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UCLA MCDBIO 191 - mcdbio191-2_syl11w

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web_191-2_11W_010211 1 Protein Folding: To be or not to be MCDB 191 Seminar, Section 2, Winter, 2011 Syllabus Class meetings Mondays, 12-1:30 PM La Kretz 101 Instructor Dr. Harumi Kasamatsu Office hours : TBA 456 Boyer Hall Phone: 825-3048 Email: [email protected] Prerequisites Life Sciences 1, 2, 3, and 4 and at least two Molecular, Cell, and Developmental Biology upper division courses (Chem 153A, MCDB 100 or 165A or M140 or MCDB 144) Course description Proper protein folding is fundamental to protein’s function and is assisted by molecular chaperones and cochaperones. With availability of structural data, we are beginning to understand how proteins fold. This seminar focuses on survey of major steps in protein folding, through reading and analysis of recent original scientific literature. Students are required to read assigned papers and to come to class prepared to ask and answer questions related to the assigned reading. Each student will also be required to analyze and present one or two papers in class. Grading is based on preparation and in-class presentation of research papers and on class participation and discussion of weekly topics. Reading materials Papers to read for presentations and class participation will be posted on the class web site. There are no textbooks. Focus: 1. A goal and brief summary of studies 2. What do authors address? 3. How do they approach their goals? 4. Pertinent results—It is important that the presenter digests results and synthesizes essence of results 5. Discussions; strengths and weaknesses of their results; other technical procedures 6. What would you do next if you are doing experiments? Presentation: 1. Power point (or overhead presentation) ---i) Do not just present as results shown in Fig.1, Fig. 2, --Fig.8 (See Focus 4); ii) Prepare concise 10-13 slides per presentation including a summary (1), goal and introduction (1), methods (2), results (4), and discussions and prospect (2); iii) Leave ample rooms for class room discussions; and iv) Class participation is essential. 2. Presenter should prepare for the class presentation, visit withweb_191-2_11W_010211 2 the instructor a week before scheduled presentation to go over prepared power point files for class presentation. 3. Presenter should call on fellow students for questions. 4. Presenter should hand in one-page critique to the instructor just before her/his presentation. 5. Class participants should read designated research articles before they come to the class, prepare for questions to ask the presenter. Grading Preparation for presentation (20), In-class paper presentation (40) and writing one-page critique (10), 70% Class participation, 30% List of Papers Reviews 1. Hartl, F.U., and Hayer-Hartl, M. (2002) Molecular chaperones in the cytosol: from naxcent chain to folded protein. Science 295, 1852-1858. 2. Deuerling, E. and Bukau, B. (2004) Chaperone-assisted protein folding of newly synthesized proteins in cytosol. Critical Reviews in Biochemistry and Molecular Biology 39, 261-277. 3. Chen, Y. and Inouye, M. (2008) The intramolecular cheprone-mediated protein folding. Current opinion in structural biology 18, 765-770. Research Papers I. Chaperones, Hsp70 4. Vogel, M., Bukau, B., Mayer, M.P. (2006) Allosteric regulation of Hsp70 chaperones by a proline switch. Mol Cell 21, 359–367. 5. Flaherty, K.M., DeLuca-Flaherty, C., McKay, D.B. (1990) Three-dimensional structure of the ATPase fragment of a 70 K heat-shock cognate protein. Nature 346, 623–628. 6. Zhu X, Zhao, X., Burkholder, W.F., Gragerov, A., Ogata, C.M., Gottesman, M.E., Hendrickson, W.A. (1996) Structural analysis of substrate binding by the molecular chaperone DnaK. Science 272,1606-1614. II. Hsp 40 7. Hennessy, F., Nicoll, W.S., Zimmermann, R., Cheetham, M.E., Blatch, G.L. (2005) Not all J domains are created equal: implications for the specificity of Hsp40-Hsp70 interactions. Protein Sci 14, 1697–1709.web_191-2_11W_010211 3 8. Fan, C.Y., Lee, S., Ren, H.Y., Cyr, D.M. (2004) Exchangeable chaperone modules contribute to specification of type I and type II Hsp40 cellular function. Mol Biol Cell 15, 761–773. III. Proline cis/trans isomerization and protein folding A. Properties of prolyl peptide bonds: PPI ase Figure 1. Non-proline (top) and proline (bottom) peptide fragments in trans and cis conformations. 9. Fischer G, Wittmann-Liebold B, Lang K, Kiefhaber T, Schmid FX. (1989). Cyclophilin and peptidyl-prolyl cis-trans isomerase are probably identical proteins. Nature. 337, 476-8. 10. Handschumacher RE, Harding MW, Rice J, Drugge RJ, Speicher DW. (1984). Cyclophilin: a specific cytosolic binding protein for cyclosporin A. Science. 226, 544-7. 11. Harding MW, Handschumacher RE, Speicher DW. (1986). Isolation and amino acid sequence of cyclophilin. J Biol Chem. 261, 8547-55. 12. Harding MW, Galat A, Uehling DE, Schreiber SL. (1989). A receptor for the immunosuppressant FK506 is a cis-trans peptidyl-prolyl isomerase. Nature. 341, 758-60. 13. Siekierka JJ, Hung SH, Poe M, Lin CS, Sigal NH. (1989). A cytosolic binding protein for the immunosuppressant FK506 has peptidyl-prolyl isomerase activity but is distinct from cyclophilin. Nature. 341, 755-7.web_191-2_11W_010211 4 14 Reimer U, Fischer G. (2002). Local structural changes caused by peptidyl-prolyl cis/trans isomerization in the native state of proteins. Biophys Chem. 96, 203-12. 15. Galat A, Metcalfe SM. (1995) Peptidylproline cis/trans isomerases. Prog Biophys Mol Biol. 63, 67-118. 16. Wedemeyer WJ, Welker E, Scheraga HA. (2002). Proline cis-trans isomerization and protein folding. Biochemistry. 41,14637-44. 17. Göthel SF, Marahiel MA. (1999). Peptidyl-prolyl cis-trans isomerases, a superfamily of ubiquitous folding catalysts. Cell Mol Life Sci. 55, 423-36. B. Cyclophilin A 18. Limacher A, Kloer DP, Flückiger S, Folkers G, Crameri R, Scapozza L. (2006). The crystal structure of Aspergillus fumigatus cyclophilin reveals 3D domain swapping of a central element. Structure. 14,185-95. 19. Howard BR, Vajdos FF, Li S, Sundquist WI, Hill CP. (2003).Structural insights into the catalytic mechanism of cyclophilin A. Nat Struct Biol.10, 475-81. C. Rapamycin binding proteinweb_191-2_11W_010211 5 20. Van Duyne GD, Standaert RF, Karplus PA, Schreiber SL, Clardy J. (1993). Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J Mol Biol. 229,


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