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Wyświetlanie 1-15 z 35
Tytuł:
An approach for the identification of microRNA with an application to Anopheles gambiae
Autorzy:
Chatterjee, Raghunath
Chaudhuri, Keya
Powiązania:
https://bibliotekanauki.pl/articles/1041242.pdf
Data publikacji:
2006
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Anopheles gambiae
RNA folding
microRNA
Opis:
MicroRNAs (miRNAs) are an abundant class of 20-27 nt long noncoding RNAs, involved in post-transcriptional regulation of genes in eukaryotes. These miRNAs are usually highly conserved between the genomes of related organisms and their pre-miRNA transcript, about 60-120 nt long, forms extended stem-loop structure. Keeping these facts in mind miRsearch is developed which relies on searching the homologues of all known miRNAs of one organism in the genome of a related organism allowing few mismatches depending on the phylogenetic distance between them, followed by assessing for the capability of formation of stem-loop structure. The precursor sequences so obtained were then screened through the RNA folding program MFOLD selecting the cut-off values on the basis of known Drosophila melanogaster pre-miRNAs. With this approach, about 91 probable candidate miRNAs along with pre-miRNAs were identified in Anopheles gambiae using known D. melanogaster miRNAs. Out of these, 41 probable miRNAs have 100% similarity with already known D. melanogaster miRNAs and others were found to be at least 85% similar to the miRNAs of various other organisms.
Źródło:
Acta Biochimica Polonica; 2006, 53, 2; 303-309
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Apparent contradiction between tectonics and deposition in overturned strata a case study from the "Moravian Culm" (Czech Republic)
Autorzy:
Otava, J.
Havir, J.
Powiązania:
https://bibliotekanauki.pl/articles/2059232.pdf
Data publikacji:
2006
Wydawca:
Państwowy Instytut Geologiczny – Państwowy Instytut Badawczy
Tematy:
Culm facies
Variscan folding
slumping
stratigraphical polarity
Opis:
An apparent contradiction between structural and sedimentological indications commonly used for discrimination of the overturned and non-overturned beds during geological mapping was found at Parsovice, a site situated in the easternmost part of the European Variscides. An outcrop of folded Lower Carboniferous siliciclastic rocks of the "Culm fades" lies on the NE margin of the Bohemian Massif, in the SE part of the Malenik Block (Moravia, Czech Republic). Flute casts in the steep overturned limb of a tectonic fold demonstrate the normal stratigraphic polarity of the bed. At the same site, a slump-related isoclinal fold was found. The apparent contradiction between structural (relation of cleavage and bedding) and sedimentological (flute casts on bed soles) indications is explained by a combination of successive phases of slump- and tectonically-related folding.
Źródło:
Geological Quarterly; 2006, 50, 3; 391-396
1641-7291
Pojawia się w:
Geological Quarterly
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Limitation of conformational space for proteins -- early stage folding simulation of human alpha and beta hemoglobin chains
Autorzy:
Bryliński, M.
Jurkowski, W.
Konieczny, L.
Roterman, I.
Powiązania:
https://bibliotekanauki.pl/articles/1954083.pdf
Data publikacji:
2004
Wydawca:
Politechnika Gdańska
Tematy:
early-stage folding
structure prediction
conformational space
Opis:
The starting structure of ab initio protein structure prediction methods is problematic as the energy minimization procedure stops searching for an optimal structure of the function's local minimum. The method presented in the paper helps to find the starting structure. Although it is based on the known native protein structure, it seems to deliver a key to the formation of a common universal starting structure. The limited conformational sub-space, defined on the basis of a geometrical model of the polypeptide backbone with the side chain-side chain interaction excluded, seems to deliver the original structure of the polypeptide, which is modified step by step as the role of the side chain interactions increases during the energy minimization procedure. Here, the method is applied to human hemoglobin chains alpha and ß to test the applicability of the method to proteins with a high content of helical forms and lacking disulphide bonds.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2004, 8, 3; 413-422
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Protein modeling with reduced representation: statistical potentials and protein folding mechanism
Autorzy:
Ekonomiuk, Dariusz
Kielbasinski, Marcin
Kolinski, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1041306.pdf
Data publikacji:
2005
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
B1 domain of protein G
statistical potentials
folding mechanism
Monte Carlo simulations
high resolution lattice proteins
protein folding
Opis:
A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational propensities and protein-like chain stiffness, a model of directional and cooperative hydrogen bonds, and properly designed knowledge-based potentials of the long-range interactions between the side groups. The folding of the model protein is cooperative and very fast. In a single trajectory, a number of folding/unfolding cycles were observed. Typically, the folding process is initiated by assembly of a native-like structure of the C-terminal hairpin. In the next stage the rest of the four-ribbon β-sheet folds. The slowest step of this pathway is the assembly of the central helix on the scaffold of the β-sheet.
