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Wyświetlanie 1-15 z 18
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:
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:
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:
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:
Attaching a spin to a protein - site-directed spin labeling in structural biology
Autorzy:
Czogalla, Aleksander
Pieciul, Aldona
Jezierski, Adam
Sikorski, Aleksander
Powiązania:
https://bibliotekanauki.pl/articles/1041067.pdf
Data publikacji:
2007
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein structure
site-directed spin labeling
electron paramagnetic resonance (EPR) spectroscopy
Opis:
Site-directed spin labeling and electron paramagnetic resonance spectroscopy have recently experienced an outburst of multiple applications in protein science. Numerous interesting strategies have been introduced for determining the structure of proteins and its conformational changes at the level of the backbone fold. Moreover, considerable technical development in the field makes the technique an attractive approach for the study of structure and dynamics of membrane proteins and large biological complexes at physiological conditions. This review focuses on a brief description of site-directed spin labeling-derived techniques in the context of their recent applications.
Źródło:
Acta Biochimica Polonica; 2007, 54, 2; 235-244
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Homologues of HSV-1 nuclear egress factor UL34 are potential phosphoinositide-binding proteins
Autorzy:
Wyrwicz, Lucjan
Koczyk, Grzegorz
Rychlewski, Leszek
Powiązania:
https://bibliotekanauki.pl/articles/1040842.pdf
Data publikacji:
2008
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
HSV-1
Herpesviridae
phosphoinositides
protein structure prediction
bioinformatics
UL34
nuclear egress
Opis:
During the herpesvirus replication cycle, viral transcription, DNA replication, formation of capsids and DNA packaging occur in the nucleus. The subsequent nuclear egress of newly synthesized nucleocapsids is performed by budding of the inner leaflet of the nuclear membrane, which creates the primary envelope. Although products of two genes conserved throughout the Herpesviridae family (HSV-1 UL34 and UL31) have previously been shown to be involved in the execution of this process, the molecular basis of their activity is not clear. Here we present results of protein structure prediction for the conserved domain of UL34. The applied methodology suggests that this protein adopts a pleckstrin homology (PH) fold to perform its function. A detailed inspection of the ligand binding site strongly supports the hypothesis that UL34 orthologs can recognize phosphoinositides. Since previous works suggest that alterations of UL34 gene product result in a drastic impairment of primary envelopment of HSV-1 and trapping of capsids in the nucleus, the presented data may lead to the development of novel anti-herpetic therapeutic strategies where analogs of phosphoinositides are administered.
Źródło:
Acta Biochimica Polonica; 2008, 55, 1; 207-213
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
On the possibility that H1 histone interaction with DNA occurs through phosphates connecting lysine and arginine side chain groups
Autorzy:
Piscopo, Marina
De Petrocellis, Luciano
Conte, Mariachiara
Pulcrano, Giovanna
Geraci, Giuseppe
Powiązania:
https://bibliotekanauki.pl/articles/1041206.pdf
Data publikacji:
2006
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Chaetopterus variopedatus
protein structure
sperm H1 histone
arginine
lysine
ionic interaction
Opis:
Gel filtration and velocity of sedimentation analyses on native and on lysine- and arginine- modified forms of the annelid worm Chaetopterus variopedatus sperm H1 histone indicate that anion-mediated lysine - arginine interactions play a relevant role in the stabilization of the oligomeric states of the molecule. CD spectroscopy shows that phosphate anions are at least an order of magnitude more efficient than chloride as negatively charged groups connecting H1 lysines and arginines. Acetylation of lysines, although not altering grossly the H1 properties, causes a tenfold decrease of the structuring efficiency of phosphates. This suggests that DNA phosphates may be sandwiched between lysine and arginine groups of H1 histone when this molecule binds to chromatin, constituting a relevant parameter for the reciprocal stabilization of the protein and of the chromatin higher order structures.
Źródło:
Acta Biochimica Polonica; 2006, 53, 3; 507-513
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Structure of small G proteins and their regulators.
Autorzy:
Paduch, Marcin
Jeleń, Filip
Otlewski, Jacek
Powiązania:
https://bibliotekanauki.pl/articles/1043851.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
small G protein
GAP
protein-protein interaction
GTPase
GDI
Rho
Ras
protein tertiary structure
GEF
Opis:
In recent years small G proteins have become an intensively studied group of regulatory GTP hydrolases involved in cell signaling. More than 100 small G proteins have been identified in eucaryotes from protozoan to human. The small G protein superfamily includes Ras, Rho Rab, Rac, Sar1/Arf and Ran homologs, which take part in numerous and diverse cellular processes, such as gene expression, cytoskeleton reorganization, microtubule organization, and vesicular and nuclear transport. These proteins share a common structural core, described as the G domain, and significant sequence similarity. In this paper we review the available data on G domain structure, together with a detailed analysis of the mechanism of action. We also present small G protein regulators: GTPase activating proteins that bind to a catalytic G domain and increase its low intrinsic hydrolase activity, GTPase dissociation inhibitors that stabilize the GDP-bound, inactive state of G proteins, and guanine nucleotide exchange factors that accelerate nucleotide exchange in response to cellular signals. Additionally, in this paper we describe some aspects of small G protein interactions with downstream effectors.
Źródło:
Acta Biochimica Polonica; 2001, 48, 4; 829-850
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Structure, function, and regulation of myosin 1C.
Autorzy:
Barylko, Barbara
Jung, Gwanghyun
Albanesi, Joseph
Powiązania:
https://bibliotekanauki.pl/articles/1041416.pdf
Data publikacji:
2005
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
myosin 1
membrane protein translocation
domain structure
Opis:
Myosin 1C, the first mammalian single-headed myosin to be purified, cloned, and sequenced, has been implicated in the translocation of plasma membrane channels and transporters. Like other forms of myosin I (of which eight exist in humans) myosin 1C consists of motor, neck, and tail domains. The neck domain binds calmodulins more tightly in the absence than in the presence of Ca^(2+). Release of calmodulins exposes binding sites for anionic lipids, particularly phosphoinositides. The tail domain, which has an isoelectic point of 10.5, interacts with anionic lipid headgroups. When both neck and tail lipid binding sites are engaged, the myosin associates essentially irreversibly with membranes. Despite this tight membrane binding, it is widely believed that myosin 1C docking proteins are necessary for targeting the enzyme to specific subcellular location. The search for these putative myosin 1C receptors is an active area of research.
Źródło:
Acta Biochimica Polonica; 2005, 52, 2; 373-380
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-15 z 18

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