Free Energy Simulations of a GTPase: GTP and GDP Binding to Archaeal Initiation Factor 2

International audienceArchaeal initiation factor 2 (aIF2) is a protein involved in the initiation of protein biosynthesis. In its GTP-bound, "ON" conformation, aIF2 binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, "OFF" conformation, it dissociates from tRNA. To understand the specific binding of GTP and GDP and its dependence on the ON or OFF conformational state of aIF2, molecular dynamics free energy simulations (MDFE) are a tool of choice. However, the validity of the computed free energies depends on the simulation model, including the force field and the boundary conditions, and on the extent of conformational sampling in the simulations. aIF2 and other GTPases present specific difficulties; in particular, the nucleotide ligand coordinates a divalent Mg(2+) ion, which can polarize the electronic distribution of its environment. Thus, a force field with an explicit treatment of electronic polarizability could be necessary, rather than a simpler, fixed charge force field. Here, we begin by comparing a fixed charge force field to quantum chemical calculations and experiment for Mg(2+):phosphate binding in solution, with the force field giving large errors. Next, we consider GTP and GDP bound to aIF2 and we compare two fixed charge force fields to the recent, polarizable, AMOEBA force field, extended here in a simple, approximate manner to include GTP. We focus on a quantity that approximates the free energy to change GTP into GDP. Despite the errors seen for Mg(2+):phosphate binding in solution, we observe a substantial cancellation of errors when we compare the free energy change in the protein to that in solution, or when we compare the protein ON and OFF states. Finally, we have used the fixed charge force field to perform MDFE simulations and alchemically transform GTP into GDP in the protein and in solution. With a total of about 200 ns of molecular dynamics, we obtain good convergence and a reasonable statistical uncertainty, comparable to the force field uncertainty, and somewhat lower than the predicted GTP/GDP binding free energy differences. The sign and magnitudes of the differences can thus be interpreted at a semiquantitative level, and are found to be consistent with the experimental binding preferences of ON- and OFF-aIF2

Na+ binding to cyclic and linear dipeptides. Bond energies, entropies of Na+ complexation, and attachment sites from the dissociation of Na+-bound heterodimers and ab initio calculations

International audienceThe Na+ affinities of simple cyclic and linear dipeptides and of selected derivatives are determined in the gas-phase based on the dissociations of Na+-bound heterodimers [peptide + Bi]Na+, in which Bi represents a reference base of known Na+ affinity (kinetic method). The decompositions of [peptide + Bi]Na+ are assessed at three different internal energies; this approach permits the deconvolution of entropic contributions from experimentally measured free energies to thus obtain affinity (i.e. enthalpy or bond energy) values. The Na+affinities of the peptides studied increase in the order (kJ mol-1) cyclo-glycylglycine (143) < cyclo-alanylglycine (149) < cyclo-alanylalanine (151) < N-acetyl glycine (172) < glycylglycine (177) < alanylglycine (178) < glycylalanine (179) < alanylalanine (180) < glycylglycine ethyl ester (181) < glycylglycine amide (183). The method used provides quantitative information about the difference in bond entropies between the peptide-Na+ and Bi-Na+ bonds, which is most significant when Na+ complexation alters rotational degrees of freedom either in the peptide or in Bi. From the relative bond entropies, it is possible to appraise absolute entropies of Na+ attachment, which are 104 and 116 J mol-1 K-1 for the cyclic and linear molecules, respectively. The combined affinity and entropy data point out that the cyclic dipeptides bind Na+ in a monodentate fashion through one of their amide carbonyl oxygens, while the linear molecules coordinate Na+ in a multidentate arrangement involving the two carbonyl oxygens and, possibly, the N-terminal amino group. High-level ab initio calculations reveal that the most stable [glycylglycine]Na+ structure arises upon bidentate chelation of Na+ by the two carbonyls and concomitant formation of a hydrogen bond between the amino group and the amide nitrogen. Such a structure agrees very well with the experimental enthalpy and entropy trends observed for the linear molecules. According to theory, zwitterionic forms of [glycylglycine]Na+ are the least stable isomers, as also suggested by the experimental results

Mechanism and Energetics for Dehydrogenation of Methane by Gaseous Iridium Ions

Ir^+ has been observed as the most efficient transition-metal ion for dehydrogenation of CH_4 in the gas phase. We carried out theoretical studies of the complete reaction profile for this process and find three salient factors responsible for the high reactivity: (i) the ability of Ir^+ to change spin easily, (ii) the strength of the Ir-C and Ir-H bonds, and (iii) the ability of Ir^+ to form up to four covalent bonds. We show that among transition-metal ions Ir^+ is unique in best possessing all three characteristics. The combination of these factors leads to a global minimum for the singlet Ir(H)_2(CH_2)^+ structure, which plays an important role in the activation. On the basis of these results, we suggest solution-phase analogues that may also activate CH_4

Mimics of Duplication Cysts: Intraperitoneal Nodules in a 14-Year-Old Boy

Hemangiomas are the most common primary hepatic tumors, but there are few reports of their occurrence elsewhere in the abdomen. The concurrent existence of multiple fibrous nodules of the omentum, mesentery, and porta hepatis, along with a gastric hemangioma, in a child raises the question of syndromic association. Our search of the English literature revealed only rare mentions of hemangiomas involving the stomach and mesentery or omentum. These lesions have attracted clinical attention by symptoms of obstruction, gastrointestinal bleeding, intussusception, infection, perforation, or vague abdominal pain. Although some tumors exist unnoticed for many decades and are identified only incidentally, others present emergently and require immediate surgical attention. We report the case of a 14-year-old boy who presented with symptoms similar to those for appendicitis or duplication cyst, who was found to have a torsed gastric hemangioma and multiple benign fibrous nodules in the abdomen. The presence of multiple vascular or fibrous lesions is associated with genetic syndromes that can have lifelong and reproductive repercussions; so it is imperative that these tumors be recognized by diagnosticians

Mechanism and Energetics for Dehydrogenation of Methane by Gaseous Iridium Ions

Ir^+ has been observed as the most efficient transition-metal ion for dehydrogenation of CH_4 in the gas phase. We carried out theoretical studies of the complete reaction profile for this process and find three salient factors responsible for the high reactivity: (i) the ability of Ir^+ to change spin easily, (ii) the strength of the Ir-C and Ir-H bonds, and (iii) the ability of Ir^+ to form up to four covalent bonds. We show that among transition-metal ions Ir^+ is unique in best possessing all three characteristics. The combination of these factors leads to a global minimum for the singlet Ir(H)_2(CH_2)^+ structure, which plays an important role in the activation. On the basis of these results, we suggest solution-phase analogues that may also activate CH_4