Źródło:
Acta Biochimica Polonica; 2005, 52, 4; 741-748
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Parametric study of friction stir welding using elastic return
Autorzy:
Serier, Mohamed
Berrahou, Mohamed
Chikh, Amina
Powiązania:
https://bibliotekanauki.pl/articles/2065774.pdf
Data publikacji:
2020
Wydawca:
Politechnika Poznańska. Wydawnictwo Politechniki Poznańskiej
Tematy:
elastic return
optimization of experiments
folding process
FSW
Opis:
Aluminum alloy is a very useful material in light manufacturing. Friction stir welding (FSW) is a solid state assembly process that is achievable for this material. This work aims to characterize the quality of the weld joint by an operation of shaping (folding), it aims to study the rate of elastic return in this weld joint after a folding operation. In this context, the elastic return for the folding process has been modeled using experimental tests under optimal welding conditions.
Źródło:
Archives of Mechanical Technology and Materials; 2020, 40; 7--11
2450-9469
Pojawia się w:
Archives of Mechanical Technology and Materials
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Denatured proteins and early folding intermediates simulated in a reduced conformational space
Autorzy:
Kmiecik, Sebastian
Kurcinski, Mateusz
Rutkowska, Aleksandra
Gront, Dominik
Kolinski, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1041278.pdf
Data publikacji:
2006
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
sequence profiles
statistical potentials
protein folding intermediates
high resolution lattice protein models
Replica Exchange Monte Carlo
molten globule
protein folding
Opis:
Conformations of globular proteins in the denatured state were studied using a high-resolution lattice model of proteins and Monte Carlo dynamics. The model assumes a united-atom and high-coordination lattice representation of the polypeptide conformational space. The force field of the model mimics the short-range protein-like conformational stiffness, hydrophobic interactions of the side chains and the main-chain hydrogen bonds. Two types of approximations for the short-range interactions were compared: simple statistical potentials and knowledge-based protein-specific potentials derived from the sequence-structure compatibility of short fragments of protein chains. Model proteins in the denatured state are relatively compact, although the majority of the sampled conformations are globally different from the native fold. At the same time short protein fragments are mostly native-like. Thus, the denatured state of the model proteins has several features of the molten globule state observed experimentally. Statistical potentials induce native-like conformational propensities in the denatured state, especially for the fragments located in the core of folded proteins. Knowledge-based protein-specific potentials increase only slightly the level of similarity to the native conformations, in spite of their qualitatively higher specificity in the native structures. For a few cases, where fairly accurate experimental data exist, the simulation results are in semiquantitative agreement with the physical picture revealed by the experiments. This shows that the model studied in this work could be used efficiently in computational studies of protein dynamics in the denatured state, and consequently for studies of protein folding pathways, i.e. not only for the modeling of folded structures, as it was shown in previous studies. The results of the present studies also provide a new insight into the explanation of the Levinthal's paradox.
