Instructing Graduate Students to Tackle the “Real World”: A Course Description (Syllabus)

Introduction and discussion of class outline/assignments

Overview of biological membranes

2

Lipid biosynthetic pathways

P. Murray, S. A. Hayward, G. G. Govan, A. Y. Gracey, A. R. Cossins, An explicit test of the phospholipid saturation hypothesis of acquired cold tolerance in Caenorhabditis elegans. Proc. Natl. Acad. Sci. U.S.A. 104, 5489–5494 (2007).

3

Lipid bilayer organization and fluidity including relevant measurement techniques [total internal reflectance fluorescence (TIRF), fluorescence recovery after photobleaching (FRAP), fluorescence loss in photobleaching (FLIP), etc.]

F. Vazquez, S. Matsuoka, W. R. Sellers, T. Yanagida, M. Ueda, P. N. Devreotes, Tumor suppressor PTEN acts through dynamic interaction with the plasma membrane. Proc. Natl. Acad. Sci. U.S.A. 103, 3633–3638 (2006).

4

Discussion for review manuscript preparation

J. Sot, F. J. Aranda, M. I. Collado, F. M. Goñi, A. Alonso, Different effects of long- and short-chain ceramides on the gel-fluid and lamellar-hexagonal transitions of phospholipids: A calorimetric, NMR, and x-ray diffraction study. Biophys. J. 88, 3368–3380 (2005).

5

Thermodynamic properties of lipid bilayers (fluidity, fusion, and transport) and relevant measurement techniques (melting points, confocal)

M. M. Baksh, M. Jaros, J. T. Groves, Detection of molecular interactions
at membrane surfaces through
colloid phase transitions. Nature 427, 139–141 (2004).

6

Interactions of integral membrane proteins with proteins (folding, lipid/protein interactions, protein composition, hydrophobic mismatch, tilt, aggregation, protein activity/stability)

H. Nymeyer, T. B. Woolf, A. E. Garcia, Folding is not required for bilayer insertion: Replica exchange simulations of an a-helical peptide with an explicit lipid bilayer.
Proteins 59,783–790 (2005).

7

Protein sorting to membranous organelles [mitochondria, nucleus, endoplasmic reticulum (ER)]

J. M. Shockey, S. K. Gidda, D. C. Chapital, J. C. Kuan, P. K. Dhanoa, J. M. Bland, S. J. Rothstein, R. T. Mullen, J. M. Dyer, Tung tree DGAT1 and DGAT2 have nonredundant functions in triacylglycerol biosynthesis and are localized to different subdomains of the endoplasmic reticulum. Plant Cell 18, 2294–2313 (2006).

8

Discussion for grant proposal preparation

W. Wickner, R. Schekman, Protein translocation across biological membranes. Science 310, 1452–1456 (2005).

9

ER protein translocation into the lumen, folding, carbohydrate sculpting, posttranslational modifications

R. Takada, Y. Satomi, T. Kurata, N. Ueno, S. Norioka, H. Kondoh, T. Takao, S. Takada, Monounsaturated fatty acid modification of Wnt protein: Its role in Wnt secretion. Dev. Cell 11, 791–801 (2006).

10

ER lipid membrane composition, scramblases, lipid modification of proteins in the ER, and stress-response pathways (PERK)

G. K. Voeltz, W. A. Prinz, Y. Shibata, J. M. Rist, T. A. Rapoport, A class of membrane proteins shaping the tubular endoplasmic reticulum. Cell 124, 573–586 (2006).

11

ER-to-Golgi trafficking (e.g., via COPI and COPII, coat protein complexes I and II) and maturation of proteins through the Golgi

Y. Guo, A. D. Lindstedt, COPII-Golgi protein interactions regulate COPII coat assembly and Golgi size. J. Cell Biol. 174, 53–63 (2006).

12

Discussion of oral presentation preparation

Y. J. Wang, J. Wang, H. Q. Sun, M. Martinez, Y. X. Sun, E. Macia, T. Kirchhausen, J. P. Albanesi, M. G. Roth, H. L. Yin, Phosphatidylinositol 4 phosphate regulates targeting of clathrin adaptor AP-1 complexes to the Golgi. Cell 114, 299–310 (2003).

