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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:
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:
Computer simulations of protein folding with a small number of distance restraints.
Autorzy:
Sikorski, Andrzej
Kolinski, Andrzej
Skolnick, Jeffrey
Powiązania:
https://bibliotekanauki.pl/articles/1043733.pdf
Data publikacji:
2002
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
lattice models
NMR structure refinement
Monte Carlo method
reduced protein models
protein folding
Opis:
A high coordination lattice model was used to represent the protein chain. Lattice points correspond to amino-acid side groups. A complicated force field was designed in order to reproduce a protein-like behavior of the chain. Long-distance tertiary restraints were also introduced into the model. The Replica Exchange Monte Carlo method was applied to find the lowest energy states of the folded chain and to solve the problem of multiple minima. In this method, a set of replicas of the model chain was simulated independently in different temperatures with the exchanges of replicas allowed. The model chains, which consisted of up to 100 residues, were folded to structures whose root-mean-square deviation (RMSD) from their native state was between 2.5 and 5 Å. Introduction of restrain based on the positions of the backbone hydrogen atoms led to an improvement in the number of successful simulation runs. A small improvement (about 0.5 Å) was also achieved in the RMSD of the folds. The proposed method can be used for the refinement of structures determined experimentally from NMR data.
Źródło:
Acta Biochimica Polonica; 2002, 49, 3; 683-692
0001-527X
Pojawia się w:
Acta Biochimica Polonica
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 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
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:
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:
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:
Komputerowa symulacja procesu składania i rozkładania ramy nośnej narzędzia rolniczego
Computer simulation of the process of folding and unfolding of main frame of agricultural implement
Autorzy:
Zbytek, Z.
Łowiński, Ł.
Talarczyk, W.
Powiązania:
https://bibliotekanauki.pl/articles/335528.pdf
Data publikacji:
2007
Wydawca:
Sieć Badawcza Łukasiewicz - Przemysłowy Instytut Maszyn Rolniczych
Tematy:
narzędzie rolnicze
rama nośna
składanie
rozkładanie
symulacja komputerowa
agricultural implement
main frame
folding
unfolding
computer simulation
Opis:
Omówiono symulacje komputerowe procesu składania i rozkładania ramy nośnej narzędzia rolniczego przeprowadzone w fazie projektowania. Opracowany model geometryczny ramy nośnej poddano analizie wpływu zmiany położenia narzędzia na reakcje w punktach zawieszenia na ciągniku, wpływu zmiany położenia ramion bocznych ramy na reakcje w miejscach mocowania siłowników oraz określono położenie i kształt zderzaków i łącznika. W wyniku podjętych prac uzyskano konstrukcję belki nośnej narzędzia rolniczego stanowiącą podstawę do przeprowadzenia analizy wytrzymałościowej modelu obliczeniowego MES całej konstrukcji wielofunkcyjnego narzędzia uprawowo-pielęgnacyjnego.
Computer simulations of the process of folding and unfolding of main frame of agricultural implement which were carried out and the phase of designing are discussed in the paper. Elaborated geometrical model of the mainframe was put to the analysis to determine the influence of implement position changes on reactions in the points of its mounting on the tractor as well as to determine the influence of changes of positions of the frame side arms on reactions in the points where hydraulic cylinders are fixed. Then the location and shape of the stops and the connecting rod were determined. As a result of these works created was construction of the agricultural implement main beam which will be a base for carrying out strength analysis of calculation model FEM of the whole construction of the agricultural multifunctional implement.
Źródło:
Journal of Research and Applications in Agricultural Engineering; 2007, 52, 2; 16-20
1642-686X
2719-423X
Pojawia się w:
Journal of Research and Applications in Agricultural Engineering
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
High throughput protein production
Autorzy:
Tworak, A.
Podkowinski, J.
Figlerowicz, M.
Powiązania:
https://bibliotekanauki.pl/articles/80317.pdf
Data publikacji:
2011
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
activity
cloning
DNA sequencing
expression
high throughput
human genome
Human Genome Project
large scale proteomics
new technology
protein folding
protein production
purification
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 2
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
O kilku osobliwościach w oddziaływaniach molekuł
On some pecularities of intermolecular and intramolecular interactions
Autorzy:
Piela, L.
