Dynamic control of selectivity in the ubiquitination pathway revealed by an ASP to GLU substitution in an intra-molecular salt-bridge network

Ubiquitination relies on a subtle balance between selectivity and promiscuity achieved through specific interactions between ubiquitin-conjugating enzymes (E2s) and ubiquitin ligases (E3s). Here, we report how a single aspartic to glutamic acid substitution acts as a dynamic switch to tip the selectivity balance of human E2s for interaction toward E3 RING-finger domains. By combining molecular dynamic simulations, experimental yeast-two-hybrid screen of E2-E3 (RING) interactions and mutagenesis, we reveal how the dynamics of an internal salt-bridge network at the rim of the E2-E3 interaction surface controls the balance between an “open”, binding competent, and a “closed”, binding incompetent state. The molecular dynamic simulations shed light on the fine mechanism of this molecular switch and allowed us to identify its components, namely an aspartate/glutamate pair, a lysine acting as the central switch and a remote aspartate. Perturbations of single residues in this network, both inside and outside the interaction surface, are sufficient to switch the global E2 interaction selectivity as demonstrated experimentally. Taken together, our results indicate a new mechanism to control E2-E3 interaction selectivity at an atomic level, highlighting how minimal changes in amino acid side-chain affecting the dynamics of intramolecular salt-bridges can be crucial for protein-protein interactions. These findings indicate that the widely accepted sequence-structure-function paradigm should be extended to sequence-structure-dynamics-function relationship and open new possibilities for control and fine-tuning of protein interaction selectivity

A protein–DNA docking benchmark

We present a protein–DNA docking benchmark containing 47 unbound–unbound test cases of which 13 are classified as easy, 22 as intermediate and 12 as difficult cases. The latter shows considerable structural rearrangement upon complex formation. DNA-specific modifications such as flipped out bases and base modifications are included. The benchmark covers all major groups of DNA-binding proteins according to the classification of Luscombe et al., except for the zipper-type group. The variety in test cases make this non-redundant benchmark a useful tool for comparison and development of protein–DNA docking methods. The benchmark is freely available as download from the internet

Impact of the 3D source geometry on time-delay measurements of lensed type-Ia Supernovae

It has recently been proposed that gravitationally lensed type-Ia supernovae can provide microlensing-free time-delay measurements provided that the measurement is taken during the achromatic expansion phase of the explosion and that color light curves are used rather than single-band light curves. If verified, this would provide both precise and accurate time-delay measurements, making lensed type-Ia supernovae a new golden standard for time-delay cosmography. However, the 3D geometry of the expanding shell can introduce an additional bias that has not yet been fully explored. In this work, we present and discuss the impact of this effect on time-delay cosmography with lensed supernovae and find that on average it leads to a bias of a few tenths of a day for individual lensed systems. This is negligible in view of the cosmological time delays predicted for typical lensed type-Ia supernovae but not for the specific case of the recently discovered type-Ia supernova iPTF16geu, whose time delays are expected to be smaller than a day.Comment: 7 pages, 4 figures, published in A&

Вимоги СОТ для державного регулювання регіонального ринку сільськогосподарської продукції України

Державне регулювання України, як країни з перехідною ринковою економікою, повинно базуватися на основних положеннях та вимогах СОТ (Світової організації торгівлі). Україна вибрала курс Європейської інтеграції, тому її економіка повинна відповідати та працювати по принципах світового ринку. Мета досліджень: проаналізувати основні положення та вимоги Світової організації торгівлі, основні моменти державного регулювання ринку сільськогосподарської продукції, що відповідають принципам світового ринку і які повинні працювати в умовах України

Характеристика механизма функционирования форм хозяйствования с иностранными инвестициями

Механизм функционирования предприятия с иностранными инвестициями неразрывно связан с понятиями "хозяйственный механизм" и "механизм функционирования предприятия". В экономической науке советского периода широко применялся термин "хозяйственный механизм". Рассматривался хозяйственный механизм отдельного предприятия, отрасли, экономики страны в целом, то есть рассматривался хозяйственный механизм экономических систем различного уровня

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

Understanding molecular recognition of small molecules by proteins in atomistic detail is key for drug design. Molecular docking is a widely used computational method to mimic ligand-protein association in silico. However, predicting conformational changes occurring in proteins upon ligand binding is still a major challenge. Ensemble docking approaches address this issue by considering a set of different conformations of the protein obtained either experimentally or from computer simulations, e.g., molecular dynamics. However, holo structures prone to host (the correct) ligands are generally poorly sampled by standard molecular dynamics simulations of the apo protein. In order to address this limitation, we introduce a computational approach based on metadynamics simulations called ensemble docking with enhanced sampling of pocket shape (EDES) that allows holo-like conformations of proteins to be generated by exploiting only their apo structures. This is achieved by defining a set of collective variables that effectively sample different shapes of the binding site, ultimately mimicking the steric effect due to the ligand. We assessed the method on three challenging proteins undergoing different extents of conformational changes upon ligand binding. In all cases our protocol generates a significant fraction of structures featuring a low RMSD from the experimental holo geometry. Moreover, ensemble docking calculations using those conformations yielded in all cases native-like poses among the top-ranked ones

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

Understanding molecular recognition of small molecules by proteins in atomistic detail is key for drug design. Molecular docking is a widely used computational method to mimic ligand–protein association in silico. However, predicting conformational changes occurring in proteins upon ligand binding is still a major challenge. Ensemble docking approaches address this issue by considering a set of different conformations of the protein obtained either experimentally or from computer simulations, e.g., molecular dynamics. However, holo structures prone to host (the correct) ligands are generally poorly sampled by standard molecular dynamics simulations of the apo protein. In order to address this limitation, we introduce a computational approach based on metadynamics simulations called ensemble docking with enhanced sampling of pocket shape (EDES) that allows holo-like conformations of proteins to be generated by exploiting only their apo structures. This is achieved by defining a set of collective variables ..