Large Oligomeric Complex Structures Can Be Computationally Assembled by Efficiently Combining Docked Interfaces

Macromolecular oligomeric assemblies are involved in many biochemical processes of living organisms. The benefits of such assemblies in crowded cellular environments include increased reaction rates, efficient feedback regulation, cooperativity and protective functions. However, an atom‐level structural determination of large assemblies is challenging due to the size of the complex and the difference in binding affinities of the involved proteins. In this study, we propose a novel combinatorial greedy algorithm for assembling large oligomeric complexes from information on the approximate position of interaction interfaces of pairs of monomers in the complex. Prior information on complex symmetry is not required but rather the symmetry is inferred during assembly. We implement an efficient geometric score, the transformation match score, that bypasses the model ranking problems of state‐of‐the‐art scoring functions by scoring the similarity between the inferred dimers of the same monomer simultaneously with different binding partners in a (sub)complex with a set of pregenerated docking poses. We compiled a diverse benchmark set of 308 homo and heteromeric complexes containing 6 to 60 monomers. To explore the applicability of the method, we considered 48 sets of parameters and selected those three sets of parameters, for which the algorithm can correctly reconstruct the maximum number, namely 252 complexes (81.8%) in, at least one of the respective three runs. The crossvalidation coverage, that is, the mean fraction of correctly reconstructed benchmark complexes during crossvalidation, was 78.1%, which demonstrates the ability of the presented method to correctly reconstruct topology of a large variety of biological complexes. Proteins 2015; 83:1887–1899. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc

EVALUATION OF CYTOKINE-MEDIATED MECHANISMS INVOLVED IN DEVELOPMENT OF RESPIRATORY MUSCLE DYSFUNCTION IN THE PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE

Respiratory muscle (RM) strength was studied in 85 men with exacerbations of chronic obstructive pulmonary disease (COPD). The strength indicators of expiratory (MEP) and inspiratory pressure (MIP, SNIP) in oral cavity were registered by means of the MicroRPM device (CareFusion, UK), as well as intranasal pressure levels by SNIP test. The measured MEP, MIP и SNIP values were compared to the proper indices. Serum concentrations of cytokines (IL-4, IL-6, IL-10, IL-17A, IL-21, TNFα, IFNγ and TGF-β) were determined. The results of the study were processed by means of canonical analysis and by clustering methods. Expiratory RM dysfunction was recorded in mild COPD, expiratory-inspiratory RM dysfunction was recorded in moderate COPD and the diaphragm dysfunction was recorded in severe COPD. Three groups of patients with different combinations of RM strength indicators and immune parameters were identified by means of cluster analysis. The cytokine profile in the first cluster was characterized by maximal concentrations of IL-17A, IL-21, TNFα and TGF-β, whereas RM strength indexes showed minimal values. In the second cluster, a decrease of RM strength indicators by 25-40% against control was associated with a sharp rise of IL-6, along with moderate increase of IL-21 and TGF-βconcentrations. In the third cluster, maximal levels of IL-6, IL-10 and IFNγwere registered, along with low levels of IL-17A, IL-21 and TGF-β concentrations, whereas MEP, MIP и SNIP values did not sufficiently differ from their levels in second cluster. The results of canonical and correlation analysis indicated to interconnections between either certain cytokines, or their pool with the RM strength indicators, dyspnea severity and functional state of COPD patients, thus suggesting involvement of cytokine-mediated mechanisms in pathogenesis of the respiratory muscle dysfunction

Combining specificity determining and conserved residues improves functional site prediction

<p>Abstract</p> <p>Background</p> <p>Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core). Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities.</p> <p>Results</p> <p>Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs), as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples.</p> <p>Conclusion</p> <p>The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.</p

Dynamics of carbon pools in post-agrogenic sandy soils of southern taiga of Russia

