Recommended Readings: Shixin Liu Ph.D. Monday November 14 2016

Monday Lectures

Monday November 14, 2016   3:45 p.m.

Caspary Auditorium

Shixin Liu   Ph.D.

Assistant Professor, The Rockefeller University

Laboratory of Nanoscale Biophysics and Biochemistry

Watching Biological Machines in Action

Recommended Readings:

 Liu, Shixin; Chistol, Gheorghe; Hetherington, Craig L.; et al.  A Viral Packaging Motor Varies Its DNA Rotation and Step Size to Preserve Subunit Coordination as the Capsid Fills.  CELL    157 (3):702-713     APR 24 2014

Chemla, Yann R.  High-Resolution, Hybrid Optical Trapping Methods, and Their Application to Nucleic Acid Processing Proteins.  BIOPOLYMERS   105(10): 704-714    OCT 2016

Ha, Taekjip.  Single-molecule methods leap aheadNATURE METHODS    11(10)1015-1018    OCT 2014

Guo, Peixuan; Grainge, Ian; Zhao, Zhengyi; et al.  Two classes of nucleic acid translocation motors: rotation and revolution without rotation. CELL AND BIOSCIENCE  4:54     SEP 16 2014

Casjens, Sherwood R.  The DNA-packaging nanomotor of tailed bacteriophages.  NATURE REVIEWS MICROBIOLOGY   9(9):647-657   SEP 2011

Chemla, YR; Aathavan, K; Michaelis, J; et al.  Mechanism of force generation of a viral DNA packaging motor. CELL   122(5 ): 683-692   : SEP 9 2005 

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: Jue Chen, Ph.D., February 27

Friday Lecture Series / Ph.D. Recruitment Lecture
Friday, February 25, 2015
3:45 p.m., Caspary Auditorium

Jue Chen, Ph.D.,
Head of Laboratory of Membrane Biology and Biophysics,
The Rockefeller University
Investigator, Howard Hughes Medical Institute

Understanding Molecular Pumps: Insights from Structural BiologyRecommended Readings

Empirical Articles

Chen, S., Oldham, M. L., Davidson, A. L., & Chen, J. (2013). Carbon catabolite repression of the maltose transporter revealed by X-ray crystallography. Nature, 499(7458), 364-368. doi:10.1038/nature12232

Jin, M. S., Oldham, M. L., Zhang, Q., & Chen, J. (2012). Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans. Nature. 490(7421), 566-569. doi:10.1038/nature11448

Oldham, M. L., Chen, S., & Chen, J. (2013). Structural basis for substrate specificity in the Escherichia coli maltose transport system. Proceedings of the National Academy of Sciences, 110(45), 18132-18137. doi:10.1073/pnas.1311407110

Review Papers

Chen, J. (2013). Molecular mechanism of the Escherichia coli maltose transporterCurrent Opinion in Structural Biology, 23(4), 492-498. doi: 10.1016/

Recommended Readings: Amédée des Georges, Ph.D. October 20

Special Lecture Series
Monday, October 20, 2014
4:00 p.m., Carson Family Auditorium

Amédée des Georges, Ph.D.
Postdoctoral Associate,
Department of Biochemistry and Molecular Biophysics,
Columbia University

Structures of Eukaryotic Translation Initiation Complexes by Single-Particle Cryo-EM, a Powerful Tool for the Study of Heterogeneous Samples

Recommended Readings

Empirical Articles

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. Nature, 503(7477), 539–543. doi:10.1038/nature12658

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29. Cell, 153(5), 1108–1119. doi:10.1016/j.cell.2013.04.036

Hashem, Y., des Georges, A., Fu, J., Buss, S. N., Jossinet, F., Jobe, A., … Frank, J. (2013). High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature, 494(7437), 385–389. doi:10.1038/nature11872

Review Papers

Jackson, R. J., Hellen, C. U. T., & Pestova, T. V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews Molecular Cell Biology, 11(2), 113–127. doi:10.1038/nrm2838

Recommended Readings: Thomas Walz, Ph.D. June 23

Special Seminar 
Monday, June 23, 2014
4:00 p.m., Carson Family Auditorium

Thomas Walz, Ph.D
Professor, Department of Cell Biology
Harvard Medical School
Investigator, Howard Hughes Medical Institute

