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完整後設資料紀錄
DC 欄位值語言
dc.contributor.advisor楊健志zh_TW
dc.contributor.advisorChien-Chih Yangen
dc.contributor.author古小波zh_TW
dc.contributor.authorHsiao-Po Kuen
dc.date.accessioned2024-08-20T16:21:56Z-
dc.date.available2024-08-21-
dc.date.copyright2024-08-20-
dc.date.issued2024-
dc.date.submitted2024-08-06-
dc.identifier.citationAibara, S., Bai, X.-C., Stewart, M. (2016) The Sac3 TPR-like region in the Saccharomyces cerevisiae TREX-2 complex is more extensive but independent of the CID region. Journal of structural biology, 195(3), 316-324.
Akbari Rokn Abadi, S., Abdosalehi, A.S., Pouyamehr, F., Koohi, S. (2022) An accurate alignment-free protein sequence comparator based on physicochemical properties of amino acids. Scientific Reports, 12(1), 11158.
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research, 25(17), 3389-3402.
Bergmann, D.C. and Sack, F.D. (2007) Stomatal development. Annu. Rev. Plant Biol., 58, 163-181.
Berk, J.M., Simon, D.N., Jenkins-Houk, C.R., Westerbeck, J.W., Grønning-Wang, L.M., Carlson, C.R., Wilson, K.L. (2014) The molecular basis of emerin–emerin and emerin–BAF interactions. Journal of Cell Science, 127(18), 3956-3969.
Bernard, G., Chan, C.X., Ragan, M.A. (2016) Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer. Scientific Reports, 6(1), 28970.
Boesch, C., Bundi, A., Oppliger, M., WüTHRICH, K. (1978) 1H nuclear‐magnetic‐resonance studies of the molecular conformation of monomeric glucagon in aqueous solution. European journal of biochemistry, 91(1), 209-214.
Bonham-Carter, O., Steele, J., Bastola, D. (2014) Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. Briefings in bioinformatics, 15(6), 890-905.
Borgia, A., Borgia, M.B., Bugge, K., Kissling, V.M., Heidarsson, P.O., Fernandes, C.B., Sottini, A., Soranno, A., Buholzer, K.J., Nettels, D. (2018) Extreme disorder in an ultrahigh-affinity protein complex. Nature, 555(7694), 61-66.
Brady, J.P., Farber, P.J., Sekhar, A., Lin, Y.-H., Huang, R., Bah, A., Nott, T.J., Chan, H.S., Baldwin, A.J., Forman-Kay, J.D. (2017) Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation. Proceedings of the National Academy of Sciences, 114(39), E8194-E8203.
Brangwynne, C.P., Tompa, P., Pappu, R.V. (2015) Polymer physics of intracellular phase transitions. Nature Physics, 11(11), 899-904.
Cai, M., Huang, Y., Ghirlando, R., Wilson, K.L., Craigie, R., Clore, G.M. (2001) Solution structure of the constant region of nuclear envelope protein LAP2 reveals two LEM‐domain structures: one binds BAF and the other binds DNA. The EMBO journal.
Cermakova, K. and Hodges, H.C. (2023) Interaction modules that impart specificity to disordered protein. Trends in biochemical sciences.
Chinnusamy, V., Ohta, M., Kanrar, S., Lee, B.-h., Hong, X., Agarwal, M., Zhu, J.-K. (2003) ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes & development, 17(8), 1043-1054.
Clarke, L. and Carbon, J. (1980) Isolation of a yeast centromere and construction of functional small circular chromosomes. Nature, 287(5782), 504-509.
Crane-Robinson, C., Dragan, A.I., Privalov, P.L. (2006) The extended arms of DNA-binding domains: a tale of tails. Trends in biochemical sciences, 31(10), 547-552.
Davey, N.E. (2019) The functional importance of structure in unstructured protein regions. Current opinion in structural biology, 56, 155-163.
Davey, N.E., Cowan, J.L., Shields, D.C., Gibson, T.J., Coldwell, M.J., Edwards, R.J. (2012a) SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic acids research, 40(21), 10628-10641.
Davey, N.E., Van Roey, K., Weatheritt, R.J., Toedt, G., Uyar, B., Altenberg, B., Budd, A., Diella, F., Dinkel, H., Gibson, T.J. (2012b) Attributes of short linear motifs. Molecular BioSystems, 8(1), 268-281.
Davies, M.N., Secker, A., Freitas, A.A., Timmis, J., Clark, E., Flower, D.R. (2008) Alignment-independent techniques for protein classification. Current Proteomics, 5(4), 217-223.
Del Conte, A., Bouhraoua, A., Mehdiabadi, M., Clementel, D., Monzon, A.M., Tosatto, S.C., Piovesan, D. (2023) CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic acids research, gkad430.
Deng, C., Ye, H., Fan, M., Pu, T., Yan, J. (2017) The rice transcription factors OsICE confer enhanced cold tolerance in transgenic Arabidopsis. Plant Signaling & Behavior, 12(5), e1316442.
Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N.P., Trave, G., Gibson, T.J. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Frontiers in Bioscience-Landmark, 13(17), 6580-6603.
