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

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

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

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

Information-Driven Antibody-Antigen Modelling with HADDOCK

In the recent years, therapeutic use of antibodies has seen a huge growth, "due to their inherent proprieties and technological advances in the methods used to study and characterize them. Effective design and engineering of antibodies for therapeutic purposes are heavily dependent on knowledge of the structural principles that regulate antibody-antigen interactions. Several experimental techniques such as X-ray crystallography, cryo-electron microscopy, NMR, or mutagenesis analysis can be applied, but these are usually expensive and time-consuming. Therefore computational approaches like molecular docking may offer a valuable alternative for the characterization of antibody-antigen complexes.Here we describe a protocol for the prediction of the 3D structure of antibody-antigen complexes using the integrative modelling platform HADDOCK. The protocol consists of (1) the identification of the antibody residues belonging to the hypervariable loops which are known to be crucial for the binding and can be used to guide the docking and (2) the detailed steps to perform docking with the HADDOCK 2.4 webserver following different strategies depending on the availability of information about epitope residues

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 ..

Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility

Intrinsic flexibility of DNA has hampered the development of efficient protein−DNA docking methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. Chem. Soc. 125, 1731–1737] to explicitly deal with DNA flexibility. HADDOCK uses non-structural experimental data to drive the docking during a rigid-body energy minimization, and semi-flexible and water refinement stages. The latter allow for flexibility of all DNA nucleotides and the residues of the protein at the predicted interface. We evaluated our approach on the monomeric repressor−DNA complexes formed by bacteriophage 434 Cro, the Escherichia coli Lac headpiece and bacteriophage P22 Arc. Starting from unbound proteins and canonical B-DNA we correctly predict the correct spatial disposition of the complexes and the specific conformation of the DNA in the published complexes. This information is subsequently used to generate a library of pre-bent and twisted DNA structures that served as input for a second docking round. The resulting top ranking solutions exhibit high similarity to the published complexes in terms of root mean square deviations, intermolecular contacts and DNA conformation. Our two-stage docking method is thus able to successfully predict protein−DNA complexes from unbound constituents using non-structural experimental data to drive the docking