<p>Abstract</p> <p>Background</p> <p>Until recently, a lot of arable lands were abandoned in many countries of the world and, especially, in Russia, where about half a million square kilometers of arable lands were abandoned in 1961-2007. The soils at these fallows undergo a process of natural restoration (or self-restoration) that changes the balance of soil organic matter (SOM) supply and mineralization.</p> <p>Results</p> <p>A soil chronosequence study, covering the ecosystems of 3, 20, 55, 100, and 170 years of self-restoration in southern taiga zone, shows that soil organic content of mineral horizons remains relatively stable during the self-restoration. This does not imply, however, that SOM pools remain steady. The C/N ratio of active SOM reached steady state after 55 years, and increased doubly (from 12.5 - 15.6 to 32.2-33.8). As to the C/N ratio of passive SOM, it has been continuously increasing (from 11.8-12.7 to 19.0-22.8) over the 170 years, and did not reach a steady condition.</p> <p>Conclusion</p> <p>The results of the study imply that soil recovery at the abandoned arable sandy lands of taiga is incredibly slow process. Not only soil morphological features of a former ploughing remained detectable but also the balance of soil organic matter input and mineralization remained unsteady after 170 years of self-restoration.</p

Оценка взаимосвязей индикаторов оксидантно-антиоксидантной системы и силы дыхательных мышц при внебольничной пневмонии

The objective: to evaluate relationships between the oxidative-antioxidative system (OAS) and the force indicators of respiratory muscles (RM) in patients with community-acquired pneumonia (CAP).Subjects and methods. 78 men from 18 to 26 years old admitted to an in-patient unit with non-severe (NSCAP) and severe community-acquired pneumonia (SCAP) were examined. Force of expiratory (MEP, MRPD) and inspiratory (MIP, MRPD, SNIP) respiration muscles was registered by MicroRPM (CareFusion, UK). The state of OAS was assessed by the level of malondialdehyde (MDA), total antioxidative activity, superoxide dismutase (SOD), catalase, glutathione reductase (GR), glutathione peroxidase (GP), and reduced glutathione. Cluster and correlation analysis methods were used for data processing.Results. CAP patients were divided into 3 clusters based on typical combinations of respiratory muscle force indicators and OAS. The first cluster included NSCAP, the second one included NSCAP and SCAP, and the third cluster included SCAP In patients of the 1st cluster, the dysfunction of expiratory respiration muscles prevailed, while in patients of the 2nd and 3rd cluster, it was inspiratory respiration muscle dysfunction. Significant negative correlations of MDA with MEP, MRPD during expiration, SNIP, and MIP were found, as well as positive correlations with GP, GR, catalase, and SOD. In convalescents of the 1st cluster, dysfunction of expiratory respiration muscles was improving, and in the 2nd and 3rd clusters, the dysfunction of expiratory and inspiratory respiration muscles was going down. In CAP patients, respiratory muscle dysfunction is associated with imbalanced OAS and the effect of these factors on respiratory muscle contractive activity.Цель: оценка взаимосвязей показателей оксидантно-антиоксидантной системы (ОАС) и силовых индикаторов дыхательных мышц (ДМ) у больных внебольничной пневмонией (ВП).Материалы и методы. В стационаре обследовано 78 мужчин в возрасте 18-26 лет с нетяжелой (НВП) и тяжелой внебольничной пневмонией (ТВП). Регистрировали показатели силы экспираторных (MEP, MRPDвыд) и инспираторных (MIP, MRPDвд,, SNIP) ДМ на аппарате MicroRPM («CareFusion», Великобритания). Состояние ОАС оценивали по уровню малонового диальдегида (МДА), общей антиоксидантной активности, супероксиддисмутазы (СОД), каталазы, глутатионредуктазы (ГР), глютатионпероксидазы (ГПО), восстановленного глутатиона. Обработка данных выполнялась методами кластерного и корреляционного анализа.Результаты. Выделено 3 кластера больных ВП с характерными комбинациями индикаторов силы ДМ и ОАС. Первый из них был представлен НВП, второй НВП и ТВП, третий - ТВП. У лиц 1-го кластера преобладала дисфункция экспираторных ДМ, а во 2-м и 3-м -инспираторных. Установлены достоверные отрицательные корреляции МДА с показателями MEP, MRPDвыд, SNIP и MIP, а положительные связи - с ГПО, ГР, каталазой и СОД. У реконвалесцентов 1-го кластера сокращалась дисфункция экспираторных ДМ, а во 2-м и 3-м -экспираторных и инспираторных ДМ. Развитие дисфункции ДМ при ВП ассоциируется с дисбалансом ОАС и влиянием этих факторов на их сократительную активность