Źródło:
Acta Biochimica Polonica; 2006, 53, 1; 131-144
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Radionuclide neutron source trajectories in the closed nuclear fuel cycle
Autorzy:
Stanisz, Przemysław
Cetnar, Jerzy
Oettingen, Mikołaj
Powiązania:
https://bibliotekanauki.pl/articles/147021.pdf
Data publikacji:
2019
Wydawca:
Instytut Chemii i Techniki Jądrowej
Tematy:
MCB
transmutation
equilibrium fuel cycle
LFR
trajectory period folding
Opis:
The highest efficiency in the usage of nuclear energy resources can be implemented in fast breeder reactors of generation IV. It is achieved thanks to the ability of consuming minor actinides (MAs) in energy production. One of the options to use this benefit is full recycling of MAs to close the nuclear fuel cycle. Monte Carlo burn up (MCB), an integrated burn-up calculation code, deals with the complexity of the burn-up process which is applied to the European Lead-cooled Fast Reactor (ELFR). MCB uses continuous energy representation of cross section and spatial effects of full core reactor model; however, it automatically calculates nuclide production in all possible reactions or decay channels. Multi-recycling of MAs can cause an intensified build-up of curium, berkelium and californium. Some of their isotopes are strong neutron emitters from spontaneous fission, which hinders fuel recycling. The implementation of a novel methodology for trajectory period folding allows us to trace the life cycle of crucial MAs from the beginning of the reactor life towards the state of adiabatic equilibrium. The result of the analysis performed is presented, showing the sources of strong contribution to the neutron production rate. The parametric sensitivity analysis method for selected nuclide reactions is applied, revealing sensitivity of transmutation chains for the production of neutron emitter isotopes.
Źródło:
Nukleonika; 2019, 64, 1; 3-9
0029-5922
1508-5791
Pojawia się w:
Nukleonika
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Functional and structural analysis of wing folding mechanism based on cockchafer (Melolontha Melolontha)
Autorzy:
Geisler, T.
Rosikoń, P.
Sochacki, W.
Topczewska, S.
Powiązania:
https://bibliotekanauki.pl/articles/386915.pdf
Data publikacji:
2014
Wydawca:
Politechnika Białostocka. Oficyna Wydawnicza Politechniki Białostockiej
Tematy:
bionic
wing
geometry
joint
folding
bionika
skrzydło
geometria
połączenie
fałdowanie
Opis:
Insects are among nature’s most nimble flyers. In this paper we present the functional and structural analysis of wing joint mechanism. Detailed action of the axillary plates and their mutual interaction was also described. Because of the small dimensionsn of the wing joint elements and the limited resolution of the light microscope, the authors used a scanning electron microscope. Based upon the knowledge of working principles of beetle flight apparatus a wing joint mechanism kinematics model has been developed.
Źródło:
Acta Mechanica et Automatica; 2014, 8, 3; 129-135
1898-4088
2300-5319
Pojawia się w:
Acta Mechanica et Automatica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Treatment of disulfide bonds in coarse-grained UNRES force field
Autorzy:
Krupa, P.
Powiązania:
https://bibliotekanauki.pl/articles/1938623.pdf
Data publikacji:
2016
Wydawca:
Politechnika Gdańska
Tematy:
molecular dynamics
protein folding
disulfide bonds
coarse-grained force field
Opis:
Disulfide bonds, despite the advances of the computational methods, are underrepresented in theoretical chemistry and the role of disulfide bonds is of ten diminished in bioinformatical studies. Most of the molecular modeling tools do not allow studying the process of disulfide bond formation and breaking, which is equally important as the sole presence of disulfide bonds in proteins and peptides. The UNRES (UNited RESidue) coarse-grained force field allows treating disulfide bonds in two ways: as static (formed or broken in the simulation) or dynamic (all specified cysteine residues can form and break disulfide bonds during simulation). The comparison between those two approaches of disulfide-bond treatment is presented for protein folding on the example of four small β - and α + β proteins with one, two, three and four disulfide bonds. The results clearly show that proper disulfide bond treatment is important in simulations and significantly enhances the quality of folded structures.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 393-398
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
New data on Caledonian, Alpine-style folding in the Holy Cross Mts., Poland
Autorzy:
Znosko, J.
