Pablo G. Jambrina

Light-Regulated Molecular Trafficking in a Synthetic Water-Soluble Host

Cucurbit[8]uril (CB[8])-mediated complexation of a dicationic azobenzene in water allows for the light-controlled encapsulation of a variety of second guest compounds, including amino acids, dyes, and fragrance molecules. Such controlled guest sequestration inside the cavity of CB[8] enables the regulation of the thermally induced phase transition of poly(N-isopropylacrylamide)-which is not photosensitive-thus demonstrating the robustness and relevancy of the light-regulated CB[8] complexation.

Molecular mechanisms of asymmetric RAF dimer activation

Protein phosphorylation is one of the most common post-translational modifications in cell regulatory mechanisms. Dimerization plays also a crucial role in the kinase activity of many kinases, including RAF, CDK2 (cyclin-dependent kinase 2) and EGFR (epidermal growth factor receptor), with heterodimers often being the most active forms. However, the structural and mechanistic details of how phosphorylation affects the activity of homo- and hetero-dimers are largely unknown. Experimentally, synthesizing protein samples with fully specified and homogeneous phosphorylation states remains a challenge for structural biology and biochemical studies. Typically, multiple changes in phosphorylation lead to activation of the same protein, which makes structural determination methods particularly difficult. It is also not well understood how the occurrence of phosphorylation and dimerization processes synergize to affect kinase activities. In the present article, we review available structural data and discuss how MD simulations can be used to model conformational transitions of RAF kinase dimers, in both their phosphorylated and unphosphorylated forms.

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation.

Abstract RAF kinases are key players in the MAPK signaling pathway and are important targets for personalized cancer therapy. RAF dimerization is part of the physiological activation mechanism, together with phosphorylation, and is known to convey resistance to RAF inhibitors. Herein, molecular dynamics simulations are used to show that phosphorylation of a key N‐terminal acidic (NtA) motif facilitates RAF dimerization by introducing several interprotomer salt bridges between the αC‐helix and charged residues upstream of the NtA motif. Additionally, we show that the R‐spine of RAF interacts with a conserved Trp residue in the vicinity of the NtA motif, connecting the active sites of two protomers and thereby modulating the cooperative interactions in the RAF dimer. Our findings provide a first structure‐based mechanism for the auto‐transactivation of RAF and could be generally applicable to other kinases, opening new pathways for overcoming dimerization‐related drug resistance.

Direct Evidence for a Peroxide Intermediate and a Reactive Enzyme-Substrate-Dioxygen Configuration in a Cofactor-Free Oxidase.

Cofactor-free oxidases and oxygenases promote and control the reactivity of O2 with limited chemical tools at their disposal. Their mechanism of action is not completely understood and structural information is not available for any of the reaction intermediates. Near-atomic resolution crystallography supported by inu2005crystallo Raman spectroscopy and QM/MM calculations showed unambiguously that the archetypical cofactor-free uricase catalyzes uric acid degradation via a C5(S)-(hydro)peroxide intermediate. Low X-ray doses break specifically the intermediate C5=OO(H) bond at 100u2005K, thus releasing O2 inu2005situ, which is trapped above the substrate radical. The dose-dependent rate of bond rupture followed by combined crystallographic and Raman analysis indicates that ionizing radiation kick-starts both peroxide decomposition and its regeneration. Peroxidation can be explained by a mechanism in which the substrate radical recombines with superoxide transiently produced in the active site.

Dynamics of the reactions of muonium and deuterium atoms with vibrationally excited hydrogen molecules: tunneling and vibrational adiabaticity

Quantum mechanical (QM) and quasiclassical trajectory (QCT) calculations have been carried out for the exchange reactions of D and Mu (Mu = muonium) with hydrogen molecules in their ground and first vibrational states. In all the cases considered, the QM rate coefficients, k(T), are in very good agreement with the available experimental results. In particular, QM calculations on the most accurate potential energy surfaces (PESs) predict a rate coefficient for the Mu + H(2) (ν = 1) reaction which is very close to the preliminary estimate of its experimental value at 300 K. In contrast to the D + H(2) (ν = 0,1) and the Mu + H(2) (ν = 0) reactions, the QCT calculations for Mu + H(2) (ν = 1) predict a much smaller k(T) than that obtained with the accurate QM method. This behaviour is indicative of tunneling. The QM reaction probabilities and total reactive cross sections show that the total energy thresholds for the reactions of Mu with H(2) in ν = 0 and ν = 1 are very similar, whereas for the corresponding reaction with D the ν = 0 total energy threshold is about 0.3 eV lower than that for ν = 1. The results just mentioned can be explained by considering the vibrational adiabatic potentials along the minimum energy path. The threshold for the reaction of Mu with H(2) in both ν = 0 and ν = 1 states is the same and is given by the height of the ground vibrational adiabatic collinear potential, whereas for the D + H(2) reaction the adiabaticity is preserved and the threshold for the reaction in ν = 1 is very close to the height of the ν = 1 adiabatic collinear barrier. For Mu + H(2) (ν = 1) the reaction takes place by crossing from the ν = 1 to the ν = 0 adiabat, since the exit channel leading to MuH (ν = 1) is not energetically accessible. At the lowest possible energies, the non-adiabatic vibrational crossing implies a strong tunneling effect through the ν = 1 adiabatic barrier. Absence of tunneling in the classical calculations results in a threshold that coincides with the height of the ν = 1 adiabatic barrier. Most interestingly, the expected tunneling effect in the reaction of Mu with hydrogen molecules occurs for H(2) (ν = 1) but not for H(2) (ν = 0) where zero-point-energy effects clearly dominate.

