Principles of Cellular Protein Unfolding and Translocation Across Membranes
How properly folded, functional proteins are either inserted into or are delivered across lipid bilayer membranes is a fundamental biological process. This process is ubiquitous and referred to by many names, including transmembrane protein translocation, secretion, protein import/export, protein dislocation, or toxin internalization. This literature survey course is interested in biophysical and molecular biology-based studies of transmembrane protein translocation and will focus on the structure and function of membrane-embedded molecular machines that are capable of unfolding and translocating proteins or peptides across membranes.
Regular Meeting Time/Place: Wednesdays at 1 pm / Stanley 421 (Unless posted otherwise; backup is in 4th floor commonroom in Stanley)
Week 1 (Sept. 5) — Bryan — Reviews — Schatz & Dobberstein and Wickner & Schekman
Week 2 (Sept. 12 / Stanley 4th Fl. Commonroom) — Geoff — Theory — Simon, Peskin & Oster
Week 3 (Sept. 19) — Adam — Theory — Shariff et al.
Week 4 (Sept. 26) — Anna — Historic — Blobel & Dobberstein
Week 5 (Oct. 3 / Stanley 4th Fl. Commonroom) — Veronica — Historic — Walter et al.
Week 6 (Oct. 10) — Hector — Sec Translocon — van der Berg et al. and Benach & Hunt
Week 7 (Oct. 17) — Sam — Sec Translocon — Hessa et al. and Bowie
Week 8 (Oct. 24) — Jerod — Sec Translocon and Theory — Glick and Matlach
Week 9 (Oct. 31) — Brie — Import into the Mitochondria & Chloroplasts — Hill
Week 10 (Nov. 7) — Charlie & Phillip (back-to-back) — Outer Membrane Biogenesis — Schleiff Clantin Kim Tommassen
Week 11 (Nov. 14) — Elaine — Secretion, Toxins & Microbial Pathogenesis — Koronakis and Postle
Week 12 (Nov. 21) — James — Secretion, Toxins & Microbial Pathogenesis — Yu
Week 13 (Dec. 3) — Back-up — TBA — TBA
Fall Semester Academic Calendar
Schatz G & Dobberstein B. (1996) "Common principles of protein translocation across membranes." Science. 271: 1519. [Local-PDF] [Abstract] [Journal]
Wickner W & Schekman R. (2005) "Protein translocation across biological membranes." Science. 310: 1452. [Local-PDF] [Abstract] [Journal]
Simon SM, Peskin CS & Oster GF. (1992) "What drives the translocation of proteins?" Proc. Natl Acad. Sci. USA. 89: 3770. [Local-PDF] [Abstract] [Journal]
Glick B. (1995) "Can Hsp70 proteins act as force-generating motors?" Cell. 80: 11. [Local-PDF] [Abstract] [Journal]
Astumian RD. (1997) "Thermodynamics and Kinetics of a Brownian Motor." Science. 276: 917. [Local-PDF] [Abstract] [Journal]
Shariff K, Ghosal S & Matouschek A. (2004) "The force exerted by the membrane potential during protein import into the mitochondrial matrix."Biophys. J. 86: 3647. [Local-PDF] [Abstract] [Journal]
Drazin R, Kandel J & Collier RJ. (1971) "Structure and activity of diphtheria Toxin II. attack by trypsin at a specific site within the intact toxin molecule." J. Biol. Chem. 246: 1504. [Local-PDF] [Abstract]
Blobel G & Dobberstein B. (1975) "Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobin light chains on membrane-bound ribosomes of murine myeloma." J. Cell Biol. 67: 835. [Local-PDF] [Abstract] [Journal]
Walter P, Ibrahimi I & Blobel G. (1981) "Translocation of proteins across the endoplasmic reticulum. I. Signal recognition protein (SRP) binds to in-vitro-assembled polysomes synthesizing secretory protein." J. Cell Biol. 91: 545. [Local-PDF] [Abstract] [Journal]
Van den Berg B, Clemons WM Jr, Collinson I, Modis Y, Hartmann E, Harrison SC & Rapoport TA. (2004) "X-ray structure of a protein-conducting channel." Nature. 427: 36. [Local-PDF] [Abstract] [Journal] [PDB: 1RHZ] [PDB: 1RH5]
Benach J & Hunt JF. (2004) "Cell biology: shape-shifting protein channel." Nature. 427: 24. [Local-PDF] [Abstract] [Journal]
Woolhead CA, McCormick PJ & Johnson AE. (2004) "Nascent Membrane and Secretory Proteins Differ in FRET-Detected Folding Far Inside the Ribosome and in Their Exposure to Ribosomal Proteins" Cell. 116: 725. [Local-PDF] [Abstract] [Journal]
Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH & von Heijne G. (2005) "Recognition of transmembrane helices by the endoplasmic reticulum translocon." Nature. 433: 377. [Local-PDF] [Abstract] [Journal]
Bowie JU. (2005) "Cell biology: Border crossing" Nature. 433: 367. [Local-PDF] [Abstract] [Journal]
Matlack KE, Misselwitz B, Plath K & Rapoport TA. (1999) "BiP acts as a molecular ratchet during posttranslational transport of prepro-alpha factor across the ER membrane." Cell. 97: 553. [Local-PDF] [Abstract] [Journal]
Import into Mitochondria & Chloroplasts
Hill K, Model K, Ryan MT, Dietmeier K, Martin F, Wagner R & Pfanner N. (1998) "Tom40 forms the hydrophilic channel of the mitochondrial import pore for preproteins." Nature. 395: 516. [Local-PDF] [Abstract] [Journal]
Schatz G. (1998) "Protein transport. The doors to organelles." Nature. 395: 439. [Local-PDF] [Abstract] [Journal]
Huang S, Ratliff KS & Matouschek A. (2002) "Protein unfolding by the mitochondrial membrane potential." Nature Struct. Biol. 9: 301. [Local-PDF] [Abstract] [Journal]
