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

Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications

Hematopoietic stem cell transplantation with alpha/beta T-lymphocyte depletion and short course of eculizumab in adolescents and young adults with paroxysmal nocturnal hemoglobinuria

The main goal is to optimize hematopoietic stem cell transplantation (HSCT) approach among adolescents and young adults with paroxysmal nocturnal hemoglobinuria (PNH) by means of Graft-versus-host disease (GVHD) and post-transplant complications risk lowering. Materials and methods. We report our experience of HSCT from HLA-matched unrelated donors using TCR alfa/beta and CD19 depletion in 5 pts (1M/4F) with PNH, developed after successful immunosuppressive therapy (IST) of acquired aplastic anemia (AA). Median age of pts at the moment of transplantation was 17,8 years (range 14,5-22,7), median interval from IST to PNH was 4 years (5mo - 6,5 y). In all patients non-severe pancytopenia was present: granulocytes 0,8х109/l (0,8-1,8 х109/l) platelets 106 х109/l (27-143 х109/l) and Hb -78 g/l, median PNH clone size in granulocytes was 94 (range 75-99)%. One pts previously developed sinus thrombosis. Conditioning consisted of thoraco-abdominal irradiation 4-6 Gy, cyclophosphamide 100 mg/kg, fludarabine 150 mg/m2 and anti-thymocyte globulin (ATG) or alemtuzumab. Eculizumab was given from day (-7) till day (+14) (every 7 days, only 4 times). GVHD prophylaxis was tacrolimus ± methotrexate. Results. Infusedgraft characteristics were: CD34+ - 8,1х106/kg, CD3TCRab·150х103/kg, CD3gd+ - 7,3х106/kg, СD19+ - 221х103/kg, NK -6,4х108/kg. Engraftment was achieved in all 5 pts with a median of 15(12-18) и 13(10-18) days for granulocytes and platelets, respectively. Skin acute GVHD grade I developed in only 1 pt, and subsided with short course of glucocorticoids. CMV reactivation occurred in 1 pt; there were no episodes of Epstein-Barr Virus (EBV) o rAdenovirus (AdV) reactivation. Full donor myeloid chimerism was established in all pts by day +30. Immune reconstitution was delayed until 6 months after transplant but no severe infections occurred. All pts are alive 1,7-5,5 years (med 4 years) after HSCT with normal hematopoiesis and immune function, full donor chimerism and no late sequelae. Conclusions. Transplantation of TCRalfa/beta and CD19 depleted hematopoietic cells from matched unrelated donor after immunoablative conditioning and supported with short course of eculizumab is perfectly safe and efficient technology leading to cure in young patients with PNH

Концентрация кальцифедола в плазме крови как маркер дефицита витамина D у новорожденных с врожденными пороками развития

Diagnosis of vitamin D deficiency and its management is the most difficult problem of modern neonatology.The objective: to study the concentration of 25(OH)D3 in newborns of St. Petersburg depending on the presence of congenital malformations (CM).Subjects and methods. 60 newborns were examined, their gestational age made 39.4 (38-41) weeks. Children were divided into 2 groups: Group 1 – healthy children, Group 2 – children with CM.Results. Regardless of the presence of CM, the calcifedol plasma concentration was below 15 ng/ml. It was found that children with CM whose plasma calcifedol concentration was below 8.0 ng/ml needed long-term invasive mechanical ventilation (80.0 vs 40.0 hours; p < 0.005) and longer treatment in ICU (7.0 vs 4.0; p < 0,002). Negative correlations were revealed between calcifedol concentration, duration of narcotic analgesics administration (R = -0.44; p = 0.01), duration of mechanical ventilation (R = -0.49; p = 0.003) and stay in ICU (R = -0.54; p = 0.001).Conclusion. The most pronounced deficiency of calcifedol was in children with severe CM requiring long-term treatment in ICU.Диагностика дефицита витамина D и его коррекция – наиболее сложная проблема современной неонатологии.Цель исследования: изучить концентрацию 25(ОН)D3 у новорожденных Санкт-Петербурга в зависимости от наличия врожденных пороков развития (ВПР).Материал и методы. Обследовано 60 новорожденных, срок гестации которых составил 39,4 (38–41) нед. Дети были разделены на две группы: 1-я – здоровые дети, 2-я – дети с ВПР.Результаты. Независимо от наличия ВПР концентрация кальцифедола в плазме крови была ниже 15 нг/мл. Установлено, что дети с ВПР, у которых концентрация кальцифедола в плазме крови была ниже 8,0 нг/мл, нуждались в длительной инвазивной искусственной вентиляции легких (ИВЛ) (80,0 против 40,0 ч; p < 0,005) и более длительном лечении в отделении реанимации и интенсивной терапии (7,0 против 4,0; p < 0,002). Выявлены отрицательные корреляционные зависимости между концентрацией кальцифедола, длительностью применения наркотических анальгетиков (R = -0,44; p = 0,01), продолжительностью ИВЛ (R = -0,49; p = 0,003) и сроками лечения в ОРИТ (R = -0,54; p = 0,001).Заключение. Наиболее выраженный дефицит кальцифедола был характерен для детей с тяжелыми ВПР, требующими длительного лечения в условиях ОРИТ

