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

Absolute affinities of alpha-amino acids for Cu+ in the gas phase. A theoretical study

International audienceAb initio calculations have been carried out on the [glycine-Cu](+), [serine-Cu](+), and [cysteine-Cu](+) complexes. Investigation of several types of structures for each complex shows that the preferred binding site of Cu+ involves chelation between the carbonyl oxygen and the amino nitrogen. With glycine, this leads to a complexation energy (best estimate of D-0) of 64.3 kcal/mol. Additional chelation with the alcohol group of serine or the thiol group of cysteine leads to larger binding energies, with cysteine binding more strongly than serine, in good agreement with a recent experimental scale of relative Cu+ affinities of all alpha-amino acids present in natural peptides. Combining this scale to the accurate determination of the Cu+ affinity of glycine from the present work leads to absolute values of Cu+ affinities of all amino acids. Calculations were also carried out on the complexes of Cu+ with water, ammonia, formaldehyde, and hydrogen sulfide. The geometrical and electronic structures of these complexes are used to analyze the binding of Cu+ to amino acids

Interaction of alkali metal cations (Li+-Cs+) with glycine in the gas phase: A theoretical study

International audienceThe complexes formed by alkali metal cations (Cat(+)) and glycine (Gly) were studied by means of ab initio quantum chemical methods. Seven types of Gly-Cat(+) interaction were considered in each case. It was found that in the most stable forms of Gly-Li+ and Gly-Na+ the metal ion is chelated between the carbonyl oxygen and nitrogen ends of glycine. For Gly-K+ an isomer involving complexation with both oxygens of the carboxylic function is found to be degenerate with the above chelate, and becomes slightly more stable for Gly-Rb+ and Gly-Cs+. In all cases, interaction of the ion with the carboxylate group of zwitterionic glycine is also low in energy. Computed binding energies (Delta H-298, kcal mol(-1)) are 54.5 (Gly-Li+), 36.3 (Gly-Na+), 26.5 (Gly-K+), 24.1 (Gly-Rb+) and 21.4 (Gly-Cs+). The values for Gly-Na+ and Gly-K+ are in good agreement with recent experimental determinations. For Gly-Li+, a revised experimental value of 54.0 kcal mol(-1) is obtained, based on the computed complexation enthalpy and entropy of Li+ with N,N-dimethylformamide (51.7 kcal mol(-1) and 23.8 cal mol(-1) K-1, respectively). Three isomers among the most stable of the lithiated dimer Gly-Li+-Gly have been determined and found to involve local Gly-Li+ interactions analogous to those in the monomer However, the relative energies of the various isomers show nonnegligible differences between the monomer and the dimer, implying that the kinetic method must be used with care for the determination of cation affinities of larger molecules. Finally, the fluxionality of the Gly-Na+ complex has been considered by locating the transition states for interconversion of the lowest energy isomers. In particular it is found that the lowest isomer can be transformed into the one involving zwitterionic Gly with a rate-determining barrier of 20.4 kcal mol(-1)

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

A quantitative basis for a scale of Na+ affinities of organic and small biological molecules in the gas phase.

International audienceHigh Pressure Mass Spectrometric experiments and ab initio calculations have been carried out in order to establish a series of accurate gas phase sodium ion affinities of organic molecules with a wide variety of functional groups. Ab initio calculations have also been performed on the sodium complexes of three amino acids, serine, cysteine and proline. A systematic critical evaluation of experimental and computational literature results shows that a significant number require revision. Based on comparisons with accurate experimental measurements, the ab initio procedure used is shown to yield sodium ion affinities with an accuracy of ca. 1 kcal.mol-1. This enables the construction of the first reliable table of gas phase Na+ affinities for organic and small biological molecules