Talk:Intrinsically disordered proteins

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Question about experimental identification[edit]

I was confused by the following in the section "Identification of intrinsically unstructured proteins"

Intrinsically unfolded proteins, once purified, can be identified by various experimental methods. Folded proteins have a high density (partial specific volume of 0.72-0.74 mL/g) and commensurately large radius of gyration.

I thought that, if unfolded proteins have relatively higher density, then would they have smaller radius of gyration instead of larger. Could anybody help explain this to me? Thanks!

--Dai mingjie (talk) 16:00, 6 September 2010 (UTC)[reply]

You are right, I think it's an error in the text. I will correct it. --Cyclopiatalk 18:09, 6 September 2010 (UTC)[reply]

Sequence signatures of disorder[edit]

I am having a problem with the following statement "Sequence signatures of disorder: Intrinsically unstructured proteins are characterized by a low content of bulky hydrophobic amino acids and a high proportion of polar and charged amino acids."

This statement is not true for many disordered protein fibers like collagen, elastin, dragline spider silk and mussel byssus. In particular Elastin's material property's likely come from the high number of bulky hydrophobic amino acids in its sequence. For a good elastin ref look up any paper by Dan Urry.

Also this wiki post needs a discussion about how the definition of "structured" vs. "disordered" is a matter of time scale. It is true that disordered proteins have sub-microsecond conformational dynamics but the underlining chemical reactions that these proteins motivate occur on picosecond times scales. So it is more appropriate to say that these proteins might be transiently structured as opposed to saying that these proteins are completely unstructured. More recent ultrafast spectroscopic data has shown that for many of these highly mobile systems there still remains innate structural preferences that persist for longer then the picosecond time scale required for a typical chemical reaction.

It's more about lack of packed globular/crystal structure rather than saying the molecule has no intrinsic structure. A given disordered region is an ensemble of many short lived more stable 3D structures that don't form a self contained stable hydrophobic core even on short time scales. A key point is that if you wanted to use X-ray crystallography to see these structures you would be there for quite some time trying, and this is not a failing of the methods employed. Also the literature does describe the full spectrum of unfolded/disordered -upto-> structured, with the concept of molten globules where secondary structure is kept in a loose ensemble that is quite flexible and often part of a more stable domain. -- MattOates (Ulti) 17:43, 21 September 2012 (UTC)[reply]

Article move to Intrinsically Disordered Proteins[edit]

I propose that we move this article to Intrinsically Disordered Proteins.

  • IDP is the more commonly used term
  • IUPs are an extreme case of IDPs and so could nest within that article
  • A large mount of the current article deals with IDPs anyway.

See the discussion on the creation of a separate article for intrinsically disordered proteins here. Does anyone have any objections to the idea? T. Shafee (Evo&Evo) (talk) 09:35, 14 March 2014 (UTC)[reply]

IDP labs and references[edit]

Not to waste people effort Lukaskoz (talk) 07:55, 23 October 2014 (UTC) moved this section to separate subpage List_of_experimental_and_computational_labs_focusing_on_IDPs.[reply]

For sure keeping this list in main article is unusual and increase unnecessarily article size by >20%. Similarly, programs for IUP prediction have their subpage.


Below is a list of great references that should be incorporated into the article. They were compiled by David Minde, however only in a bullet-point list. Ideally they should be incorporated into the prose in the history and analysis sections. T. Shafee (Evo&Evo) (talk) 12:13, 14 March 2014 (UTC) Hi Evo-Evo,[reply]

great initiative in principle. Only I doubt, many people will read the talk part of this Wiki. Dont you think it will be easier to create a new IDP page (sort of pretenting there is no IUP wiki) and then let the WIKI-community decide whats best (merge/coexistence or whatever)? David P Minde (talk) 17:16, 18 March 2014 (UTC)[reply]
I more meant that the list shouldn't appear on the main page as it is, but rather that the references would appear in the rest of the article. E.g. references to Keith Dunker will appear in the history section, references to Ursula Jakob's work would appear in the coupled folding and binding section. All the information from the list would appear when the lab's work is summarised in the article and the list itself coud be removed. T. Shafee (Evo&Evo) (talk) 23:24, 19 October 2014 (UTC)[reply]
Hi, I am wondering whether it makes sense to include such a list in this article. Deciding which labs are pioneering is very subjective. I don't recall seeing such a list elsewhere on Wikipedia. I realise a lot of work has gone into this, but perhaps the word pioneering should be replaced with something else. But if it was simply list of labs involved in IDP research, then I think we may get hundreds of entries. So perhaps its best to create a new article called IDP Research Labs and move this content there. Alexbateman (talk) 11:56, 15 April 2014 (UTC)[reply]
  • Experimental and computational labs focusing on IDPs:
    • Keith Dunker coined the term IDP, recognised IDPs as distinc class of proteins with important biological functions, established many prediction algorithms to characterise IDPs in thousands 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 IDPs in transcription control.[7][8]
    • Jim Bardwell is a pioneer in the discovery of intrinsically disordered molecular chaperones.[9][10]
    • Ursula Jakob is a pioneer in conditional disorder and its role for molecular chaperoning.[11][12]
    • Philipp Selenko is a pioneer in in-cell characterisation of IDPs.[13][14]
    • Michael Woodside pioneered optical tweezers studies on aggregation.[15][16]
    • Madelon Maurice is a pioneer in IDP scaffolds in Wnt signalling.[17][18]
    • Sir Alan Fersht pioneered structural studies on the most frequently cancer-mutated IDP, p53.[19][20]
    • Stefan Rudiger is a pioneer in Hsp90-associated IDP recognition mechanisms.[21][22]
    • Tobias Madl pioneered SAXS-NMR protein complex determination methodology development.[23][24]
    • Yongli Zhang is a pioneer in IDP unfolding.[25][26]
    • Peter Wright pioneered the mechanistic analysis of coupled folding and binding of IDPs.[27][28]
    • Jane Dyson is a pioneer in NMR studies on various biologically important IDPs.[29][30]
    • Rohit Pappu pioneered modelling of electrostatic malleability of IDP ensembles.[31][32]
    • Inke Nathke pioneered research on APC, one of the largest IDPs.[33][34]
    • Richard Kriwacki pioneered structural studies on binding-induced folding of IDPs.[35][36]
    • Benjamin Schuler pioneered single-molecule fluorescence studies on IDPs.[37][38]
    • Ashok Deniz pioneered single-molecule fluorescence studies on IDPs.[39][40]
    • David Klenerman pioneered single-molecule fluorescence studies on IDPs.[41][42]

