Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling

The mechanism of enzymatic peptide hydrolysis in matrix metalloproteinase-2 (MMP-2) was studied at atomic resolution through quantum mechanics/molecular mechanics (QM/MM) simulations. An all-atom three-dimensional molecular model was constructed on the basis of a crystal structure from the Protein Data Bank (ID: 1QIB), and the oligopeptide Ace-Gln-Gly∼Ile-Ala-Gly-Nme was considered as the substrate. Two QM/MM software packages and several computational protocols were employed to calculate QM/MM energy profiles for a four-step mechanism involving an initial nucleophilic attack followed by hydrogen bond rearrangement, proton transfer, and C—N bond cleavage. These QM/MM calculations consistently yield rather low overall barriers for the chemical steps, in the range of 5–10 kcal/mol, for diverse QM treatments (PBE0, B3LYP, and BB1K density functionals as well as local coupled cluster treatments) and two MM force fields (CHARMM and AMBER). It, thus, seems likely that product release is the rate-limiting step in MMP-2 catalysis. This is supported by an exploration of various release channels through QM/MM reaction path calculations and steered molecular dynamics simulations

The concept, structures in management and importance of integrated logistic

З’яўленне інтэграцыйнай лагістыкі мае вынікам прынцыпова новыя паводле формы дзейнасці фірмы (forth - party logistics provider альбо 4PL), якія аб’ядноўваюць лагістычныя паслугі ў інтэграцыйны пакет. Выканана спроба аналізу эфектыўнасці дзейнасці фірм тыпу 4PL

Evolution of in vitro digestibility techniques: a systematic review

The inability to reproduce certain digestive processes in vivo, high research costs and ethical aspects have led to the development of a large number of in vitro digestion models. These models allow us to take into account various factors of modeling complex multistage physiological processes occurring in the gastrointestinal tract, which makes them promising and widely used. A significant part of in vitro methods includes assessment by enzymatic digestion and are based on the calculation of nitrogen remaining after digestion in relation to the initial total nitrogen (according to the Dumas, Kjeldahl method, spectrophotometric or chromatographic method). There are also a number of titrometric methods (pH‑stat), which are mainly used to assess the digestibility of feed, most successfully for aquatic animals due to the simplicity of their digestive tract. Methods for assessing the digestibility of food products by enzymatic digestion have undergone various stages of evolution (since 1947) and have been widely modified by including various enzymes (pepsin, trypsin, pancreatin, erepsin, etc.) in model systems, indices for various products have been determined on their basis (pepsin-digest-residue (PDR) index, 1956; pepsin pancreatin digest (PPD) index, 1964; pepsin digest dialysate (PDD), 1989). As a result, a single protocol was formed to study the digestibility of food — INFOGEST (2014–2019), which includes three stages of digestion (oral, gastric and intestinal). It allows researchers to accurately reproduce the conditions of the human gastrointestinal tract and is widely used by scientists around the world

Comparative estimation of biochemical composition of fruits of Ericaceae species under conditions of Belarus

Thus, as a result of biochemical screening of 30 taxons of Ericaceae species taking into account 32 parameters in a long-term cycle of observation it has been established the different degree of dependence of variability level of biochemical structure components of fruits of alien crops on genotype and a hydrothermal mode of the period of their maturing has been revealed. The similarity of parameters of genotypic variability of some traits of all investigated Ericaceae species is also revealed: low one – for the general contents in fruits of soluble sugars, flavonols, of potassium, calcium, magnesium and high one – for the contents of anthocyanins, and also the ratio of fractions of pectinaceous substances and bioflavonoids. Specific features of genetic determinacy of the analyzed traits, testifying the greatest degree of its displays of V. corymbosum for total accumulation of soluble sugars and bioflavonoids, flavonols contents, calcium and magnesium and by the lowest degree – for the contents of titratable acids, vitamin C, anthocyanins and values of a sugar-acid index were established. If to mention V. vitis-idaea L., the parameters of general accumulation in fruits of soluble sugars, dry substances and all major mineral elements were characterized by the greatest degree of genetic determinacy, whereas by the least degree – the contents of anthocyanins, catechines and tannins. If to mention V. macrocarpon, the parameters of accumulation in fruits of dry substances, nitrogen, potassium, calcium, phenol-carboxylic acids have been noted by the most expressed genetic determinacy, and by the least expressed – the contents of anthocyanins, sucrose and pectinaceous substances in fruits

Genotypic distinctions of variability of biochemical composition of fruits of Vacciniaceae species under conditions of Belarus