13

Trafficking of vesicles to the plasma membrane and SNARE (synaptosomal protein receptor) complexes

T. Weber, B. V. Zemelman, J. A. McNew, B. Westermann, M. Gmachl, F. Parlati, T. H. Söllner, J. E. Rothman, SNAREpins: Minimal machinery for membrane fusion. Cell 92, 759–772 (1998).

14

Trafficking between the plasma membrane and the recycling endosome

P. Zimmermann, Z. Zhang, G. Degeest, E. Mortier, I. Leenaerts, C. Coomans, J. Schulz, F. N’Kuli, P. J. Courtoy, G. David, Syndecan recycling is controlled by syntenin-PIP2 interaction and Arf6. Dev. Cell 9, 377–388 (2005).

15

Palmitylation, farnesylation, geranylgeranylation of proteins

A. El-Husseini, E. Schnell, S. Dakoji, N. Sweeney, Q. Zhou, O. Prange, C. Gauthier-Campbell, A. Aguilera-Moreno, R. A. Nicoll, D. S. Bredt, Synaptic strength regulated by palmitate cycling on PSD-95. Cell 108, 849–863 (2002).

16

Oral presentations

3 or 4 students per class

17

Oral presentations

3 or 4 students per class

18

Oral presentations

3 or 4 students per class

19

TRPC (transient receptor potential ion channel) regulation by lipids

V. J. Bezzerides, I. S. Ramsey, S. Kotecha, A. Greka, D. E. Claphan, Rapid vesicular translocation and insertion of TRP channels. Nat. Cell Biol. 6, 709–720 (2004).

20

Potassium channel regulation by lipids

H. Zhang, L. C. Cracium, T. Mirshahi, T. Rohacs, C. M. Lopes, T. Jin, D. E. Logethis, PIP2 activates KCNQ channels, and its hydrolysis underlies receptor-mediated inhibition of M currents. Neuron 37, 963–975 (2003).

21

Calcium channel regulation by lipids

M. Toselli, G. Biella, V. Taglietti, E. Cazzaniga, M. Parenti, Caveolin-1 expression and membrane cholesterol content modulate N-type calcium channel activity in NG108-15 cells. Biophys. J. 89, 2443–2457 (2005).

22

Review Paper presentations for critique

23

Review Paper presentations for critique

24

Review Paper presentations for critique

25

Viral invasion of the cell

E. Wessels, D. Duijsings, T.-K. Niu, S. Neumann, V. M. Oorschot, F. de Lange, K. H. W. Lanke, J. Klumperman, A. Henke, C. L. Jackson, W. J. G. Melchers, F. J. M. van Kuppeveld, A viral protein that blocks Arf1-mediated COP-I assembly by inhibiting the guanine nucleotide exchange factor GBF1. Dev. Cell 11, 191–201, (2006).

26

Bacterial invasion of the cell and pore-forming toxins

S. J. Tilley, E. V. Orlova, R. J. Gilbert, P. W. Andrew, H. R Saibil, Structural basis of pore formation by the bacterial toxin pneumolysin. Cell 121, 247–256 (2005)

27

Grant Proposal presentations for critique

28

Grant Proposal presentations for critique

29

Grant Proposal presentations for critique

30

GTP-binding protein (G protein)-coupled receptors (GPCR)–regulated lipid signaling (phospholipase C, PI 3-kinase, PI 5-kinase alpha, etc.)

S. Santagata, T. J. Boggon, C. L. Baird, C. A. Gomez, J. Zhao, W. S. Shan, D. G. Myszka, L. Shapiro, G-protein signaling through tubby proteins. Science 292, 2041–2050 (2001).

31

Tyrosine kinase receptor–regulated lipid signaling (phospholipase C–g, PI 3-kinase, dicacylglycerol kinase, phosphatidic acid, etc)

O. Sukocheva, C. Wadham, A. Holmes, N. Albanese, E. Verrier, F. Feng, A. Bernal, C. K. Derian, A. Ullrich, M. A. Vadas, P. Xia, Estrogen transactivates EGFR via the sphingosine 1-phosphate receptor Edg-3: The role of sphingosine kinase-1. J. Cell Biol. 173, 301–310 (2006).