Recommended Readings: Tom Maniatis, Ph.D., Friday October 6th, 2017

Friday Lectures

Friday, October 06, 2017  3:45 p.m.

Caspary Auditorium

Tom Maniatis, Ph.D.

Isidore S. Edelman Professor and Chair

Department of Biochemistry and Molecular Biophysics

Columbia University Medical Center

The Generation and Function of Protocadherin Cell Surface Diversity in Mammalian Neural Circuit Assembly

Recommended Readings:

Technology Networks Wrong Wiring Causes Depression. Apr 28, 2017

Rubinstein, Rotem; Goodman, Kerry Marie; Maniatis, Tom; et al. (2017). Structural origins of clustered protocadherin-mediated neuronal barcoding. SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 69 (SI): 140-150. PLEASE REQUEST FROM MARKUS LIBRARY.

Chen, Weisheng V.; Nwakeze, Chiamaka L.; Denny, Christine A.; et al. (2017). Pcdh alpha c2 is required for axonal tiling and assembly of serotonergic circuitries in mice. SCIENCE. 356 (6336): 406-410

Mountoufaris, George; Chen, Weisheng V.; Hirabayashi, Yusuke; et al. (2017). Multicluster Pcdh diversity is required for mouse olfactory neural circuit assembly. SCIENCE. 356 (6336): 411-413  

Goodman, Kerry Marie; Rubinstein, Rotem; Thu, Chan Aye; et al. (2016). gamma-Protocadherin structural diversity and functional implications. ELIFE. 5: e20930  

Chen, Weisheng V.; Maniatis, Tom (2013). Clustered protocadherins. DEVELOPMENT. 140 (16): 3297-3302

Lefebvre, Julie L.; Kostadinov, Dimitar; Chen, Weisheng V.; et al. (2012). Protocadherins mediate dendritic self-avoidance in the mammalian nervous system. NATURE. 488 (7412): 517-+

Recommended Readings: Sue Biggins, Ph.D., Friday May 5th, 2017

Friday Lectures

Friday, May 5th, 2017   3:45 p.m.

Caspary Auditorium

Sue Biggins, Ph.D.

Member and Associate Director

Division of Basic Sciences

Fred Hutchinson Cancer Research Center

Sensing Tension at Kinetochores

Recommended Readings: 

Miller, Matthew P.; Asbury, Charles L.; Biggins, Sue (2016). A TOG Protein Confers Tension Sensitivity to Kinetochore-Microtubule Attachments. CELL. 165(6): 1428-1439

Musacchio, Andrea (2015). The Molecular Biology of Spindle Assembly Checkpoint Signaling Dynamics. CURRENT BIOLOGY.  25(20): R1002-R1018

Biggins, Sue (2015). Under tension: Kinetochores and Basic Research. GENETICS. 200(3): 681-682

London, Nitobe; Biggins, Sue (2014). Signalling dynamics in the spindle checkpoint response. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 15 (11): 735-747

Sarangapani, Krishna K.; Duro, Eris; Deng, Yi; et al. (2014). Sister kinetochores are mechanically fused during meiosis I in yeast. SCIENCE. 346(6206): 248-251

Biggins, Sue (2013). The Composition, Functions, and Regulation of the Budding Yeast Kinetochore. GENETICS. 194(4): 817-846

Gonen, Shane; Akiyoshi, Bungo; Iadanza, Matthew G.; et al. (2012). The structure of purified kinetochores reveals multiple microtubule-attachment sites. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 19( 9): 925-929







Recommended Readings: Tarun Kapoor, Ph.D., April 18

Monday Lecture Series
Monday, April 18, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Tarun Kapoor, Ph.D.
Pels Family Professor and Head,
Selma and Lawrence Ruben Laboratory of Chemistry and Cell Biology,
The Rockefeller University

New Chemical Probes for Ribosome Biogenesis and Cytoskeleton Organization

Recommended Readings

Kasap, C., Elemento, O., & Kapoor, T. M. (2014). DrugTargetSeqR: a genomics-and CRISPR-Cas9–based method to analyze drug targets. Nature Chemical Biology, 10(8), 626-628. doi: 10.1038/nchembio.1551

See, S. K., Hoogendoorn, S., Chung, A. H., Ye, F., Steinman, J. B., Sakata-Kato, T., … & Chen, J. K. (2015). Cytoplasmic dynein antagonists with improved potency and isoform selectivity. ACS Chemical Biology, 11(1), 53-60. doi:10.1021/acschembio.5b00895

Shimamoto, Y., Forth, S., & Kapoor, T. M. (2015). Measuring pushing and braking forces generated by ensembles of kinesin-5 crosslinking two microtubules. Developmental Cell, 34(6), 669-681. doi:10.1016/j.devcel.2015.08.017

Recommended Readings: Xiaoliang “Sunney” Xie, Ph.D, January 15

Friday Lecture Series
Friday, January 15, 2016
3:45 p.m., Caspary Auditorium

Xiaoliang “Sunney” Xie, Ph.D.
Mallinckrodt Professor of Chemistry and Chemical Biology,
Harvard University

Life at the Single Molecule Level: From Single Molecule  Enzymology to MALBAC Babies

Recommended Reading

Empirical Articles

Hou, Y., Fan, W., Yan, L., Li, R., Lian, Y., Huang, J., … & Qiao, J. (2013). Genome analyses of single human oocytes. Cell, 155(7), 1492-1506. doi: 10.1016/j.cell.2013.11.040.

