scholarly journals Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8569
Author(s):  
Tatjana Sjakste ◽  
Elina Leonova ◽  
Rudolfs Petrovs ◽  
Ilva Trapina ◽  
Marion S. Röder ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Cd Spectra ◽  
Structural Genes ◽  
Blast Search ◽  
Positive Band ◽  
Topologically Associating Domains ◽  
Topologically Associating Domain ◽  
Guanine Quadruplex ◽  
Protein Group ◽  
Good Agreement

Background The concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings. Methods The tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocellulose or exhaustive digestion of DNA with DNase I. Cloning and transformation were performed using pMOSBBlue Blunt Ended Cloning Kit. Inserts were amplified by PCR, and sequencing was performed on the MegaBace 1000 Sequencing System. The BLAST search was performed using sequence databases at NCBI, CR-EST, and TREP and Ensembl Plants databases. Comparison to MAR/SAR sequences was performed using http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi database. The prediction of G quadruplexes (GQ) was performed with the aid of R-studio library pqsfinder. CD spectra were recorded on a Chirascan CS/3D spectrometer. Results Although the barley genome is AT-rich (43% of GC pairs), most DNA fragments associated with TBP were GC-rich (up to 70% in some fractions). Both fractionation procedures yielded a high proportion of CT-motif sequences presented predominantly by the 16-bp CC(TCTCCC)2 TC fragment present in clones derived from the TBP-bound DNA and absent in free DNA. BLAST analysis revealed alignment with different barley repeats. Some clones, however, aligned with both nuclear and chloroplast structural genes. Alignments with MAR/SAR motifs were very few. The analysis produced by the pqsfinder program revealed numerous potential quadruplex-forming sites in the TBP-bound sequences. A set of oligonucleotides containing sites of possible GQs were designed and ordered. Three of them represented the minus strand of the CT-repeat. Two were derived from sequences of two clones of nitrocellulose retained fraction from leaves and contained GC-rich motifs different from the CT motif. Circular dichroism spectroscopy revealed profound changes in spectra when oligonucleotides were incubated with 100 mM KCl. There was either an increase of positive band in the area of 260 nm or the formation of a positive band at 290 nm. In the former case, changes are typical for parallel G-quadruplexes and, in the latter, 3 + 1 structures. Discussion The G-quadruplexes anchor proteins are probably involved in the maintenance of the topologically associated domain structure.

scholarly journals Electrophoretic pattern of the polypeptide component in the tight DNA-protein complexes in rat and chicken tissues and its partial characterisation in rat liver

2010 ◽  
Vol 64 (5-6) ◽  
pp. 188-193
Author(s):  
Normunds Legzdiņš ◽  
Danute Labeikytė ◽  
Nikolajs Sjakste
Keyword(s):  
Rat Liver ◽  
Protein Complexes ◽  
Regulation Of Gene Expression ◽  
Electrophoretic Pattern ◽  
Covalent Bonds ◽  
Chicken Tissues ◽  
Repair Enzymes ◽  
Protein Group ◽  
Ubiquitin Proteasome ◽  
Partial Characterisation

Electrophoretic pattern of the polypeptide component in the tight DNA-protein complexes in rat and chicken tissues and its partial characterisation in rat liverTightly bound to DNA proteins (TBP) are a protein group that remain attached to DNA with covalent or non-covalent bonds after its deproteinisation. The distribution of TBP in genes reflects the type of cell differentiation. It has been hypothesised that TBP binding is involved in regulation of gene expression. Early studies reported uniformity of the TBPs from different sources. Later it was shown that TBPs obtained from DNA, isolated in mild conditions from evolutionary distant species, are different. Application of chloroform DNA extraction without use of externally added enzymes enabled us to reveal differences in the TBP spectrum in plant organs and changes of this spectrum in the course of plant development. The goal of this work was to study the electrophoretic pattern of the polypeptide component in the tight DNA-protein complexes in organs of animals: a mammal (rat) and a bird (chicken). Rat thymus TBPs were represented by 70 and 60 kDa proteins, and the same polypeptides were observed also in brain and skeletal muscles. Kidney TBPs were represented by 85, 70, 65, 60 and 37 kDa polypeptides; 85, 77, 70, 60, 50 and 37 kDa TBPs were characteristic of liver. Numerous minor peptides were observed in all samples studied. The spectrum of chicken liver and blood TBPs differed in distribution of proteins of 25-35 kDa. Mass-spectrometry of 14 bands from rat liver TBP gel revealed 43 different proteins. Chromatin modifying proteins and repair enzymes, transcription factors, serpins, ATPase, kinases and enzymes of ubiquitin-proteasome pathway were found among the TBPs. Thus, TBPs appear to be a vast protein group involved in several intranuclear processes. It is hypothesised that numerous functions ascribed to the nuclear matrix are performed in the TBP complexes.

