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Wyświetlanie 1-15 z 55
Tytuł:
MOFOID - not only the protein modeling server.
Autorzy:
Szczesny, Pawel
Wieczorek, Grzegorz
Zielenkiewicz, Piotr
Powiązania:
https://bibliotekanauki.pl/articles/1041488.pdf
Data publikacji:
2005
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein structure prediction
homology modeling
Opis:
MOFOID is a new server developed mainly for automated modeling of protein structures by their homology to the structures deposited in the PDB database. Selection of a template and calculation of the alignment is performed with the Smith-Waterman or Needleman-Wunsch algorithms implemented in the EMBOSS package. The final model is built and optimised with programs from the JACKAL package. The wide spectrum of options in the web-based interface and the possibility of uploading user's own alignment make MOFOID a suitable platform for testing new approaches in the alignment building. The server is available at https:// valis.ibb.waw.pl/mofoid/.
Źródło:
Acta Biochimica Polonica; 2005, 52, 1; 267-269
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Comparison of proteins based on segments structural similarity.
Autorzy:
Plewczynski, Dariusz
Pas, Jakub
von Grotthuss, Marcin
Rychlewski, Leszek
Powiązania:
https://bibliotekanauki.pl/articles/1043336.pdf
Data publikacji:
2004
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
3D-hit
protein structure comparison
liveBench
protein structure
toolShop
structural hashing
Opis:
We present here a simple method for fast and accurate comparison of proteins using their structures. The algorithm is based on structural alignment of segments of Ca chains (with size of 99 or 199 residues). The method is optimized in terms of speed and accuracy. We test it on 97 representative proteins with the similarity measure based on the SCOP classification. We compare our algorithm with the LGscore2 automatic method. Our method has the same accuracy as the LGscore2 algorithm with much faster processing of the whole test set, which is promising. A second test is done using the ToolShop structure prediction evaluation program and shows that our tool is on average slightly less sensitive than the DALI server. Both algorithms give a similar number of correct models, however, the final alignment quality is better in the case of DALI. Our method was implemented under the name 3D-Hit as a web server at http://3dhit.bioinfo.pl/ free for academic use, with a weekly updated database containing a set of 5000 structures from the Protein Data Bank with non-homologous sequences.
Źródło:
Acta Biochimica Polonica; 2004, 51, 1; 161-172
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Improving protein structure prediction, refinement and quality assessment techniques
Autorzy:
Leelananda, S. P.
Pawłowski, M.
Faraggi, E.
Kloczkowski, A.
Powiązania:
https://bibliotekanauki.pl/articles/1954426.pdf
Data publikacji:
2014
Wydawca:
Politechnika Gdańska
Tematy:
protein structure prediction
model quality assessment
structure refinement
Opis:
Several novel techniques have been combined to improve protein structure prediction, structural refinement and quality assessment of protein models. We discuss in brief the development of four-body potentials that take into account dense packing and cooperativity of interactions of proteins, and its success. We have developed a method that uses whole protein information filtered through machine learning to score protein models based on their likeness to native structure. Here we consider electrostatic interactions and residue depth, and use these for structure prediction. These potentials were tested to be successful in CASP9 and CASP10. We have also developed a Quality Assessment technique, MQAP single, which is a quasi-single-model MQAP, by combining advantages of both “pure” single-model MQAPs and clustering MQAP s. This technique can be used in ranking and assessing the absolute global quality of single protein models. This model (Pawlowski-Kloczkowski) was ranked 3rd in Model Quality Assessment in CASP 10. Consideration of protein flexibility and its fluctuation dynamics improves protein structure prediction and leads to better refinement of computational models of proteins. Here we also discuss how Anisotropic Network Model (ANM) of protein fluctuation dynamics and Go-like model of energy score can be used for novel protein structure refinement.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 231--243
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Structural studies of algal lectins with anti-HIV activity
Autorzy:
Ziółkowska, Natasza
Wlodawer, Alexander
Powiązania:
https://bibliotekanauki.pl/articles/1041149.pdf
Data publikacji:
2006
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
topical antivirals
protein structure
HIV
lectin
AIDS
Opis:
A number of antiviral lectins, small proteins that bind carbohydrates found on viral envelopes, are currently in pre-clinical trials as potential drugs for prevention of transmission of human immunodeficiency virus (HIV) and other enveloped viruses, such as the Ebola virus and the coronavirus responsible for severe acute respiratory syndrome (SARS). Lectins of algal origin whose antiviral properties make them candidate agents for prevention of viral transmission through topical applications include cyanovirin-N, Microcystis viridis lectin, scytovirin, and griffithsin. Although all these proteins exhibit significant antiviral activity, their structures are unrelated and their mode of binding of carbohydrates differs significantly. This review summarizes the current state of knowledge of the structures of algal lectins, their mode of binding of carbohydrates, and their potential medical applications.
