Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases

Most proteins assume different conformations to perform their cellular functions. This conformational dynamics is physiologically regulated by binding events and post-translational modifications, but can also be affected by pathogenic mutations. Atomistic molecular dynamics simulations complemented by enhanced sampling approaches are increasingly used to probe the effect of mutations on the conformational dynamics and on the underlying conformational free energy landscape of proteins. In this short review we discuss recent successful examples of simulations used to understand the molecular mechanism underlying the deregulation of physiological conformational dynamics due to non-synonymous single point mutations. Our examples are mostly drawn from the protein kinase family

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

p38α is a Ser/Thr protein kinase involved in a variety of cellular processes and pathological conditions, which makes it a promising pharmacological target. Although the activity of the enzyme is highly regulated, its molecular mechanism of activation remains largely unexplained, even after decades of research. By using state-of-the-art molecular dynamics simulations, we decipher the key elements of the complex molecular mechanism refined by evolution to allow for a fine tuning of p38α kinase activity. Our study describes for the first time the molecular effects of different regulators of the enzymatic activity, and provides an integrative picture of the activation mechanism that explains the seemingly contradictory X-ray and NMR data

Soil C and N Changes with Afforestation of Grasslands Across Gradients of Precipitation and Plantation Age

Afforestation, the conversion of unforested lands to forests, is a tool for sequestering anthropogenic carbon dioxide into plant biomass. However, in addition to altering biomass, afforestation can have substantial effects on soil organic carbon (SOC) pools, some of which have much longer turnover times than plant biomass. An increasing body of evidence suggests that the effect of afforestation on SOC may depend on mean annual precipitation (MAP). The goal of this study was to test how labile and bulk pools of SOC and total soil nitrogen (TN) change with afforestation across a rainfall gradient of 600–1500 mm in the Rio de la Plata grasslands of Argentina and Uruguay. The sites were all former grasslands planted with Eucalyptus spp. Overall, we found that afforestation increased (up to 1012 kg C·ha−1·yr−1) or decreased (as much as 1294 kg C·ha−1·yr−1) SOC pools in this region and that these changes were significantly related to MAP. Drier sites gained, and wetter sites lost, SOC and TN (r2 = 0.59, P = 0.003; and r2 = 0.57, P = 0.004, respectively). Labile C and N in microbial biomass and extractable soil pools followed similar patterns to bulk SOC and TN. Interestingly, drier sites gained more SOC and TN as plantations aged, while losses reversed as plantations aged in wet sites, suggesting that plantation age in addition to precipitation is a critical driver of changes in soil organic matter with afforestation. This new evidence implies that longer intervals between harvests for plantations could improve SOC storage, ameliorating the negative trends found in humid sites. Our results suggest that the value of afforestation as a carbon sequestration tool should be considered in the context of precipitation and age of the forest stand

Quantum transport through a DNA wire in a dissipative environment

Electronic transport through DNA wires in the presence of a strong dissipative environment is investigated. We show that new bath-induced electronic states are formed within the bandgap. These states show up in the linear conductance spectrum as a temperature dependent background and lead to a crossover from tunneling to thermal activated behavior with increasing temperature. Depending on the strength of the electron-bath coupling, the conductance at the Fermi level can show a weak exponential or even an algebraic length dependence. Our results suggest a new environmental-induced transport mechanism. This might be relevant for the understanding of molecular conduction experiments in liquid solution, like those recently performed on poly(GC) oligomers in a water buffer (B. Xu et al., Nano Lett 4, 1105 (2004)).Comment: 5 pages, 3 figure

An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase

Phosphorylation of the activation loop is a fundamental step in the activation of most protein kinases. In the case of the Src tyrosine kinase, a prototypical kinase due to its role in cancer and its historic importance, phosphorylation of tyrosine 416 in the activation loop is known to rigidify the structure and contribute to the switch from the inactive to a fully active form. However, whether or not phosphorylation is able per-se to induce a fully active conformation, that efficiently binds ATP and phosphorylates the substrate, is less clear. Here we employ a combination of solution NMR and enhanced-sampling molecular dynamics simulations to fully map the effects of phosphorylation and ATP/ADP cofactor loading on the conformational landscape of Src tyrosine kinase. We find that both phosphorylation and cofactor binding are needed to induce a fully active conformation. What is more, we find a complex interplay between the A-loop and the hinge motion where the phosphorylation of the activation-loop has a significant allosteric effect on the dynamics of the C-lobe

Complex microwave conductivity of Na-DNA powders

We report the complex microwave conductivity, $\sigma=\sigma_1-i\sigma_2$, of Na-DNA powders, which was measured from 80 K to 300 K by using a microwave cavity perturbation technique. We found that the magnitude of $\sigma_1$ near room temperature was much larger than the contribution of the surrounding water molecules, and that the decrease of $\sigma_1$ with decreasing temperature was sufficiently stronger than that of the conduction of counterions. These results clearly suggest that the electrical conduction of Na-DNA is intrinsically semiconductive.Comment: 16 pages, 7 figure