Powiązania:
https://bibliotekanauki.pl/articles/2059266.pdf
Data publikacji:
2001
Wydawca:
Państwowy Instytut Geologiczny – Państwowy Instytut Badawczy
Tematy:
Caledonian folding
Cambrian
Ordovician
Brzeziny Syncline
Devonian-Cenozoic platform cover
Opis:
There has been a century-long debate on the nature of the major orogeny in the Holy Cross Mts. Some research workers consider that they were folded during the Variscan orogeny, and that Caledonian movements were responsible only for the formation of mesostructures. Others provide evidence for great folding movements and detachments, suggesting that strong Caledonian compression formed or "squeezed out" Ordovician-Silurian synclines; they consider Variscan deformation to be of platform-type. Laramide and Late Alpine platform-type faults also deformed the Holy Cross Mts. Ordovician haematites show 3 generations of folds in the Brzeziny Syncline, showing it to be over 250 m in amplitude. This structure is thus not a mesostructure but a large-scale structure formed as a result of orogenic compression. The Devonian-Carboniferous cover shows a platform tectonic style. Differences in style between the folded Cambro-Silurian basement and the unconformably overlying Devonian-Carboniferous sedimentary cover are great and cannot be explained in terms of different rock competence. These tectonic relationships are supported by borehole and geophysical evidence. The Caledonian faulting style is identical in the southern part of the Holy Cross Mts. and the northern Łysogóry area. Laramide and Late Alpine stresses are likely related to Atlantic ocean-floor spreading; stresses acting on the crystalline margin of the East European Craton rejuvenated tectonic lineaments in the Holy Cross Mts. and deformed the Devonian-Cenozoic cover throughout the Polish Lowlands.
Źródło:
Geological Quarterly; 2001, 45, 2; 155-164
1641-7291
Pojawia się w:
Geological Quarterly
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Analysis of the wing mechanism movement parameters of selected beetle species (Coleoptera)
Autorzy:
Geisler, T.
Topczewska, S.
Powiązania:
https://bibliotekanauki.pl/articles/265526.pdf
Data publikacji:
2015
Wydawca:
Uniwersytet Zielonogórski. Oficyna Wydawnicza
Tematy:
bionic
wing
movement parameters
folding
chrząszcze
skrzydło owada
parametry ruchu
Opis:
This study presents a structural and functional analysis of the wing bending and folding mechanism of a selected beetle species. Insect motility studies, with regard to the anatomical structure, were performed. The main inner wing structures were highlighted and their mechanical properties and functions were determined. The structure parameters as mechanisms bodies that allow wings of various beetle species to bend and fold were defined.
Źródło:
International Journal of Applied Mechanics and Engineering; 2015, 20, 1; 53-64
1734-4492
2353-9003
Pojawia się w:
International Journal of Applied Mechanics and Engineering
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Monte Carlo simulations of protein-like heteropolymers.
Autorzy:
Sikorski, Andrzej
Romiszowski, Piotr
Powiązania:
https://bibliotekanauki.pl/articles/1044166.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
lattice models
protein structure
Monte Carlo method
protein dynamics
protein folding
Opis:
Properties of a simple model of polypeptide chains were studied by the means of the Monte Carlo method. The chains were built on the (310) hybrid lattice. The residues interacted with long-range potential. There were two kinds of residues: hydrophobic and hydrophilic forming a typical helical pattern -HHPPHPP-. Short range potential was used to prefer helical conformations of the chain. It was found that at low temperatures the model chain formes dense and partially ordered structures (non-unique). The presence of the local potential led to an increase of helicity. The effect of the interplay between the two potentials was studied. After the collapse of the chain further annealing caused rearrangement of helical structures. Dynamic properties of the chain at low temperature depended strongly on the local chain ordering.
Źródło:
Acta Biochimica Polonica; 2001, 48, 1; 77-81
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Determining critical amino acid contacts for knotted protein folding
Autorzy:
Dąbrowski-Tumański, P.
Niewieczerzał, S.
Sułkowska, J. I.
