• Title/Summary/Keyword: Protein motif

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Implementation of Protein Motif Prediction System Using integrated Motif Resources (모티프 자원 통합을 이용한 단백질 모티프 예측 시스템 구현)

  • Lee, Bum-Ju;Choi, Eun-Sun;Ryu, Keun-Ho
    • The KIPS Transactions:PartD
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    • v.10D no.4
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    • pp.679-688
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    • 2003
  • Motif databases are used in the function and structure prediction of proteins which appear on new and rapid release of raw data from genome sequencing projects. Recently, the frequency of use about these databases increases continuously. However, existing motif databases were developed and extended independently and were integrated mainly by using a web-based cross-reference, thus these databases have a heterogeneous search result problem, a complex query process problem and a duplicate database entry handling problem. Therefore, in this paper, we suppose physical motif resource integration and describe the integrated search method about a family-based protein prediction for solving above these problems. Finally, we estimate our implementation of the motif integration database and prediction system for predicting protein motifs.

MOTIF BASED PROTEIN FUNCTION ANALYSIS USING DATA MINING

  • Lee, Bum-Ju;Lee, Heon-Gyu;Ryu, Keun-Ho
    • Proceedings of the KSRS Conference
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    • v.2
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    • pp.812-815
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    • 2006
  • Proteins are essential agents for controlling, effecting and modulating cellular functions, and proteins with similar sequences have diverged from a common ancestral gene, and have similar structures and functions. Function prediction of unknown proteins remains one of the most challenging problems in bioinformatics. Recently, various computational approaches have been developed for identification of short sequences that are conserved within a family of closely related protein sequence. Protein function is often correlated with highly conserved motifs. Motif is the smallest unit of protein structure and function, and intends to make core part among protein structural and functional components. Therefore, prediction methods using data mining or machine learning have been developed. In this paper, we describe an approach for protein function prediction of motif-based models using data mining. Our work consists of three phrases. We make training and test data set and construct classifier using a training set. Also, through experiments, we evaluate our classifier with other classifiers in point of the accuracy of resulting classification.

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Protein Motif Extraction via Feature Interval Selection

  • Sohn, In-Suk;Hwang, Chang-Ha;Ko, Jun-Su;Chiu, David;Hong, Dug-Hun
    • Journal of the Korean Data and Information Science Society
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    • v.17 no.4
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    • pp.1279-1287
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    • 2006
  • The purpose of this paper is to present a new algorithm for extracting the consensus pattern, or motif from sequence belonging to the same family. Two methods are considered for feature interval partitioning based on equal probability and equal width interval partitioning. C2H2 zinc finger protein and epidermal growth factor protein sequences are used to demonstrate the effectiveness of the proposed algorithm for motif extraction. For two protein families, the equal width interval partitioning method performs better than the equal probability interval partitioning method.

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Novel TGACG-Motif Binding Protein of Soybean

  • Hong, Jong-Chan
    • Proceedings of the Botanical Society of Korea Conference
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    • 1996.07a
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    • pp.40-47
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    • 1996
  • The promoters of a variety of plant genes are characterized by the presence of TGACG motif-containing sequences. These genes often exhibit quite diverse expression characteristics and in many case the TGACG-motif has been demonstrated to be essential for expression. Here we report the isolation and characterization of a soybean cDNA that encodes a novel basic/leucine zipper (bZIP) protein, STF1, that specifically interacts with Hex (TGACGTGG) and CRE (TGACGTCA) sequences. This protein contains a bZIP motif at C-teminus and an acidic domain at N-terminus. DNA binding specificities, heterodimer formation, and expression characteristics of STF1 were compared with a soybean TGA1 protein, STGA1. The soybean STF1 interacts with TGACG-sequences containing an ACGT core, while STGA1 requires TGACG as a sufficient binding sequence. The flanking sequences to the TGACG motif affected DNA binding of STF1 siginificantly. The STF1 mRNA is found mainly in dark grown soybean seedling with higher expression in apical and elongating hypocotyl, while STGA1 mRNA is highly abundant in roots of light grown plants. Furthermore, we demonstrate that STF1 heterodimerzes with G-box binding factorss (GBFs) which was not observed with TGA1. The fact that STF1 possesses both distinct DNA binding speficities and heterodimerization properties suggest that STF1 belongs to a new family of plant bZIP proteins which recognize the Hex/CRE motif.