H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments

BACKGROUND: A multiple sequence alignment (MSA) generated for a protein can be used to characterise residues by means of a statistical analysis of single columns. In addition to the examination of individual positions, the investigation of co-variation of amino acid frequencies offers insights into function and evolution of the protein and residues. RESULTS: We introduce conn(k), a novel parameter for the characterisation of individual residues. For each residue k, conn(k) is the number of most extreme signals of co-evolution. These signals were deduced from a normalised mutual information (MI) value U(k, l) computed for all pairs of residues k, l. We demonstrate that conn(k) is a more robust indicator than an individual MI-value for the prediction of residues most plausibly important for the evolution of a protein. This proposition was inferred by means of statistical methods. It was further confirmed by the analysis of several proteins. A server, which computes conn(k)-values is available at http://www-bioinf.uni-regensburg.de. CONCLUSION: The algorithms H2r, which analyses MSAs and computes conn(k)-values, characterises a specific class of residues. In contrast to strictly conserved ones, these residues possess some flexibility in the composition of side chains. However, their allocation is sensibly balanced with several other positions, as indicated by conn(k)

Movement Protein Pns6 of Rice dwarf phytoreovirus Has Both ATPase and RNA Binding Activities

Cell-to-cell movement is essential for plant viruses to systemically infect host plants. Plant viruses encode movement proteins (MP) to facilitate such movement. Unlike the well-characterized MPs of DNA viruses and single-stranded RNA (ssRNA) viruses, knowledge of the functional mechanisms of MPs encoded by double-stranded RNA (dsRNA) viruses is very limited. In particular, many studied MPs of DNA and ssRNA viruses bind non-specifically ssRNAs, leading to models in which ribonucleoprotein complexes (RNPs) move from cell to cell. Thus, it will be of special interest to determine whether MPs of dsRNA viruses interact with genomic dsRNAs or their derivative sRNAs. To this end, we studied the biochemical functions of MP Pns6 of Rice dwarf phytoreovirus (RDV), a member of Phytoreovirus that contains a 12-segmented dsRNA genome. We report here that Pns6 binds both dsRNAs and ssRNAs. Intriguingly, Pns6 exhibits non-sequence specificity for dsRNA but shows preference for ssRNA sequences derived from the conserved genomic 5′- and 3′- terminal consensus sequences of RDV. Furthermore, Pns6 exhibits magnesium-dependent ATPase activities. Mutagenesis identified the RNA binding and ATPase activity sites of Pns6 at the N- and C-termini, respectively. Our results uncovered the novel property of a viral MP in differentially recognizing dsRNA and ssRNA and establish a biochemical basis to enable further studies on the mechanisms of dsRNA viral MP functions

Оценка взаимосвязи силы дыхательных мышц и показателей цитокинового статуса у больных внебольничной пневмонией

