PlantMWpIDB: a database of molecular weights and isoelectric points of plant proteomes

  • Mohanta, TK, Khan, AL, Hashem, A., Abd Allah, EF & Al-Harrasi, A. The molecular mass and isoelectric point of plant proteomes. BMC Genom. 20631 (2019).

    CAS Google Scholar Article

  • Mohanta, TK et al. Virtual 2D map of the fungal proteome. Science. representing 116676 (2021).

    ADS CAS PubMed PubMed Central Article Google Scholar

  • Uversky, VN In Post-translational modification (eds Maloy, S. & Hughes, KBT) 425–430 (Academic Press, 2013). https://doi.org/10.1016/B978-0-12-374984-0.01203-1.

    Google Scholar Chapter

  • Sun, q. et al. PPDB, the plant proteomics database at cornell. Nucleic Acids Res. 37D969–D974 (2009).

    CAS PubMed Google Scholar Article

  • Mohanta, T., Syed, A., Ameen, F. & Bae, H. New genomic and evolutionary perspective of cyanobacterial tRNAs. Before. Broom. 8200 (2017).

    PubMed PubMed Central CAS Article Google Scholar

  • Ochsenreiter, T., Cipriano, M. & Hajduk, SL Alternative mRNA editing in trypanosomes is important and may contribute to mitochondrial protein diversity. PLOS ONE 3e1566 (2008).

    ADS PubMed PubMed Central CAS Article Google Scholar

  • Reid, DW & Nicchitta, CV Diversity and selectivity in mRNA translation on the endoplasmic reticulum. Nat. Rev. Mol. Cell Biol. 16221-231 (2015).

    CAS PubMed PubMed Central Google Scholar Article

  • Livingstone, M., Atas, E., Meller, A. & Sonenberg, N. Mechanisms governing the control of mRNA translation. Phys. Biol. 721001 (2010).

    CAS Google Scholar Article

  • Li, X. et al. Quantitative approach of chemical proteomics to identify protein-protein interactions induced by post-translational modification. Jam. Chem. Soc. 1341982-1985 (2012).

    CAS PubMed PubMed Central Google Scholar Article

  • Eisenhaber, BE Post-translational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure?. Fluent. Sci protein peptide. 8197–203 (2007).

    CAS Google Scholar Article

  • Finkemeier, I., Laxa, M., Miguet, L., Howden, AJM, and Sweetlove, LJ Proteins of various subcellular functions and locations are acetylated by lysine in Arabidopsis. Plant Physics. 1551779–1790 (2011).

    CAS PubMed PubMed Central Google Scholar Article

  • Wolf, S., Lucas, WJ, Deom, CM & Beachy, RN Tobacco mosaic virus movement protein alters plasmodesmatous size exclusion limit. Science 246377–379 (1989).

    ADS CAS PubMed Google Scholar Article

  • Ivankov, D.N. et al. Contact order revisited: Influence of protein size on folding rate. Sci protein. 122057-2062 (2003).

    CAS PubMed PubMed Central Google Scholar Article

  • Hishigaki, H., Nakai, K., Ono, T., Tanigami, A. & Takagi, T. Assessing the accuracy of protein function prediction from protein-protein interaction data. Yeast 18523–531 (2001).

    CAS PubMed Google Scholar Article

  • Kudlow, JE Post-translational modification by O-GlcNAc: another way to modify protein function. J. Cell. Biochemistry. 981062-1075 (2006).

    CAS PubMed Google Scholar Article

  • Belizaire, R. & Unanue, ER Targeting proteins to distinct subcellular compartments reveals unique requirements for MHC class I and II presentation. proc. Natl. Acad. Science. 10617463–17468 (2009).

    ADS CAS PubMed PubMed Central Article Google Scholar

  • Park, D., Choi, SS & Ha, K.-S. Transglutaminase 2: A multifunctional protein in multiple subcellular compartments. Amino acids 39619-631 (2010).

    CAS PubMed Google Scholar Article

  • Ugo, P., Marafini, P. & Meneghello, M. List of symbols 21–22 (De Gruyter, 2021). https://doi.org/10.1515/9783110589160-206.

    Book Google Scholar

  • Erickson, HP Kinetics of protein-protein association and dissociation. Principles of protein-protein association 5–8 (2019) doi: https://doi.org/10.1088/2053-2563/ab19bach8.

  • Wu, YC, Koch, WF, Berezansky, PA & Holland, LA Amino acid dissociation constant by conductometric method: I. pK1 of MOPSO-HCl at 25°C. J.Solution Chem. 21597–605 (1992).

    CAS Google Scholar Article

  • Das, RK, Crick, SL & Pappu, RV N-terminal segments modulate the α-helical propensities of the intrinsically disordered basic regions of bZIP proteins. J.Mol. Biol. 416287–299 (2012).

    CAS PubMed Google Scholar Article

  • Vamvaca, K., Volles, MJ & Lansbury, PT The first N-terminal amino acids of α-synuclein are essential for in vitro α-helical structure formation and membrane binding in yeast. J.Mol. Biol. 389413–424 (2009).

    CAS PubMed PubMed Central Google Scholar Article

  • Requiao, DR et al. Distribution of protein charge in proteomes and its impact on translation. PLOS calculation. Biol. 13e1005549 (2017).

