Langevin dynamics with a tilted periodic potential

We study a Langevin equation for a particle moving in a periodic potential in the presence of viscosity $\gamma$ and subject to a further external field $\alpha$. For a suitable choice of the parameters $\alpha$ and $\gamma$ the related deterministic dynamics yields heteroclinic orbits. In such a regime, in absence of stochastic noise both confined and unbounded orbits coexist. We prove that, with the inclusion of an arbitrarly small noise only the confined orbits survive in a sub-exponential time scale.Comment: 38 pages, 6 figure

Folding of dimeric methionine adenosyltransferase III: identification of two folding intermediates

Methionine adenosyl transferase (MAT) is an essential enzyme that synthesizes AdoMet. The liver-specific MAT isoform, MAT III, is a homodimer of a 43.7-kDa subunit that organizes in three nonsequential alpha-beta domains. Although MAT III structure has been recently resolved, little is known about its folding mechanism. Equilibrium unfolding and refolding of MAT III, and the monomeric mutant R265H, have been monitored using different physical parameters. Tryptophanyl fluorescence showed a three-state folding mechanism. The first unfolding step was a folding/association process as indicated by its dependence on protein concentration. The monomeric folding intermediate produced was the predominant species between 1.5 and 3 m urea. It had a relatively compact conformation with tryptophan residues and hydrophobic surfaces occluded from the solvent, although its N-terminal region may be very unstructured. The second unfolding step monitored the denaturation of the intermediate. Refolding of the intermediate showed first order kinetics, indicating the presence of a kinetic intermediate within the folding/association transition. Its presence was confirmed by measuring the 1,8-anilinonaphtalene-8-sulfonic acid binding in the presence of tripolyphosphate. We propose that the folding rate-limiting step is the formation of an intermediate, probably a structured monomer with exposed hydrophobic surfaces, that rapidly associates to form dimeric MAT III

Methionine adenosyltransferase S-nitrosylation is regulated by the basic and acidic amino acids surrounding the target thiol

S-Adenosylmethionine serves as the methyl donor for many biological methylation reactions and provides the propylamine group for the synthesis of polyamines. S-Adenosylmethionine is synthesized from methionine and ATP by the enzyme methionine adenosyltransferase. The cellular factors regulating S-adenosylmethionine synthesis have not been well defined. Here we show that in rat hepatocytes S-nitrosoglutathione monoethyl ester, a cell-permeable nitric oxide donor, markedly reduces cellular S-adenosylmethionine content via inactivation of methionine adenosyltransferase by S-nitrosylation. Removal of the nitric oxide donor from the incubation medium leads to the denitrosylation and reactivation of methionine adenosyltransferase and to the rapid recovery of cellular S-adenosylmethionine levels. Nitric oxide inactivates methionine adenosyltransferase via S-nitrosylation of cysteine 121. Replacement of the acidic (aspartate 355) or basic (arginine 357 and arginine 363) amino acids located in the vicinity of cysteine 121 by serine leads to a marked reduction in the ability of nitric oxide to S-nitrosylate and inactivate hepatic methionine adenosyltransferase. These results indicate that protein S-nitrosylation is regulated by the basic and acidic amino acids surrounding the target cysteine

A neutron diffraction study and mode analysis of compounds of the system La_1−xSr_xFeO_3−xF_x (x=1, 0.8, 0.5, 0.2) and an investigation of their magnetic properties

AbstractWe report here a detailed study of the system La1−xSrxFeO3−xFx, by neutron powder diffraction- and magnetic-measurements. All the compounds are robust antiferromagnetics with ordering temperatures well above room temperature. Magnetic moments are shown to align parallel to the c-axis. FC-ZFC measurements indicate a small canting of the magnetic moments, resulting in a ferromagnetic component with a maximum for La0.5Sr0.5FeO2.5F0.5. We show that the system exhibits a composition-driven transition from a phase, for low fluorination levels (x≤0.5), with Pnma symmetry and the usual system of octahedral tiltings, to a phase with space group Imma for higher fluorine contents, where a correlated distortion of the oxygen octahedra plays a significant role. The consistency of the structural models, with respect to the expected continuity of the amplitudes of the different distortion modes and the invariance of their internal form, was monitored through the symmetry mode decomposition of the structures

Biochemical basis for the dominant inheritance of hypermethioninemia associated with the R264H mutation of the MAT1A gene. A monomeric methionine adenosyltransferase with tripolyphosphatase activity

Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine (AdoMet), the main alkylating agent in living cells. Additionally, in the liver, MAT is also responsible for up to 50% of methionine catabolism. Humans with mutations in the gene MAT1A, the gene that encodes the catalytic subunit of MAT I and III, have decreased MAT activity in liver, which results in a persistent hypermethioninemia without homocystinuria. The hypermethioninemic phenotype associated with these mutations is inherited as an autosomal recessive trait. The only exception is the dominant mild hypermethioninemia associated with a G-A transition at nucleotide 791 of exon VII. This change yields a MAT1A-encoded subunit in which arginine 264 is replaced by histidine. Our results indicate that in the homologous rat enzyme, replacement of the equivalent arginine 265 by histidine (R265H) results in a monomeric MAT with only 0.37% of the AdoMet synthetic activity. However the tripolyphosphatase activity is similar to that found in the wild type (WT) MAT and is inhibited by PP(i). Our in vivo studies demonstrate that the R265H MAT I/III mutant associates with the WT subunit resulting in a dimeric R265H-WT MAT unable to synthesize AdoMet. Tripolyphosphatase activity is maintained in the hybrid MAT, but is not stimulated by methionine and ATP, indicating a deficient binding of the substrates. Our data indicate that the active site for tripolyphosphatase activity is functionally active in the monomeric R265H MAT I/III mutant. Moreover, our results provide a molecular mechanism that might explain the dominant inheritance of the hypermethioninemia associated with the R264H mutation of human MAT I/III