Ding, Y., Li, H., Zhang, X., Xie, Q., Gong, Z., Yang, S. (2015) OST1 kinase modulates freezing tolerance by enhancing ICE1 stability in Arabidopsis. Developmental cell, 32(3), 278-289.
Donaldson, L.W., Gish, G., Pawson, T., Kay, L.E., Forman-Kay, J.D. (2002) Structure of a regulatory complex involving the Abl SH3 domain, the Crk SH2 domain, and a Crk-derived phosphopeptide. Proceedings of the National Academy of Sciences, 99(22), 14053-14058.
Dong, C.-H., Agarwal, M., Zhang, Y., Xie, Q., Zhu, J.-K. (2006) The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proceedings of the National Academy of Sciences, 103(21), 8281-8286.
Dosztanyi, Z., Csizmok, V., Tompa, P., Simon, I. (2005) The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. Journal of molecular biology, 347(4), 827-839.
Dosztányi, Z., Csizmok, V., Tompa, P., Simon, I. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21(16), 3433-3434.
Duffy, S., Shackelton, L.A., Holmes, E.C. (2008) Rates of evolutionary change in viruses: patterns and determinants. Nature Reviews Genetics, 9(4), 267-276.
Dunker, A.K., Brown, C.J., Lawson, J.D., Iakoucheva, L.M., Obradović, Z. (2002) Intrinsic disorder and protein function. Biochemistry, 41(21), 6573-6582.
Dunker, A.K., Oldfield, C.J., Meng, J., Romero, P., Yang, J.Y., Chen, J.W., Vacic, V., Obradovic, Z., Uversky, V.N. (2008) The unfoldomics decade: an update on intrinsically disordered proteins. BMC genomics, 9(2), 1-26.
Dyson, H.J. (2011) Expanding the proteome: disordered and alternatively folded proteins. Quarterly reviews of biophysics, 44(4), 467-518.
Dyson, H.J. and Wright, P.E. (2002) Coupling of folding and binding for unstructured proteins. Current opinion in structural biology, 12(1), 54-60.
Dyson, H.J. and Wright, P.E. (2005) Intrinsically unstructured proteins and their functions. Nature reviews Molecular cell biology, 6(3), 197-208.
Earl, D., Nguyen, N., Hickey, G., Harris, R.S., Fitzgerald, S., Beal, K., Seledtsov, I., Molodtsov, V., Raney, B.J., Clawson, H. (2014) Alignathon: a competitive assessment of whole-genome alignment methods. Genome research, 24(12), 2077-2089.
Eddy, S.R. (2004) What is dynamic programming? Nature biotechnology, 22(7), 909-910.
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32(5), 1792-1797.
Fernandez, A., Bautista, M., Wu, L., Pinaud, F. (2022) Emerin self-assembly and nucleoskeletal coupling regulate nuclear envelope mechanics against stress. Journal of Cell Science, 135(6), jcs258969.
Fischer, T., Sträßer, K., Rácz, A., Rodriguez‐Navarro, S., Oppizzi, M., Ihrig, P., Lechner, J., Hurt, E. (2002) The mRNA export machinery requires the novel Sac3p–Thp1p complex to dock at the nucleoplasmic entrance of the nuclear pores. The EMBO journal.
Fonin, A.V., Antifeeva, I.A., Kuznetsova, I.M., Turoverov, K.K., Zaslavsky, B.Y., Kulkarni, P., Uversky, V.N. (2022) Biological soft matter: intrinsically disordered proteins in liquid–liquid phase separation and biomolecular condensates. Essays in Biochemistry, 66(7), 831-847.
Fuxreiter, M., Tompa, P., Simon, I. (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics, 23(8), 950-956.
Galea, C.A., Wang, Y., Sivakolundu, S.G., Kriwacki, R.W. (2008) Regulation of cell division by intrinsically unstructured proteins: intrinsic flexibility, modularity, and signaling conduits. Biochemistry, 47(29), 7598-7609.
Go, Y.-M. and Jones, D.P. (2010) Redox control systems in the nucleus: mechanisms and functions. Antioxidants & redox signaling, 13(4), 489-509.
Han, K.-K. and Martinage, A. (1993) Post-translational chemical modifications of proteins—III. Current developments in analytical procedures of identification and quantitation of post-translational chemically modified amino acid (s) and its derivatives. International journal of biochemistry, 25(7), 957-970.
Han, S.-K., Qi, X., Sugihara, K., Dang, J.H., Endo, T.A., Miller, K.L., Kim, E.-D., Miura, T., Torii, K.U. (2018) MUTE directly orchestrates cell-state switch and the single symmetric division to create stomata. Developmental cell, 45(3), 303-315. e305.
Hao, Y., Zong, X., Ren, P., Qian, Y., Fu, A. (2021) Basic Helix-Loop-Helix (bHLH) transcription factors regulate a wide range of functions in Arabidopsis. International Journal of Molecular Sciences, 22(13), 7152.
