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.
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References
Anon (1967a) Ribonuclease structure – some implications. Nature 213:960
Anon (1967b) Structure and function of proteins. Nature 215(5105):1066–1067
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
Berndt A, Deisseroth K (2015) Optogenetics. Expanding the optogenetics toolkit. Science 349(6248):590–591. https://doi.org/10.1126/science.aac7889
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
Cate JH (2016) Structure. A big bang in spliceosome structural biology. Science 351(6280):1390–1392. https://doi.org/10.1126/science.aaf4465
Cruse M (2014) 100 years of crystallography. Biochemist 36(1):40–42
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):69–77
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.
Hemmer P, Gomes C (2015) Physics. Single proteins under a diamond spotlight. Science 347(6226):1072–1073. https://doi.org/10.1126/science.aaa7440
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
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):662–666
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
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
Laskowski RA (2016) Protein structure databases. Methods Mol Biol 1415:31–53. https://doi.org/10.1007/978-1-4939-3572-7_2
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
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
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
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):1149–1152
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
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
Schwartz TW, Sakmar TP (2011) Structural biology: snapshot of a signalling complex. Nature 477(7366):540–541. https://doi.org/10.1038/477540a
Tools & Databases (2017) EMBL-EBI. http://www.ebi.ac.uk/services/all. Accessed 15 Feb 2017
Ward AB, Sali A, Wilson IA (2013) Biochemistry. Integrative structural biology. Science 339(6122):913–915. https://doi.org/10.1126/science.1228565
Wells JA, Estell DA (1988) Subtilisin – an enzyme designed to be engineered. Trends Biochem Sci 13(8):291–297
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
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Skern, T. (2018). The Rationale Behind This Workbook. In: Exploring Protein Structure: Principles and Practice. Learning Materials in Biosciences. Springer, Cham. https://doi.org/10.1007/978-3-319-76858-8_1
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DOI: https://doi.org/10.1007/978-3-319-76858-8_1
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