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

Molecular complexes of small alkanes with Co+

International audienceUsing ab initio methods, including extensive electron correlation, we studied the molecular complexes of Co+ with H-2 and a number of small alkanes (CH4, C2H6, and C3H8). We found that the bond energies increase with ligand size, ranging from 17.2 (for Co(H2)+) to 29.3 kcal/mol (for Co(C3H8)+), in close agreement with recent experiments. For methane, Co+ coordinates to either two or three C-H bonds, with the eta2 geometry more stable by 1.3 kcal/mol out of 21.4 kcal/mol. For ethane, eta2 and eta3 coordinations of Co+ to the C-H bonds are also favorable, but these bonds can be on either the same carbon center or different centers (strict coordination to the C-C bond was not found). Adding a second CH4 to Co(CH4)+, we found that the second bond is stronger than the first by 1.7 kcal/mol. In addition, with both methanes in the eta2 Configuration, we found that the C-H bonds are eclipsed (8.3 kcal/mol better than the staggered conformation). With both methanes in the eta3 configuration, however, they are staggered

Vibrational Signature Of Charge Solvation Vs Salt Bridge Isomers Of Sodiated Amino Acids In The Gas Phase

International audienceThe vibrational spectra of the gaseous sodium complexes of glycine (Gly-Na+) and proline (Pro-Na+) have been recorded in the spectral range 1150-2000 cm-1. The complexes were formed by matrix-assisted laser desorption-ionisation, introduced in the cell of a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer, and their infrared absorption spectra were recorded using photons of variable energy emitted by a free electron laser. Photon absorption was probed by the diminished intensity of the parent ion, due to its infrared induced dissociation into bare sodium cation and the free amino acid, and the appearance of Na+. The observed absorption bands are assigned using ab initio computations of the IR spectra of the lowest energy isomers in each case. They provide the first experimental evidence that the salt bridge isomer is formed in the case of Pro-Na+. In contrast, charge solvation by chelation of Na+ between nitrogen and the carbonyl oxygen seems to be most favorable for Gly-Na+, but a mixture of isomers cannot be ruled out in this case

The sodium ion affinities of cytosine and its methylated derivatives.

International audienceThe sodium ion affinities of cytosine (Cyt), 5-methylcytosine (5MeCyt) and 1-methylcytosine (1MeCyt) have been determined by experimental and quantum chemical methods. Na(+)-bound heterodimers were produced carrying one cytosine or methylated cytosine ligand (designated as C) and one peptide or amino acid reference base (designated as Pep); the Pep molecules included the peptides GlyLeu, GlyPhe, SerGly, and PheGly, and the amino acid His. The dissociation kinetics of these C--Na(+)--Pep ions were determined by collisionally activated dissociation (CAD) and converted to relative and absolute Na(+) affinities via kinetic method approaches. Relative Na(+) affinities increase in the order (kJ/mol): GlyLeu (0) < Cyt (3) < GlyPhe (4) < SerGly (6) < 5MeCyt (8) < PheGly (11) < 1MeCyt (13) < His (17). Anchoring the relative values of the nucleobases to the absolute affinities of the reference bases leads to absolute Na(+) affinities of 214 +/- 8, 219 +/- 8, and 224 +/- 8 kJ/mol for Cyt, 5MeCyt, and 1MeCyt, respectively. Ab initio calculations were used to confirm these results. The computed affinities of Cyt (213 kJ/mol) and 1MeCyt (217 kJ/mol) are in very good agreement with the experiments. These values unambiguously correspond to Na(+) complexes with the keto form of cytosine and its methyl derivatives. Ab initio calculations on tautomerization mechanisms in the gas versus condensed phase are used to discuss why the sodiated keto isomers were formed in the present electrospray ionization (ESI) experiments, but the enol isomers in previous fast atom bombardment (FAB) experiments

Is delocalization a driving force in chemistry ? Benzene, allyl radical, cyclobutadiene and their isoelectronic species.

International audienceThe VB correlation diagram model (Figure 1) is used to answer the title question. It is shown that only atoms that form weak two-electron bonds with low triplet excitation energies may generate delocalized species that are stable toward a localizing distortion. Electronic delocaliaztion is, then, seldom expected to be a significant driving force in chemistry. By this principle, the pi-components of delocalized species, like C6H6 or C3H5, are predicted to be distortive electronic systems that are trapped, within rigidly symmetric sigma frames, and are thereby delocalized despite their opposite inherent tendency. The predictions are examined by means of ab initio investigations at the level of STO-3G, 6-31G and 6-311G with extensive correlation (CI) calculations (up tp 6*10+6 determinants). sigma-pi energy partitions show that the pi-components of C6H6 and C3H5 are indeed distortive much like the pi-electrons of C4H4, and all the pi-components resemble, in turn, their isoelectronic Hn (n=3,4,6) species in the common reluctance to adopt geometries that lead to electronic delocalization. Electronic delocalization in C3H5 and C6H6 turns out to be a byproduct of the sigma-imposed geometric symmetry and not a driving force by itself. The pi-distortive propensities are shown to coexist harmoniously with the thermochemical stability of benzene and the rotational barrier of allyl radical. Further application of the model shows that pi-delocalization, per se, is seldom expected to be a driving force in organic molecules containing C, N and O. In this manner the delocalization problem is unified and shown not to be merely a matter of electron count and mode of delocalization

Internal Proton Transfer Leading to Stable Zwitterionic Structures in a Neutral Isolated Peptide

No solution for the zwitterion: An acid- and base-containing pentapeptide was designed to explore the possibility of zwitterion formation in the gas phase, in the absence of a net charge. Internal proton transfer between peptide side chains in vacuo gave a zwitterion (highlighted in yellow; the canonical form is highlighted in blue), which was identified by gas-phase IR spectroscopy

Influence de dépôt particulaire de pluie sur les processus microbiens et biogéochimiques dans un milieu d'infiltration poreux

International audienceIn aquatic ecosystems, deposition of fine particles at the surface of bed sediments has a great influence on biogeochemical processes and organic matter mineralization. In urban area, the fine particle deposits collected in stormwater infiltration basins can strongly increase the concentrations of reduced solutes (as NH4+) in interstitial water infiltrating in the porous media. The purpose of this study was to test the relative influence of organic matter characteristics (quantity and quality) and the pollutant content of a stormwater particle deposit on mineralization processes, bacterial characteristics, and the release of nutrients in infiltration sediment systems. In microcosm experiments, two other natural particle deposits (one low and one rich particulate organic matter deposits) were studied to compare their effects with those of the stormwater deposit. The results showed that the biogeochemical processes (aerobic respiration, denitrification, fermentative processes) and the microbial metabolism (enzymatic activities) were stimulated in presence of the stormwater deposit and the natural particulate organic matter (POM)-rich deposit because of the quantity of the POM in these surface particle deposits. The high availability of the POM (indicated by its low C/N ratio) produced a higher stimulation of the microbial metabolism than the POM-rich deposit (with a high C/N ratio). In contrast, presence of pollutants (metals and hydrocarbons) in the stormwater deposit did not have significant influence on microbial processes in the porous media. Thus, stormwater sedimentary deposits strongly loaded in POM and pollutants have a great impact on functioning of water-sediment interfaces by stimulating biogeochemical and microbial processes: (1) interstitial water was deoxygenated, (2) several solutes (NH4+, PO43-, DOC) originating from POM were released to interstitial water and (3) these solutes, particularly DOC, that were transferred at depth can significantly affect the functional diversity of micro-organisms in the whole infiltration system