BP Scheine
BIOPHYSIK-SCHEINE 2005
www.biochemtech.uni-halle.de/xray/Seminars_2005.html
The Biophysik-Scheine will be awarded on the basis of seminars on a recent structural paper. These seminars will take place on Thursdays from 13.00 - 14.30, starting on 14. April 2005.
Things to know from the paper:
1. Function: what does (do) the protein(s) do?
2. Methods: how was the structure obtained?
3. Structure: how does the structure explain the function?
4. Critical points? Does the structure REALLY explain the function?
Some or all of this should come across in the presentation – in Powerpoint if you like; look at the structure from the Protein Data Bank and display it using PyMol if you want (see "Protein structure visualisation" from our Technische Biochemie Praktikum for more information)..... Your talk can be in English or German, as you wish.
Note: some of the papers also have supplementary information (such as movies), links are provided. If you have any problems with these, please contact me.
For some very useful notes (in German) on how to prepare your seminar, follow this link (courtesy of Prof. Dr. Jochen Balbach, Fachbereich Physik).
Seminars should last ca. 15 minutes, with 5 minutes left for discussion....
Donnerstag, 14. April 2005: Vorbesprechung
0.0 Milton T. Stubbs
Donnerstag, 21. April 2005: Proteins at the membrane interface
1.1 Annett Weichert & Jörg Schildhauer
Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating. Fotin A, Cheng Y, Grigorieff N, Walz T, Harrison SC, Kirchhausen T. Nature. 2004 Dec 2;432(7017):649-53.
1.2 Benjamin Schmiedel & Sebastian Vogt
Insights into assembly from structural analysis of bacteriophage PRD1. Abrescia NG, Cockburn JJ, Grimes JM, Sutton GC, Diprose JM, Butcher SJ, Fuller SD, San Martin C, Burnett RM, Stuart DI, Bamford DH, Bamford JK. Nature. 2004 Nov 4;432(7013):68-74.
1.2a, 1.2b,
1.3 Stephan Götz & Wiebke Chemnitz
Structural basis for the function of the beta subunit of the eukaryotic signal recognition particle receptor. Schwartz T, Blobel G. Cell. 2003 Mar 21;112(6):793-803.
Donnerstag, 28. April 2005: Chaperone activity
2.1 Marie-Christine Mouttey & Birgit Grote
X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex. Griffith JP, Kim JL, Kim EE, Sintchak MD, Thomson JA, Fitzgibbon MJ, Fleming MA, Caron PR, Hsiao K, Navia MA. Cell. 1995 Aug 11;82(3):507-22.
2.2 Swetlana Rot & Dajana Reuter
X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli. Choudhury D, Thompson A, Stojanoff V, Langermann S, Pinkner J, Hultgren SJ, Knight SD. Science. 1999 Aug 13;285(5430):1061-6.
2.3 Anja Hellwege & Jana Leise
Crystal structure of Mip, a prolylisomerase from Legionella pneumophila. Riboldi-Tunnicliffe A, Konig B, Jessen S, Weiss MS, Rahfeld J, Hacker J, Fischer G, Hilgenfeld R. Nat Struct Biol. 2001 Sep;8(9):779-83.
Donnerstag, 12. Mai 2005: Getting proteins across membranes
3.1 Sophie Winterfeld & Chris Oschatz
Crystal structure of LexA: a conformational switch for regulation of self-cleavage. Luo Y, Pfuetzner RA, Mosimann S, Paetzel M, Frey EA, Cherney M, Kim B, Little JW, Strynadka NC. Cell. 2001 Sep 7;106(5):585-94.
3.2 Anja Bräutigam & Sabrina von Einem
X-ray structure of a protein-conducting channel. Van den Berg B, Clemons WM Jr, Collinson I, Modis Y, Hartmann E, Harrison SC, Rapoport TA. Nature. 2004 Jan 1;427(6969):36-44.
3.2a, 3.2b 3.2c 3.2d 3.2e 3.2f 3.2g 3.2h 3.2i
3.3 Heike Berudt & Anne Rietz
Structural basis for the assembly of a nuclear export complex. Matsuura Y, Stewart M. Nature. 2004 Dec 16;432(7019):872-7.
3.3a, 3.3b 3.3c 3.3d
Donnerstag, 19. Mai 2005: Anthrax toxins
4.1 Andreas Hoffmann & Jörg Wenze
Crystal structure of the anthrax lethal factor. Pannifer AD, Wong TY, Schwarzenbacher R, Renatus M, Petosa C, Bienkowska J, Lacy DB, Collier RJ, Park S, Leppla SH, Hanna P, Liddington RC. Nature. 2001 Nov 8;414(6860):229-33.
