Wyniki wyszukiwania

1

FunPred-1: Protein function prediction from a protein interaction network using neighborhood analysis

100%

Saha S., Chatterjee P., Basu S., Kundu M., Nasipuri M.

Cellular and Molecular Biology Letters

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2014

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tom 19

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nr 4

Proteins are responsible for all biological activities in living organisms. Thanks to genome sequencing projects, large amounts of DNA and protein sequence data are now available, but the biological functions of many proteins are still not annotated in most cases. The unknown function of such non-annotated proteins may be inferred or deduced from their neighbors in a protein interaction network. In this paper, we propose two new methods to predict protein functions based on network neighborhood properties. FunPred 1.1 uses a combination of three simple-yet-effective scoring techniques: the neighborhood ratio, the protein path connectivity and the relative functional similarity. FunPred 1.2 applies a heuristic approach using the edge clustering coefficient to reduce the search space by identifying densely connected neighborhood regions. The overall accuracy achieved in FunPred 1.2 over 8 functional groups involving hetero-interactions in 650 yeast proteins is around 87%, which is higher than the accuracy with FunPred 1.1. It is also higher than the accuracy of many of the state-of-the-art protein function prediction methods described in the literature. The test datasets and the complete source code of the developed software are now freely available at http://code.google.com/p/cmaterbioinfo/.

2

L1-ORF1p and Ago2 are involved in a siRNA-mediated regulation for promoter activity of L1-5’UTR

86%

Shi L., Shi H., Lou L., Yuan X., Zhu Y.

Folia Histochemica et Cytobiologica

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2019

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tom 57

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nr 2

3

Structural determinants of cooperativity in acto-myosin interactions

86%

Moraczewska J.

Acta Biochimica Polonica

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2002

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tom 49

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nr 4

Regulation of muscle contraction is a very cooperative process. The presence of tropomyosin on the thin filament is both necessary and sufficient for cooperativity to occur. Data recently obtained with various tropomyosin isoforms and mutants help us to understand better the structural requirements in the thin filament for cooperative protein interactions. Forming an end-to-end overlap between neighboring tropomyosin molecules is not necessary for the cooperativity of the thin filament activation. When direct contacts between tropomyosin molecules are disrupted, the conformational changes in the filament are most probably transmitted cooperatively through actin subunits, although the exact nature of these changes is not known. The function of tropomyosin ends, alternatively expressed in various isoforms, is to confer specific actin affinity. Tropomyosin's affinity or actin is directly related to the size of the apparent cooperative unit defined as the number of actin subunits turned into the active state by binding of one myosin head. Inner sequences of tropomyosin, particularly actin-binding periods 3 to 5, play crucial role in myosin-induced activation of the thin filament. A plausible mechanism of tropomyosin function in this process is that inner tropomyosin regions are either specifically recognized by myosin or they define the right actin conformation required for tropomyosin movement from its blocking position.

4

Studies of HIV-Rev in living cells

86%

Brokstad K. A., Andersen V., Kanestrom A., Szilvay A. M., Haukenes G., Kalland K. H.

Cellular and Molecular Biology Letters

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1997

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tom 02

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nr 2

5

The interactions between SATB1 and F-actin are important for mechanisms of active cell death

72%

Grzanka D., Kowalczyk A. E., Izdebska M., Klimaszewska- -Wisniewska A., Gagat M.

Folia Histochemica et Cytobiologica

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2015

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tom 53

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nr 2

6

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Identification of cell cycle proteins interacting with Arabidopsis thaliana proliferating cell nuclear antigen using bimolecular fluorescence complementation assay

72%

Strzalka W., Jakubowska A., Bartnicki F., Pels K., Kowalska E.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

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nr 3

7

Conformational stability of six truncated cHMG1a proteins studied in their mixture by H-D exchange and electrospray ionization mass spectrometry

72%

Petry I., Wisniewski J. R., Szewczuk Z.

