Representation of amino acid sequences in terms of interaction energy in protein globules

AbstractWe suggest a new simple approach for comparing the primary structure of proteins and their spatial structure. It relies on the one-to-one correspondence between each residue of the polypeptide chain and the energy of van der Waals interactions between the regions of the native globule flanking this residue. The method obviates the sophisticated geometrical criteria for estimating similarity between spatial structures. Besides, it permits one to analyze structural units of different scale

Seasonal dynamics of microbiological indices of water in the Ingulets and Berezovka rivers under different antropogenic burden

Проаналізовано сезонну динаміку мікробіологічних показників санітарного стану досліджуваних річок у весняно-осінній період. Проведене санітарне районування річок у межах м. Олександрія. Встановлено, що за показниками індексу лактозопозитивних кишкових паличок (ЛКП) найбільше забруднення води річок у більшості випадків спостерігалось у серпні.Проанализированы сезонную динамику микробиологических показателей санитарного состояния исследуемых рек в весенне-осенний период. Проведенное санитарное районирование рек в пределах г. Александрия.. Установлено, что по показателям индекса лактозоположительных кишечных палочек (ЛКП) наибольшее загрязнение воды рек в большинстве случаев наблюдалось в августе.The seasonal dynamics of microbiological indices of sanitary situation in Ingulets and Berezovka Rivers was analysed at spring-autumn period. The sanitary mapping of the rivers was done for the Alexandria area. In most cases maximal level of the rivers contamination by the lactose-positive E. coli index was found in August

Protein-DNA interactions: statistical analysis of interatomic contacts in major and minor grooves

The interactions between protein and DNA in essence underlie all processes in a living cell. Understanding the principles of specific recognition of DNA sites will open the way to understand how these processes are controlled and to interfere in their operation. In the paper we studied contacts between the protein and DNA at the atomic level in the structures of all the 3 518 protein­DNA complexes available in PDB by the Voronoi–Delaunay tessellation method. The method unambiguously defines contacts between atoms without any parameters, and characterizes each contact by the distance between atoms and the contact area, which is determined by the corresponding face of the Voronoi polyhedron. It was shown that most contacts are formed between the protein atoms and the sugarphosphate backbone of the DNA (72.9 %). The contact with the atoms of the nucleic bases emerging into the grooves of DNA is 17.0 % for a major groove and 10.1 % for all atomic contacts for a minor groove. Totally, the interaction between protein atoms and nucleic base atoms accounts for 27.1 % of all contacts. Analysis of the accessible surface area of atoms in the major and the minor grooves showed a correlation with the number of contacts (coefficient of linear correlation 0.94 and 0.93, respectively), however, nucleic acid atoms forming hydrogen bonds make contacts more often than may be expected from statistical considerations. It was shown that conformationally stable peptides occur sometimes in the binding regions with DNA. Analysis of the residues in a predefined conformation in 3 518 protein­DNA complexes revealed 159 amino acid residues in a predefined β­bend type I conformation, 15 residues in the conformation of β­bend type I’, and 6 residues in the conformation of β­bend type II. No residues in the conformation of β­bend type II’ were found. Analysis of contacts showed that such residues virtually do not form contacts with DNA. Contacts with nucleic base atoms are found only in the two homologous structures 3qea and 3qe9, where threonine atoms form contacts with atoms of nucleotide bases of the AT­pair

Гемодинамическая оценка устройства генерации пульсирующего потока в системах обхода левого желудочка сердца