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The Ring-H2 Finger Motif of CKBBP1/SAG Is Necessary for Interaction with Protein Kinase CKII and Optimal Cell Proliferation

  • Kim, Yun-Sook;Ha, Kwon-Soo;Kim, Young-Ho;Bae, Young-Seuk
    • BMB Reports
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    • v.35 no.6
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    • pp.629-636
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    • 2002
  • Protein kinase CKII (CKII) is required for progression through the cell division cycle. We recently reported that the $\beta$ subunit of protein kinase CKII ($CKII{\beta}$) associates with CKBBP1 that contains the Ring-H2 finger motif in the yeast two-hybrid system. We demonstrate here that the Ring-H2 finger-disrupted mutant of CKBBP1 does not interact with purified $CKII{\beta}$ in vitro, which shows that the Ring-H2 finger motif is critical for direct interaction with $CKII{\beta}$. The CKII holoenzyme is efficiently co-precipitated with the wild-type CKBBP1, but not with the Ring-H2 finger-disrupted CKBBP1, from whole cell extracts when epitope-tagged CKBBP1 is transiently expressed in HeLa cells. Disruption of the Ring-H2 finger motif does not affect the cellular localization of CKBBP1 in HeLa cells. The increased expression of either the wild-type CKBBP1 or Ring-H2 finger-disrupted CKBBP1 does not modulate the protein or the activity levels of CKII in HeLa cells. However, the stable expression of Ring-H2 finger-disrupted CKBBP1 in HeLa cells suppresses cell proliferation and causes the accumulation of the G1/G0 peak of the cell cycle. The Ring-H2 finger motif is required for maximal CKBBP1 phosphorylation by CKII, suggesting that the stable binding of CKBBP1 to CKII is necessary for its efficient phosphorylation. Taken together, these results suggest that the complex formation of $CKII{\beta}$ with CKBBP1 and/or CKII-mediated CKBBP1 phosphorylation is important for the G1/S phase transition of the cell cycle.

Display of green fluorescent protein (GFP) on the cell surface of Zymomonas mobilis using N-terminal domain of ice nucleation protein (빙핵활성단백질의 N-terminal 부분을 이용한 녹색형광단백질의 Zymomonas mobilis 세포 표면 발현)

  • Lee, Eun-Mo;Choi, Shin-Geon
    • Journal of Industrial Technology
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    • v.29 no.B
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    • pp.115-119
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    • 2009
  • Green fluorescent protein (GFPuv) was displayed on the surface of ethanol-producing bacteria Zymomonas mobilis using N-terminal domain of ice nucleation protein (INP) as an anchoring motif. To evaluate the ice nucleation protein as plausible anchor motif in Z. mobilis, GFPuv gene was subcloned into Zymomonas expression vector yielding pBBR1MCS-3/pPDC/INPN/GFPuv plasmid., INP-GFPuv fusion protein was expressed in Z. mobilis and its fluorescence was verified by confocal microscopy. The successful display of GFPuv on Zymomonas mobilis suggest that INP anchor motif could be used for future fusion partner in Z. mobilis strain improvement.

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Structural Effects of the GXXXG Motif on the Oligomer Formation of Transmembrane Domain of Syndecan-4

  • Song, Jooyoung;Kim, Ji-Sun;Choi, Sung-Sub;Kim, Yongae
    • Bulletin of the Korean Chemical Society
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    • v.34 no.12
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    • pp.3577-3585
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    • 2013
  • Syndecan-4 (heparan sulfate proteoglycan), biologically important in cell-to-cell interactions and tumor suppression, was studied through mutation of the GXXXG motif of its transmembrane domain (Syd4-TM), a motif which governs dimerization. The expression and purification of the mutant (mSyd4-TM) were optimized here to assess the function of the GXXXG motif in the dimerization of Syd4-TM. mSyd4-TM was obtained in M9 minimal media and its oligomerization was identified by SDS PAGE, Circular Dichroism (CD) spectroscopy, mass spectrometry and NMR spectroscopy. The mutant, unlike Syd4-TM, did not form dimers and was observed as monomers. The GXXXG motif of Syd-4TM was shown to be an important structural determinant of its dimerization.

