Interactive 3D Complements in Proteopedia

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Articles in Proteopedia can be designed to complement publications in scientific journals. A link, within the publication, to an interactive 3D complement (I3DC) in Proteopedia can enable readers to rotate molecular scenes having the same initial orientation, color schemes, and labeling as figures in the publication. Links to the interactive 3D complement in Proteopedia can be placed in the text of the publication, and/or in the .doc file included on the journal website as supplementary materials. The I3DC article can be developed in advance of publication, yet hidden from viewing by visitors to Proteopedia until publication occurs (see Proteopedia:Workbench). Authors of the associated publications are able and encouraged to review the I3DC page before publication, and to interact with the Proteopedia editor at any time. I3DC are protected from editing by anyone.

Proteopedia is working with Journals to develop, in close collaboration with authors, interactive 3D complement articles in Proteopedia, thus rendering the structural data more comprehensible to a wider audience. In addition, Proteopedia welcomes author-initiated development of interactive 3D complement articles for individual publications in any journal. List of I3DC pages available for open access.

For more details, please Contact us.

Contents

Journals Adopting I3DC

The Journal of Biological Inorganic Chemistry seeks to promote this field internationally. This journal is primarily concerned with advances in the understanding of systems involving one or more metal ions set in a biological matrix--particularly, metalloproteins and metal-nucleic acid complexes--in order to understand biological function at the atomic level. Manuscripts describing high quality and original research concerned with metal ions or other inorganic species and having biological relevance are invited for submission to this journal. Mini-reviews, Reports, and Commentaries are also encouraged. Examples can be found in the list of I3DC articles for JBIC.

Author-Initiated I3DC

Proteopedia encourages authors of any scientific publication to develop an interactive 3D complement in Proteopedia. Members of the Proteopedia team stand ready to assist: Contact. Here are some examples of author-initiated I3DC. Years are dates of journal publication.

2015-Present

  • 2021: Structure of Geobacter pili reveals secretory rather than nanowire behavior. Gu, Srikanth, et al., Nature, in press. See Malvankar/3.
  • 2019: Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Wang, Gu et al., Cell [1], see Malvankar/2.
  • 2017: An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook. Barker et al., BMC Biology [2], see Samatey/5.
  • 2016: Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions. Matsunami et al., Nature Communications[3], see Samatey/4.
  • 2016: Structural insights into bacterial flagellar hook similarities and specifities. Yoon et al., Scientific Reports[4], see Samatey/3.
  • 2016: Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in Salmonella enterica. Matsunami et al., Scientific Reports[5], see Samatey/2.
  • 2016: Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of Geobacter sulfurreducens Pili. Xiao et al.[6], Scientific Reports, see Ke Xiao/1.
  • 2015: Structural basis for metallic-like conductivity in microbial nanowires. Malvankar et al.[7], see Journal:mBio:1.

2008-2014

  • 2013: Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins. V. A. Meshcheryakov, A. Kitao, H. Matsunami and F. A. Samatey. Acta Crystallographica D D69, 812-820. See Samatey/1.
  • 2011: The publication of "Structural and functional insights into a dodecameric molecular machine – The RuvBL1/RuvBL2 complex" in JSB[8] was accompanied by an I3DC at Journal:JSB:1.
  • 2011: User:Janice C. Telfer/Group B SRCR domains provides interactive 3D complements linked into the discussion of the publication Scavenger receptor WC1 contributes to the γδ T cell response to Leptospira[9].
  • 2011: The publication of "Structural linkage between ligand discrimination and receptor activation by type I interferon" in Cell[10] was accompanied by an I3DC at Journal:Cell:1. The structures in the paper were of interferon and interferon receptor complexes: 3s98 (IFNAR1ΔSD4), 3s8w (IFNAR2-D2), 3s9d (binary IFNα-IFNAR2 complex), 3se4 (ternary IFNω complex), and 3se3 (ternary IFNα complex).
  • 2011: The publication of "Antiviral Activity of 3(2H)- and 6-Chloro-3(2H)-Isoflavenes against Highly Diverged, Neurovirulent Vaccine-Derived, Type2 Poliovirus Sewage Isolates" in PLoS ONE[11] was accompanied by an I3DC at Journal:PLoS_ONE:1.
  • 2010: Interconversion of the Specificities of Human Lysosomal Enzymes Associated with Fabry and Schindler Diseases[12] by Tomasic IB1, Metcalf MC, Guce AI, Clark NE, Garman SC. (J. Biol. Chem.) is illustrated at Garman lab: Interconversion of lysosomal enzyme specificities.
  • 2010: Engineered mutants of HlyIIR provides interactive 3D complements for a publication in Proteins[13].
  • 2008: The publication of 3btp in Proc. Natl. Acad. Sci. USA[14] was accompanied by an I3DC.

I3DC vs. Supplementary Materials

Interactive 3D complements in Proteopedia have some functions in common with supplementary materials, but are distinguished because

  1. The journal does not hold a copyright to the the interactive 3D complement (I3DC).
  2. I3DC fall under the the same licenses as do all contributions to Proteopedia (for details, please see Proteopedia:Terms of Service).
  3. The I3DC is not housed on the journal's website.
  4. The I3DC is not frozen. It can be edited by the authors of the publication, subsequent to publication, should the authors wish to do so.

Protection From Editing

Unlike most articles in Proteopedia, I3DC are not open to editing by the general community of Proteopedia account holders.