Hatos, A., Hajdu-Soltész, B., Monzon, A.M., Palopoli, N., Álvarez, L., Aykac-Fas, B., Bassot, C., Benítez, G.I., Bevilacqua, M., Chasapi, A. (2020) DisProt: intrinsic protein disorder annotation in 2020. Nucleic acids research, 48(D1), D269-D276.
Herrada, I., Samson, C., Velours, C., Renault, L., Östlund, C., Chervy, P., Puchkov, D., Worman, H.J., Buendia, B., Zinn-Justin, S. (2015a) Muscular Dystrophy Mutations Impair the Nuclear Envelope Emerin Self-assembly Properties. ACS chemical biology, 10(12), 2733-2742.
Herrada, I., Samson, C., Velours, C., Renault, L., Östlund, C., Chervy, P., Puchkov, D., Worman, H.J., Buendia, B., Zinn-Justin, S. (2015b) Muscular dystrophy mutations impair the nuclear envelope emerin self-assembly properties. ACS chemical biology, 10(12), 2733-2742.
Ho, W.L., Huang, H.C., Huang, J.r. (2023) IFF: Identifying key residues in intrinsically disordered regions of proteins using machine learning. Protein Science, 32(9), e4739.
Holt, L.J., Tuch, B.B., Villén, J., Johnson, A.D., Gygi, S.P., Morgan, D.O. (2009) Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science, 325(5948), 1682-1686.
Hu, Y., Jiang, L., Wang, F., Yu, D. (2013) Jasmonate regulates the inducer of CBF expression–c-repeat binding factor/DRE binding factor1 cascade and freezing tolerance in Arabidopsis. The Plant Cell, 25(8), 2907-2924.
Huang, D.-B., Huxford, T., Chen, Y.-Q., Ghosh, G. (1997) The role of DNA in the mechanism of NFκB dimer formation: crystal structures of the dimerization domains of the p50 and p65 subunits. Structure, 5(11), 1427-1436.
Jun, S.-R., Sims, G.E., Wu, G.A., Kim, S.-H. (2010) Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. Proceedings of the National Academy of Sciences, 107(1), 133-138.
Köhler, A. and Hurt, E. (2007) Exporting RNA from the nucleus to the cytoplasm. Nature reviews Molecular cell biology, 8(10), 761-773.
Kanaoka, M.M., Pillitteri, L.J., Fujii, H., Yoshida, Y., Bogenschutz, N.L., Takabayashi, J., Zhu, J.-K., Torii, K.U. (2008) SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to Arabidopsis stomatal differentiation. The Plant Cell, 20(7), 1775-1785.
Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., Kanehisa, M. (2007) AAindex: amino acid index database, progress report 2008. Nucleic acids research, 36(suppl_1), D202-D205.
Kendrew, J.C., Bodo, G., Dintzis, H.M., Parrish, R., Wyckoff, H., Phillips, D.C. (1958) A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature, 181(4610), 662-666.
Kidokoro, S., Kim, J.-S., Ishikawa, T., Suzuki, T., Shinozaki, K., Yamaguchi-Shinozaki, K. (2020) DREB1A/CBF3 is repressed by transgene-induced DNA methylation in the Arabidopsis ice1-1 mutant. The Plant Cell, 32(4), 1035-1048.
Kim, D.-H. and Han, K.-H. (2018) PreSMo target-binding signatures in intrinsically disordered proteins. Molecules and Cells, 41(10), 889.
Kim, J.-S., Kidokoro, S., Shinozaki, K., Yamaguchi-Shinozaki, K. (2020) DNA demethylase ROS1 prevents inheritable DREB1A/CBF3 repression by transgene-induced promoter methylation in the Arabidopsis ice1-1 mutant. Plant molecular biology, 104(6), 575-582.
Kumar, M., Gouw, M., Michael, S., Sámano-Sánchez, H., Pancsa, R., Glavina, J., Diakogianni, A., Valverde, J.A., Bukirova, D., Čalyševa, J. (2020) ELM—the eukaryotic linear motif resource in 2020. Nucleic acids research, 48(D1), D296-D306.
Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. Journal of molecular biology, 157(1), 105-132.
Lee, B.-h., Henderson, D.A., Zhu, J.-K. (2005) The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. The Plant Cell, 17(11), 3155-3175.
Lee, J.H., Jung, J.H., Park, C.M. (2015) INDUCER OF CBF EXPRESSION 1 integrates cold signals into FLOWERING LOCUS C‐mediated flowering pathways in Arabidopsis. The Plant Journal, 84(1), 29-40.
Lee, K.K., Haraguchi, T., Lee, R.S., Koujin, T., Hiraoka, Y., Wilson, K.L. (2001) Distinct functional domains in emerin bind lamin A and DNA-bridging protein BAF. Journal of Cell Science, 114(24), 4567-4573.
Lee, S.-H., Kim, D.-H., J Han, J., Cha, E.-J., Lim, J.-E., Cho, Y.-J., Lee, C., Han, K.-H. (2012) Understanding pre-structured motifs (PreSMos) in intrinsically unfolded proteins. Current Protein and Peptide Science, 13(1), 34-54.
