Advertisement

The Rationale Behind This Workbook

  • Tim Skern
Chapter
Part of the Learning Materials in Biosciences book series (LMB)

Abstract

This book developed from a course on protein structure and function that I have been offering at the University of Vienna since 1999. The course arose because I sensed a need to support my students to move forward from the theoretical knowledge of protein structure obtained in their biochemistry courses to a more active interaction that would enable them to make use of the huge amount of information on macromolecular structures stored in the Protein Data Bank (PDB). Students are used to seeing ribbon diagrams of proteins and other macromolecules in publications. However, they usually are unsure of how to interpret them and how they can be generated.

References

  1. Anon (1967a) Ribonuclease structure – some implications. Nature 213:960Google Scholar
  2. Anon (1967b) Structure and function of proteins. Nature 215(5105):1066–1067CrossRefGoogle Scholar
  3. Bartesaghi A, Merk A, Banerjee S, Matthies D, Wu X, Milne JL, Subramaniam S (2015) 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor. Science 348(6239):1147–1151.  https://doi.org/10.1126/science.aab1576 CrossRefPubMedGoogle Scholar
  4. Berndt A, Deisseroth K (2015) Optogenetics. Expanding the optogenetics toolkit. Science 349(6248):590–591.  https://doi.org/10.1126/science.aac7889 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Callaway E (2015) The revolution will not be crystallized: a new method sweeps through structural biology. Nature 525(7568):172–174.  https://doi.org/10.1038/525172a CrossRefPubMedGoogle Scholar
  6. Cate JH (2016) Structure. A big bang in spliceosome structural biology. Science 351(6280):1390–1392.  https://doi.org/10.1126/science.aaf4465 CrossRefPubMedGoogle Scholar
  7. Cruse M (2014) 100 years of crystallography. Biochemist 36(1):40–42Google Scholar
  8. Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, MacKinnon R (1998) The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280(5360):69–77CrossRefPubMedGoogle Scholar
  9. Hall KT (2014) The man in the monkeynut coat: William Astbury and the Forgotten Road to the Double-Helix. Oxford University Press, Oxford, U.K.Google Scholar
  10. Hemmer P, Gomes C (2015) Physics. Single proteins under a diamond spotlight. Science 347(6226):1072–1073.  https://doi.org/10.1126/science.aaa7440 CrossRefPubMedGoogle Scholar
  11. Kang Y, Zhou XE, Gao X, He Y, Liu W, Ishchenko A, Barty A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Ke J, Tan MH, Zhang C, Moeller A, West GM, Pascal BD, Van Eps N, Caro LN, Vishnivetskiy SA, Lee RJ, Suino-Powell KM, Gu X, Pal K, Ma J, Zhi X, Boutet S, Williams GJ, Messerschmidt M, Gati C, Zatsepin NA, Wang D, James D, Basu S, Roy-Chowdhury S, Conrad CE, Coe J, Liu H, Lisova S, Kupitz C, Grotjohann I, Fromme R, Jiang Y, Tan M, Yang H, Li J, Wang M, Zheng Z, Li D, Howe N, Zhao Y, Standfuss J, Diederichs K, Dong Y, Potter CS, Carragher B, Caffrey M, Jiang H, Chapman HN, Spence JC, Fromme P, Weierstall U, Ernst OP, Katritch V, Gurevich VV, Griffin PR, Hubbell WL, Stevens RC, Cherezov V, Melcher K, Xu HE (2015) Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature 523(7562):561–567.  https://doi.org/10.1038/nature14656 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, Phillips DC (1958) A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181(4610):662–666CrossRefPubMedGoogle Scholar
  13. Khoshouei M, Radjainia M, Baumeister W, Danev R (2017) Cryo-EM structure of haemoglobin at 3.2 A determined with the Volta phase plate. Nat Commun 8:16099.  https://doi.org/10.1038/ncomms16099 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Kobilka B (2013) The structural basis of G-protein-coupled receptor signaling (Nobel Lecture). Angew Chem Int Ed Engl 52(25):6380–6388.  https://doi.org/10.1002/anie.201302116 CrossRefPubMedPubMedCentralGoogle Scholar
  15. Laskowski RA (2016) Protein structure databases. Methods Mol Biol 1415:31–53.  https://doi.org/10.1007/978-1-4939-3572-7_2 CrossRefPubMedGoogle Scholar
  16. Lin DH, Stuwe T, Schilbach S, Rundlet EJ, Perriches T, Mobbs G, Fan Y, Thierbach K, Huber FM, Collins LN, Davenport AM, Jeon YE, Hoelz A (2016) Architecture of the symmetric core of the nuclear pore. Science 352(6283):aaf1015.  https://doi.org/10.1126/science.aaf1015 CrossRefPubMedPubMedCentralGoogle Scholar
  17. MacKinnon R (2004) Potassium channels and the atomic basis of selective ion conduction (Nobel Lecture). Angew Chem Int Ed Engl 43(33):4265–4277.  https://doi.org/10.1002/anie.200400662 CrossRefPubMedGoogle Scholar
  18. Manglik A, Kruse AC, Kobilka TS, Thian FS, Mathiesen JM, Sunahara RK, Pardo L, Weis WI, Kobilka BK, Granier S (2012) Crystal structure of the micro-opioid receptor bound to a morphinan antagonist. Nature 485(7398):321–326.  https://doi.org/10.1038/nature10954 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Miller M, Schneider J, Sathyanarayana BK, Toth MV, Marshall GR, Clawson L, Selk L, Kent SB, Wlodawer A (1989) Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. Science 246(4934):1149–1152CrossRefPubMedGoogle Scholar
  20. Ramakrishnan V (2014) The ribosome emerges from a black box. Cell 159(5):979–984.  https://doi.org/10.1016/j.cell.2014.10.052 CrossRefPubMedGoogle Scholar
  21. Rasmussen SG, DeVree BT, Zou Y, Kruse AC, Chung KY, Kobilka TS, Thian FS, Chae PS, Pardon E, Calinski D, Mathiesen JM, Shah ST, Lyons JA, Caffrey M, Gellman SH, Steyaert J, Skiniotis G, Weis WI, Sunahara RK, Kobilka BK (2011) Crystal structure of the beta2 adrenergic receptor-Gs protein complex. Nature 477(7366):549–555.  https://doi.org/10.1038/nature10361 CrossRefPubMedPubMedCentralGoogle Scholar
  22. Schwartz TW, Sakmar TP (2011) Structural biology: snapshot of a signalling complex. Nature 477(7366):540–541.  https://doi.org/10.1038/477540a CrossRefPubMedPubMedCentralGoogle Scholar
  23. Tools & Databases (2017) EMBL-EBI. http://www.ebi.ac.uk/services/all. Accessed 15 Feb 2017
  24. Ward AB, Sali A, Wilson IA (2013) Biochemistry. Integrative structural biology. Science 339(6122):913–915.  https://doi.org/10.1126/science.1228565 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Wells JA, Estell DA (1988) Subtilisin – an enzyme designed to be engineered. Trends Biochem Sci 13(8):291–297CrossRefPubMedGoogle Scholar
  26. Worrall LJ, Hong C, Vuckovic M, Deng W, Bergeron JR, Majewski DD, Huang RK, Spreter T, Finlay BB, Yu Z, Strynadka NC (2016) Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body. Nature 540:597–601.  https://doi.org/10.1038/nature20576 CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Tim Skern
    • 1
  1. 1.Max F. Perutz LaboratoriesMedical University of ViennaViennaAustria

Personalised recommendations