Objective: to investigate the efficiency of a device that generates pulsatile flow during constant-speed axial-flow pump operation for use in left ventricular assist devices.Materials and methods. The pulsatile flow-generating device, hereinafter referred to as «pulsator», consists of a variable hydraulic resistance made in the form of a hull. A tube of elastic biocompatible material featuring an inner diameter of 11 mm is installed inside it. In the systolic phase of the left ventricle, due to systolic pressure, the elastic tube is fully opened, minimizing resistance to blood ejection. In the diastolic phase, due to suction action of the flow pump operating in constant revolutions, the elastic tube partially closes, creating additional hydraulic resistance to blood flow, which leads to reduced diastolic aortic pressure. Comparative assessment of axial-flow pump operation in pulsating and non-pulsating modes was carried out on a hydrodynamic stand that simulated the cardiovascular system. The following indices were calculated: arterial pressure pulsation (Ip), in-pump flow pulsation (AQ), energy equivalent pressure (EEP) and surplus hemodynamic energy (SHE).Results. When comparing axial-flow pump operation in pulsatile and continuous mode, arterial pressure pulsation index, in-pump pulsation index, and SHE index increased by 2.13 ± 0.2, 3.2 ± 0.2, and 2.7 ± 0.15 times, respectively, while EER index remained unchanged.Цель работы: исследование эффективности устройства генерации пульсирующего потока крови при работе осевого насоса с постоянной скоростью вращения для использования в системе обхода левого желудочка сердца.Материалы и методы. Устройство генерации пульсирующего потока, именуемое в дальнейшем «пульсатор», состоит из переменного гидравлического сопротивления, выполненного в виде корпуса с установленной внутри него трубкой из эластичного биосовместимого материала с внутренним диаметром 11 мм. В систолической фазе левого желудочка сердца за счет систолического давления эластичная трубка полностью раскрывается, минимизируя сопротивление выброса крови. В диастолической фазе за счет присасывающего действия насоса, работающего в режиме постоянных оборотов, эластичная трубка частично смыкается, создавая потоку крови дополнительное гидравлическое сопротивление, что приводит к уменьшению диастолического аортального давления. Сравнительная оценка работы осевого насоса в пульсирующем и непульсирующем режиме проводилась на гидродинамическом стенде, имитирующем сердечно-сосудистую систему с расчетом индексов: пульсации артериального давления (Ip), внутринасосной пульсации потока (AQ), энергии эквивалентного давления (ЕЕР) и избыточной гемодинамической энергии (SHE).Результаты. При сравнении работы осевого насоса в пульсирующем и непрерывном режиме индекс пульсации артериального давления увеличивался в 2,13 ± 0,2 раза, индекс внутринасосной пульсации увеличивался в 3,2 ± 0,2 раза, индекс SHE увеличивался в 2,7 ± 0,15 раза, индекс ЕЕР оставался без изменения

Clusters of primordial black holes

The Primordial Black Holes (PBHs) are gradually involved into consideration as the phenomenon having reliable basis. We discuss here the possibility of their agglomeration into clusters that may have several prominent observable features. The clusters can form due to closed domain walls appearance in the natural and the hybrid inflation with subsequent evolution and gravitational collapse. Early dustlike stages of dominance of heavy metastable dissipative particles, at which star-like objects are formed, can also naturally lead to formation of black hole clusters, remaining in the Universe after decay of particles, from which they have originated. The dynamical evolution of such clusters discussed here is of the crucial importance. Such a model inherits all the advantages of the single PBHs like possible explanation of existence of supermassive black holes (origin of the early quasars), binary BH merges registered by LIGO/Virgo through gravitational waves, contribution to reionization of the Universe, but also has additional benefits. The cluster could alleviate or completely avoid existing constraints on the single PBH abundance making PBHs a real dark matter candidate. The most of existing constraints on (single) PBH density should be re-considered as applied to the clusters. Also unidentified cosmic gamma-ray point-like sources could be (partially) accounted for by them. One can conclude, that it seems really to be much more viable model with respect to the single PBHs.Comment: v2: both the text and bibliography are essentially extended, coincides with EPJC versio

Comparative study of thermostability and structure of close homologues - bamase and binase