scholarly journals Mitochondrial сomplexome of etiolated pea shoots

2022 ◽  
Vol 11 (4) ◽  
pp. 570-580
Author(s):  
I. V. Ukolova ◽  
I. G. Kondratov ◽  
M. A. Kondakova ◽  
I. V. Lyubushkina ◽  
O. I. Grabelnykh ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Pyruvate Dehydrogenase Complex ◽  
Energy System ◽  
Physiological Status ◽  
Major Protein ◽  
Functional Categories ◽  
Sds Page ◽  
Acid Processing ◽  
Oxphos System ◽  
Protein Group

Studies into mitochondrial сomplexomes in various organisms provide an insight into the native organization of proteins and metabolic pathways in the organelles of the subject under study. “Complexome” is a relatively recent concept describing the proteome of protein complexes, supercomplexes, and oligomeric proteins. Complexome analysis is performed using current electrophoretic and mass spectrometric techniques, in particular, by two-dimensional electrophoresis (2D BN/SDS-PAGE) in combination with mass spectrometry (MS). Unlike 2D IEF/SDS-PAGE, this method enables analysis of not only hydrophilic proteins of the mitochondrial matrix, but also membrane proteins and their associations, thus expanding the possibilities of studying the organelle proteome. In the present work, the complexome of etiolated pea shoots was studied for the first time using 2D BN/SDS-PAGE followed by MALDI-TOF MS. To this end, 145 protein spots excised from the gel were analyzed; 110 polypeptides were identified and assigned to different functional groups. A densitometric analysis revealed that the major protein group comprised the enzymes of the mitochondrial energy system (1), accounting for an average of 43% of the total polypeptide content. The remaining 57% was primarily distributed among the following functional categories: pyruvate dehydrogenase complex and citric acid cycle (2); amino acid metabolism (3); nucleic acid processing (4); protein folding (5); antioxidant protection (6); carrier proteins (7); other proteins (8); proteins having unknown functions (9). The obtained data indicate the complex organization of the pea proteome. In addition to the enzymes of the OXPHOS system, the proteins of other functional categories are found to form supramolecular structures. It is suggested that the presence of proteins from other cellular compartments may indicate the interaction of mitochondria with the enzymes or structures of corresponding organelles. In general, the obtained data on the pea complexome represent a kind of a mitochondrial “passport” that reflects the native state of the proteome of organelles corresponding to their physiological status.

scholarly journals An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks

2008 ◽  
Vol 2008 ◽  
pp. 1-10 ◽  
Author(s):  
Guangyu Cui ◽  
Yu Chen ◽  
De-Shuang Huang ◽  
Kyungsook Han
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Network ◽  
Protein Complexes ◽  
Interaction Network ◽  
Connected Subgraph ◽  
Protein Protein Interaction ◽  
Group Form ◽  
Protein Protein Interaction Networks ◽  
Protein Protein Interaction Network ◽  
Good Agreement

Biological processes are often performed by a group of proteins rather than by individual proteins, and proteins in a same biological group form a densely connected subgraph in a protein-protein interaction network. Therefore, finding a densely connected subgraph provides useful information to predict the function or protein complex of uncharacterized proteins in the highly connected subgraph. We have developed an efficient algorithm and program for finding cliques and near-cliques in a protein-protein interaction network. Analysis of the interaction network of yeast proteins using the algorithm demonstrates that 59% of the near-cliques identified by our algorithm have at least one function shared by all the proteins within a near-clique, and that 56% of the near-cliques show a good agreement with the experimentally determined protein complexes catalogued in MIPS.

scholarly journals Guanine-quadruplex-enriched sequences in the tight DNA-protein complexes of barley seedlings

2019 ◽  
Vol 35 (3) ◽  
pp. 234-234
Author(s):  
T. Sjakste ◽  
E. Leonova ◽  
R. Petrovs ◽  
M. Röder ◽  
N. Sjakste
Keyword(s):  
Protein Complexes ◽  
Guanine Quadruplex

scholarly journals Protein complex similarity based on Weisfeiler-Lehman labeling

