c-Src and c-Abl are two closely related protein kinases that constitute important anticancer targets. Despite their high sequence identity, they show different sensitivities to the anticancer drug imatinib, which binds specifically to a particular inactive conformation in which the Asp of the conserved DFG motif points outward (DFG-out). We have analyzed the DFG conformational transition of the two kinases using massive molecular dynamics simulations, free energy calculations, and isothermal titration calorimetry. On the basis of the reconstruction of the free energy surfaces for the DFG-in to DFG-out conformational changes of c-Src and c-Abl, we propose that the different flexibility of the two kinases results in a different stability of the DFG-out conformation and might be the main determinant of imatinib selectivity.

Density functional theory (DFT) Becke3LYP calculations including full and restricted geometry optimizations are carried out on the complexes [Co(Cor)(Benz)(CH 3 )] (Cor ) corrin, Benz ) benzimidazole), [Co(Cor)(Benz)], [Co(Cor)(CH 3 )], and [Co(Cor)]. These systems, despite the absence of side-chains, constitute the most realistic models used to date for DFT calculations on cofactor B 12 and its homolysis product. The calculations prove that both thermodynamics and kinetics of the homolytic bond cleavage of the Co-C bond have very little dependence on the position of the axial benzimidazole ligand. The generality of these results is confirmed by additional calculations on [Co(Cor)(Benz)(CH 2 R)] (R ) tetrahydrofuran), [Co(Cor)(Im)-(CH 3 )] (Im ) imidazole), and [Co(Cor-CH 3 )(Benz)(CH 3 )] (Cor-CH 3 ) methylated corrin).

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Alpha-solenoid proteins are suggested to constitute highly flexible macromolecules, whose structural variability and large surface area is instrumental in many important protein-protein binding processes. By equilibrium and nonequilibrium molecular dynamics simulations, we show that importin-beta, an archetypical alpha-solenoid, displays unprecedentedly large and fully reversible elasticity. Our stretching molecular dynamics simulations reveal full elasticity over up to twofold end-to-end extensions compared to its bound state. Despite the absence of any long-range intramolecular contacts, the protein can return to its equilibrium structure to within 3 A backbone RMSD after the release of mechanical stress. We find that this extreme degree of flexibility is based on an unusually flexible hydrophobic core that differs substantially from that of structurally similar but more rigid globular proteins. In that respect, the core of importin-beta resembles molten globules. The elastic behavior is dominated by nonpolar interactions between HEAT repeats, combined with conformational entropic effects. Our results suggest that alpha-solenoid structures such as importin-beta may bridge the molecular gap between completely structured and intrinsically disordered proteins.