    PubMed PubMed Central CAS Article Google Scholar

  • von Heijne, G. Net NC charge imbalance may be important for signal sequence function in bacteria. J.Mol. Biol. 192287–290 (1986).

    Google Scholar article

  • von Heijne, G. Analysis of the distribution of charged residues in the N-terminal region of signal sequences: implications for protein export in prokaryotic and eukaryotic cells. EBO J. 32315–2318 (1984).

    Google Scholar article

  • Dinçbas-Renqvist, V. et al. A post-translational modification of the GGQ motif of Escherichia coli RF2 stimulates translational arrest. EBO J. 196900–6907 (2000).

    PubMed PubMed Central ArticleGoogle Scholar

  • Phelps, DS, Floros, J. & Taeusch, HW Jr. Post-translational modification of major human surfactant-associated proteins. Biochemistry. J 237373–377 (1986).

    CAS PubMed PubMed Central Google Scholar Article

  • Aitken, A. Post-translational modification of 14-3-3 isoforms and regulation of cell function. Semin. Dev cell. Biol. 22673–680 (2011).

    CAS PubMed Google Scholar Article

  • Nussinov, R., Tsai, C.-J., Xin, F. & Radivojac, P. Allosteric post-translational modification codes. Biochem Trends. Science. 37447–455 (2012).

    CAS PubMed Google Scholar Article

  • Zhang, L. et al. Towards post-translational modification of the royal jelly proteome. J. Proteom. 755327–5341 (2012).

    CAS Google Scholar Article

  • Li, F.-ML Prediction of the subcellular location of proteins using pseudo-amino acid composition of cabbage and an improved hybrid approach. Lett protein peptide. 15612–616 (2008).

    Article on Google Scholar Ads

  • Park, K.-J. & Kanehisa, M. Prediction of subcellular locations of proteins by support vector machines using amino acid and amino acid pair compositions. Bioinformatics 191656-1663 (2003).

    CAS PubMed Google Scholar Article

  • Pierleoni, A., Martelli, PL, Fariselli, P. & Casadio, R. eSLDB: Eukaryotic Subcellular Localization Database. Nucleic Acids Res. 35D208–D212 (2007).

    CAS PubMed Google Scholar Article

  • Rastogi, S. & Rost, B. LocDB: Experimental localization annotations for Homo sapiens and Arabidopsis thaliana. Nucleic Acids Res. 39D230–D234 (2011).

    CAS PubMed Google Scholar Article

  • Negi, S., Pandey, S., Srinivasan, SM, Mohammed, A. & Guda, C. LocSigDB: a database of protein localization signals. Database 20152 (2015).

    Google Scholar article

  • Guo, X., Liu, F., Ju, Y., Wang, Z., and Wang, C. Subcellular localization of human proteins with integrated source and multi-tag ensemble classifier. Science. representing 628087 (2016).

    ADS CAS PubMed PubMed Central Article Google Scholar

  • Orre, LM et al. SubCellBarCode: Proteome-wide mapping of protein localization and relocalization. Mol. Cell 73166-182.e7 (2019).

    CAS PubMed Google Scholar Article

  • Wan, S., Mak, M.-W. & Kung, S.-Y. mGOASVM: Subcellular localization of multi-tag proteins based on gene ontology and supporting vector machines. BMC Bioinform. 13290 (2012).

    Google Scholar article

  • Bunkute, E. et al. PIP-DB: The Protein Isoelectric Point Database. Bioinformatics 31295-296 (2015).

    CAS PubMed Google Scholar Article

  • Kozlowski, LP Proteome-pI: Proteome Isoelectric Point Database. Nucleic Acids Res. 45D1112–D1116 (2017).

    CAS PubMed Google Scholar Article

  • Kozlowski, LP IPC — isoelectric point calculator. Biol. Direct 1155 (2016).

    PubMed PubMed Central CAS Article Google Scholar

  • Kozlowski, LP Proteome-pI 2.0: Proteome isoelectric point database update. Nucleic Acids Res. 50D1535–D1540 (2022).

    CAS PubMed Google Scholar Article

  • Su, B., Qian, Z., Li, T., Zhou, Y. & Wong, A. PlantMP: A Database for Dark Plant Proteins. Database 20192 (2019).

    CAS Google Scholar Article

  • Brown, JWS, Shaw, PJ, Shaw, P. & Marshall, DF Arabidopsis Nucleolar Protein Database (AtNoPDB). Nucleic Acids Res. 33D633–D636 (2005).

    CAS PubMed Google Scholar Article

  • Na Ayutthaya, PP, Lundberg, D., Weigel, D. & Li, L. Blue native polyacrylamide gel electrophoresis (BN-PAGE) for the analysis of protein oligomers in plants. Fluent. Biol Plant Protocol. 5e20107 (2020).

    CAS PubMed Google Scholar Article

  • Lee, PY, Saraygord-Afshari, N. & Low, TY The evolution of two-dimensional gel electrophoresis – from proteomics to emerging alternative applications. J. Chromatogr. A 1615460763 (2020).

    CAS PubMed Google Scholar Article

  • Toledo Silva, SH, Bader-Mittermaier, S., Silva, LB, Doer, G. & Eisner, P. Electrophoretic characterization, amino acid composition, and solubility properties of Macauba (Acrocomia aculeata L.) nucleus globulins. Food bioscience. 40100908 (2021).

    CAS Google Scholar Article

  • Maria H. Underwood