Abstract
In recent years it was shown that a large number of proteins are either fully or partially disordered. Intrinsically disordered proteins are ubiquitary proteins that fulfill essential biological functions while lacking a stable 3D structure. Despite the large abundance of disorder, disordered regions are still poorly detected. The identification of disordered regions facilitates the functional annotation of proteins and is instrumental in delineating boundaries of protein domains amenable to crystallization. This chapter focuses on the methods currently employed for predicting disorder and identifying regions involved in induced folding.
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References
Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F., Jones, D. T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337(3), 635–645.
Bogatyreva, N. S., Finkelstein, A. V., Galzitskaya, O. V. (2006) Trend of amino acid composition of proteins of different taxa. J Bioinform Comput Biol 4(2), 597–608.
Haynes, C., Oldfield, C. J., Ji, F., Klitgord, N., Cusick, M. E., Radivojac, P., Uversky, V. N., Vidal, M., Iakoucheva, L. M. (2006) Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol 2(8), e100.
Radivojac, P., Iakoucheva, L. M., Oldfield, C. J., Obradovic, Z., Uversky, V. N., Dunker, A. K. (2007) Intrinsic disorder and functional proteomics. Biophys J 92(5), 1439–1456.
Lobley, A., Swindells, M. B., Orengo, C. A., Jones, D. T. (2007) Inferring function using patterns of native disorder in proteins. PLoS Comput Biol 3(8), e162.
Ferron, F., Longhi, S., Canard, B., Karlin, D. (2006) A practical overview of protein disorder prediction methods. Proteins 65(1), 1–14.
Bourhis, J., Canard, B., Longhi, S. (2007) Predicting protein disorder and induced folding: from theoretical principles to practical applications. Curr Protein Peptide Sci 8, 135–149.
Uversky, V. N., Radivojac, P., Iakoucheva, L. M., Obradovic, Z., Dunker, A. K. (2007) Prediction of intrinsic disorder and its use in functional proteomics. Methods Mol Biol 408, 69–92.
Vucetic, S., Brown, C., Dunker, K., Obradovic, Z. (2003) Flavors of protein disorder. Proteins 52, 573–584.
Karlin, D., Ferron, F., Canard, B., Longhi, S. (2003) Structural disorder and modular organization in Paramyxovirinae N and P. J Gen Virol 84(Pt 12), 3239–3252.
Ferron, F., Rancurel, C., Longhi, S., Cambillau, C., Henrissat, B., Canard, B. (2005) VaZyMolO: a tool to define and classify modularity in viral proteins. J Gen Virol 86(Pt 3), 743–749.
Severson, W., Xu, X., Kuhn, M., Senutovitch, N., Thokala, M., Ferron, F., Longhi, S., Canard, B., Jonsson, C. B. (2005) Essential amino acids of the hantaan virus N protein in its interaction with RNA. J Virol 79(15), 10032–10039.
Llorente, M. T., Barreno-Garcia, B., Calero, M., Camafeita, E., Lopez, J. A., Longhi, S., Ferron, F., Varela, P. F., Melero, J. A. (2006) Structural analysis of the human respiratory syncitial virus phosphoprotein: characterization of an a-helical domain involved in oligomerization. J Gen Virol 87, 159–169.
Sickmeier, M., Hamilton, J. A., LeGall, T., Vacic, V., Cortese, M. S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V. N., Obradovic, Z., Dunker, A. K. (2007) DisProt: the database of disordered proteins. Nucleic Acids Res 35(Database issue), D786–D793.
Romero, P., Obradovic, Z., Li, X., Garner, E. C., Brown, C. J., Dunker, A. K. (2001) Sequence complexity of disordered proteins. Proteins 42(1), 38–48.
Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., Dunker, A. K. (2005) Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins. 61(Suppl. 7), 176–182.
Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., Brown, C. J., Dunker, A. K. (2003) Predicting intrinsic disorder from amino acid sequence. Proteins 53(Suppl 6), 566–572.
Peng, K., Vucetic, S., Radivojac, P., Brown, C. J., Dunker, A. K., Obradovic, Z. (2005) Optimizing long intrinsic disorder predictors with protein evolutionary information. J Bioinform Comput Biol 3(1), 35–60.
Linding, R., Russell, R. B., Neduva, V., Gibson, T. J. (2003) GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res 31(13), 3701–3708.
Linding, R., Jensen, L. J., Diella, F., Bork, P., Gibson, T. J., Russell, R. B. (2003) Protein disorder prediction: implications for structural proteomics. Structure (Camb) 11(11), 1453–1459.
Ward, J. J., McGuffin, L. J., Bryson, K., Buxton, B. F., Jones, D. T. (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics 20(13), 2138–2139.
Yang, Z. R., Thomson, R., McNeil, P., Esnouf, R. M. (2005) RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21(16), 3369–3376.
Cheng, J., Sweredoski, M., Baldi, P. (2005) Accurate prediction of protein disordered regions by mining protein structure data. Data Mining Knowledge Discov 11, 213–222.
Pollastri, G., McLysaght, A. (2005) Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics 21(8), 1719–1720.
Coeytaux, K., Poupon, A. (2005) Prediction of unfolded segments in a protein sequence based on amino acid composition. Bioinformatics 21(9), 1891–1900.
Schlessinger, A., Punta, M., Rost, B. (2007) Natively unstructured regions in proteins identified from contact predictions. Bioinformatics 23(18), 2376–2384.
