, with the developed model shown to be in excellent agreement with experiment.

Mechanism of the Nitric Oxide Dioxygenase Reaction of Mycobacterium tuberculosis Hemoglobin N.

Many globins convert •NO to innocuous NO3- through their nitric oxide dioxygenase (NOD) activity. Mycobacterium tuberculosis fights the oxidative and nitrosative stress imposed by its host (the toxic effects of O2•- and •NO species and their OONO- and •NO2 derivatives) through the action of truncated hemoglobin N (trHbN), which catalyzes the NOD reaction with one of the highest rates among globins. The general NOD mechanism comprises the following steps: binding of O2 to the heme, diffusion of •NO into the heme pocket and formation of peroxynitrite (OONO-), isomerization of OONO-, and release of NO3-. Using quantum mechanics/molecular mechanics free-energy calculations, we show that the NOD reaction in trHbN follows a mechanism in which heme-bound OONO- undergoes homolytic cleavage to give FeIV═O2- and the •NO2 radical but that these potentially harmful intermediates are short-lived and caged by the heme pocket residues. In particular, the simulations show that Tyr33(B10) side chain is shielded from FeIV═O2- and •NO2 (and protected from irreversible oxidation and nitration) by forming stable hydrogen bonds with Gln58(E11) side chain and Leu54(E7) backbone. Aromatic residues Phe46(CD1), Phe32(B9), and Tyr33(B10) promote NO3- dissociation via C-H···O bonding and provide stabilizing interactions for the anion along its egress route.

Loss of hepatic DEPTOR alters the metabolic transition to fasting.

OBJECTIVE: The mechanistic target of rapamycin (mTOR) is a serine/threonine kinase that functions into distinct protein complexes (mTORC1 and mTORC2) that regulates growth and metabolism. DEP-domain containing mTOR-interacting protein (DEPTOR) is part of these complexes and is known to reduce their activity. Whether DEPTOR loss affects metabolism and organismal growth in vivo has never been tested. METHODS: We have generated a conditional transgenic mouse allowing the tissue-specific deletion of DEPTOR. This model was crossed with CMV-cre mice or Albumin-cre mice to generate either whole-body or liver-specific DEPTOR knockout (KO) mice. RESULTS: Whole-body DEPTOR KO mice are viable, fertile, normal in size, and do not display any gross physical and metabolic abnormalities. To circumvent possible compensatory mechanisms linked to the early and systemic loss of DEPTOR, we have deleted DEPTOR specifically in the liver, a tissue in which DEPTOR protein is expressed and affected in response to mTOR activation. Liver-specific DEPTOR null mice showed a reduction in circulating glucose upon fasting versus control mice. This effect was not associated with change in hepatic gluconeogenesis potential but was linked to a sustained reduction in circulating glucose during insulin tolerance tests. In addition to the reduction in glycemia, liver-specific DEPTOR KO mice had reduced hepatic glycogen content when fasted. We showed that loss of DEPTOR cell-autonomously increased oxidative metabolism in hepatocytes, an effect associated with increased cytochrome c expression but independent of changes in mitochondrial content or in the expression of genes controlling oxidative metabolism. We found that liver-specific DEPTOR KO mice showed sustained mTORC1 activation upon fasting, and that acute treatment with rapamycin was sufficient to normalize glycemia in these mice. CONCLUSION: We propose a model in which hepatic DEPTOR accelerates the inhibition of mTORC1 during the transition to fasting to adjust metabolism to the nutritional status.

Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field.

A polarizable potential function for the hydration of alkali and halide ions is developed on the basis of the recent SWM4-DP water model [Lamoureux, G.; MacKerell, A. D., Jr.; Roux, B. J. Chem. Phys. 2003, 119, 5185]. Induced polarization is incorporated using classical Drude oscillators that are treated as auxiliary dynamical degrees of freedom. The ions are represented as polarizable Lennard-Jones centers, whose parameters are optimized to reproduce the binding energies of gas-phase monohydrates and the hydration free energies in the bulk liquid. Systematic exploration of the parameters shows that the monohydrate binding energies can be consistent with a unique hydration free energy scale if the computed hydration free energies incorporate the contribution from the air/water interfacial electrostatic potential (-540 mV for SWM4-DP). The final model, which can satisfyingly reproduce both gas and bulk-phase properties, corresponds to an absolute scale in which the intrinsic hydration free energy of the proton is -247 kcal/mol.