List of experimental and computational labs focusing on IDPs
List of experimental and computational labs focusing on IDPs. In the last ten years, a great number of laboratories have investigated protein disorders using both experimental (e.g. SAXS-NMR, single-molecule fluorescence) and computational (analysis of protein structure) techniques.
- Keith Dunker coined the term IDP, recognised IDPs as distinct class of proteins with important biological functions, established many prediction algorithms to characterise IDPs in thousands of proteomes.[1][2]
- Peter Tompa contributed early studies of oversized IDPs and disordered plant chaperones.[3][4]
- Vladimir Uversky is a pioneer in theoretical and experimental biophysics of IDPs.[5][6]
- Madan Babu is a pioneer in cellular regulation of IDPs and studied how IDP expression and degradation are controlled.[7][8][9]
- Jim Bardwell is a pioneer in the discovery of intrinsically disordered molecular chaperones.[10][11]
- Ursula Jakob is a pioneer in conditional disorder and its role for molecular chaperoning.[12][13]
- Philipp Selenko is a pioneer in in-cell characterisation of IDPs.[14][15]
- Michael Woodside pioneered optical tweezers studies on aggregation.[16][17]
- Sir Alan Fersht pioneered structural studies on the most frequently cancer-mutated IDP, p53.[18][19]
- Stefan Rudiger is a pioneer in Hsp90-associated IDP recognition mechanisms.[20][21]
- Tobias Madl pioneered SAXS-NMR protein complex determination methodology development.[22][23]
- Yongli Zhang is a pioneer in IDP unfolding.[24][25]
- Peter Wright pioneered the mechanistic analysis of coupled folding and binding of IDPs.[26][27]
- Jane Dyson is a pioneer in NMR studies on various biologically important IDPs.[28][29]
- Rohit Pappu pioneered modelling of electrostatic malleability of IDP ensembles.[30][31] and developed powerful modeling tools to predict ensembles of highly charged IDPs based on their charge distributions.[32]
- Inke Nathke pioneered research on APC, one of the largest IDPs.[33][34]
- Madelon Maurice is a pioneer in cellular mechanisms of IDP scaffolds in Wnt signalling.[35][36][37][38]
- Richard Kriwacki pioneered structural studies on binding-induced folding of IDPs.[39][40]
- Benjamin Schuler pioneered single-molecule fluorescence studies on IDPs.[41][42]
- Ashok Deniz pioneered single-molecule fluorescence studies on IDPs.[43][44]
- David Klenerman pioneered single-molecule fluorescence studies on IDPs.[45][46]
- Vincent Hilser extended the theory of allostery and demonstrated that IDPs have an ensemble allosteric advantage.[47]
- Yosef Shaul pioneered large-scale experimental investigations of IDPs in cells using 20S Proteasome assays.[48]
- David Eliezer pioneered NMR and ESR studies on IDPs such as alpha-synuclein and tau.[49][50]
See also
References
- ↑ "About Us - Keith Dunker Lab - Center for Computational Biology and Bioinformatics". Compbio.iupui.edu. Retrieved 2014-03-11.
- ↑ Dunker, A. K.; Lawson, J. D.; Brown, C. J.; Williams, R. M.; Romero, P; Oh, J. S.; Oldfield, C. J.; Campen, A. M.; Ratliff, C. M.; Hipps, K. W.; Ausio, J; Nissen, M. S.; Reeves, R; Kang, C; Kissinger, C. R.; Bailey, R. W.; Griswold, M. D.; Chiu, W; Garner, E. C.; Obradovic, Z (2001). "Intrinsically disordered protein". Journal of molecular graphics & modelling. 19 (1): 26–59. doi:10.1016/s1093-3263(00)00138-8. PMID 11381529.
- ↑ "Peter Tompa Lab". Vib.be. 2011-05-11. Retrieved 2014-03-11.