Parameters of heat denaturation and intrinsic fluorescence of bamase and its close homologue, binase in the pH region 2-6 have been determined. The bamase heat denaturation (pH 2.85.5) proceeds according to the “all-or-none” principle. Bamase denaturation temperature is lower than that of binase and this difference increases from 2.5 °C at pH 5 to 7 °C at pH 3. Enthalpy values of bamase and binase denaturation coincide only at pH 4.5-5.5, but as far as pH decreases the bamase denaturation enthalpy decreases significantly and in this respect it differs from binase. The fluorescence and CD techniques do not reveal any distinctions in the local environment of aromatic residues in the two proteins, and the obtained difference in the parameters of intrinsic fluorescence is due to fluorescence quenching of the bamase Trp94 by the His 18 residue, absent in binase. Secondary structures of both native and denaturated proteins also do not differ. Some differences in the barnase and binase electrostatic characteristics, revealed in the character of the dipole moments distribution, have been found. © 1993 Taylor & Francis Ltd

8-оксо-2’-дезоксигуанозин - биомаркер окислительного стресса

Free radical mechanism of a cell damage is one of the universal non-specific pathogenic pathways in a cause of many diseases, including cancer, neurodegenerative diseases, atherosclerosis and aging. So in nuclear and mitochondrial DNA, guanine hydroxylation to 8-position gives 8­hydroxy­2'­deoxyguanosine (8­OH­dG) and 8­oxo­7,8­dihydro­2'­deoxyguanosine (8­oxo­dG). These substances are one of the predominant products of free radical­induced oxidative damages. They are usually been applied as biomarkers of oxidative stress and carcinogenesis. The direct oxidation of guanine or incorrect inclusion of 8-oxo-dGTP from the nucleotide pool by polymerases, lead to a lack of specificity of the base pairing in DNA, favoring mutagenesis. Firstly 8-oxo-dG has been described by H. Kasai and S. Nishimura in 1983. Since then, this damage has been widely measured in various tissues and body fluids as blood, urine, brain, liver, and others. Today 8-oxo-dG is already used not only as a marker of oxidative stress, but also as a tool for prognosis of diseases and results of applied therapy. Now many efforts are focused on developing the procedure of measurement of 8-oxo-dG content in tissues and body fluids. In this paper we also discuss the role of the 8-oxo-dG as a biomarker of oxidative stress and a predictor of diseases and results of the applied therapy.8-Оксо-2’-дезоксигуанозин (8-oxo-dG) является преобладающей формой свободнорадикального повреждения ДНК. C момента его обнаружения в 1983 году, это соединение определяют в различных тканях и жидкостях организма: в крови, моче, мозге, печени и др. В данном обзоре рассматривается роль 8-oxo-dG в качестве биомаркера окислительного стресса, предиктора течения заболевания и успеха применяемой терапии у больных, а также методы, с помощью которых он сегодня детектируется в биологических образцах

Синтез нового аналога пептида ProGlyPro

A novel analogue of the biologically active peptide ProGlyPro containing an isosteric pseudopeptide bond instead of an amide one has been synthesized.существлен синтез нового аналога биологически активного пептида ProGlyPro, содержащего изостерическую псевдопептидную связь вместо амидной

Фурье-преобразование в сферических системах как инструмент решения физических задач структурной биологии

Applications of the most common adaptation of Fourier analysis in spherical coordinate systems used to solve a number of problems in structural biology, namely, flat wave decomposition (flat waves are represented as spherical functions decomposition), are herein considered. Arguments in favor of this decomposition are compared with other decompositions in superposition of special functions. A more general justification for the correctness of this decomposition is obtained than that existing today. A method for representing groups of atoms in the form of a Fourier object is proposed. It is also considered what opportunities give such a representation. The prospects for the application of Fourier analysis in structural biophysics are discussed.Рассмотрено применение наиболее распространенной адаптации Фурье-анализа в сферических системах координат для решения ряда задач структурной биологии, а именно: разложения по плоским волнам (при этом плоские волны представляются в виде разложения по сферическим функциям). Приводятся аргументы в пользу этого разложения в сравнении с другими разложениями по суперпозициям специальных функций. Получено более общее обоснование корректности данного разложения, чем существующие в настоящее время. Предложен способ представления групп атомов в виде Фурье-объекта и рассмотрены его возможности. Обсуждаются перспективы применения Фурье-анализа в структурной биофизике