2018 ◽  
Author(s):  
Bianca K Stöcker ◽  
Till Schäfer ◽  
Petra Mutzel ◽  
Johannes Köster ◽  
Nils Kriege ◽  
...  
Keyword(s):  
Protein Complex ◽  
Large Scale ◽  
Protein Complexes ◽  
Similarity Measures ◽  
Interaction Networks ◽  
Protein Protein Interaction ◽  
Protein Complex Prediction ◽  
Protein Protein Interaction Networks ◽  
Human Integrin ◽  
Good Agreement

Being able to quantify the similarity between two protein complexes is essential for numerous applications. Prominent examples are database searches for known complexes with a given query complex, comparison of the output of different protein complex prediction algorithms, or summarizing and clustering protein complexes, e.g., for visualization. While the corresponding problems have received much attention on single proteins and protein families, the question about how to model and compute similarity between protein complexes has not yet been systematically studied. Because protein complexes can be naturally modeled as graphs, in principle general graph similarity measures may be used, but these are often computationally hard to obtain and do not take typical properties of protein complexes into account. Here we propose a parametric family of similarity measures based on Weisfeiler-Lehman labeling. We evaluate it on simulated complexes of the extended human integrin adhesome network. Because the connectivity (graph topology) of real complexes is often unknown and hard to obtain experimentally, we use both known protein-protein interaction networks and known interdependencies (constraints) between interactions to simulate more realistic complexes than from interaction networks alone. We empirically show that the defined family of similarity measures is in good agreement with edit similarity, a similarity measure derived from graph edit distance, but can be much more efficiently computed. It can therefore be used in large-scale studies and simulations and serve as a basis for further refinements of modeling protein complex similarity.

scholarly journals Protein complex similarity based on Weisfeiler-Lehman labeling

2018 ◽  
Author(s):  
Bianca K Stöcker ◽  
Till Schäfer ◽  
Petra Mutzel ◽  
Johannes Köster ◽  
Nils Kriege ◽  
...  
Keyword(s):  
Protein Complex ◽  
Large Scale ◽  
Protein Complexes ◽  
Similarity Measures ◽  
Interaction Networks ◽  
Protein Protein Interaction ◽  
Protein Complex Prediction ◽  
Protein Protein Interaction Networks ◽  
Human Integrin ◽  
Good Agreement

Being able to quantify the similarity between two protein complexes is essential for numerous applications. Prominent examples are database searches for known complexes with a given query complex, comparison of the output of different protein complex prediction algorithms, or summarizing and clustering protein complexes, e.g., for visualization. While the corresponding problems have received much attention on single proteins and protein families, the question about how to model and compute similarity between protein complexes has not yet been systematically studied. Because protein complexes can be naturally modeled as graphs, in principle general graph similarity measures may be used, but these are often computationally hard to obtain and do not take typical properties of protein complexes into account. Here we propose a parametric family of similarity measures based on Weisfeiler-Lehman labeling. We evaluate it on simulated complexes of the extended human integrin adhesome network. Because the connectivity (graph topology) of real complexes is often unknown and hard to obtain experimentally, we use both known protein-protein interaction networks and known interdependencies (constraints) between interactions to simulate more realistic complexes than from interaction networks alone. We empirically show that the defined family of similarity measures is in good agreement with edit similarity, a similarity measure derived from graph edit distance, but can be much more efficiently computed. It can therefore be used in large-scale studies and simulations and serve as a basis for further refinements of modeling protein complex similarity.

scholarly journals RobusTAD: A Tool for Robust Annotation of Topologically Associating Domain Boundaries

2018 ◽  
Author(s):  
Rola Dali ◽  
Guillaume Bourque ◽  
Mathieu Blanchette
Keyword(s):  
Comparative Analysis ◽  
Noise Level ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Desktop Computer ◽  
Experimental Conditions ◽  
Heterogeneous Samples ◽  
Topologically Associating Domains ◽  
Topologically Associating Domain ◽  
Domain Boundaries

AbstractMotivationTopologically Associating Domains (TADs) are chromatin structures that can be identified by analysis of Hi-C data. Tools currently available for TAD identification are sensitive to experimental conditions such as coverage, resolution and noise level.ResultsHere, we present RobusTAD, a tool to score TAD boundaries in a manner that is robust to these parameters. In doing so, RobusTAD eases comparative analysis of TAD structures across multiple heterogeneous samples.AvailabilityRobusTAD is implemented in R and released under a GPL license. RobusTAD can be downloaded from https://github.com/rdali/RobusTAD and runs on any standard desktop [email protected], [email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals Size, shape and secondary structure of calponin.