Regulation of amyloid precursor protein processing by its KFERQ motif

  • Park, Ji-Seon;Kim, Dong-Hou;Yoon, Seung-Yong
    • BMB Reports
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    • v.49 no.6
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    • pp.337-343
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    • 2016
  • Understanding of trafficking, processing, and degradation mechanisms of amyloid precursor protein (APP) is important because APP can be processed to produce β-amyloid (Aβ), a key pathogenic molecule in Alzheimer's disease (AD). Here, we found that APP contains KFERQ motif at its C-terminus, a consensus sequence for chaperone-mediated autophagy (CMA) or microautophagy which are another types of autophagy for degradation of pathogenic molecules in neurodegenerative diseases. Deletion of KFERQ in APP increased C-terminal fragments (CTFs) and secreted N-terminal fragments of APP and kept it away from lysosomes. KFERQ deletion did not abolish the interaction of APP or its cleaved products with heat shock cognate protein 70 (Hsc70), a protein necessary for CMA or microautophagy. These findings suggest that KFERQ motif is important for normal processing and degradation of APP to preclude the accumulation of APP-CTFs although it may not be important for CMA or microautophagy.

RTP1, a Rat Homologue of Adenovirus ElA-associated Protein BS69, Interacts with DNA Topoisomerase II

  • Oh, Misook;Rha, Geun-Bae;Yoon, Jeong-Ho;Sunwoo, Yang-Il;Hong, Seung-Hwan;Park, Sang-Dai
    • Animal cells and systems
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    • v.6 no.3
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    • pp.277-282
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    • 2002
  • Topoisomearse II is an essential enzyme in all organisms with several independent roles in DNA metabolism. Recently, it has been demonstrated that the C-terminal region of topoisomerases II is associated with hetero-logous protein-protein interactions in human and yeast. In this study, we identified that RTP1, a rat homologue of EIA binding protein BS69, is another topoisomerae II interacting protein by yeast two-hybrid screening. RTP1 has an E1A-binding domain and a MYND motif, which are known to be required for transcriptional regulation by binding to other proteins and interaction with the leucine zipper motif of topoisomerase II. The physical interaction between RTP1 and topoisomerase ll$\alpha$ was examined by GST pull-down assay in vitro. The expression level of RTP1 peaks in S phase as that of topoisomerase ll$\alpha$. These results suggest that the interaction between topoisomerase ll$\alpha$ and RTP1 might play an important role in regulating the transcription of genes involved in DNA metabolism in higher eukaryotes.

A Big Data Based Random Motif Frequency Method for Analyzing Human Proteins (인간 단백질 분석을 위한 빅 데이타 기반 RMF 방법)

  • Kim, Eun-Mi;Jeong, Jong-Cheol;Lee, Bae-Ho
    • The Journal of the Korea institute of electronic communication sciences
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    • v.13 no.6
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    • pp.1397-1404
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    • 2018
  • Due to the technical difficulties and high cost for obtaining 3-dimensional structure data, sequence-based approaches in proteins have not been widely acknowledged. A motif can be defined as any segments in protein or gene sequences. With this simplicity, motifs have been actively and widely used in various areas. However, the motif itself has not been studied comprehensively. The value of this study can be categorized in three fields in order to analyze the human proteins using artificial intelligence method: (1) Based on our best knowledge, this research is the first comprehensive motif analysis by analyzing motifs with all human proteins in Protein Data Bank (PDB) associated with the database of Enzyme Commission (EC) number and Structural Classification of Proteins (SCOP). (2) We deeply analyze the motif in three different categories: pattern, statistical, and functional analysis of clusters. (3) At the last and most importantly, we proposed random motif frequency(RMF) matric that can efficiently distinct the characteristics of proteins by identifying interface residues from non-interface residues and clustering protein functions based on big data while varying the size of random motif.