Lu, S., Zong, C., Fan, W., Yang, M., Li, J., Chapman, A. R., … & Bai, F. (2012). Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science, 338(6114), 1627-1630. doi: 10.1126/science.1229112.

Taniguchi, Y., Choi, P. J., Li, G. W., Chen, H., Babu, M., Hearn, J., … & Xie, X. S. (2010). Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science, 329(5991), 533-538. doi: 10.1126/science.1188308.

Zong, C., Lu, S., Chapman, A. R., & Xie, X. S. (2012). Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338(6114), 1622-1626. doi: 10.1126/science.1229164.

Review Papers

Li, G. W., & Xie, X. S. (2011). Central dogma at the single-molecule level in living cells. Nature, 475(7356), 308-315. doi: 10.1038/nature10315.

Xie, X. S. (2010). Enzymology and life at the single molecule level. In Single Molecule Spectroscopy in Chemistry, Physics and Biology (pp. 435-448). Springer Berlin Heidelberg.

Recommended Readings: David Baker, Ph.D., April 29

Special Lecture Series
Wednesday, April 29, 2015
3:45 p.m., Carson Family Auditorium (CRC)

David Baker, Ph.D.,
Professor of Biochemistry,
University of Washington
Investigator, Howard Hughes Medical Institute

Post-Evolutionary Biology: Design of Novel Protein Structures, Functions and Assemblies

Recommended Readings

Empirical Articles

Bradley, P., Misura, K. M., & Baker, D. (2005). Toward high-resolution de novo structure prediction for small proteins. Science, 309(5742), 1868-1871.

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., … & Popović, Z. (2010). Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. doi:10.1038/nature09304

Eiben, C. B., Siegel, J. B., Bale, J. B., Cooper, S., Khatib, F., Shen, B. W., … & Baker, D. (2012). Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology, 30(2), 190-192. doi:10.1038/nbt.2109

Jiang, L., Althoff, E. A., Clemente, F. R., Doyle, L., Röthlisberger, D., Zanghellini, A., … & Baker, D. (2008). De novo computational design of retro-aldol enzymes. Science, 319(5868), 1387-1391. doi:10.1126/science.1152692

Review Papers

Adams, P. D., Baker, D., Brunger, A. T., Das, R., DiMaio, F., Read, R. J., … & Terwilliger, T. C. (2013). Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics, 42, 265-287.doi: 10.1146/annurev-biophys-083012-130253

Das, R., & Baker, D. (2008). Macromolecular modeling with Rosetta. Annual Review of Biophysics, 77, 363-382. doi:10.1146/annurev.biochem.77.062906.171838

Recommended Readings: Tom Muir, Ph.D., March 27

Friday Lecture Series
Friday, March 27, 2015
3:45 p.m., Caspary Auditorium

Tom Muir, Ph.D.
Van Zandt Williams Jr. Class of ‘65 Professor of Chemistry,
Chair, Department of chemistry
Princeton University

‘Houdini’ Proteins: Discovery and Applications of Ultrafast Inteins

Recommended Readings

Empirical Articles

Shah, N. H., Dann, G. P., Vila-Perelló, M., Liu, Z., & Muir, T. W. (2012). Ultrafast protein splicing is common among cyanobacterial split inteins: Implications for protein engineering. Journal of the American Chemical Society, 134(28), 11338–11341. doi:10.1021/ja303226x

Shah, N. H., Eryilmaz, E., Cowburn, D., & Muir, T. W. (2013). Naturally split inteins assemble through a “capture and collapse” mechanism. Journal of the American Chemical Society, 135(49), 18673–18681. doi:10.1021/ja4104364

Shah, N. H., Vila-Perelló, M., & Muir, T. W. (2011). Kinetic control of one-pot trans-splicing reactions by using a wild-type and designed split intein. Angewandte Chemie, 50(290, 6511–6515. doi:10.1002/anie.201102909

Vila-Perelló, M., Liu, Z., Shah, N. H., Willis, J. A., Idoyaga, J., & Muir, T. W. (2013). Streamlined expressed protein ligation using split inteins. Journal of the American Chemical Society, 135(1), 286–292. doi:10.1021/ja309126m

Review Papers

Eryilma, E., Shah, N. H., Muir, T. W., & Cowburn, D. (2014). Structural and dynamical features of Inteins and implications on protein splicing. Journal of Biological Chemistry, 289(21), 14506–14511. doi:10.1074/jbc.R113.540302