Powiązania:
https://bibliotekanauki.pl/articles/1954247.pdf
Data publikacji:
2022-02-01
Wydawca:
Politechnika Gdańska
Tematy:
knotted protein
slipknot
2efv folding
contact map
native
non-native
Opis:
Proteins with a non-trivial topological structure are currently well recognized, while a knotted protein chain represents a new motif in protein three dimensional folds. Recent comprehensive analysis of the Protein Data Base shows that knotted proteins represent 1.5% of known protein structures. Determination of a free energy landscape of knotted proteins, and its understanding provides a serious challenge for both experimentalists and theoreticians. Moreover the role of a knot for biological activity of protein still remains elusive. In this work we study the smallest knotted proteins ( PDB code 2efv) to understand/investigate their free energy landscape, by means of extensive molecular dynamics simulations. We explore the dependence of the thermodynamics, kinetics and protein folding pathways on the native-likes contact maps and on the length of the chain. We analyze two sets of native-like contacts , which differ by a number of long range interactions, and we consider the 2efv protein with two different lengths of its C-terminus end. We identify the subset of native contacts sufficient to explore the entire free energy landscape. Then, we analyze the influence of the remaining set of native contacts – we show that the set of additional contacts may enhance folding kinetics, and that it has an influence on folding pathways.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 265--279
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Coarse-grained modeling of protein structure, dynamics and protein-protein interactions
Autorzy:
Koliński, A.
Kmiecik, S.
Jamróz, M.
Błaszczyk, M.
Kouza, M.
Kurciński, M.
Powiązania:
https://bibliotekanauki.pl/articles/1954428.pdf
Data publikacji:
2014
Wydawca:
Politechnika Gdańska
Tematy:
coarse-grained modeling
protein folding
protein dynamics
molecular docking
protein docking
Opis:
Theoretical prediction of protein structures and dynamics is essential for understanding the molecular basis of drug action, metabolic and signaling pathways in living cells, designing new technologies in the life science and material sciences . We developed and validated a novel multiscale methodology for the study of protein folding processes including flexible docking of proteins and peptides. The new modeling technique starts from coarse-grained large-scale simulations, followed by selection of the most plausible final structures and intermediates and, finally, by an all-atom rectification of the obtained structures. Except for the most basic bioinformatics tools, the entire computational methodology is based on the models and algorithms developed in our lab. The coarse-grained simulations are based on a high-resolution lattice representation of protein structures, a knowledge based statistical force field and efficient Monte Carlo dynamics schemes, including Replica Exchange algorithms. This paper focuses on the description of the coarse-grained CABS model and its selected applications.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 219--229
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Protein modeling and structure prediction with a reduced representation.
Autorzy:
Kolinski, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1043267.pdf
Data publikacji:
2004
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Monte Carlo simulations
structure prediction
comparative modeling
lattice proteins
protein folding
Opis:
Protein modeling could be done on various levels of structural details, from simplified lattice or continuous representations, through high resolution reduced models, employing the united atom representation, to all-atom models of the molecular mechanics. Here I describe a new high resolution reduced model, its force field and applications in the structural proteomics. The model uses a lattice representation with 800 possible orientations of the virtual alpha carbon-alpha carbon bonds. The sampling scheme of the conformational space employs the Replica Exchange Monte Carlo method. Knowledge-based potentials of the force field include: generic protein-like conformational biases, statistical potentials for the short-range conformational propensities, a model of the main chain hydrogen bonds and context-dependent statistical potentials describing the side group interactions. The model is more accurate than the previously designed lattice models and in many applications it is complementary and competitive in respect to the all-atom techniques. The test applications include: the ab initio structure prediction, multitemplate comparative modeling and structure prediction based on sparse experimental data. Especially, the new approach to comparative modeling could be a valuable tool of the structural proteomics. It is shown that the new approach goes beyond the range of applicability of the traditional methods of the protein comparative modeling.
Źródło:
Acta Biochimica Polonica; 2004, 51, 2; 349-371
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-15 z 35

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