Quantum interference between H + D2 quasiclassical reaction mechanisms

Interferences are genuine quantum phenomena that appear whenever two seemingly distinct classical trajectories lead to the same outcome. They are common in elastic scattering but are seldom observable in chemical reactions. Here we report experimental measurements of the state-to-state angular distribution for the Hu2009+u2009D2 reaction using the photoloc technique. For products in low rotational and vibrational states, a characteristic oscillation pattern governs backward scattering. The comparison between the experiments, rigorous quantum calculations and classical trajectories on an accurate potential energy surface allows us to trace the origin of that structure to the quantum interference between different quasiclassical mechanisms, a phenomenon analogous to that observed in the double-slit experiment.

Understanding the reaction between muonium atoms and hydrogen molecules: zero point energy, tunnelling, and vibrational adiabaticity

The advent of very precise measurements of rate coefficients in reactions of muonium (Mu), the lightest hydrogen isotope, with H2 in its ground and first vibrational state and of kinetic isotope effects with respect to heavier isotopes has triggered a renewed interests in the field of muonic chemistry. The aim of the present article is to review the most recent results about the dynamics and mechanism of the reaction Mu+H2 to shed light on the importance of quantum effects such as tunnelling, the preservation of the zero point energy, and the vibrational adiabaticity. In addition to accurate quantum mechanical (QM) calculations, quasiclassical trajectories (QCT) have been run in order to check the reliability of this method for this isotopic variant. It has been found that the reaction with H2(v=0) is dominated by the high zero point energy (ZPE) of the products and that tunnelling is largely irrelevant. Accordingly, both QCT calculations that preserve the products’ ZPE as well as those based on the Ring Polymer Molecular Dynamics methodology can reproduce the QM rate coefficients. However, when the hydrogen molecule is vibrationally excited, QCT calculations fail completely in the prediction of the huge vibrational enhancement of the reactivity. This failure is attributed to tunnelling, which plays a decisive role breaking the vibrational adiabaticity when v=1. By means of the analysis of the results, it can be concluded that the tunnelling takes place through the ν1=1 collinear barrier. Somehow, the tunnelling that is missing in the Mu+H2(v=0) reaction is found in Mu+H2(v=1).

Elucidation of the O(1D) + HF → F + OH mechanism by means of quasiclassical trajectories

The dynamics and mechanism of the O((1)D) + HF → F + OH reaction have been studied through quasi-classical trajectory calculations carried out on the 1(1)A Potential Energy Surface (PES) fitted by Gómez-Carrasco et al. [Chem. Phys. Lett., 2007, 435, 188]. The influence of the collision energy and the initial rovibrational state on the reaction has been considered. As a result of this study, we conclude that for v = 0 the reactive collisions take place exclusively through an indirect mechanism that involves a long-lived complex. Interestingly and somewhat unexpectedly for a barrierless reaction, vibrational excitation causes a large enhancement of the reactivity due to the concurrence of a direct abstraction mechanism. Unlike other reactions also taking place on a barrierless PES featuring deep wells, no insertion mechanism is observed in O((1)D) + HF reactive collisions.

Communication: Rate coefficients from quasiclassical trajectory calculations from the reverse reaction: The Mu + H2 reaction re-visited

In a previous paper [P. G. Jambrina et al., J. Chem. Phys. 135, 034310 (2011)] various calculations of the rate coefficient for the Mu + H(2) → MuH + H reaction were presented and compared to experiment. The widely used standard quasiclassical trajectory (QCT) method was shown to overestimate the rate coefficients by several orders of magnitude over the temperature range 200-1000 K. This was attributed to a major failure of that method to describe the correct threshold for the reaction owing to the large difference in zero-point energies (ZPE) of the reactant H(2) and product MuH (∼0.32 eV). In this Communication we show that by performing standard QCT calculations for the reverse reaction and then applying detailed balance, the resulting rate coefficient is in very good agreement with the other computational results that respect the ZPE, (as well as with the experiment) but which are more demanding computationally.

Cold and ultracold dynamics of the barrierless D+ + H2 reaction: Quantum reactive calculations for ∼R−4 long range interaction potentials

Quantum reactive and elastic cross sections and rate coefficients have been calculated for D(+) + H2 (v = 0, j = 0) collisions in the energy range from 10(-8) K (deep ultracold regime), where only one partial wave is open, to 150 K (Langevin regime) where many of them contribute. In systems involving ions, the ∼R(-4) behavior extends the interaction up to extremely long distances, requiring a special treatment. To this purpose, we have used a modified version of the hyperspherical quantum reactive scattering method, which allows the propagations up to distances of 10(5)u2009a0 needed to converge the elastic cross sections. Interpolation procedures are also proposed which may reduce the cost of exact dynamical calculations at such low energies. Calculations have been carried out on the PES by Velilla et al. [J. Chem. Phys. 129, 084307 (2008)] which accurately reproduces the long range interactions. Results on its prequel, the PES by Aguado et al. [J. Chem. Phys. 112, 1240 (2000)], are also shown in order to emphasize the significance of the inclusion of the long range interactions. The calculated reaction rate coefficient changes less than one order of magnitude in a collision energy range of ten orders of magnitude, and it is found in very good agreement with the available experimental data in the region where they exist (10-100 K). State-to-state reaction probabilities are also provided which show that for each partial wave, the distribution of HD final states remains essentially constant below 1 K.