Disorder, oscillatory dynamics and state switching: the role of c-Myc.

In this paper, using the intrinsically disordered oncoprotein Myc as an example, we present a mathematical model to help explain how protein oscillatory dynamics can influence state switching. Earlier studies have demonstrated that, while Myc overexpression can facilitate state switching and transform a normal cell into a cancer phenotype, its downregulation can reverse state-switching. A fundamental aspect of the model is that a Myc threshold determines cell fate in cells expressing p53. We demonstrate that a non-cooperative positive feedback loop coupled with Myc sequestration at multiple binding sites can generate bistable Myc levels. Normal quiescent cells with Myc levels below the threshold can respond to mitogenic signals to activate the cyclin/cdk oscillator for limited cell divisions but the p53/Mdm2 oscillator remains nonfunctional. In response to stress, the p53/Mdm2 oscillator is activated in pulses that are critical to DNA repair. But if stress causes Myc levels to cross the threshold, Myc inactivates the p53/Mdm2 oscillator, abrogates p53 pulses, and pushes the cyclin/cdk oscillator into overdrive sustaining unchecked proliferation seen in cancer. However, if Myc is downregulated, the cyclin/cdk oscillator is inactivated and the p53/Mdm2 oscillator is reset and the cancer phenotype is reversed.

On the anisotropy of van der Waals atomic radii of O, S, Se, F, Cl, Br, and I.

The Cambridge Structural Database (CSD) was used to obtain flattening factors to describe the overall anisotropy of nonbonding van der Waals (vdW) contacts between several main group elements. The method for obtaining the flattening factors is based on a novel minimization process. Results show that the vdW contact distances are significantly dependent on the environment and the orientations of the surrounding covalently bonded atoms: head-on vdW contacts are generally shorter than sideways contacts in overall agreement with earlier results by Nyburg and Faerman (Acta Crystallogr., Sect. B: Struct. Sci. 1985, 41, 274-279). With the exception of Se, we find flattening factors that are somewhat smaller than those found earlier. High-level ab initio quantum chemical calculations using Ar and Ne as a probe also confirm the flattening effect and its dependency on the environment. A dozen popular long-range corrected and dispersion supplemented density functionals are compared with the CCSD(T) data. While several of them perform quite poorly, four DFT-D methods, especially B3LYP-GD3BJ, provided vdW flattening similar to those found by the CCSD(T) theory and experiment.