4.1a,
4.2 Katharina Müller & Andrea Steinmetz
Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin. Drum CL, Yan SZ, Bard J, Shen YQ, Lu D, Soelaiman S, Grabarek Z, Bohm A, Tang WJ. Nature. 2002 Jan 24;415(6870):396-402.
4.2a, 4.2b
4.3 Romy Klausnitzer & Jan Heumann
Crystal structure of a complex between anthrax toxin and its host cell receptor. Santelli E, Bankston LA, Leppla SH, Liddington RC. Nature. 2004 Aug 19;430(7002):905-8.
4.4 Andreas Kirsten
Structure of heptameric protective antigen bound to an anthrax toxin receptor: a role for receptor in pH-dependent pore formation. Lacy DB, Wigelsworth DJ, Melnyk RA, Harrison SC, Collier RJ. Proc Natl Acad Sci U S A. 2004 Sep 7;101(36):13147-51.
Donnerstag, 26. Mai 2005: RNA polymerase, RNA silencing
5.1 Julia Rohrberg & Grit Mehnert
Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase. Thompson AA, Peersen OB. EMBO J. 2004 Sep 1;23(17):3462-71.
5.2 Anke Liepelt & Ulf Liebal
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. Martin G, Keller W, Doublie S. EMBO J. 2000 Aug 15;19(16):4193-203.
5.3 Anne Baude & Nina Kreißig
Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Parker JS, Roe SM, Barford D. Nature. 2005 Mar 31;434(7033):663-6.
5.3a 5.3b 5.3c 5.3d
Donnerstag, 2. Juni 2005: Ubiquitin and partners
6.1 Martin Dippe & Sebastian Kirsch
Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1. Lois LM, Lima CD. EMBO J. 2005 Feb 9;24(3):439-51
6.1a, 6.1b
6.2 Irene Müller& Isabel Naarmann
SUMO modification of the ubiquitin-conjugating enzyme E2-25K. Pichler A, Knipscheer P, Oberhofer E, van Dijk WJ, Korner R, Olsen JV, Jentsch S, Melchior F, Sixma TK. Nat Struct Mol Biol. 2005 Mar;12(3):264-9.
6.2a,
6.3 Jens Primpke & Christian Wölfer
Structural basis of NEDD8 ubiquitin discrimination by the deNEDDylating enzyme NEDP1. Shen LN, Liu H, Dong C, Xirodimas D, Naismith JH, Hay RT. EMBO J. 2005 Mar 17
6.4 Juliane Braun
Unique binding interactions among Ubc9, SUMO and RanBP2 reveal a mechanism for SUMO paralog selection. Tatham MH, Kim S, Jaffray E, Song J, Chen Y, Hay RT. Nat Struct Mol Biol. 2005 Jan;12(1):67-74.
6.4a, 6.4b,
Donnerstag, 9. Juni 2004: Enzymes at work
7.1 Alexander Bepperling & Franziska Hamann
Insight into steroid scaffold formation from the structure of human oxidosqualene cyclase. Thoma R, Schulz-Gasch T, D'Arcy B, Benz J, Aebi J, Dehmlow H, Hennig M, Stihle M, Ruf A. Nature. 2004 Nov 4;432(7013):118-22.
7.1a,
7.2 Tina Strauß & Sabine Bergelt
High-resolution crystal structures of Caldicellulosiruptor strain Rt8B.4 carbohydrate-binding module CBM27-1 and its complex with mannohexaose. Roske Y, Sunna A, Pfeil W, Heinemann U. J Mol Biol. 2004 Jul 9;340(3):543-54.
7.3 Stephan Fischer & Matthias Bosse
KIF1A alternately uses two loops to bind microtubules. Nitta R, Kikkawa M, Okada Y, Hirokawa N. Science. 2004 Jul 30;305(5684):678-83.
7.3a, 7.3b 7.3c
Donnerstag, 16. Juni 2004: DNA repair
8.1 Rene Geißler & Paul Knick
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Banerjee A, Yang W, Karplus M, Verdine GL. Nature. 2005 Mar 31;434(7033):612-8.
8.1a 8.1b 8.1c 8.1d 8.1e 8.1f 8.1g
8.2 Andre Steven & Stephan Zimmermann
Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Mees A, Klar T, Gnau P, Hennecke U, Eker AP, Carell T, Essen LO. Science. 2004 Dec 3;306(5702):1789-93.
8.2a
8.3 Mario Träger & Franka Gaede
Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Singleton MR, Dillingham MS, Gaudier M, Kowalczykowski SC, Wigley DB. Nature. 2004 Nov 11;432(7014):187-93.