Źródło:
Acta Biochimica Polonica; 2006, 53, 4; 617-626
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Understanding the evolution of restriction-modification systems: Clues from sequence and structure comparisons.
Autorzy:
Bujnicki, Janusz
Powiązania:
https://bibliotekanauki.pl/articles/1044038.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein structure
methyltransferases
bioinformatics
molecular evolution
endonucleases
Opis:
Restriction-modification (RM) systems comprise two opposing enzymatic activities: a restriction endonuclease, that targets specific DNA sequences and performs endonucleolytic cleavage, and a modification methyltransferase that renders these sequences resistant to cleavage. Studies on molecular genetics and biochemistry of RM systems have been carried out over the past four decades, laying foundations for modern molecular biology and providing important models for mechanisms of highly specific protein-DNA interactions. Although the number of known, relevant sequences 3D structures of RM proteins is growing steadily, we do not fully understand their functional diversities from an evolutionary perspective and we are not yet able to engineer new sequence specificities based on rational approaches. Recent findings on the evolution of RM systems and on their structures and mechanisms of action have led to a picture in which conserved modules with defined function are shared between different RM proteins and other enzymes involved in nucleic acid biochemistry. On the other hand, it has been realized that some of the modules have been replaced in the evolution by unrelated domains exerting similar function. The aim of this review is to give a survey on the recent progress in the field of structural phylogeny of RM enzymes with special emphasis on studies of sequence-structure-function relationships and emerging potential applications in biotechnology.
Źródło:
Acta Biochimica Polonica; 2001, 48, 4; 935-967
0001-527X
Pojawia się w:
Acta Biochimica Polonica
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:
Unexpected domain composition of MACC1 links MET signaling and apoptosis
Autorzy:
Kokoszyńska, Katarzyna
Kryński, Jacek
Rychlewski, Leszek
Wyrwicz, Lucjan
Powiązania:
https://bibliotekanauki.pl/articles/1040592.pdf
Data publikacji:
2009
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein structure modeling
colorectal cancer
bioinformatics
death domain
Opis:
Colorectal cancer, one of the most challenging malignancies, still has a limited number of recognized prognostic and predictive markers indicating appropriate treatment. MACC1 (metastasis-associated in colon cancer-1), a novel regulator of tumor growth and metastasis has recently been identified as an important prognostic factor of metastatic disease in colorectal cancer. The mechanism of MACC1 activity remains undetermined. Here we apply a combination of fold recognition and homology modeling algorithms to draft MACC1 function. The applied methods revealed that the MACC1 protein consists of four domains: ZU5, SH3, and two C-terminal death domains (DD). Previously a similar domain architecture (ZU5-DD) was observed in other proteins, involved mainly in signal transduction and apoptosis regulation. Based on the specific aspects of the closest homologues' biology functional hypotheses on MACC1 are proposed. A broad range of bioinformatic analyzes indicates that MACC1, besides its involvement in signal transduction from the MET receptor, links MET signaling and apoptosis.