Li, H., Ding, Y., Shi, Y., Zhang, X., Zhang, S., Gong, Z., Yang, S. (2017) MPK3-and MPK6-mediated ICE1 phosphorylation negatively regulates ICE1 stability and freezing tolerance in Arabidopsis. Developmental cell, 43(5), 630-642. e634.
Li, M. and Vitányi, P. (2008) An introduction to Kolmogorov complexity and its applications Springer.
Liang, C.-H. and Yang, C.-C. (2015) Identification of ICE1 as a negative regulator of ABA-dependent pathways in seeds and seedlings of Arabidopsis. Plant molecular biology, 88, 459-470.
Liu, J., Perumal, N.B., Oldfield, C.J., Su, E.W., Uversky, V.N., Dunker, A.K. (2006) Intrinsic disorder in transcription factors. Biochemistry, 45(22), 6873-6888.
Liu, Y., Wang, X., Liu, B. (2019) A comprehensive review and comparison of existing computational methods for intrinsically disordered protein and region prediction. Briefings in bioinformatics, 20(1), 330-346.
London, N., Movshovitz-Attias, D., Schueler-Furman, O. (2010) The structural basis of peptide-protein binding strategies. Structure, 18(2), 188-199.
Longbotham, J.E., Chio, C.M., Dharmarajan, V., Trnka, M.J., Torres, I.O., Goswami, D., Ruiz, K., Burlingame, A.L., Griffin, P.R., Fujimori, D.G. (2019) Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling. Nature communications, 10(1), 94.
Longbotham, J.E., Kelly, M.J., Fujimori, D.G. (2021) Recognition of histone H3 methylation states by the PHD1 domain of histone demethylase KDM5A. ACS chemical biology, 18(9), 1915-1925.
Lopez-Anido, C.B., Vatén, A., Smoot, N.K., Sharma, N., Guo, V., Gong, Y., Gil, M.X.A., Weimer, A.K., Bergmann, D.C. (2021) Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf. Developmental cell, 56(7), 1043-1055. e1044.
Lyons, H., Veettil, R.T., Pradhan, P., Fornero, C., De La Cruz, N., Ito, K., Eppert, M., Roeder, R.G., Sabari, B.R. (2023) Functional partitioning of transcriptional regulators by patterned charge blocks. Cell, 186(2), 327-345. e328.
Mészáros, B., Dosztányi, Z., Simon, I. (2012) Disordered binding regions and linear motifs—bridging the gap between two models of molecular recognition.
MacAlister, C.A., Ohashi-Ito, K., Bergmann, D.C. (2007) Transcription factor control of asymmetric cell divisions that establish the stomatal lineage. Nature, 445(7127), 537-540.
Miura, K., Jin, J.B., Lee, J., Yoo, C.Y., Stirm, V., Miura, T., Ashworth, E.N., Bressan, R.A., Yun, D.-J., Hasegawa, P.M. (2007) SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis. The Plant Cell, 19(4), 1403-1414.
Miura, K., Ohta, M., Nakazawa, M., Ono, M., Hasegawa, P.M. (2011) ICE1 Ser403 is necessary for protein stabilization and regulation of cold signaling and tolerance. The Plant Journal, 67(2), 269-279.
Miura, K., Shiba, H., Ohta, M., Kang, S.W., Sato, A., Yuasa, T., Iwaya-Inoue, M., Kamada, H., Ezura, H. (2012) SlICE1 encoding a MYC-type transcription factor controls cold tolerance in tomato, Solanum lycopersicum. Plant Biotechnology, 29(3), 253-260.
Már, M., Nitsenko, K., Heidarsson, P.O. (2023) Multifunctional intrinsically disordered regions in transcription factors. Chemistry–A European Journal, 29(21), e202203369.
Moesa, H.A., Wakabayashi, S., Nakai, K., Patil, A. (2012) Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification. Molecular BioSystems, 8(12), 3262-3273.
Mohan, A., Oldfield, C.J., Radivojac, P., Vacic, V., Cortese, M.S., Dunker, A.K., Uversky, V.N. (2006) Analysis of molecular recognition features (MoRFs). Journal of molecular biology, 362(5), 1043-1059.
Monahan, Z., Ryan, V.H., Janke, A.M., Burke, K.A., Rhoads, S.N., Zerze, G.H., O'Meally, R., Dignon, G.L., Conicella, A.E., Zheng, W. (2017) Phosphorylation of the FUS low‐complexity domain disrupts phase separation, aggregation, and toxicity. The EMBO journal, 36(20), 2951-2967.
Morgenstern, B. and Atchley, W.R. (1999) Evolution of bHLH transcription factors: modular evolution by domain shuffling? Molecular biology and evolution, 16(12), 1654-1663.
Motlagh, H.N., Wrabl, J.O., Li, J., Hilser, V.J. (2014) The ensemble nature of allostery. Nature, 508(7496), 331-339.
Mu, Z., Yu, T., Qi, E., Liu, J., Li, G. (2019) DCGR: feature extractions from protein sequences based on CGR via remodeling multiple information. BMC bioinformatics, 20(1), 1-10.