2000 ◽  
Vol 47 (3) ◽  
pp. 791-806 ◽  
Author(s):  
E A Czurylo ◽  
W Eimer ◽  
N Kulikova ◽  
T Hellweg
Keyword(s):  
Secondary Structure ◽  
Hydrodynamic Radius ◽  
Translational Diffusion ◽  
Cd Spectra ◽  
Beta Turns ◽  
Translational Diffusion Coefficient ◽  
X Ray ◽  
Ellipsoidal Model ◽  
Hydrodynamic Calculations ◽  
Good Agreement

The overall size and shape of the chicken gizzard calponin (CaP) h1 molecule was investigated by dynamic light scattering (DLS) measurements. From the DLS experiments, a z-averaged translational diffusion coefficient is derived (5.75 +/- 0.3) x 10(-7) cm(2) s(-1), which corresponds to a hydrodynamic radius of 3.72 nm for calponin. The frictional ratio (1.8 for the unhydrated molecule and 1.5 for the hydrated one) suggests a pronounced anisotropic structure for the molecule. An ellipsoidal model in length 19.4 nm and with a diameter of 2.6 nm used for hydrodynamic calculations was found to reproduce the DLS experimental data. The evaluation of the secondary structure of CaP h1 from the CD spectra by two independent methods has revealed that it contains, on average, 23% helix, 19% beta-strand, 18% beta-turns and loops, and 40% of remainder structures. These values are in good agreement with those predicted from the amino-acid sequence. Predictions used for CaP h1 were applied to other isoforms of known sequences and revealed that all calponins share a common secondary structure. Moreover, the predicted structure of the calponin CH domain is identical to that found by X-ray studies of the spectrin, fimbrin and utrophin CH domains.

Oscillator Strength Measurements in the Vacuum-Ultraviolet by the Emission Method

1988 ◽  
Vol 102 ◽  
pp. 353-356
Author(s):  
C. Goldbach ◽  
G. Nollez
Keyword(s):  
Oscillator Strength ◽  
Vacuum Ultraviolet ◽  
Oscillator Strengths ◽  
Emission Method ◽  
Absolute Scale ◽  
Good Agreement

AbstractThe principles and the realization of an experiment devoted to oscillator strength measurements in the vacuum-ultraviolet by the emission method are briefly presented. The results obtained for the strong multiplets of neutral nitrogen and carbon in the 1200-2000 Å range yield an absolute scale of oscillator strengths in good agreement with the most recent calculations.

A High Voltage Electron Microscopy Study of Sub-Oxide Formation in Vanadium

1971 ◽  
Vol 29 ◽  
pp. 212-213
Author(s):  
R. H. Geiss ◽  
R. L. Ladd ◽  
K. R. Lawless
Keyword(s):  
High Vacuum ◽  
Microscopy Study ◽  
Electron Microscopy Study ◽  
Ultra High Vacuum ◽  
Pure Oxygen ◽  
Pressure Oxidation ◽  
High Voltage Electron Microscopy ◽  
Oxidation Study ◽  
Voltage Electron ◽  
Good Agreement

Detailed electron microscope and diffraction studies of the sub-oxides of vanadium have been reported by Cambini and co-workers, and an oxidation study, possibly complicated by carbon and/or nitrogen, has been published by Edington and Smallman. The results reported by these different authors are not in good agreement. For this study, high purity polycrystalline vanadium samples were electrochemically thinned in a dual jet polisher using a solution of 20% H2SO4, 80% CH3OH, and then oxidized in an ion-pumped ultra-high vacuum reactor system using spectroscopically pure oxygen. Samples were oxidized at 350°C and 100μ oxygen pressure for periods of 30,60,90 and 160 minutes. Since our primary interest is in the mechanism of the low pressure oxidation process, the oxidized samples were cooled rapidly and not homogenized. The specimens were then examined in the HVEM at voltages up to 500 kV, the higher voltages being necessary to examine thick sections for which the oxidation behavior was more characteristic of the bulk.

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