  • For journals with formal I3DC adoption policies, the I3DC are placed within the Journal: namespace. This protects them.
  • Author-initiated I3DC should be placed within an author's User: space, which protects them (see Help:Protected Pages).

See Also

  • BAMBED, a journal that publishes abstracts of selected articles from Proteopedia.

Literature Cited

  1. ↑ Wang F, Gu Y, O'Brien JP, Yi SM, Yalcin SE, Srikanth V, Shen C, Vu D, Ing NL, Hochbaum AI, Egelman EH, Malvankar NS. Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Cell. 2019 Apr 4;177(2):361-369.e10. doi: 10.1016/j.cell.2019.03.029. PMID:30951668 doi:http://dx.doi.org/10.1016/j.cell.2019.03.029
  2. ↑ Barker CS, Meshcheryakova IV, Kostyukova AS, Freddolino PL, Samatey FA. An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook. BMC Biol. 2017 Oct 27;15(1):97. doi: 10.1186/s12915-017-0438-7. PMID:29078764 doi:http://dx.doi.org/10.1186/s12915-017-0438-7
  3. ↑ Matsunami H, Barker CS, Yoon YH, Wolf M, Samatey FA. Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions. Nat Commun. 2016 Nov 4;7:13425. doi: 10.1038/ncomms13425. PMID:27811912 doi:http://dx.doi.org/10.1038/ncomms13425
  4. ↑ Yoon YH, Barker CS, Bulieris PV, Matsunami H, Samatey FA. Structural insights into bacterial flagellar hooks similarities and specificities. Sci Rep. 2016 Oct 19;6:35552. doi: 10.1038/srep35552. PMID:27759043 doi:http://dx.doi.org/10.1038/srep35552
  5. ↑ Matsunami H, Yoon YH, Meshcheryakov VA, Namba K, Samatey FA. Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in Salmonella enterica. Sci Rep. 2016 Jun 7;6:27399. doi: 10.1038/srep27399. PMID:27273476 doi:http://dx.doi.org/10.1038/srep27399
  6. ↑ Xiao K, Malvankar NS, Shu C, Martz E, Lovley DR, Sun X. Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of Geobacter sulfurreducens Pili. Sci Rep. 2016 Mar 22;6:23385. doi: 10.1038/srep23385. PMID:27001169 doi:http://dx.doi.org/10.1038/srep23385
  7. ↑ Malvankar NS, Vargas M, Nevin K, Tremblay PL, Evans-Lutterodt K, Nykypanchuk D, Martz E, Tuominen MT, Lovley DR. Structural basis for metallic-like conductivity in microbial nanowires. MBio. 2015 Mar 3;6(2):e00084. doi: 10.1128/mBio.00084-15. PMID:25736881 doi:http://dx.doi.org/10.1128/mBio.00084-15
  8. ↑ Gorynia S, Bandeiras TM, Pinho FG, McVey CE, Vonrhein C, Round A, Svergun DI, Donner P, Matias PM, Carrondo MA. Structural and functional insights into a dodecameric molecular machine - The RuvBL1/RuvBL2 complex. J Struct Biol. 2011 Sep 10. PMID:21933716 doi:10.1016/j.jsb.2011.09.001
  9. ↑ Wang F, Herzig CT, Chen C, Hsu H, Baldwin CL, Telfer JC. Scavenger receptor WC1 contributes to the gammadelta T cell response to Leptospira. Mol Immunol. 2011 Mar;48(6-7):801-9. Epub 2011 Jan 11. PMID:21227509 doi:10.1016/j.molimm.2010.12.001
  10. ↑ Thomas C, Moraga I, Levin D, Krutzik PO, Podoplelova Y, Trejo A, Lee C, Yarden G, Vleck SE, Glenn JS, Nolan GP, Piehler J, Schreiber G, Garcia KC. Structural Linkage between Ligand Discrimination and Receptor Activation by Type I Interferons. Cell. 2011 Aug 19;146(4):621-32. PMID:21854986 doi:10.1016/j.cell.2011.06.048
  11. ↑ Shulman LM, Sofer D, Manor Y, Mendelson E, Balanant J, Salvati AL, Delpeyroux F, Fiore L. Antiviral activity of 3(2H)- and 6-chloro-3(2H)-isoflavenes against highly diverged, neurovirulent vaccine-derived, type2 poliovirus sewage isolates. PLoS One. 2011;6(5):e18360. Epub 2011 May 25. PMID:21904594 doi:10.1371/journal.pone.0018360
  12. ↑ Tomasic IB, Metcalf MC, Guce AI, Clark NE, Garman SC. Interconversion of the specificities of human lysosomal enzymes associated with Fabry and Schindler diseases. J Biol Chem. 2010 Jul 9;285(28):21560-6. Epub 2010 May 5. PMID:20444686 doi:10.1074/jbc.M110.118588
  13. ↑ Kovalevskiy OV, Solonin AS, Antson AA. Structural investigation of transcriptional regulator HlyIIR: Influence of a disordered region on protein fold and dimerization. Proteins. 2010 Feb 3. PMID:20225260 doi:10.1002/prot.22700
  14. ↑ Dym O, Albeck S, Unger T, Jacobovitch J, Branzburg A, Michael Y, Frenkiel-Krispin D, Wolf SG, Elbaum M. Crystal structure of the Agrobacterium virulence complex VirE1-VirE2 reveals a flexible protein that can accommodate different partners. Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11170-5. Epub 2008 Aug 4. PMID:18678909

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Eric Martz, Jaime Prilusky, Joel L. Sussman, David Canner

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