Aim. Assessment of the role of cytokine-mediated changes in the development of respiratory muscle (RM) dysfunction in patients with community-acquired pneumonia (СAP). Methods. 84 men aged 18 – 26 years with a median of age 19.5 [18.4; 22.8]. Mild to moderate CAP (MCAP) was diagnosed in 62 (73.8%) patients and severe (SCAP) in 22 (26.2%). The expiratory (MEP, MRPDout) and inspiratory (MIP, MRPDin. SNIP) strength indices of RM were recorded on a MicrоRPM apparatus (CareFusion, UK). The severity of endogenous intoxication was verified using the following indices: hematologic (HII), leukocyte (LII), and nuclear. Serum concentrations of interleukins-2, -8, -10, basic fibroblast growth factor, transforming growth factor-beta, tumor necrosis factor-alpha (TNF-α), and a soluble receptor for TNF-α. Data processing was performed by cluster and correlation analysis methods. Results. Three clusters of patients with CAP were identified by the characteristic combinations of indicators of RM strength, endogenous intoxication, and cytokine status. The first cluster had MCAP, the second – both MCAP and SCAP, the third – SCAP. In the first cluster, dysfunction of expiratory RM prevailed, and in the second and third – dysfunction of inspiratory RM. In the midst of CAP, significant negative correlations of RM strength indicators with LII, HII, TNF-α, IL-10, IL-8, and IL-2 levels were recorded. The endogenous intoxication indices reached control values in all patients during recovery. The first cluster showed a decrease in the level of analyzed cytokines against isolated dysfunction of expiratory RM. The second cluster showed a tendency toward restoration of TNF-α and IL-8 levels, and only their SNIP index was normal. The third cluster showed minimal medians of RM strength against the continuing imbalance in the profile of pro- and anti-inflammatory cytokines during recovery. Conclusion. RM dysfunction in CAP is associated with cytokine-mediated dysfunction. The degree of cytokine involvement in this process depends on the severity of endogenous intoxication and the volume of alveolar inflammation.Целью исследования явилась оценка роли цитокин-опосредованных механизмов в развитии дисфункции дыхательных мышц (ДМ) у больных внебольничной пневмонией (ВП). Материалы и методы. Обследованы мужчины (n = 84; возраст – 18–26 лет; медиана – 19,5 (18,4; 22,8) года), госпитализированные в стационар по поводу ВП. Нетяжелая ВП (НВП) диагностирована у 62 (73,8 %) больных, тяжелая (ТВП) – у 22 (26,2 %). При помощи аппарата MicrоRPM (CareFusion, Великобритания) зарегистрированы показатели силы экспираторных (MEP, MRPDвыд.) и инспираторных (MIP, MRPDвд., SNIP) ДМ. Верификация тяжести эндогенной интоксикации проводилась с использованием гематологического (ГИИ), лейкоцитарного (ЛИИ) и ядерного индексов. В сыворотке крови определялась концентрация интерлейкинов (IL)-2, -8, -10, базисного фактора роста фибробластов, трансформирующего фактора роста-β, фактора некроза опухоли-α (TNF-α) и растворимого рецептора к TNF-α. Обработка данных выполнялась методами кластерного и корреляционного анализа. Результаты. Выделены 3 кластера больных ВП с характерными комбинациями индикаторов силы ДМ, эндогенной интоксикации и цитокинового статуса. Первый из них представлен больными НВП, 2-й – НВП и ТВП, 3-й – лицами с ТВП. У лиц 1-го кластера преобладала дисфункция экспираторных, 2-го и 3-го – инспираторных ДМ. В разгар ВП зарегистрированы достоверные отрицательные взаимосвязи показателей силы ДМ с ЛИИ, ГИИ, TNF-α, IL-10, IL-8, IL-2. В период реконвалесценции у всех пациентов индексы эндогенной интоксикации достигали контрольных значений. У лиц 1-го кластера установлено снижение уровня анализируемых цитокинов на фоне изолированной дисфункции экспираторных ДМ. У пациентов 2-го кластера зафиксирована тенденция к восстановлению TNF-α и IL-8, а уровню, наблюдаемому у здоровых, соответствовал только показатель SNIP. У реконвалесцентов 3-го кластера отмечены минимальные средние показатели силы ДМ на фоне сохраняющегося дисбаланса в профиле про- и противовоспалительных цитокинов. Заключение. Дисфункция ДМ при ВП ассоциируется с участием в ее патогенезе цитокин-опосредованных механизмов, интенсивность вовлечения которых в данный процесс зависит от тяжести эндогенной интоксикации и распространенности альвеолярного воспаления

Detection of Pionium with DIRAC

The aim of the DIRAC experiment at CERN is to provide an accurate determination of S-wave pion-pion scattering lengths from the measurement of the lifetime of the pi+ pi- atom. The measurement will be done with precision comparable to the level of accuracy of theoretical predictions, formulated in the context of Chiral Perturbation Theory. Therefore, the understanding of chiral symmetry breaking of QCD will be submitted to a stringent test