Result of research of quantitative characteristics of biochemical composition of fruits of 30 taxons of 3 Vacciniaceae species (such as V. corymbosum L. (highbush blueberry), V. vitis-idaea L. (lingonberry) and Oxycoccus macrocarpus (Ait.) Pers. (cranberry)) inter-specific distinctions of a degree of stability of its separate components to complex influence of meteorological factors are revealed by 32 parameters (traits) describing the contents in fruits of some organic acids, carbohydrates, phenolic compounds, terpenoids and major mineral elements are presented. The cultivars possessing by the greatest and accordingly by the least levels of dependence on abiotic factors are identified

Влияние продолжительности светодиодного освещения на биохимический состав микрозелени капусты белокочанной

In recent years, there has been a steady increase in public interest in healthy and balanced foods all over the world. In this respect, the microgreens of white cabbage is a source of a wide range of useful substances and is characterized by a higher content of those, compared with a similar commercial vegetable. At the same time, information about technological aspects of cultivation, which relate to the duration of lighting, about their correlation with biochemical composition of microgreens of industrial varieties and hybrids of this crop is insufficient and is limited to a very narrow set of their parameters. For this reason, it is of particular relevance to identify the optimal duration of LED lighting in the white cabbage microgreens crop, which ensures accumulation of the highest nutritional and vitamin value and determines the taste qualities of this product. The results of a comparative study of 14 quantitative parameters of biochemical composition of white cabbage microgreens (content of dry, tannic and pectin substances, free organic, ascorbic and hydroxycinnamic acids, soluble sugars, the main groups of bioflavonoids – i.e. anthocyanins, leucoanthocyanins, catechins, flavonols and the indicator of sugar acid index) with different duration of LED lighting are presented (8, 10, 12, 14 and 16 hours). The less significant effect of the studied factor on biochemical composition of microgreens was revealed at 10 hour exposure, while the maximum, exceeding it three times, was at 16 hour exposure. It has been shown that the highest integral level of nutritional and vitamin value of products according to the total analyzed indicators was provided at 16 hours of LED lighting, while the minimum – at 8 hours. For the first time in the Republic of Belarus, the optimal duration of LED lighting for the accumulation of physiologically valuable compounds by microgreens of white cabbage was revealed, which made it possible to recommend it to be used for industrial production.В последние годы во всем мире наблюдается устойчивое повышение интереса общества к здоровым и сбалансированным продуктам питания. Микрозелень капусты белокочанной в этом отношении является источником широкого спектра полезных веществ и отличается более высоким их содержанием по сравнению с аналогичным товарным овощем. Вместе с тем информация о технологических аспектах выращивания, к которым в первую очередь относится продолжительность освещения, об их связи с биохимическим составом микрозелени промышленных сортов и гибридов данной культуры недостаточна и ограничивается весьма узким набором их характеристик. По этой причине особую актуальность обретает выявление оптимальной продолжительности светодиодного освещения в культуре микрозелени капусты белокочанной, обеспечивающей накопление наиболее высокой питательной и витаминной ценности и определяющей вкусовые качества данной продукции. Приведены результаты сравнительного исследования 14 количественных характеристик биохимического состава микрозелени капусты белокочанной (содержание сухих, дубильных и пектиновых веществ, свободных органических, аскорбиновой и гидроксикоричных кислот, растворимых сахаров, основных групп биофлавоноидов – собственно антоцианов, лейкоантоцианов, катехинов, флавонолов и показатель сахарокислотного индекса) при разной продолжительности светодиодного освещения (8, 10, 12, 14, 16 ч). Наименее значительное влияние исследуемого фактора на биохимический состав микрозелени выявлено при 10-часовой экспозиции, тогда как максимальное, превышавшее его в три раза, – при 16-часовой. Показано, что наиболее высокий интегральный уровень питательной и витаминной ценности продукции по совокупности анализируемых показателей обеспечивался при 16-часовой продолжительности светодиодного освещения, тогда как минимальный – при 8-часовой. Впервые в Республике Беларусь выявлена оптимальная продолжительность светодиодного освещения для накопления физиологически ценных соединений микрозеленью капусты белокочанной, что дало возможность рекомендовать ее для использования при промышленном производстве данной продукции

Ассоциация полиморфных вариантов генов ферментов биотрансформации ксенобиотиков с восприимчивостью к заболеваемости туберкулезом легких