- ↑ Tompa, P (2002). "Intrinsically unstructured proteins". Trends in Biochemical Sciences. 27 (10): 527–33. doi:10.1016/s0968-0004(02)02169-2. PMID 12368089.
- ↑ https://hsccf.hsc.usf.edu/facultyDirectory/researchDirectory/search_profile.cfm?person_id=2838234
- ↑ Uversky, V. N.; Gillespie, J. R.; Fink, A. L. (2000). "Why are "natively unfolded" proteins unstructured under physiologic conditions?". Proteins: Structure, Function, and Genetics. 41 (3): 415–27. doi:10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7. PMID 11025552.
- ↑ "Research | M. Madan Babu's Lab". Mbgroup.mrc-lmb.cam.ac.uk. Retrieved 2014-03-11.
- ↑ Gsponer, J; Futschik, M. E.; Teichmann, S. A.; Babu, M. M. (2008). "Tight regulation of unstructured proteins: From transcript synthesis to protein degradation". Science. 322 (5906): 1365–8. doi:10.1126/science.1163581. PMC 2803065. PMID 19039133.
- ↑ van der Lee, Robin; Lang, Benjamin; Kruse, Kai; Gsponer, Jörg; Sánchez de Groot, Natalia; Huynen, Martijn A.; Matouschek, Andreas; Fuxreiter, Monika; Babu, M. Madan. "Intrinsically Disordered Segments Affect Protein Half-Life in the Cell and during Evolution". Cell Reports. 8 (6): 1832–1844. doi:10.1016/j.celrep.2014.07.055. ISSN 2211-1247. PMC 4358326. PMID 25220455.
- ↑ "The Bardwell Lab the University of Michigan". Labs.mcdb.lsa.umich.edu. Retrieved 2014-03-11.
- ↑ Bardwell, J. C.; Jakob, U (2012). "Conditional disorder in chaperone action". Trends in Biochemical Sciences. 37 (12): 517–25. doi:10.1016/j.tibs.2012.08.006. PMC 3508372. PMID 23018052.
- ↑ "Ursula Jakob, Ph.D. | University of Michigan Department of Biological Chemistry". Biochem.med.umich.edu. Retrieved 2014-03-11.
- ↑ Bardwell, J. C.; Jakob, U (2012). "Conditional disorder in chaperone action". Trends in Biochemical Sciences. 37 (12): 517–25. doi:10.1016/j.tibs.2012.08.006. PMC 3508372. PMID 23018052.
- ↑ "Welcome to the Selenko Lab". In-cell NMR. Retrieved 2014-03-11.
- ↑ Binolfi, A.; Theillet, F. X.; Selenko, P. (2012). "Bacterial in-cell NMR of human α-synuclein: A disordered monomer by nature?". Biochemical Society Transactions. 40 (5): 950–4. doi:10.1042/BST20120096. PMID 22988846.
- ↑ "Woodside Lab". Ualberta.ca. 2012-08-22. Retrieved 2014-03-11.
- ↑ Yu, H; Liu, X; Neupane, K; Gupta, A. N.; Brigley, A. M.; Solanki, A; Sosova, I; Woodside, M. T. (2012). "Direct observation of multiple misfolding pathways in a single prion protein molecule". Proceedings of the National Academy of Sciences. 109 (14): 5283–8. doi:10.1073/pnas.1107736109. PMC 3325692. PMID 22421432.
- ↑ UK (2013-11-21). "Alan Fersht | MRC Laboratory of Molecular Biology". .mrc-lmb.cam.ac.uk. Retrieved 2014-03-11.
- ↑ Binolfi, A.; Theillet, F. X.; Selenko, P. (2012). "Bacterial in-cell NMR of human α-synuclein: A disordered monomer by nature?". Biochemical Society Transactions. 40 (5): 950–4. doi:10.1042/BST20120096. PMID 22988846.
- ↑ "dr. S.G.D. (Stefan) Rüdiger - Betawetenschappen - Universiteit Utrecht". Uu.nl. Retrieved 2014-03-11.