Źródło:
Acta Biochimica Polonica; 2009, 56, 2; 317-324
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Improving of functional properties of oilseed and legume proteins by structural changes
Poprawa właściwości funkcjonalnych białek nasion roślin oleistych i strączkowych przez zmiany strukturalne
Autorzy:
Schwenke, K.D.
Powiązania:
https://bibliotekanauki.pl/articles/1399315.pdf
Data publikacji:
1988
Wydawca:
Instytut Rozrodu Zwierząt i Badań Żywności Polskiej Akademii Nauk w Olsztynie
Tematy:
protein structure
oilseed globulins
protein modification
functional properties
legume seed globulina
Opis:
The structure modification of the main proteins from oilseeds and legumes by means of alkali- or acid-denaturation and succinylation, respectively, and its influence on the protein functionality is discussed. This kind of modification enables to improve the functional properties with minimal energy input.
Główne białka z nasion roślin oleistych i strączkowych reprezentowane są przez frakcje globulinowe 11S i 7S o bardzo podobnej strukturze oligomerycznej w każdej z tych frakcji. Przez zmianę struktury przestrzennej można osiągnąć poprawę właściwości funkcjonalnych tych białek. Przedyskutowane są podstawowe kierunki modyfikacji struktury: łagodna denaturacja w środowisku kwaśnym lub alkalicznym i sukcylynowanie. Ostatnia z wymienionych metod pozwala na stopniową zmianę struktury białka i jego właściwości funkcjonalnych. Obydwie metody umożliwiają poprawę właściwości funkcjonalnych bez wysokiego nakładu energii.
Źródło:
Acta Alimentaria Polonica; 1988, 14(38), 1; 15-23
0137-1495
Pojawia się w:
Acta Alimentaria Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The effect of the Glu342Lys mutation in α1-antitrypsin on its structure, studied by molecular modelling methods.
Autorzy:
Jezierski, Grzegorz
Pasenkiewicz-Gierula, Marta
Powiązania:
https://bibliotekanauki.pl/articles/1044164.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
serpins
protein structure
energy minimisation
molecular dynamics simulation
Opis:
The structure of native α1-antitrypsin, the most abundant protease inhibitor in human plasma, is characterised primarily by a reactive loop containing the centre of proteinase inhibition, and a β-sheet composed of five strands. Mobility of the reactive loop is confined as a result of electrostatic interactions between side chains of Glu342 and Lys290, both located at the junction of the reactive loop and the β structure. The most common mutation in the protein, resulting in its inactivation, is Glu342→Lys, named the Z mutation. The main goal of this work was to investigate the influence of the Z mutation on the structure of α1-antitrypsin. Commonly used molecular modelling methods have been applied in a comparative study of two protein models: the wild type and the Z mutant. The results indicate that the Z mutation introduces local instabilities in the region of the reactive loop. Moreover, even parts of the protein located far apart from the mutation region are affected. The Z mutation causes a relative change in the total energy of about 3%. Relatively small root mean square differences between the optimised structures of the wild type and the Z mutant, together with detailed analysis of 'conformational searching' process, lead to the hypothesis that the Z mutation principally induces a change in the dynamics of α1-antitrypsin.
Źródło:
Acta Biochimica Polonica; 2001, 48, 1; 65-75
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Scanning electron microscopic picture of the concentration and distribution of protein structures in the seed endosperm of low and high protein varietes of rye (Secale cereale L.)
Badania porównawcze ilości i rozmieszczenia białek w komórkach endospermy ziarniaków nisko- i wysokobiałkowych odmian żyta
Autorzy:
Kubiczek, R.
Luczak, W.
Molski, B.
Moczydłowski, J.
