Crosslinking constraints and computational models as complementary tools in modeling the extracellular domain of the glycine receptor

The glycine receptor (GlyR), a member of the pentameric ligand-gated ion channel superfamily, is the major inhibitory neurotransmitter-gated receptor in the spinal cord and brainstem. In these receptors, the extracellular domain binds agonists, antagonists and various other modulatory ligands that act allosterically to modulate receptor function. The structures of homologous receptors and binding proteins provide templates for modeling of the ligand-binding domain of GlyR, but limitations in sequence homology and structure resolution impact on modeling studies. The determination of distance constraints via chemical crosslinking studies coupled with mass spectrometry can provide additional structural information to aid in model refinement, however it is critical to be able to distinguish between intra- and inter-subunit constraints. In this report we model the structure of GlyBP, a structural and functional homolog of the extracellular domain of human homomeric α1 GlyR. We then show that intra- and intersubunit Lys-Lys crosslinks in trypsinized samples of purified monomeric and oligomeric protein bands from SDS-polyacrylamide gels may be identified and differentiated by MALDI-TOF MS studies of limited resolution. Thus, broadly available MS platforms are capable of providing distance constraints that may be utilized in characterizing large complexes that may be less amenable to NMR and crystallographic studies. Systematic studies of state-dependent chemical crosslinking and mass spectrometric identification of crosslinked sites has the potential to complement computational modeling efforts by providing constraints that can validate and refine allosteric models. © 2014 Liu et al

ВЛИЯНИЕ ТЕРМИЧЕСКОЙ ОБРАБОТКИ НА СТРУКТУРУ И СВОЙСТВА ЛИСТОВЫХ ПОЛУФАБРИКАТОВ ИЗ ЖАРОПРОЧНОГО СПЛАВА НА ОСНОВЕ ТИТАНА, ЛЕГИРОВАННОГО РЗМ

This paper is a continuation of studies on the effect of microalloying with gadolinium, a rare earth metal, on the structure formation and properties of a titanium alloy under thermal action. It was previously shown that the introduction of gadolinium into an experimental heat-resistant alloy promotes cast structure transformation and reduces the size of structural components, and affects the rate of growth and nucleation of particles. It has been established that additional alloying of gadolinium has no significant influence on the microstructure formation of hot-rolled sheets made of the heat-resistant experimental alloy after annealing at 950 °C. The structure is represented by equiaxial particles of the primary α-phase, secondary α-phase of lamellar morphology and a small amount of β-phase.It has been established that the ordering processes occur in primary α-phase particles and α2-phase particles are formed during isothermal aging at 700 °C for 100 h with the formation of silicides at the α-β interface. It is shown that the α2 phase is formed in the body of the primary α-phase particles, and its border regions are free from precipitations that is due to their aluminum depletion as a result of β→α transformation. It has been established that the silicide particle size is reduced as the gadolinium content in the alloy increases. The average particle size is 0,2–0,3 μm in the alloy with 0 % Gd, and it is reduced to 0,05–0,1 μm in the alloy with 0,2 % Gd.It was shown that the introduction of 0,2 % of gadolinium into the heat-resistant titanium alloy leads to a decrease in the gas-saturated layer depth, and to an increase in the cyclic durability and short-term strength at 700 °C by 30 %.Продолжены исследования, посвященные изучению влияния микролегирования редкоземельным металлом гадолинием на формирование структуры и свойства титанового сплава при термическом воздействии. Как установлено ранее, введение в опытный жаропрочный сплав гадолиния способствует преобразованию структуры в литом состоянии, приводит к уменьшению размера структурных составляющих, а также воздействует на скорости роста и зарождения частиц. Выявлено, что дополнительное легирование гадолинием не оказывает существенного влияния на формирование микроструктуры горячекатаных листов из жаропрочного опытного сплава после отжига при температуре 950 °С. Структура представлена равноосными частицами первичной α-фазы, вторичной α-фазы пластинчатой морфологии и небольшим количеством β-фазы. Определено, что в процессе изотермической выдержки (t = 700 °С, τ = 100 ч) в частицах первичной α-фазы протекают процессы упорядочения и отмечается выделение частиц α2-фазы, а на межфазной α/β-границе – образование химических соединений в виде силицидов. Показано, что формирование α2-фазы происходит в теле частиц первичной α-фазы, а приграничные ее области свободны от выделений, что обусловлено их обеднением алюминием вследствие протекания β→α-превращения. Установлено, что с увеличением в сплаве содержания гадолиния размеры выделяющихся частиц силицида уменьшаются. Если в сплаве с 0 % Gd средний размер частиц составляет 0,2–0,3 мкм, то в сплаве с 0,2 % Gd он снижается до 0,05–0,1 мкм. Показано, что введение в жаропрочный титановый сплав 0,2 % Gd приводит к уменьшению глубины «альфированного» слоя, повышению на 30 % циклической долговечности и кратковременной прочности при температуре 700 °С

Experiments with the Linear Automata and Synthesis Test to Them

The overview of results in area of the experiments theory with linear automata is given. This theory is a fundamental base to devise methods of discrete systems technical diagnosis

About Search of Optimal Paths in Fuzzy Graphs

A large variety of problems in different fields, including the problems of the creation of optimal solutions of different kinds, can be formulated in graph theory language in the form of search tasks at given graphs of optimal paths of special character. Many results in these courses are now obtained which refer to classical graph theory. In this theory, a graph is assumed to be a deterministic object and there are no any uncertainties (fuzzinesses) in its description and in the description of its functioning process. Nowadays, science has come to the realization that the majority of our knowledge and links with the external world do not correspond to formerly established classical notions about them. New approaches to these areas are now being developed, which imply principal impossibility to do without fuzzinesses that are accepted as a reality of human existence. This requires the development of complex of concepts and methods which in, this fuzziness should be taken into account really in practical applications. In the proposed article, the tasks of searching optimal paths according to some criteria in the frames of currently accepted fuzzy graph model are considered. When solving the problem of the shortest paths, the rule of choosing the “best” arc is introduced and motivated. The method of solving the tasks with the use of the design of oriented graph path tree is proposed. The notion of path feasibility in fuzzy graph is introduced, the feasibility is evaluated as the probability of path real existence in given graph. The method for calculation of path feasibility, based on the reduction of belonging degree of each arc in the path of graph path to its probability, is proposed. The task on the search of path with maximum feasibility is solved on this basis.</jats:p