Powiązania:
https://bibliotekanauki.pl/articles/172004.pdf
Data publikacji:
2011
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
globalna optymalizacja
zwijanie białek
oddziaływanie dipol-dipol
choroba prionowa
autokataliza
global optimization
protein folding
dipole-dipole interaction
prion disease
autocatalysis
Opis:
The ground state electronic energy represents a complicated function of the nuclear coordinates. Even for relatively small molecules this function may have many minima in the corresponding "energy landscape", very often myriads of minima, each of them corresponding to a stable configuration of the nuclei. This is why predicting the lowest-energy conformation or configuration represents a formidable task. There were many attempts to solve this problem for protein molecules, for which it is believed their native conformation corresponds to the lowest free energy. The challenge to find this conformation from a given sequence of amino acids is known as a "second genetic code". In fact all of these attempts based on some smoothing of the energy landscape. In the article some of these smoothing techniques are described, from a generic one to those, which finally turned out to be highly successful in finding native structures of globular proteins. When discussing the contributions to the conformational energy the importance of the hydrophobic effect as well as of the electrostatic interactions has been stressed. In particular it turned out that the dipole moments of the NH and of the CO bonds in proteins functioning in nature are oriented to good accuracy along the local intramolecular electric field. Thanks to enormous effort of the protein folding community it is possible to design such amino acid sequences, which fold to the desired protein 3D structure. A certain reliable theoretical technique of protein folding has been used to study a possibility of conformational autocatalysis. It turned out that a small protein of 32 amino acids, with carefully predesigned amino acid sequence, exhibits indeed such an effect, which may be seen as a model of the prion disease propagation.
Źródło:
Wiadomości Chemiczne; 2011, 65, 11-12; 935-952
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Analysis of the Structure and Mechanism of Wing Folding and Flexion in Xylotrupes Gideon Beetle (L. 1767) (Coloptera, Scarabaeidae)
Autorzy:
Geisler, T.
Powiązania:
https://bibliotekanauki.pl/articles/386995.pdf
Data publikacji:
2012
Wydawca:
Politechnika Białostocka. Oficyna Wydawnicza Politechniki Białostockiej
Tematy:
tylne skrzydła
budowa
mechanizm
składanie skrzydeł
zgięcie skrzydeł
hind wings
structure
mechanism
folding and flexion of wings
Opis:
This study presents the structure and functions of flying wings in beetles (Coloptera). Structural analysis and function of multiplanar flexion and the structure of the wings in selected beetles were also carried out. The author developed a method of determination of points, structures and surfaces on the wing in folding and flexing motions. The paper describes the system of veins, foils and folds in the wing. Photographs of the wing in different phases of folding and flexion are presented in the paper. The paper emphasizes practical applications of the method of analysis in bionic mechanisms.
Źródło:
Acta Mechanica et Automatica; 2012, 6, 3; 37-44
1898-4088
2300-5319
Pojawia się w:
Acta Mechanica et Automatica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Mosty składane - przykłady zastosowania izolacji nowej generacji
Autorzy:
Czopek, G.
Powiązania:
https://bibliotekanauki.pl/articles/364200.pdf
Data publikacji:
2012
Wydawca:
Nowoczesne Budownictwo Inżynieryjne
Tematy:
bridgemaster
eliminator
izolacja
most składany
nawierzchnia
nawierzchnia antypoślizgowa Safetrack
Bridgemaster
folding bridge
insulation
surface
Opis:
27 września 2012 r. w krakowskim hotelu Aspel Związek Mostowców Rzeczpospolitej Polskiej Oddział Małopolski oraz Małopolska Okręgowa Izba Inżynierów Budownictwa zorganizowały szóste szkolenie Mosty składane - przykłady zastosowania izolacji nowej generacji.
Źródło:
Nowoczesne Budownictwo Inżynieryjne; 2012, 6; 53
1734-6681
Pojawia się w:
Nowoczesne Budownictwo Inżynieryjne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Nurt fałdowania, a problem działania architektury
Folding and performance in architecture
Autorzy:
Więcek, K.
Powiązania:
https://bibliotekanauki.pl/articles/370252.pdf
Data publikacji:
2012
Wydawca:
Zachodniopomorski Uniwersytet Technologiczny w Szczecinie. Wydawnictwo Uczelniane ZUT w Szczecinie
Tematy:
Gilles Deleuze
folding
fałdowanie
fałda
działanie
znaczenie
tekst
fold
performance
meaning
text
Opis:
Artykuł skrótowo prezentuje problemy, genezę i potencjał nurtu fałdowania (foldingu) na polu teorii, jak i praktyki architektonicznej w ciągu ostatnich 20 lat oraz jego związków z pewnymi kwestiami badanymi przez teorię architektury, w szczególności problemem działania architektury i jej recepcją.
The following article presents theoretical assessment and evaluation of certain theoretical problems regarding folding movement inspired by Gilles Deleuze, as well as its connections with the notion of architecture's influence of users' behavior, and its reception.
Źródło:
Przestrzeń i Forma; 2012, 17; 291-300
1895-3247
2391-7725
Pojawia się w:
Przestrzeń i Forma
Dostawca treści:
Biblioteka Nauki
Artykuł
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