References

  1. ^ "About Us - Keith Dunker Lab - Center for Computational Biology and Bioinformatics". Compbio.iupui.edu. Retrieved 2014-03-11.
  2. ^ 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. PMID 11381529.
  3. ^ "Peter Tompa Lab". Vib.be. 2011-05-11. Retrieved 2014-03-11.
  4. ^ Tompa, P (2002). "Intrinsically unstructured proteins". Trends in Biochemical Sciences. 27 (10): 527–33. doi:10.1016/s0968-0004(02)02169-2. PMID 12368089.
  5. ^ https://hsccf.hsc.usf.edu/facultyDirectory/researchDirectory/search_profile.cfm?person_id=2838234
  6. ^ 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.
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  9. ^ "The Bardwell Lab the University of Michigan". Labs.mcdb.lsa.umich.edu. Retrieved 2014-03-11.
  10. ^ 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.
  11. ^ "Ursula Jakob, Ph.D. | University of Michigan Department of Biological Chemistry". Biochem.med.umich.edu. Retrieved 2014-03-11.
  12. ^ 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.
  13. ^ "Welcome to the Selenko Lab". In-cell NMR. Retrieved 2014-03-11.
  14. ^ 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.
  15. ^ "Woodside Lab". Ualberta.ca. 2012-08-22. Retrieved 2014-03-11.
  16. ^ 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.
  17. ^ "Maurice - Cell Biology UMC Utrecht". Cellbiology-utrecht.nl. Retrieved 2014-03-11.
  18. ^ 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  19. ^ UK (2013-11-21). "Alan Fersht | MRC Laboratory of Molecular Biology". .mrc-lmb.cam.ac.uk. Retrieved 2014-03-11.
  20. ^ 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.
  21. ^ "dr. S.G.D. (Stefan) Rüdiger - Betawetenschappen - Universiteit Utrecht". Uu.nl. Retrieved 2014-03-11.
  22. ^ 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.
  23. ^ "Emmy-Noether Nachwuchsgruppe: Startseite". Madllab.ch.tum.de. Retrieved 2014-03-11.
  24. ^ 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.
  25. ^ "Yongli Zhang, PhD > Biological & Biomedical Sciences | Yale University". Bbs.yale.edu. 2012-12-12. Retrieved 2014-03-11.
  26. ^ 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.
  27. ^ "Peter Wright". Scripps.edu. Retrieved 2014-03-11.
  28. ^ 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.
  29. ^ "Jane Dyson". Scripps.edu. Retrieved 2014-03-11.
  30. ^ 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.
  31. ^ Alex Holehouse (2014-02-11). "Pappu Lab". Pappulab.wustl.edu. Retrieved 2014-03-11.
  32. ^ 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.
  33. ^ "Inke Nathke |". Lifesci.dundee.ac.uk. Retrieved 2014-03-11.
  34. ^ 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.
  35. ^ "Kriwacki laboratory". St. Jude Research. Retrieved 2014-03-11.
  36. ^ 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.
  37. ^ "Ben Schuler research group". Bioc.uzh.ch. 2013-10-31. Retrieved 2014-03-11.
  38. ^ 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.
  39. ^ "The Deniz Lab". Scripps.edu. 2014-01-23. Retrieved 2014-03-11.
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New/improved image?[edit]

An ensemble of NMR structures of the Thylakoid soluble phosphoprotein TSP9, which shows a largely flexible protein chain.[1]

The lead and only figure in this article is terribly pixelated. Does anyone have a better image to include? There must be some out there.T. Shafee (Evo&Evo) (talk) 23:23, 19 October 2014 (UTC) [reply]

References

  1. ^ Song J, Lee MS, Carlberg I, Vener AV, Markley JL (December 2006). "Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications". Biochemistry. 45 (51): 15633–43. doi:10.1021/bi062148m. PMC 2533273. PMID 17176085.{{cite journal}}: CS1 maint: multiple names: authors list (link)

Assessment comment[edit]

The comment(s) below were originally left at Talk:Intrinsically disordered proteins/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

Changed rating from high to mid; in comparison to other topics in the "high" class, this appears to be less important. - tameeria 20:49, 18 February 2007 (UTC)[reply]

Substituted at 18:23, 17 July 2016 (UTC)

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