Wang, L., Sauer, U. H. (2008) OnD-CRF: predicting order and disorder in proteins using [corrected] conditional random fields. Bioinformatics 24(11), 1401–1402.
Shimizu, K., Hirose, S., Noguchi, T. (2007) POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. Bioinformatics 23(17), 2337–2338.
Su, C. T., Chen, C. Y., Ou, Y. Y. (2006) Protein disorder prediction by condensed PSSM considering propensity for order or disorder. BMC Bioinformatics 7, 319.
Uversky, V. N., Gillespie, J. R., Fink, A. L. (2000) Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins 41(3), 415–427.
Zeev-Ben-Mordehai, T., Rydberg, E. H., Solomon, A., Toker, L., Auld, V. J., Silman, I., Botti, S., Sussman, J. L. (2003) The intracellular domain of the Drosophila cholinesterase-like neural adhesion protein, gliotactin, is natively unfolded. Proteins 53(3), 758–767.
Liu, J., Rost, B. (2003) NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res 31(13), 3833–3835.
Liu, J., Tan, H., Rost, B. (2002) Loopy proteins appear conserved in evolution. J Mol Biol 322(1), 53–64.
Dosztanyi, 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.
Galzitskaya, O. V., Garbuzynskiy, S. O., Lobanov, M. Y. (2006) FoldUnfold: web server for the prediction of disordered regions in protein chain. Bioinformatics 22(23), 2948–2949.
Callebaut, I., Labesse, G., Durand, P., Poupon, A., Canard, L., Chomilier, J., Henrissat, B., Mornon, J. P. (1997) Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives. Cell Mol Life Sci 53(8), 621–645.
Vacic, V., Oldfield, C. J., Mohan, A., Radivojac, P., Cortese, M. S., Uversky, V. N., Dunker, A. K. (2007) Characterization of molecular recognition features, MoRFs, and their binding partners. J Proteome Res 6(6), 2351–2366.
Oldfield, C. J., Cheng, Y., Cortese, M. S., Romero, P., Uversky, V. N., Dunker, A. K. (2005) Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 44(37), 12454–12470.
Bourhis, J., Johansson, K., Receveur-Bréchot, V., Oldfield, C. J., Dunker, A. K., Canard, B., Longhi, S. (2004) The C-terminal domain of measles virus nucleoprotein belongs to the class of intrinsically disordered proteins that fold upon binding to their pohysiological partner. Virus Res 99, 157–167.
John, S. P., Wang, T., Steffen, S., Longhi, S., Schmaljohn, C. S., Jonsson, C. B. (2007) Ebola virus VP30 is an RNA binding protein. J Virol 81(17), 8967–8976.
Wootton, J. C. (1994) Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 18(3), 269–285.
Kall, L., Krogh, A., Sonnhammer, E. L. (2007) Advantages of combined transmembrane topology and signal peptide prediction – the Phobius web server. Nucleic Acids Res 35(Web Server issue), W429–W432.
Bornberg-Bauer, E., Rivals, E., Vingron, M. (1998) Computational approaches to identify leucine zippers. Nucleic Acids Res 26(11), 2740–2746.
Lupas, A., Van Dyke, M., Stock, J. (1991) Predicting coiled coils from protein sequences. Science 252(5009), 1162–1164.
Baldi, P., Cheng, J., Vullo, A. (2004) Large-scale prediction of disulphide bond connectivity. Adv Neural Inf Process Syst 17, 97–104.
McGuffin, L. J., Bryson, K., Jones, D. T. (2000) The PSIPRED protein structure prediction server. Bioinformatics 16(4), 404–405.
Lieutaud, P., Canard, B., Longhi, S. (2008) MeDor: a metaserver for predicting protein disorder. BMC Genomics 9(Suppl 2), S25.
Chandonia, J. M. (2007) StrBioLib: a Java library for development of custom computational structural biology applications. Bioinformatics 23(15), 2018–2020.
Longhi, S., Receveur-Brechot, V., Karlin, D., Johansson, K., Darbon, H., Bhella, D., Yeo, R., Finet, S., Canard, B. (2003) The C-terminal domain of the measles virus nucleoprotein is intrinsically disordered and folds upon binding to the C-terminal moiety of the phosphoprotein. J Biol Chem 278(20), 18638–18648.
Kingston, R. L., Hamel, D. J., Gay, L. S., Dahlquist, F. W., Matthews, B. W. (2004) Structural basis for the attachment of a paramyxoviral polymerase to its template. Proc Natl Acad Sci USA 101(22), 8301–8306.
Morin, B., Bourhis, J. M., Belle, V., Woudstra, M., Carrière, F., BGuigliarelli, B., Fournel, A., Longhi, S. (2006) Assessing induced folding of an intrinsically disordered protein by site-directed spin-labeling EPR spectroscopy. J. Phys. Chem. B 110(41), 20596–20608.
Acknowledgments
MeDor was developed with the financial support of the EU VIZIER (http://www.vizier-europe.org). program (CT 2004-511960) and the ANR (ANR-05-MIIM-035-02).
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Longhi, S., Lieutaud, P., Canard, B. (2010). Conformational Disorder. In: Carugo, O., Eisenhaber, F. (eds) Data Mining Techniques for the Life Sciences. Methods in Molecular Biology, vol 609. Humana Press. https://doi.org/10.1007/978-1-60327-241-4_18
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DOI: https://doi.org/10.1007/978-1-60327-241-4_18
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