- ↑ Karagöz, G. E.; Duarte, A. M.; Akoury, E; Ippel, H; Biernat, J; Morán Luengo, T; Radli, M; Didenko, T; Nordhues, B. A.; Veprintsev, D. B.; Dickey, C. A.; Mandelkow, E; Zweckstetter, M; Boelens, R; Madl, T; Rüdiger, S. G. (2014). "Hsp90-tau complex reveals molecular basis for specificity in chaperone action". Cell. 156 (5): 963–74. doi:10.1016/j.cell.2014.01.037. PMID 24581495.
- ↑ "Emmy-Noether Nachwuchsgruppe: Startseite". Madllab.ch.tum.de. Retrieved 2014-03-11.
- ↑ MacKereth, C. D.; Madl, T; Bonnal, S; Simon, B; Zanier, K; Gasch, A; Rybin, V; Valcárcel, J; Sattler, M (2011). "Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF". Nature. 475 (7356): 408–11. doi:10.1038/nature10171. PMID 21753750.
- ↑ "Yongli Zhang, PhD > Biological & Biomedical Sciences | Yale University". Bbs.yale.edu. 2012-12-12. Retrieved 2014-03-11.
- ↑ Gao, Y; Zorman, S; Gundersen, G; Xi, Z; Ma, L; Sirinakis, G; Rothman, J. E.; Zhang, Y (2012). "Single reconstituted neuronal SNARE complexes zipper in three distinct stages". Science. 337 (6100): 1340–3. doi:10.1126/science.1224492. PMC 3677750. PMID 22903523.
- ↑ "Peter Wright". Scripps.edu. Retrieved 2014-03-11.
- ↑ Demarest, S. J.; Martinez-Yamout, M.; Chung, J.; Chen, H.; Xu, W.; Dyson, H. J.; Evans, R. M.; Wright, P. E. (2002). "Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators". Nature. 415 (6871): 549–553. doi:10.1038/415549a. PMID 11823864.
- ↑ "Jane Dyson". Scripps.edu. Retrieved 2014-03-11.
- ↑ Dyson, H. J. (2011). "Expanding the proteome: Disordered and alternatively folded proteins". Quarterly Reviews of Biophysics. 44 (4): 467–518. doi:10.1017/S0033583511000060. PMC 3189428. PMID 21729349.
- ↑ Alex Holehouse (2014-02-11). "Pappu Lab". Pappulab.wustl.edu. Retrieved 2014-03-11.
- ↑ Das, R. K.; Pappu, R. V. (2013). "Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues". Proceedings of the National Academy of Sciences. 110 (33): 13392–7. doi:10.1073/pnas.1304749110. PMC 3746876. PMID 23901099.
- ↑ Das, R. K.; Pappu, R. V. (2013). "Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues". Proceedings of the National Academy of Sciences. 110 (33): 13392–7. doi:10.1073/pnas.1304749110. PMC 3746876. PMID 23901099.
- ↑ "Inke Nathke |". Lifesci.dundee.ac.uk. Retrieved 2014-03-11.
- ↑ Nelson, S; Näthke, I. S. (2013). "Interactions and functions of the adenomatous polyposis coli (APC) protein at a glance". Journal of Cell Science. 126 (Pt 4): 873–7. doi:10.1242/jcs.100479. PMID 23589686.
- ↑ "Maurice - Cell Biology UMC Utrecht". Cellbiology-utrecht.nl. Retrieved 2014-03-11.
- ↑ Minde, D. P.; Anvarian, Z.; Rüdiger, S. G.; Maurice, M. M. (2011). "Messing up disorder: How do missense mutations in the tumor suppressor protein APC lead to cancer?". Molecular Cancer. 10: 101. doi:10.1186/1476-4598-10-101. PMC 3170638. PMID 21859464.