Pfanner N & Truscott KN. (2002) "Powering mitochondrial protein import." Nature Struct. Biol. 9: 234. [Local-PDF] [Abstract] [Journal]
Wilcox AJ, Choy J, Bustamante C & Matouschek A. (2005) "Effect of protein structure on mitochondrial import." Proc. Natl Acad. Sci. USA. 89: 3770. [Local-PDF] [Abstract] [Journal]
Schleiff E & Soll J. (2005) "Membrane protein insertion: mixing eukaryotic and prokaryotic concepts" EMBO reports. 6: 1023. [Local-PDF] [Abstract] [Journal]
Clantin B, Delattre A, Rucktooa P, Saint N, Méli AC, Locht C, Jacob-Dubuisson F, Villeret V. (2007) "Structure of the Membrane Protein FhaC: A Member of the Omp85-TpsB Transporter Superfamily." Science. 317: 957. [Local-PDF] [Abstract] [Journal] [PDB: 2QDZ]
Kim S, Malinverni JC, Sliz P, Silhavy TJ, Harrison SC, Kahne D. (2007) "Structure and Function of an Essential Component of the Outer Membrane Protein Assembly Machine." Science. 317: 961. [Local-PDF] [Abstract] [Journal] [PDB: 2QCZ] [PDB: 2QDF]
Tommassen J. (2007) "Getting Into and Through the Outer Membrane" Science. 317: 903. [Local-PDF] [Abstract] [Journal]
Secretion, Toxins & Microbial Pathogenesis
Koronakis V, Sharff A, Koronakis E, Luisi B & Hughes C. (2000) "Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export." Nature. 405: 914. [Local-PDF] [Abstract] [Journal] [PDB: 1EK9]
Postle K & Vakharia H. (2000) "TolC, a macromolecular periplasmic 'chunnel' " Nature Struct. Biol. 7: 527. [Local-PDF] [Abstract] [Journal]
Yu EW, McDermott G, Zgurskaya HI, Nikaido H & Koshland DE Jr. (2003) "Structural Basis of Multiple Drug-Binding Capacity of the AcrB Multidrug Efflux Pump" Science. 300: 976. [Local-PDF] [Abstract] [Journal]
Oomen CJ, van Ulsen P, van Gelder P, Feijen M, Tommassen J & Gross P. (2004) "Structure of the translocator domain of a bacterial autotransporter." EMBO J. 23: 1257. [Local-PDF] [Abstract] [Journal] [PDB: 1UYN]
Meng G, Surana NK, St Geme III JW, Waksman G. (2006) "Structure of the outer membrane translocator domain of the Haemophilus influenzae Hia trimeric autotransporter." EMBO J. 25: 2297. [Local-PDF] [Abstract] [Journal] [PDB: 2GR8] [PDB: 2GR7]
Galán JE & Wolf-Watz H. (2006) "Protein delivery into eukaryotic cells by type III secretion machines." Nature. 444: 567. [Local-PDF] [Abstract] [Journal]
Krantz BA, Finkelstein A & Collier RJ. (2006) "Protein translocation through the anthrax toxin transmembrane pore is driven by a proton gradient." J. Mol. Biol. 355: 968. [Local-PDF] [Abstract] [Journal]
Krantz BA, Melnyk RA, Zhang S, Juris SJ, Lacy DB, Wu Z, Finkelstein A & Collier RJ. (2005) "A phenylalanine clamp catalyzes protein translocation through the anthrax toxin pore." Science. 309: 777. [Local-PDF] [Abstract] [Journal] [Supporting materials]
von Heijne G. (2005) "Translocation of Anthrax Toxin: Lord of the Rings" Science. 309: 709. [Local-PDF] [Abstract] [Journal]
Nature and Purpose of the MCB 290 Format
An MCB 290 course is a special topics seminar course for graduate students that focuses on a reasonably well-defined area of current research from within the broad range of disciplines represented in the MCB Dept. Faculty should strive to make the subject material as topical and up-to-date as possible. One purpose of this kind of class is to expose students to the most recent conceptual and methodological advances in a particular field.
A 290 seminar meets once a week for 1-2 hours, and carries one unit of credit. It is graded on a letter grade basis. During the first session (organizational meeting), a convenient day, time and place for the course meetings will be established. In addition, at the first meeting or very shortly thereafter, the instructor will distribute to all of the participating students a list of recent papers on the topics to be covered, and each student should select (or be assigned) the paper(s) that will be presented. The instructor should also give the students a clear picture of the nature of the presentation expected.
In general, the presentation should be a chalk talk, judiciously augmented by slides or overheads when useful, and the student should prepare a general reference list and hand-out be distributed to the rest of the class. During each meeting one (or sometimes two) students give a presentation. These presentations should provide sufficient background on the subject being covered, review the current state of knowledge in the area, and then critically analyze, in detail, the assigned paper(s). All students in the class are expected to read the specific paper(s) that will be presented at each session, which should be limited to one or two. In addition, regular attendance and active participation in discussions is required of all students in the seminar in order to receive a passing grade. A main role of the instructor is to ensure that an atmosphere is created that encourages lots of discussion and the free exchange of ideas and information.