Nadeau, J.A. and Sack, F.D. (2002) Stomatal development in Arabidopsis. The Arabidopsis book/American Society of Plant Biologists, 1.
Nilsson, J., Grahn, M., Wright, A.P. (2011) Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins. Genome Biology, 12(7), 1-17.
Oates, M.E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M.J., Xue, B., Dosztányi, Z., Uversky, V.N., Obradovic, Z., Kurgan, L. (2012) D2P2: database of disordered protein predictions. Nucleic acids research, 41(D1), D508-D516.
Ohashi-Ito, K. and Bergmann, D.C. (2006) Arabidopsis FAMA controls the final proliferation/differentiation switch during stomatal development. The Plant Cell, 18(10), 2493-2505.
Panova, S., Cliff, M.J., Macek, P., Blackledge, M., Jensen, M.R., Nissink, J.W.M., Embrey, K.J., Davies, R., Waltho, J.P. (2019) Mapping hidden residual structure within the Myc bHLH-LZ domain using chemical denaturant titration. Structure, 27(10), 1537-1546. e1534.
Peng, Z., Yan, J., Fan, X., Mizianty, M.J., Xue, B., Wang, K., Hu, G., Uversky, V.N., Kurgan, L. (2015) Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life. Cellular and Molecular Life Sciences, 72, 137-151.
Pentony, M.M. and Jones, D.T. (2010) Modularity of intrinsic disorder in the human proteome. Proteins: Structure, Function, and Bioinformatics, 78(1), 212-221.
Perriches, T. and Singleton, M.R. (2012) Structure of yeast kinetochore Ndc10 DNA-binding domain reveals unexpected evolutionary relationship to tyrosine recombinases. Journal of Biological Chemistry, 287(7), 5173-5179.
Pillitteri, L.J., Sloan, D.B., Bogenschutz, N.L., Torii, K.U. (2007) Termination of asymmetric cell division and differentiation of stomata. Nature, 445(7127), 501-505.
Piovesan, D., Del Conte, A., Clementel, D., Monzon, A.M., Bevilacqua, M., Aspromonte, M.C., Iserte, J.A., Orti, F.E., Marino-Buslje, C., Tosatto, S.C. (2023) MobiDB: 10 years of intrinsically disordered proteins. Nucleic acids research, 51(D1), D438-D444.
Piovesan, D., Tabaro, F., Mičetić, I., Necci, M., Quaglia, F., Oldfield, C.J., Aspromonte, M.C., Davey, N.E., Davidović, R., Dosztányi, Z. (2017) DisProt 7.0: a major update of the database of disordered proteins. Nucleic acids research, 45(D1), D219-D227.
Potenza, E., Domenico, T.D., Walsh, I., Tosatto, S.C. (2015) MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins. Nucleic acids research, 43(D1), D315-D320.
Prilusky, J., Felder, C.E., Zeev-Ben-Mordehai, T., Rydberg, E.H., Man, O., Beckmann, J.S., Silman, I., Sussman, J.L. (2005) FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics, 21(16), 3435-3438.
Putarjunan, A., Ruble, J., Srivastava, A., Zhao, C., Rychel, A.L., Hofstetter, A.K., Tang, X., Zhu, J.-K., Tama, F., Zheng, N. (2019) Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP kinases to SPEECHLESS. Nature plants, 5(7), 742-754.
Quaglia, F., Mészáros, B., Salladini, E., Hatos, A., Pancsa, R., Chemes, L.B., Pajkos, M., Lazar, T., Peña-Díaz, S., Santos, J. (2022) DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic acids research, 50(D1), D480-D487.
Remaut, H. and Waksman, G. (2006) Protein–protein interaction through β-strand addition. Trends in biochemical sciences, 31(8), 436-444.
Riley, A.C., Ashlock, D.A., Graether, S.P. (2023) The difficulty of aligning intrinsically disordered protein sequences as assessed by conservation and phylogeny. PloS one, 18(7), e0288388.
Romero, P., Obradovic, Z., Kissinger, C., Villafranca, J., Dunker, A.K. (1997) Identifying disordered regions in proteins from amino acid sequence. In Proceedings of International Conference on Neural Networks (ICNN'97), IEEE: pp 90-95.
Romero, P., Obradovic, Z., Li, X., Garner, E.C., Brown, C.J., Dunker, A.K. (2001) Sequence complexity of disordered protein. Proteins: Structure, Function, and Bioinformatics, 42(1), 38-48.
Sakaki, M., Koike, H., Takahashi, N., Sasagawa, N., Tomioka, S., Arahata, K., Ishiura, S. (2001) Interaction between emerin and nuclear lamins. The Journal of Biochemistry, 129(2), 321-327.
Samson, C., Herrada, I., Celli, F., Theillet, F.-X., Zinn-Justin, S. (2016) 1 H, 13 C and 15 N backbone resonance assignment of the intrinsically disordered region of the nuclear envelope protein emerin. Biomolecular NMR assignments, 10, 179-182.