Using Two-dimensional Crystals of Aquaporin-0 to Investigate Lipid-Protein Interactions

Recommended Readings:

Empirical Articles

Aponte-Santamaría, C., Briones, R., Schenk, A. D., Walz, T., & de Groot, B. L. (2012). Molecular driving forces defining lipid positions around aquaporin-0. Proceedings of the National Academy of Sciences, 109(25), 9887–9892. doi:10.1073/pnas.1121054109

Gonen, T., Cheng, Y., Sliz, P., Hiroaki, Y., Fujiyoshi, Y., Harrison, S. C., & Walz, T. (2005). Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature, 438(7068), 633–638. doi:10.1038/nature04321

Gonen, T., Sliz, P., Kistler, J., Cheng, Y., & Walz, T. (2004). Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature, 429(6988), 193–197. doi:10.1038/nature02503

Hite, R. K., Li, Z., & Walz, T. (2010). Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals. The EMBO Journal, 29(10), 1652–1658. doi:10.1038/emboj.2010.68

Review Papers

Gonen, T., & Walz, T. (2006). The structure of aquaporins. Quarterly Reviews of Biophysics, 39(4), 361–396. doi:10.1017/S0033583506004458

Raunser, S., & Walz, T. (2009). Electron crystallography as a technique to study the structure on membrane proteins in a lipidic environment. Annual Review of Biophysics, 38, 89–105. doi:10.1146/annurev.biophys.050708.133649

Recommended Readings: Angeline Lyon, Ph.D. Monday, January 6

Monday, January 6, 2014
4:00 p.m., Carson Family Auditorium

Angeline Lyon, Ph.D.
American Heart Association Postdoctoral Fellow
Life Sciences Institute, University of Michigan

Molecular Mechanisms of Phospholipase Cβ Regulation

Recommended Readings:

Empirical Articles

Hicks, S. N., Jezyk, M. R., Gershburg, S., Seifert, J. P., Harden, T. K., & Sondek, J. (2008). General and versatile autoinhibition of PLC isozymes. Molecular Cell, 31(3), 383–394. doi:10.1016/j.molcel.2008.06.018

Lyon, A. M., Dutta, S., Boguth, C. A., Skiniotis, G., & Tesmer, J. J. G. (2013). Full-length Gα(q)-phospholipase C-β3 structure reveals interfaces of the C-terminal coiled-coil domain. Nature: Structural & Molecular Biology, 20(3), 355–362. doi:10.1038/nsmb.2497

Lyon, A. M., Tesmer, V. M., Dhamsania, V. D., Thal, D. M., Gutierrez, J., Chowdhury, S., … Tesmer, J. J. G. (2011). An autoinhibitory helix in the C-terminal region of phospholipase C-β mediates Gαq activation. Nature: Structural & Molecular Biology, 18(9), 999–1005. doi:10.1038/nsmb.2095

Tadano, M., Edamatsu, H., Minamisawa, S., Yokoyama, U., Ishikawa, Y., Suzuki, N., … Kataoka, T. (2005). Congenital semilunar valvulogenesis defect in mice deficient in phospholipase C epsilon. Molecular and Cellular Biology, 25(6), 2191–2199. doi:10.1128/MCB.25.6.2191-2199.2005

Wang, H., Oestreich, E. A., Maekawa, N., Bullard, T. A., Vikstrom, K. L., Dirksen, R. T., … Smrcka, A. V. (2005). Phospholipase C epsilon modulates beta-adrenergic receptor-dependent cardiac contraction and inhibits cardiac hypertrophy. Circulation Research, 97(12), 1305–13. doi:10.1161/

Review Papers

Gresset, A., Sondek, J., & Harden, T. K. (2012). The phospholipase C isozymes and their regulationSub-Cellular Biochemistry58, 61–94. doi:10.1007/978-94-007-3012-0_3

Suh, P.-G., Park, J.-I., Manzoli, L., Cocco, L., Peak, J. C., Katan, M., … Ryu, S. H. (2008). Multiple roles of phosphoinositide-specific phospholipase C isozymesBMB Reports41(6), 415–434.