- ↑ Li, V. S.; Ng, S. S.; Boersema, P. J.; Low, T. Y.; Karthaus, W. R.; Gerlach, J. P.; Mohammed, S; Heck, A. J.; Maurice, M. M.; Mahmoudi, T; Clevers, H (2012). "Wnt signaling through inhibition of β-catenin degradation in an intact Axin1 complex". Cell. 149 (6): 1245–56. doi:10.1016/j.cell.2012.05.002. PMID 22682247.
- ↑ Koo, B. K.; Spit, M; Jordens, I; Low, T. Y.; Stange, D. E.; Van De Wetering, M; Van Es, J. H.; Mohammed, S; Heck, A. J.; Maurice, M. M.; Clevers, H (2012). "Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors". Nature. 488 (7413): 665–9. doi:10.1038/nature11308. PMID 22895187.
- ↑ "Kriwacki laboratory". St. Jude Research. Retrieved 2014-03-11.
- ↑ Wang, Y; Fisher, J. C.; Mathew, R; Ou, L; Otieno, S; Sublet, J; Xiao, L; Chen, J; Roussel, M. F.; Kriwacki, R. W. (2011). "Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21". Nature Chemical Biology. 7 (4): 214–21. doi:10.1038/nchembio.536. PMC 3124363. PMID 21358637.
- ↑ "Ben Schuler research group". Bioc.uzh.ch. 2013-10-31. Retrieved 2014-03-11.
- ↑ Brucale, M; Schuler, B; Samorì, B (2014). "Single-Molecule Studies of Intrinsically Disordered Proteins". Chemical Reviews. 114 (6): 140117081415006. doi:10.1021/cr400297g. PMID 24432838.
- ↑ "The Deniz Lab". Scripps.edu. 2014-01-23. Retrieved 2014-03-11.
- ↑ Ferreon, A. C.; Ferreon, J. C.; Wright, P. E.; Deniz, A. A. (2013). "Modulation of allostery by protein intrinsic disorder". Nature. 498 (7454): 390–4. doi:10.1038/nature12294. PMC 3718496. PMID 23783631.
- ↑ "Klenerman | Department of Chemistry". Ch.cam.ac.uk. Retrieved 2014-03-11.
- ↑ Cremades, N; Cohen, S. I.; Deas, E; Abramov, A. Y.; Chen, A. Y.; Orte, A; Sandal, M; Clarke, R. W.; Dunne, P; Aprile, F. A.; Bertoncini, C. W.; Wood, N. W.; Knowles, T. P.; Dobson, C. M.; Klenerman, D (2012). "Direct observation of the interconversion of normal and toxic forms of α-synuclein". Cell. 149 (5): 1048–59. doi:10.1016/j.cell.2012.03.037. PMC 3383996. PMID 22632969.
- ↑ Hilser, V. J.; Thompson, E. B. (2007). "Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins". Proceedings of the National Academy of Sciences. 104 (20): 8311–5. doi:10.1073/pnas.0700329104. PMC 1895946. PMID 17494761.
- ↑ Tsvetkov, P.; Myers, N.; Moscovitz, O.; Sharon, M.; Prilusky, J.; Shaul, Y. (2012). "Thermo-resistant intrinsically disordered proteins are efficient 20S proteasome substrates". Molecular BioSystems. Royal Society of Chemistry. 8 (1): 368–373. doi:10.1039/c1mb05283g. PMID 22027891.
- ↑ Eliezer, D; Kutluay, E; Bussell Jr, R; Browne, G (2001). "Conformational properties of alpha-synuclein in its free and lipid-associated states". Journal of Molecular Biology. 307 (4): 1061–73. doi:10.1006/jmbi.2001.4538. PMID 11286556.
- ↑ Eliezer, D; Barré, P; Kobaslija, M; Chan, D; Li, X; Heend, L (2005). "Residual structure in the repeat domain of tau: Echoes of microtubule binding and paired helical filament formation". Biochemistry. 44 (3): 1026–36. doi:10.1021/bi048953n. PMID 15654759.
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