Saw, A.K., Tripathy, B.C., Nandi, S. (2019) Alignment-free similarity analysis for protein sequences based on fuzzy integral. Scientific Reports, 9(1), 2775.
Schad, E., Fichó, E., Pancsa, R., Simon, I., Dosztányi, Z., Mészáros, B. (2017) DIBS: a repository of disordered binding sites mediating interactions with ordered proteins. Bioinformatics, 34(3), 535-537.
Schwabe, J.W., Chapman, L., Finch, J.T., Rhodes, D., Neuhaus, D. (1993) DNA recognition by the oestrogen receptor: from solution to the crystal. Structure, 1(3), 187-204.
Seo, H., Sepuru, K.M., Putarjunan, A., Aguirre, L., Burrows, B.A., Torii, K.U. (2022) Intragenic suppressors unravel the role of the SCREAM ACT-like domain for bHLH partner selectivity in stomatal development. Proceedings of the National Academy of Sciences, 119(9), e2117774119.
Sicoli, G., Kress, T., Vezin, H., Ledolter, K., Kurzbach, D. (2020) A Switch between Two Intrinsically Disordered Conformational Ensembles Modulates the Active Site of a Basic-Helix–Loop–Helix Transcription Factor. The Journal of Physical Chemistry Letters, 11(21), 8944-8951.
Siebenlist, U., Franzoso, G., Brown, K. (1994) Structure, regulation and function of NF-kappaB. Annual review of cell biology, 10(1), 405-455.
Song, N., Joseph, J.M., Davis, G.B., Durand, D. (2008) Sequence similarity network reveals common ancestry of multidomain proteins. PLoS computational biology, 4(5), e1000063.
Stein, A. and Aloy, P. (2008) Contextual specificity in peptide-mediated protein interactions. PloS one, 3(7), e2524.
Tanabe, N., Noshi, M., Mori, D., Nozawa, K., Tamoi, M., Shigeoka, S. (2019) The basic helix-loop-helix transcription factor, bHLH11 functions in the iron-uptake system in Arabidopsis thaliana. Journal of plant research, 132, 93-105.
Taneja, I. and Holehouse, A.S. (2021) Folded domain charge properties influence the conformational behavior of disordered tails. Current Research in Structural Biology, 3, 216-228.
Terrapon, N., Weiner, J., Grath, S., Moore, A.D., Bornberg-Bauer, E. (2014) Rapid similarity search of proteins using alignments of domain arrangements. Bioinformatics, 30(2), 274-281.
Thomashow, M.F. and Torii, K.U. (2020) SCREAMing twist on the role of ICE1 in freezing tolerance, American Society of Plant Biologists.
Thompson, J.D., Higgins, D.G., Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research, 22(22), 4673-4680.
Toledo-Ortiz, G., Huq, E., Quail, P.H. (2003) The Arabidopsis basic/helix-loop-helix transcription factor family. The Plant Cell, 15(8), 1749-1770.
Tompa, P. (2002) Intrinsically unstructured proteins. Trends in biochemical sciences, 27(10), 527-533.
Tompa, P. (2005) The interplay between structure and function in intrinsically unstructured proteins. FEBS letters, 579(15), 3346-3354.
Tompa, P. and Fuxreiter, M. (2008) Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions. Trends in biochemical sciences, 33(1), 2-8.
Tompa, P., Fuxreiter, M., Oldfield, C.J., Simon, I., Dunker, A.K., Uversky, V.N. (2009) Close encounters of the third kind: disordered domains and the interactions of proteins. Bioessays, 31(3), 328-335.
Uversky, V.N., Gillespie, J.R., Fink, A.L. (2000) Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins: Structure, Function, and Bioinformatics, 41(3), 415-427.
Van Der Lee, R., Buljan, M., Lang, B., Weatheritt, R.J., Daughdrill, G.W., Dunker, A.K., Fuxreiter, M., Gough, J., Gsponer, J., Jones, D.T. (2014) Classification of intrinsically disordered regions and proteins. Chemical reviews, 114(13), 6589-6631.
Van Hoy, M., Leuther, K.K., Kodadek, T., Johnston, S.A. (1993) The acidic activation domains of the GCN4 and GAL4 proteins are not α helical but form β sheets. Cell, 72(4), 587-594.
Van Roey, K., Gibson, T.J., Davey, N.E. (2012) Motif switches: decision-making in cell regulation. Current opinion in structural biology, 22(3), 378-385.
Van Roey, K., Uyar, B., Weatheritt, R.J., Dinkel, H., Seiler, M., Budd, A., Gibson, T.J., Davey, N.E. (2014) Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation. Chemical reviews, 114(13), 6733-6778.
Vinga, S. (2014) Alignment-free methods in computational biology, Oxford University Press: pp 341-342.
Vinogradova, M., Gehling, V.S., Gustafson, A., Arora, S., Tindell, C.A., Wilson, C., Williamson, K.E., Guler, G.D., Gangurde, P., Manieri, W. (2016) An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells. Nature chemical biology, 12(7), 531-538.