Woodcock, E. a, Kistler, P. M., & Ju, Y.-K. (2009). Phosphoinositide signalling and cardiac arrhythmiasCardiovascular Research82(2), 286–295. doi:10.1093/cvr/cvn283

Recommended Readings: Seth Darst, Ph.D. Monday, Dec. 9

Monday Lecture Series
Structural studies of bacterial transcription: Bacteriophage T7 Gp2 inhibition of Escherichia coli RNA polymerase
Seth Darst, Ph.D.
Jack Fishman Professor
Laboratory of Molecular Biophysics
The Rockefeller University
4:00 p.m., Carson Family Auditorium

Recommended Readings

Review Paper

Samson, J. E., Magadán, A. H., Sabri, M., & Moineau, S. (2013). Revenge of the phages: defeating bacterial defenses. Nature Reviews Microbiology, 11(10), 675–687. doi:10.1038/nrmicro3096

Empirical Articles

Bae, B., Davis, E., Brown, D., Campbell, E. a, Wigneshweraraj, S., & Darst, S. a. (In Press). Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ70 domain 1.1. Proceedings of the National Academy of Sciences of the United States of America. doi:10.1073/pnas.1314576110

Cámara, B., Liu, M., Reynolds, J., Shadrin, A., Liu, B., Kwok, K., … Wigneshweraraj, S. R. (2010). T7 phage protein Gp2 inhibits the Escherichia coli RNA polymerase by antagonizing stable DNA strand separation near the transcription start site. Proceedings of the National Academy of Sciences of the United States of America, 107(5), 2247–2252. doi:10.1073/pnas.0907908107

James, E., Liu, M., Sheppard, C., Mekler, V., Cámara, B., Liu, B., … Wigneshweraraj, S. (2012). Structural and mechanistic basis for the inhibition of Escherichia coli RNA polymerase by T7 Gp2. Molecular Cell, 47(5), 755–766. doi:10.1016/j.molcel.2012.06.013

Sheppard, C., Cámara, B., Shadrin, A., Akulenko, N., Liu, M., Baldwin, G., … Wigneshweraraj, S. R. (2011). Inhibition of Escherichia coli RNAp by T7 Gp2 protein: role of negatively charged strip of amino acid residues in Gp2. Journal of Molecular Biology, 407(5), 623–632. doi:10.1016/j.jmb.2011.02.013

Recommended Readings: Benjamin Judkewitz Ph.D. Monday September 16, 2013

Monday Seminar   September 16, 2013

Deep Tissue Fluorescence Imaging With Time-reversed Light

Benjamin Judkewitz, Ph.D.

Sir Henry Wellcome Postdoctoral Fellow

Departments of Bioengineering and Electrical Engineering

California Institute of Technology

4:00 p.m. Carson Family Auditorium

Recommended Readings:

Judkewitz, Benjamin; Wang, Ying Min; Horstmeyer, Roarke; et al.  2013.  Speckle-scale focusing in the diffusive regime with time reversal of variance-encoded light (TROVE).  NATURE PHOTONICS  7(4):300-305   DOI: 10.1038/NPHOTON.2013.31  

Wang, Ying Min; Judkewitz, Benjamin; DiMarzio, Charles A.; et al. 2012. Deep-tissue focal fluorescence imaging with digitally time-reversed ultrasound-encoded light.   NATURE COMMUNICATIONS   3(Article 928):   DOI: 10.1038/ncomms1925

Suzuki, Yuta; Xu, Xiao; Lai, Puxiang; et al   2012.  Energy enhancement in time-reversed ultrasonically encoded optical focusing using a photorefractive polymer.   JOURNAL OF BIOMEDICAL OPTICS   17(8): Article Number: 080507   DOI: 10.1117/1.JBO.17.8.080507  

Makale, Milan; McElroy, Michele; O’Brien, Peter; et al.  2009.  Extended-working-distance multiphoton micromanipulation microscope for deep-penetration imaging in live mice and tissue.   JOURNAL OF BIOMEDICAL OPTICS   14(2): Article Number 024032   DOI:10.1117/1.3103783  

Lai, Puxiang; Xu, Xiao; Liu, Honglin; et al.  2012.  Time-reversed ultrasonically encoded optical focusing in biological tissue.   JOURNAL OF BIOMEDICAL OPTICS   17(3): Article Number 030506   DOI: 10.1117/1.JBO.17.3.030506  

Liu, Honglin; Xu, Xiao; Wang, Lihong V.  2011. Focusing light into turbid media: time-reversed ultrasonically encoded (TRUE) focusing. Book Editor(s): Oraevsky, AA; Wang, LV.   Conference on Photons Plus Ultrasound – Imaging and Sensing  Location: San Francisco, CA Date: JAN 23-25,  Proceedings of SPIE   7899:Article Number 78991A   DOI: 10.1117/12.876956  

Recommended Readings: Roderick MacKinnon, M.D.

