Single-point mutations in the transmembrane (TM) region of receptor tyrosine kinases (RTKs) can lead to abnormal ligand-independent activation. We use a combination of computational modeling, NMR spectroscopy and cell experiments to analyze in detail the mechanism of how TM domains contribute to the activation of wild-type (WT) PDGFRA and its oncogenic V536E mutant. Using a computational framework, we scan all positions in PDGFRA TM helix for identification of potential functional mutations for the WT and the mutant and reveal the relationship between the receptor activity and TM dimerization via different interfaces. This strategy also allows us design a novel activating mutation in the WT (I537D) and a compensatory mutation in the V536E background eliminating its constitutive activity (S541G). We show both computationally and experimentally that single-point mutations in the TM region reshape the TM dimer ensemble and delineate the structural and dynamic determinants of spontaneous activation of PDGFRA via its TM domain. Our atomistic picture of the coupling between TM dimerization and PDGFRA activation corroborates the data obtained for other RTKs and provides a foundation for developing novel modulators of the pathological activity of PDGFRA.
In situ XRD and NMR experiments combined with molecular dynamics simulations using the grand canonical ensemble (GCMD) show that cation size, charge and solvation energy play critical roles in determining the interlayer expansion of smectite clay minerals when exposed to dry supercritical CO2 under conditions relevant to the earthâ€™s upper crust, petroleum reservoirs, and geological CO2 sequestration conditions (323 K and 90 bar). The GCMD results show that the smectite mineral, hectorite, containing interlayer alkali and alkaline earth cations with relatively small ionic radii and high solvation and hydration energies (e.g., Li+, Na+ Mg2+, and Ca2+) does not intercalate dry CO2 and that the fully collapsed interlayer structure is the energetically most stable configuration. With increasing cation size and decreasing cation solvation energy, the energy barrier to CO2 intercalation decreases. With K+, Rb+, Cs+, Sr2+, and Ba2+ the monolayer structure is the stable configuration, and CO2 should spontaneously enter the interlayer. With Cs+ there is not even an energy barrier for CO2 intercalation, in agreement with the experimental XRD and NMR results that show clay layer expansion and CO2 incorporation. The number of intercalated CO2 molecules decreases with increasing size of the alkali cation but does not vary with ion size for the alkaline earth cations. 13C NMR spectroscopy and the GCMD simulations show that the average orientation of the intercalated CO2 molecules is with their O-C-O axes parallel to the basal clay surface and that they undergo a combination of rapid rotation about an axis perpendicular to the main molecular axis and wobbling motion with respect to the basal surface. Incorporation of CO2 in the interlayer decreases the coordination of Cs+ by the oxygen atoms of the basal surfaces, which is compensated by CO2 molecules entering their solvation shell, as predicted based on previously published NMR results. The GCMD simulations show that the strength of the interaction between the exchangeable cation and the clay structure dominates the intercalation energetics in dry scCO2. With relatively small cations, the cation-clay interactions outcompete cation solvation by CO2 molecules. The computed residence times for coordination among of interlayer species are consistent with the computed energetics.
The intercalation of H2O, CO2, and other fluid species in expandable clay minerals (smectites) may play a significant role in controlling the behavior of these species in geological C-sequestration and enhanced petroleum production and has been the subject of intensive study in recent years. This paper reports the results of a computational study of the effects of the properties of the charge balancing, exchangeable cations on H2O and CO2 intercalation in the smectite mineral, hectorite, in equilibrium with an H2O-saturated supercritical CO2 fluid under reservoir conditions using Grand Canonical Molecular Dynamics (GCMD) methods. The results show that the intercalation behavior is greatly different with cations with relatively low hydration energies and high affinities for CO2 (here Cs+) than with cations with higher hydration energies (here Ca2+). With Cs+, CO2 intercalation occurs in a 1-layer structure and does not require H2O intercalation, whereas with Ca2+ the presence of a sub-monolayer of H2O is required for CO2 intercalation. The computational results provide detailed structural, dynamical and energetic insight into the differences in intercalation behavior and are in excellent agreement with in situ experimental XRD, IR, quartz crystal microbalance, and NMR results for smectite materials obtained under reservoir conditions.