Wei, D., Liu, M., Chen, H., Zheng, Y., Liu, Y., Wang, X., Yang, S., Zhou, M., Lin, J. (2018) INDUCER OF CBF EXPRESSION 1 is a male fertility regulator impacting anther dehydration in Arabidopsis. PLoS genetics, 14(10), e1007695.
Wright, P.E. and Dyson, H.J. (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. Journal of molecular biology, 293(2), 321-331.
Wright, P.E. and Dyson, H.J. (2015) Intrinsically disordered proteins in cellular signalling and regulation. Nature reviews Molecular cell biology, 16(1), 18-29.
Wu, C.-L., Lin, L.-F., Hsu, H.-C., Huang, L.-F., Hsiao, C.-D., Chou, M.-L. (2021) Saussurea involucrata (Snow Lotus) ICE1 and ICE2 orthologues involved in regulating cold stress tolerance in transgenic Arabidopsis. International Journal of Molecular Sciences, 22(19), 10850.
Xiong, J. (2006) Essential bioinformatics Cambridge University Press.
Xu, J. and Zhang, S. (2015) Mitogen-activated protein kinase cascades in signaling plant growth and development. Trends in Plant Science, 20(1), 56-64.
Xu, W., Jiao, Y., Li, R., Zhang, N., Xiao, D., Ding, X., Wang, Z. (2014) Chinese wild-growing Vitis amurensis ICE1 and ICE2 encode MYC-type bHLH transcription activators that regulate cold tolerance in Arabidopsis. PloS one, 9(7), e102303.
Xue, B., Dunker, A.K., Uversky, V.N. (2012) Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life. Journal of Biomolecular Structure and Dynamics, 30(2), 137-149.
Yu, L., Zhang, Y., Gutman, I., Shi, Y., Dehmer, M. (2017) Protein sequence comparison based on physicochemical properties and the position-feature energy matrix. Scientific Reports, 7(1), 46237.
Zhang, X., Tanaka, K., Yan, J., Li, J., Peng, D., Jiang, Y., Yang, Z., Barton, M.C., Wen, H., Shi, X. (2013) Regulation of estrogen receptor α by histone methyltransferase SMYD2-mediated protein methylation. Proceedings of the National Academy of Sciences, 110(43), 17284-17289.
Zhang, Y., Li, Z., Sacks, D.B., Ames, J.B. (2012) Structural Basis for Ca2+-induced Activation and Dimerization of Estrogen Receptor α by Calmodulin. Journal of Biological Chemistry, 287(12), 9336-9344.
Zhang, Y., Zhang, M., Hu, H., Yang, J., Cui, J., Xu, J. (2021) Cloning and cold-resistance analyses of CfICE1 gene in Cryptomeria fortunei. Plant Physiology and Biochemistry, 162, 456-467.
Zhao, C., Wang, P., Si, T., Hsu, C.-C., Wang, L., Zayed, O., Yu, Z., Zhu, Y., Dong, J., Tao, W.A. (2017) MAP kinase cascades regulate the cold response by modulating ICE1 protein stability. Developmental cell, 43(5), 618-629. e615.
Zhou, J., Oldfield, C.J., Yan, W., Shen, B., Dunker, A.K. (2019) Intrinsically disordered domains: Sequence➔ disorder➔ function relationships. Protein Science, 28(9), 1652-1663.
Zielezinski, A., Vinga, S., Almeida, J., Karlowski, W.M. (2017) Alignment-free sequence comparison: benefits, applications, and tools. Genome Biology, 18(1), 186.
Zielinska, D.F., Gnad, F., Schropp, K., Wiśniewski, J.R., Mann, M. (2012) Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery. Molecular cell, 46(4), 542-548.