Shah, N. H., & Muir, T. W. (2014). Inteins: Nature’s Gift to Protein Chemists. Chemical Science, 5(1), 446–461. doi:10.1016/j.biotechadv.2011.08.021.Secreted

Recommended Readings: Lingyin Li, Ph.D., February 25

Special Lecture
Wednesday, February 25, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Lingyin Li, Ph.D.,
Merck Fellow of the Jane Coffins Child Memorial Fund,
Department of Systems Biology,
Harvard Medical School

Chemical Biology of Anti-Cancer Innate Immunity

Recommended Readings

Kim, S., Li, L., Maliga, Z., Yin, Q., Wu, H., & Mitchison, T. J. (2013). Anticancer flavonoids are mouse-selective STING agonists. ACS Chemical Biology, 8(7), 1396–1401. doi:10.1021/cb400264n

Li, L., Yin, Q., Kuss, P., Maliga, Z., Wu, H., & Mitchison, T. J. (2014). Hydrolysis of 2′3′-cGAMP by ENPP1 and design of nonhydrolyzable analogs. Nature Chemical Biology, 10(12), 1043–1048. doi:10.1038/nchembio.1661

Recommended Readings: Howard Hang, Ph.D. November 17

Monday Lecture Series
Monday, November 17, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Howard Hang, Ph.D.
Professor and Head,
Laboratory of Chemical Biology and Microbial Pathogenesis,
The Rockefeller University

A C. elegans Model for Commensal Bacteria Function Reveals a Secreted Peptidoglycan Hydrolase Activator of Host Immunity

Recommended Readings

Empirical Articles

Charron, G., Zhang, M. M., Yount, J. S., Wilson, J., Raghavan, A. S., Shamir, E., & Hang, H. C. (2009). Robust fluorescent detection of protein fatty-acylation with chemical reporters. Journal of the American Chemical Society, 131(13), 4967–4975. doi:10.1021/ja810122f

Hang, H. C., Geutjes, E.-J., Grotenbreg, G., Pollington, A. M., Bijlmakers, M. J., & Ploegh, H. L. (2007). Chemical probes for the rapid detection of Fatty-acylated proteins in Mammalian cells. Journal of the American Chemical Society, 129(10), 2744–2745. doi:10.1021/ja0685001

Yount, J. S., Moltedo, B., Yang, Y.-Y., Charron, G., Moran, T. M., López, C. B., & Hang, H. C. (2010). Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3. Nature Chemical Biology, 6(8), 610–614. doi:10.1038/nchembio.405

Review Paper

Grammel, M., & Hang, H. C. (2013). Chemical reporters for biological discovery. Nature Chemical Biology, 9(8), 475–484. doi:10.1038/nchembio.1296

The Much Maligned Tick: Key to a New Class of Antibiotics?

Yale researchers have discovered a glycoprotein in ticks (Ixodidae) that kicks in during winter to protect them from the cold also fights infection.  This protein may be the key to a new class of an antibiotics to help  in the battle against dangers pathogens such as MRSA.
Read more at:

Recommended Readings: Daniel Finley, Ph.D. May 30

Friday Lecture Series
Friday, May 30, 2014
3:45 p.m., Caspary Auditorium

Daniel Finley, Ph.D.
Department of Cell Biology
Harvard Medical School

Regulation of Proteasome Activity by Ubiquitin Chain Editing

Recommended Readings:

Empirical Articles

Crosas, B., Hanna, J., Kirkpatrick, D. S., Zhang, D. P., Tone, Y., Hathaway, N. a, … Finley, D. (2006). Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities. Cell, 127(7), 1401–1413. doi:10.1016/j.cell.2006.09.051

Hanna, J., Hathaway, N. a, Tone, Y., Crosas, B., Elsasser, S., Kirkpatrick, D. S., … Finley, D. (2006). Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation. Cell, 127(1), 99–111. doi:10.1016/j.cell.2006.07.038

Lee, B.-H., Lee, M. J., Park, S., Oh, D.-C., Elsasser, S., Chen, P.-C., … Finley, D. (2010). Enhancement of proteasome activity by a small-molecule inhibitor of USP14. Nature, 467(7312), 179–184. doi:10.1038/nature09299

Leggett, D. S., Hanna, J., Borodovsky, A., Crosas, B., Schmidt, M., Baker, R. T., … Finley, D. (2002). Multiple associated proteins regulate proteasome structure and function. Molecular Cell, 10(3), 495–507.

Review Papers

Finley, D. (2009). Recognition and Processing of Ubiquitin-Protein Conjugates by the Proteasome. Annual Review of Biochemistry, 78(1), 477–513. doi:10.1146/annurev.biochem.78.081507.101607

Schmidt, M., & Finley, D. (2014). Regulation of proteasome activity in health and disease. Biochimica et Biophysica Acta, 1843(1), 13–25. doi:10.1016/j.bbamcr.2013.08.012