Real-Space Mesh Techniques in Density Functional Theory

This review discusses progress in efficient solvers which have as their foundation a representation in real space, either through finite-difference or finite-element formulations. The relationship of real-space approaches to linear-scaling electrostatics and electronic structure methods is first discussed. Then the basic aspects of real-space representations are presented. Multigrid techniques for solving the discretized problems are covered; these numerical schemes allow for highly efficient solution of the grid-based equations. Applications to problems in electrostatics are discussed, in particular numerical solutions of Poisson and Poisson-Boltzmann equations. Next, methods for solving self-consistent eigenvalue problems in real space are presented; these techniques have been extensively applied to solutions of the Hartree-Fock and Kohn-Sham equations of electronic structure, and to eigenvalue problems arising in semiconductor and polymer physics. Finally, real-space methods have found recent application in computations of optical response and excited states in time-dependent density functional theory, and these computational developments are summarized. Multiscale solvers are competitive with the most efficient available plane-wave techniques in terms of the number of self-consistency steps required to reach the ground state, and they require less work in each self-consistency update on a uniform grid. Besides excellent efficiencies, the decided advantages of the real-space multiscale approach are 1) the near-locality of each function update, 2) the ability to handle global eigenfunction constraints and potential updates on coarse levels, and 3) the ability to incorporate adaptive local mesh refinements without loss of optimal multigrid efficiencies.Comment: 70 pages, 11 figures. To be published in Reviews of Modern Physic

A community effort in SARS-CoV-2 drug discovery.

peer reviewedThe COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against Covid-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.R-AGR-3826 - COVID19-14715687-CovScreen (01/06/2020 - 31/01/2021) - GLAAB Enric

The Effect of the Physical Activity of Disabled Children on the Social Suffi ciency of their Families in the Light of Pierre Bourdieu’s Sociological Theory

Рукопись поступила в редакцию 10 октября 2019 г.Проблема диагностики и критериев оценки социального самочувствия семьи с ребенком-инвалидом является одной из ключевых в формировании социальной политики государства. В статье предложен способ коррекции и накопления социального капитала данной категории семей через вовлечение в регулярную физическую активность ребенка с особенностями развития. Согласно социологической теории Пьера Бурдье взаимодействие всех членов семьи с социальным полем, в данном случае — с полем физкультурной деятельности, предполагает расширение репертуара социальных связей родителей. Проведено исследование структуры семейной физической активности и видов семейного отдыха, определена степень вовлеченности родителей в активный образ жизни, в совместные физкультурные занятия с детьми. Выявлены дефицит двигательной активности ребенка-инвалида на фоне низкого уровня бытовой общей физической подготовленности и слабая мотивация родителей к поддержанию семейных форм физкультурной деятельности.The problem of diagnostics and criteria for assessing the social well-being of families with disabled children is one of the key issues in shaping the state social policy. The article proposes a method of correction and accumulation of social capital of this category of families by involving a child with developmental disabilities in regular physical activity. According to Pierre Bourdieu’s sociological theory, the interaction of all family members with the social fi eld, in this case with the fi eld of physical activity, involves the repertoire expansion of parents’ social connections. The analysis focused on the structure of family physical activity and types of family vacations, the degree of parental involvement in an active lifestyle and physical education activities with children. The research has revealed a defi ciency in the motor activity of a disabled child, which is usually accompanied by the low level of general physical fi tness in the family and insuffi cient motivation of parents to maintain family forms of physical education

OSTEOPOROZ U MUZhChIN S SAKhARNYM DIABETOM 2 TIPA I ANDROGENNYM DEFITsITOM

У каждого третьего мужчины старше 50 лет возникает малотравматичный перелом, последствия которого тяжелее, чем у женщин. Среди факторов риска важное место занимает сахарный диабет (СД) и гипогонадизм. До сих пор существует проблема несвоевременной диагностики и лечения остеопороза(ОП) у мужчин. Цель. Установить частоту остеопороза у мужчин с СД 2 типа в зависимости от андрогенного статуса. Материал и методы. Обследовано 40 мужчин с СД 2 в возрасте 50-60 лет, которые были разделены на 2 сопоставимые группы в зависимости от андрогенной обеспеченности: 20 человек 1 группы имели возрастной андрогенный дефицит и 20 человек 2 группы - с нормальным уровнем тестостерона. Проводилось исследование крови на общий тестостерон (Т), глобулин связывающий половые гормоны (ГСПГ), пролактин, тиреотропный гормон (ТТГ), лютеинизирующий гормон (ЛГ), кальций (Ca), фосфор (P), кре-атинин. Всем мужчинам проводилась рентгеновская денситометрия (DXA) с целью оценки минеральной плотности костной ткани (МПКТ) бедра. Результаты. Частота остеопороза у мужчин 1 группы составила 20%, а во 2 группе - 10%. Кроме того, у мужчин с уровнем эстрадиола 20 пг/мл - 5%. Однако, низкие уровни общего тестостерона и вычисленного свободного тестостерона сильнее коррелировали со снижением МПКТ, чем низкие уровни эстрадиола. Выводы. Дефицит половых гормонов (тестостерона и эстрадиола) оказывает значимое влияние на развитие остеопороза у мужчин с СД 2 типа