-
dc.identifier.urihttp://tdr.lib.ntu.edu.tw/jspui/handle/123456789/94879-
dc.description.abstractICE1 (Inducer of CBF Expression 1) 為阿拉伯芥轉錄因子中的鹼性螺旋-環-螺旋 (basic helix-loop-helix , bHLH) 家族的一員,參與許多不同植物逆境反應與生長調控機制。AtICE1共有494個胺基酸,除了bHLH (300-365 a.a.) 和ACTL (405-494 a.a.) 具有可摺疊構造, 其餘約 70% 的序列被預測為本質無序區域 (intrinsically disorder regions, IDRs),這些區域多由親水性或極性的胺基酸組成,其在分子層次的功能仍不確定。根據IDRs的胺基酸組成特性,許多序列分析方法被開發出來以預測特性區域的存在或其功能。具有摺疊結構的蛋白,其結構可以與其序列密切相關,所以可以以對齊序列比較法 (Alignment-based sequence comparison) 找尋到類似構造或功能的蛋白質,然而,對於保守性低的IDRs,對齊序列分析方法搜尋類似蛋白質的差異性較大。因此,若以胺基酸物化特性作為序列對應的比較方式,便可以去除對齊序列比對中保守性序列的限制,有利於 IDRs 的序列對應與分析。本研究採用一種片段化分析法,利用提取胺基酸特性的免對齊序列比對法 (Alignment-free sequence comparison) 分析不同長度的 AtICE1 片段序列,並與 Disprot 資料庫收集的 IDRs 進行對應搜尋,嘗試以對應到的IDR做為AtICE1參考的功能探索。相對於整個蛋白質胺基酸特性的計算,片段化序列分析法可避免蛋白質序列長度的差異而影響分析。在序列對應上, AtICE1的長片段 IDRs有初步的對應,且在 ICE1的不同物種同源蛋白上也有看到類似的對應,說明此方法的可行性。這些分析結果將有助於 AtICE1 潛在功能的探討。zh_TW
dc.description.abstractICE1 (Inducer of CBF Expression 1) is a member of the basic helix-loop-helix (bHLH) family of transcription factors in Arabidopsis thaliana, involved in various plant stress responses and plant growth development. AtICE1 consists of 494 amino acids, with the bHLH (300-365 a.a.) and ACTL (405-494 a.a.) regions forming foldable structured domains. Approximately 70% of the remaining sequence is predicted to be intrinsically disordered regions (IDRs), which are primarily composed of hydrophilic or polar amino acids. The molecular functions of these IDRs remain uncertain. Based on the unique amino acid composition of IDRs, various sequence analysis methods have been developed to predict the presence of IDR. For proteins with structured domains, their structure is typically determined by their sequence, allowing alignment-based sequence comparison methods to identify proteins with similar structures or functions. However, for IDRs with low sequence conservation, alignment-based methods is limiting its accountability. Therefore, comparing sequences based on the physicochemical properties of amino acids can eliminate the constraints of the necessity of a sequential arrangement in alignment-based sequence comparisons, facilitating finding counterpart of IDRs. This study employs a fragment-based analysis method, utilizing an alignment-free sequence comparison that extracts amino acid properties to analyze AtICE1 IDRs. These IDRs properties are then matched with IDPs/Rs collected in the DisProt database, attempting to find the corresponding IDRs as functional references for AtICE1. Compared to calculating the physicochemical properties of entire protein sequences, the fragment-based analysis method avoids the influence of protein sequence length differences on the analysis. In terms of sequence correspondence, the IDRs of long AtICE1 fragments showed correspondences, and similar matches were observed in homologous proteins of ICE1 across different species, demonstrating the feasibility of this method. These analysis results will contribute to exploring the potential functions of AtICE1.en
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dc.description.tableofcontents致謝………………………………………………………….……….…...i
中文摘要……………………………………………………………..…..ii
Abstract…………………………………………………………..……...iii
目次………………………………………………………..……………vii
圖次………...……………………………………………………………vi
表次……………………………………………………………………...xi
附錄…………………………………………………………………….xii
縮寫表…………………………………………………………………xiii
壹、前言…………………………………………………………………1
1.1阿拉伯芥bHLH轉錄因子Inducer of CBF Expression (ICE1) …….1
1.2本質無序蛋白質/蛋白質區域 (Intrinsically disordered proteins /regions,IDPs/Rs)………………………………………………………5
1.3 序列比對…………………………………………………………...12
1.4 研究動機與目標…………………………………………………...15
貳、相關研究資料 (related work) ……………………...……………..17
2.1 PCV序列比對……………………………………………………..17
參、研究方法………………………………………………………22
3.1資料庫與使用軟體…………………………………………………22
3.2建立片段化序列比對………………………………………………23
肆、結果與討論……………………………………………………….24
4.1比較片段化免對齊序列比對和PCV序列比對…………………..25
4.2片段化免對齊分析法各長度對應分析……………….……………26
4.3比較片段化免對齊分析法與MobiDB資料庫序列註……….……31
4.4 Emerin 1-187位點對應於氣孔發育蛋白質上分析…….................33
4.5 Emerin 1-187位點對應於不同物種的ICE1上分析.........................33
4.6不同物種ICE1在歐式距離小於13的篩選下長片段對應分析…..35
伍、結論與未來展望………………………………………………….37
參考資料………………………………………………………………38
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dc.language.isozh_TW-
dc.title免對齊序列比對法分析片段化阿拉伯芥轉錄因子ICE1之本質無序區域zh_TW
dc.titleFragment-Based Sequence Alignment-Free Analysis of the Intrinsically Disordered Region of Arabidopsis thaliana Transcription Factor ICE1en
dc.typeThesis-
dc.date.schoolyear112-2-
dc.description.degree碩士-
dc.contributor.oralexamcommittee陳倩瑜;廖憶純;鄭梅君;陳佩燁zh_TW
dc.contributor.oralexamcommitteeChien-Yu Chen;Yi-Chun Liao;Mei-Chun Cheng;Rita P.-Y. Chenen
dc.subject.keyword免對齊序列比較法,本質無序區域,ICE1,zh_TW
dc.subject.keywordAlignment-free Sequence Comparison,Intrinsically Disordered Regions,ICE1,en
dc.relation.page81-
dc.identifier.doi10.6342/NTU202402932-
dc.rights.note未授權-
dc.date.accepted2024-08-09-
dc.contributor.author-college生命科學院-
dc.contributor.author-dept生化科技學系-
顯示於系所單位:生化科技學系

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