The objective: to investigate the relationship of polymorphic variants of genes of xenobiotic biotransformation metabolism enzymes (NAT2 (590G>A (rs1799930)), CYP2E1 (9896C>G (rs2070676)), ABCB1 (3435T>C (rs1045642)), GSTM1 (E/D), GSTT1 (E/D) with the risk of pulmonary tuberculosis.Subjects and Methods. Within the framework of this study, a population sample of unrelated 1081 individuals of Slavic nationalities (mainly Russians) living in the territory of Kursk Oblast was used.Results. The del/del (D/D) GSTM1 genotype was associated with an increased risk of developing tuberculosis, while carrying the del/del (D/D) GSTT1 genotype was associated with a lower risk of developing the disease. Polymorphism 3435T>C ABCB1 (TC genotype) was associated with increased susceptibility to pulmonary tuberculosis in the codominization model, while TT+TC genotypes had the same association in the dominance model.Цель исследования: исследовать взаимосвязь полиморфных вариантов генов ферментов метаболизма биотрансформации ксенобиотиков (NAT2 (590G>A (rs1799930)), CYP2E1 (9896C>G (rs2070676)), ABCB1 (3435T>C (rs1045642)), GSTM1 (E/D), GSTT1 (E/D) с риском развития туберкулеза легких.Материал и методы. В рамках исследования использовалась гомогенная по этническому составу популяционная выборка неродственных индивидов славянских национальностей (преимущественно русских), проживающих на территории Курской области, общей численностью 1 081 индивид.Результаты. Генотип del/del (D/D) GSTM1 ассоциировался с повышенным риском развития туберкулеза, тогда как носительство генотипа del/del (D/D) GSTT1 было ассоциировано с пониженным риском развития болезни. Полиморфизм 3435T>C ABCB1 (генотип TС) ассоциировался с повышенной восприимчивостью к туберкулезу легких в рамках модели кодоминирования, а генотипы ТТ+ТС в рамках модели доминирования

СРАВНИТЕЛЬНЫЙ АНАЛИЗ ВОССТАНОВЛЕНИЯ CYP124 M. TUBERCULOSIS РАЗЛИЧНЫМИ РЕДОКС-ПАРТНЕРАМИ

In order to determine the optimal redox partners of CYP124 M. tuberculosis in reconstituted in vitro system we carried out heterologous expression, isolation and purification of recombinant CYP124 Mycobacterium tuberculosis and candidate redox partners: Fdx, FdR, FprA, Adx, AdR, CPR, Arh1_A18G, Etpfd. CYP124 was shown to exhibit the highest catalytic activity in system with S. pombe mitochondrial electron transfer proteins: Etp1fd и Arh1_A18G.С целью определения оптимальных редокс-партнеров CYP124 M. tuberculosis в in vitro реконструированной системе осуществлена гетерологическая экспрессия, выделение и очистка рекомбинантных цитохрома CYP124 M. tuberculosis и потенциальных редокс-партнеров: Fdx, FdR, FprA, Adx, AdR, CPR, Arh1_A18G, Etpfd. Показано, что CYP124 проявляет наибольшую каталитическую активность в системе с митохондриальными электрон-транспортными белками S. pombe: Etp1fd и Arh1_A18G

ВЛИЯНИЕ ПОГОДНЫХ УСЛОВИЙ НА ИЗМЕНЧИВОСТЬ ХАРАКТЕРИСТИК БИОХИМИЧЕСКОГО СОСТАВА ПЛОДОВ ИНТРОДУЦИРОВАННЫХ СОРТОВ OXYCOCCUS MACROCARPUS (AIT.) PERS. В УСЛОВИЯХ БЕЛАРУСИ

The article presents the results of a comparative study of the variability of the biochemical composition of the fruits of six cultivars introduced in Belarus: Oxycoccus macrocarpus (Ait.) Pers. – Stevens, Bain Favorit, Hiliston, Holistar Red, Stankovic and WSU 108 during contrast moistening seasons. It has been established that the least pronounced intersectional differences are characterized by the parameters of accumulation in the fruits of dry substances, ascorbic and hydroxycinnamic acids, as well as the total amount of antoniated pigments and bioflavonoids in general, while of most significance are the sugar-dependent concentration and the content of soluble sugars, pectins, leucoanthocyanins and flavonols. It is shown that in the taxonomic series of large-fruited cranberries the Stankovich cultivar was characterized by the greatest resistance of the biochemical composition of the fruits to weather factors, while the lowest cultivar was Bain Favorit and especially Hiliston. Приведены результаты сравнительного исследования изменчивости биохимического состава плодов 6 новых интродуцированных в Беларуси сортов: Oxycoccus macrocarpus (Аit.) Рers. – Stevens, Bain Favorit, Hiliston, Holistar Red, Stankovich и WSU 108 в контрастные по режиму увлажнения сезоны. Установлено, что наименее выраженными межсезонными различиями характеризовались параметры накопления в плодах сухих веществ, аскорбиновой и гидроксикоричных кислот, а также общее количество антоциановых пигментов и биофлавоноидов в целом, тогда как наиболее значительными – показатель сахарокислотного индекса и содержание в них растворимых сахаров, пектиновых веществ, лейкоантоцианов и флавонолов. Показано, что в таксономическом ряду клюквы крупноплодной наибольшей устойчивостью биохимического состава плодов к погодным факторам характеризовался сорт Stankovich, тогда как наименьшей – сорта Bain Favorit и особенно Hiliston.