Friday Lecture Series

Inaugural Bruce Merrifield Distinguished Lecture; Ph.D. Recruitment Lecture

The Incredible Diversity of K+ Channels

Roderick MacKinnon, M.D., John D. Rockefeller Jr. Professor, and head,

Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University;

investigator, Howard Hughes Medical Institute

 March 1, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Hansen, S. B., Tao, X., & MacKinnon, R. (2011). Structural basis of PIP 2 activation of the classical inward rectifier K + channel Kir2.2. Nature, 477(7365), 495-498

Lee, S. -., Banerjee, A., & MacKinnon, R. (2009). Two separate interfaces between the voltage sensor and pore are required for the function of voltage-dependent K + channels. PLoS Biology, 7(3)

Lee, S. -., Lee, A., Chen, J., & MacKinnon, R. (2005). Structure of the KvAP voltage-dependent K + channel and its on the lipid membrane. Proceedings of the National Academy of Sciences of the United States of America, 102(43), 15441-15446

Long, S. B., Tao, X., Campbell, E. B., & MacKinnon, R. (2007). Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature, 450(7168), 376-382

Schmidt, D., & MacKinnon, R. (2008). Voltage-dependent K + channel gating and voltage sensor toxin sensitivity depend on the mechanical state of the lipid membrane. Proceedings of the National Academy of Sciences of the United States of America, 105(49), 19276-19281

Tao, X., Avalos, J. L., Chen, J., & MacKinnon, R. (2009). Crystal structure of the eukaryotic strong inward-rectifier K + channel Kir2.2 at 3.1 Å resolution. Science, 326(5960), 1668-1674


Recommended Readings: Kazuhiro Yamada, PhD October 1, 2012

Crystallographic Studies of Large Complexes: From the Yeast Chromatin

Remodeling Factor ISW1a to the Entire Nucleosome-Traversing

Transcription Machinery

Kazuhiro Yamada,  PhD

Senior Scientist/Over-assistant

Institute of Molecular Biology and Biophysics

ETH Zurich

Monday, October 1, 2012

4 p.m. , Caspary Auditorium.   Refreshments 3:45 p.m.

 Recommended Readings:

Yen, K.; Vinayachandran, V.; Batta, K.; et al.   2012. Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers.  CELL   149(7):1461-1473   DOI: 10.1016/j.cell.2012.04.036

Richmond, Timothy J.  2012. Nucleosome recognition and spacing by chromatin remodelling factor ISW1a.   BIOCHEMICAL SOCIETY TRANSACTIONS,  40: 347-350  DOI: 10.1042/BST20110748   Please request from Markus Library.

De Cian, A; Praly, E; Ding, F; et al.  2012.  ATP-Independent Cooperative Binding of Yeast Isw1a to Bare and Nucleosomal DNA.    PLOS ONE   7(2): e31845   DOI: 10.1371/journal.pone.0031845

Sharma, A.; Jenkins, K. R.; Heroux, A.; et al.  2011. Crystal Structure of the Chromodomain Helicase DNA-binding Protein 1 (Chd1) DNA-binding Domain in Complex with DNA.  JOURNAL OF BIOLOGICAL CHEMISTRY    286(49):42099-42104   DOI: 10.1074/jbc.C111.294462

Yamada, K.; Frouws, T. D.; Angst, B.; et al. 2011.  Structure and mechanism of the chromatin remodelling factor ISW1a.   NATURE.  472(7344):U448-U536   DOI: 10.1038/nature09947

Pinskaya, M.; Nair, A.; Clynes, D.; et al.  2009.  Nucleosome Remodeling and Transcriptional Repression Are Distinct Functions of Isw1 in Saccharomyces cerevisiae.  MOLECULAR AND CELLULAR BIOLOGY   29(9): 2419-2430   DOI: 10.1128/MCB.01050-08