Acta Biochimica Polonica

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2001

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tom 48

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nr 4

The high mobility group (HMG) proteins are abundant non-histone components of eukaryotic chromatin. The presence of C-terminal acidic tails is a common feature of the majority of HMG proteins. Although the biological significance of the acidic domains is not clear, they are conferring conformational and metabolic stability to the proteins in vitro. Moreover, the length and net charge of the acidic tails affect the strength of HMG protein interaction with DNA. Synthesis of an insect HMG protein by standard recombinant technology in bacteria leads to a mixture of the intact protein (cHMG1a-(1-113) (I)) and a series of its degradation products truncated at the C tail: cHMGla-(l-lll) (II); cHMG1a-(1-110) (III); cHMG1a-(1-109) (IV); cHMG1a-(1-108) (V); cHMG1a-(1-107) (VI); cHMG1a-(1-106) (VII). The proteins differ from each other only by the number of amino-acid residues at the C-terminal tail. We used H/D exchange mass spectrometry to characterize the stability of the proteins directly in their mixture. The results show that the proteins I-V and VII have very similar conformations. The protein VI is less compact and exchanges its protons faster than the others. It may be concluded that the C-terminal tail influences the conformation of the cHMGla protein and that individual residues in this part of the protein play a key role in its compactness.

8

Using yeast two-hybrid system for identification of the proteins interacting with the product of a novel plant gene induced by sulphur deficiency stress

58%

Kaminska J., Lewandowska M., Wawrzynska A., Gaganidze D., Liszewska F., Sirko A.

Biological Letters

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2005

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tom 42

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nr 2 Spec.Vol.

9

Application of capillary electrophoresis for DNA-protein binding tests

58%

Kazmierczak A., Kazmierczak J. M.

Acta Physiologiae Plantarum

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2003

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tom 25

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nr 1

10

Bacterial DNA repair genes and their aukaryotic homologues: 1. Mutations in genes involved in base excision repair [BER] and DNA-end processors and their implication in mutagenesis and human disease

58%

Krwawicz J., Arczewska K. D., Speina E., Maciejewska A., Grzesiuk E.

Acta Biochimica Polonica

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2007

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tom 54

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nr 3

Base excision repair (BER) pathway executed by a complex network of proteins is the major system responsible for the removal of damaged DNA bases and repair of DNA single strand breaks (SSBs) generated by environmental agents, such as certain cancer therapies, or arising spontaneously during cellular metabolism. Both modified DNA bases and SSBs with ends other than 3'-OH and 5'-P are repaired either by replacement of a single or of more nucleotides in the processes called short-patch BER (SP-BER) or long-patch BER (LP-BER), respectively. In contrast to Escherichia coli cells, in human ones, the two BER sub-pathways are operated by different sets of proteins. In this review the selection between SP- and LP-BER and mutations in BER and end-processors genes and their contribution to bacterial mutagenesis and human diseases are considered.

11

Interakcja azotanow [III] z wybranymi polifenolami w procesie enzymatycznej hydrolizy bialka

44%

Pokorska-Lis G., Tokarz A., Sawicka J., Wiacek K.

Bromatologia i Chemia Toksykologiczna

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2005

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tom 38

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nr Supl.

165-170

W oparciu o proste modele enzymatycznego trawienia białka - kazeiny in vitro oznaczono stopień oddziaływania między wprowadzonymi do układu azotanami a wybranymi polifenolami. Aktywność polifenoli określano na podstawie ilości azotanów (III) i (V) przechodzących do dializatu. Stwierdzono, że interakcje polifenoli zachodzą głównie z azotanami (III).

Ograniczanie wyników

FunPred-1: Protein function prediction from a protein interaction network using neighborhood analysis

L1-ORF1p and Ago2 are involved in a siRNA-mediated regulation for promoter activity of L1-5’UTR

Structural determinants of cooperativity in acto-myosin interactions

Studies of HIV-Rev in living cells

The interactions between SATB1 and F-actin are important for mechanisms of active cell death

Identification of cell cycle proteins interacting with Arabidopsis thaliana proliferating cell nuclear antigen using bimolecular fluorescence complementation assay

Conformational stability of six truncated cHMG1a proteins studied in their mixture by H-D exchange and electrospray ionization mass spectrometry

Using yeast two-hybrid system for identification of the proteins interacting with the product of a novel plant gene induced by sulphur deficiency stress

Application of capillary electrophoresis for DNA-protein binding tests

Bacterial DNA repair genes and their aukaryotic homologues: 1. Mutations in genes involved in base excision repair [BER] and DNA-end processors and their implication in mutagenesis and human disease

Interakcja azotanow [III] z wybranymi polifenolami w procesie enzymatycznej hydrolizy bialka