First-principles study of the ferroelastic phase transition in CaCl_2

First-principles density-functional calculations within the local-density approximation and the pseudopotential approach are used to study and characterize the ferroelastic phase transition in calcium chloride (CaCl_2). In accord with experiment, the energy map of CaCl_2 has the typical features of a pseudoproper ferroelastic with an optical instability as ultimate origin of the phase transition. This unstable optic mode is close to a pure rigid unit mode of the framework of chlorine atoms and has a negative Gruneisen parameter. The ab-initio ground state agrees fairly well with the experimental low temperature structure extrapolated at 0K. The calculated energy map around the ground state is interpreted as an extrapolated Landau free-energy and is successfully used to explain some of the observed thermal properties. Higher-order anharmonic couplings between the strain and the unstable optic mode, proposed in previous literature as important terms to explain the soft-phonon temperature behavior, are shown to be irrelevant for this purpose. The LAPW method is shown to reproduce the plane-wave results in CaCl_2 within the precision of the calculations, and is used to analyze the relative stability of different phases in CaCl_2 and the chemically similar compound SrCl_2.Comment: 9 pages, 6 figures, uses RevTeX

Reply to “Structural and magnetic behavior of the cubic oxyfluoride SrFeO₂F studied by neutron diffraction”

In this article we comment on the results published by Thompson et al. (,J. Solid State Chem. 219 (2014) 173-178) on the crystal structure of SrFeO2F, who claim the compound to crystallize in the cubic space group Pm-3m. We give a more detailed explanation of the determination of our previously reported structural model with Imma symmetry (Clemens et al., J. Solid State Chem. 206 (2013) 158-169), with addition of variable temperature XRD measurements with high counting time to provide unambiguous evidence for the Imma model being correct for our sample. (C) 2015 Elsevier Inc. All rights reserved

Creation of a functional S-nitrosylation site in vitro by single point mutation

Here we show that in extrahepatic methionine adenosyltransferase replacement of a single amino acid (glycine 120) by cysteine is sufficient to create a functional nitric oxide binding site without affecting the kinetic properties of the enzyme. When wild-type and mutant methionine adenosyltransferase were incubated with S-nitrosoglutathione the activity of the wild-type remained unchanged whereas the activity of the mutant enzyme decreased markedly. The mutant enzyme was found to be S-nitrosylated upon incubation with the nitric oxide donor. Treatment of the S-nitrosylated mutant enzyme with glutathione removed most of the S-nitrosothiol groups and restored the activity to control values. In conclusion, our results suggest that functional S-nitrosylation sites can develop from existing structures without drastic or large-scale amino acid replacement

Importance of a deficiency in S-adenosyl-L-methionine synthesis in the pathogenesis of liver injury

One of the features of liver cirrhosis is an abnormal metabolism of methionine--a characteristic that was described more than a half a century ago. Thus, after an oral load of methionine, the rate of clearance of this amino acid from the blood is markedly impaired in cirrhotic patients compared with that in control subjects. Almost 15 y ago we observed that the failure to metabolize methionine in cirrhosis was due to an abnormally low activity of the enzyme methionine adenosyltransferase (EC 2.5.1.6). This enzyme converts methionine, in the presence of ATP, to S-adenosyl-L-methionine (SAMe), the main biological methyl donor. Since then, it has been suspected that a deficiency in hepatic SAMe may contribute to the pathogenesis of the liver in cirrhosis. The studies reviewed here are consistent with this hypothesis

S-Adenosylmethionine revisited: its essential role in the regulation of liver function

Dietary methionine is mainly metabolized in the liver where it is converted into S-adenosylmethionine (AdoMet), the main biologic methyl donor. This reaction is catalyzed by methionine adenosyltransferase I/III (MAT I/III), the product of MAT1A gene, which is exclusively expressed in this organ. It was first observed that serum methionine levels were elevated in experimental models of liver damage and in liver cirrhosis in human beings. Results of further studies showed that this pathological alteration was due to reduced MAT1A gene expression and MAT I/III enzyme inactivation associated with liver injury. Synthesis of AdoMet is essential to all cells in the organism, but it is in the liver where most of the methylation reactions take place. The central role played by AdoMet in cellular function, together with the observation that AdoMet administration reduces liver damage caused by different agents and improves survival of alcohol-dependent patients with cirrhosis, led us to propose that alterations in methionine metabolism could play a role in the onset of liver disease and not just be a consequence of it. In the present work, we review the recent findings that support this hypothesis and highlight the mechanisms behind the hepatoprotective role of AdoMet