Powiązania:
https://bibliotekanauki.pl/articles/1399430.pdf
Data publikacji:
1989
Wydawca:
Instytut Rozrodu Zwierząt i Badań Żywności Polskiej Akademii Nauk w Olsztynie
Tematy:
rye
scanning electron microscopy
endosperm structures
protein structure
Opis:
Comparative studies of subaleurone and inner endosperm cells of dry mature caryopses from 8 low-protein and 7 high-protein varieties of rye, grown in similar conditions of isolated collection, were performed by means of scanning electron microscopy technique. Low protein varieties contained starch granules differentiated in the diameter embedded in the less dense protein matrix of the wide subaluerone region. High protein varieties, besides the larger aleurone cells had in some examples wider subaluerone layer with the dense protein matrix, which was very regular and less packed with starch granules. The inner endosperm cells of high-protein caryopses contained much more dense protein matrix all around the starch granules in contrast to low-protein caryopses, which were tightly packed with starch and had only a thin layer of protein matrix around them. Comparative pronase treatment of low- and high-protein rye caryopses confirmed the above observations. No granular protein bodies in any cells, besides the aleurone ones, could be observed.
Przeprowadzono badania porównawcze ilości i rozmieszczenia składników białkowych komórek warstw podaleuronowych i głębszych warstw endospermy w suchych, dojrzałych ziarniakach 8 niskobiałkowych i 7 wysokobiałkowych odmian żyta (tab.), wyhodowanych w 1974/75 r. w Skierniewicach i 1976/77 r. w Powsinie w identycznych warunkach izolowanej kolekcji zachowawczej z wykorzystaniem skaningowego mikroskopu elektronowego (SEM). W odmianach niskobiałkowych ziarna skrobiowe o zróżnicowanej średnicy były zatopione w grubej warstwie matrycy białkowej w komórkach cienkiej warstwy podaleuronowej (fot. 1, 2, 3). W odmianach wysokobiałkowych, oprócz zdarzających się w wypadku niektórych odmian większych komórek warstwy aleuronowej, warstwa podaleuronowa była lepiej wykształcona z dużą ilością matrycy białkowej i regularnymi i mniej upakowanymi w niej ziarnami skrobi (fot. 4, 5). Również w głębszych warstwach endospermy komórki ziarniaków odmian wysokobiałkowych zawierały więcej matrycy białkowej otaczającej ziarna skrobi w przeciwieństwie do niskobiałkowych, których komórki wypełnione są szczelnie ziarnami skrobi i zawierają niewielkie ilości białek pomiędzy nimi oraz białko cytoplazmatyczne pod ścianami komórek. Porównawcze trawienie pronazą skrawków ziarniaków odmian nisko- i wysokobiałkowych (fot.8) potwierdziło powyższe twierdzenia. Nie zauważono w komórkach innych niż aleuronowe granularnych ciał białkowych w żadnej z badanych odmian żyta.
Źródło:
Acta Alimentaria Polonica; 1989, 15(39), 2; 185-195
0137-1495
Pojawia się w:
Acta Alimentaria Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Novel roles for glutathione in linking oxidative stress to phytohormone-dependent signalling
Autorzy:
Noctor, G.
Han, Y.
Chaouch, S.
Mhamdi, A.
Powiązania:
https://bibliotekanauki.pl/articles/80088.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
conference
glutathione
oxidative stress
phytohormone
antioxidant
protein structure
protein function
signalling
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 2
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage.
Autorzy:
Bujnicki, Janusz
Radlińska, Monika
Zaleski, Piotr
Piekarowicz, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1044039.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein structure
sequence specificity
DNA methyltransferase
bioinformatics
molecular evolution
Opis:
In this paper we report cloning and experimental characterization of the DNA adenine methyltransferase (dam) gene from Haemophilus influenzae and comparison of ts product with the Dam protein from the lysogenic phage of H. influenzae, HP1. Molecular modeling of M.HinDam and M.HP1Dam was carried out, providing a framework for a comparative analysis of these enzymes and their close homologs in the tructural context. Both proteins share the common fold and essential cofactor-bind ng and catalytic residues despite overall divergence. However, subtle but significant differences in the cofactor-binding pocket have been identified. Moreover, while M.HinDam seems to contact its target DNA sequence using a number of loops, most of them are missing from M.HP1Dam. Analysis of both MTases suggests that their catalytic activity was derived from a common ancestor, but similar sequence specificities rose by convergence.
Źródło:
Acta Biochimica Polonica; 2001, 48, 4; 969-983
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Cytomegalovirus immediate early gene UL37 encodes a novel MHC-like protein
Autorzy:
Wyrwicz, Lucjan
Rychlewski, Leszek
Powiązania:
https://bibliotekanauki.pl/articles/1040815.pdf
Data publikacji:
2008
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Betaherpesvirinae
CMV
protein structure prediction
MHC I class
bioinformatics
apoptosis
Opis:
The cytomegalovirus (CMV) genome encodes four clusters of genes expressed immediately after infection - i.e.: UL36-38, UL122-123, TRS1-IRS1, and US3. The general function of these genes is associated with inhibition of cellular mechanisms of antiviral response. Although several biological processes have been mapped onto specific gene products, the knowledge of the molecular mechanism of their activity remains fragmentary. Here, we report the application of protein structure prediction methods in assigning the function to a glycosylated domain encoded by UL37 of CMV (gpUL37, UL37x3). The discerned similarity clearly points out that this domain represents a novel type of a major histocompatibility complex (MHC)-like protein, and consequently may play a central role in an additional mechanism of escape from antiviral response.
Źródło:
Acta Biochimica Polonica; 2008, 55, 1; 67-74
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases.
Autorzy:
Wlodawer, Alexander
Li, Mi
Gustchina, Alla
Oyama, Hiroshi
Dunn, Ben
Oda3, Kohei
Powiązania:
https://bibliotekanauki.pl/articles/1043650.pdf
Data publikacji:
2003
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
enzyme families
sequence conservation
active site
enzymatic machanism
protein structure
Opis:
Sedolisins (serine-carboxyl peptidases) are proteolytic enzymes whose fold resembles that of subtilisin; however, they are considerably larger, with the mature catalytic domains containing approximately 375 amino acids. The defining features of these enzymes are a unique catalytic triad, Ser-Glu-Asp, as well as the presence of an aspartic acid residue in the oxyanion hole. High-resolution crystal structures have now been solved for sedolisin from Pseudomonas sp. 101, as well as for kumamolisin from a thermophilic bacterium, Bacillus novo sp. MN-32. The availability of these crystal structures enabled us to model the structure of mammalian CLN2, an enzyme which, when mutated in humans, leads to a fatal neurodegenerative disease. This review compares the structural and enzymatic properties of this newly defined MEROPS family of peptidases, S53, and introduces their new nomenclature.
Źródło:
Acta Biochimica Polonica; 2003, 50, 1; 81-102
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A short review on proteomics and its applications
Autorzy:
Chandrasekhar, K.
Dileep, A.
Lebonah, D.E.
Pramoda Kumari, J.
Powiązania:
https://bibliotekanauki.pl/articles/11309.pdf
Data publikacji:
2014
Wydawca:
Przedsiębiorstwo Wydawnictw Naukowych Darwin / Scientific Publishing House DARWIN
Tematy:
proteomics
application
protein function
protein structure
stress condition
metabolism
2-D electrophoresis
disease treatment
novel protein
Opis:
Proteomics is the large scale of study of proteins, particularly their function and structure. Proteomics is an excellent approach for studying changes in metabolism in response to different stress conditions. In the present review focused on different types of techniques for the analysis of expressed proteins. The techniques includes 2-D gel electrophoresis, MALDI-TOF/MS etc., play a vital role for the analysis of novel proteins and their role in disease maintenance and treatment. The review also concentrated on applicative perspective of proteomics in the fields of biomedical, agriculture and food.
Źródło:
International Letters of Natural Sciences; 2014, 12, 1
2300-9675
Pojawia się w:
International Letters of Natural Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
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