Seminars and Journal Club
Speakers in the biophysics seminar program have focused on molecular and cellular structure, and interactions between molecules. Outstanding speakers from leading laboratories in the US and abroad speak weekly, and students have the opportunity to meet with them on an informal basis over lunch. Student Research Talks and Journal Clubs are held weekly. In the course of the year each student presents at least one journal article outside of his or her immediate study and a discussion of current work. These seminars are open to faculty and other interested colleagues. This activity serves two purposes, both broadening the interests of students and giving them the opportunity for oral presentations.
Twice monthly first and second year students invite a member of the faculty to speak informally, followed by dinner. In this way, students can be assured of meeting every faculty member associated with the group and learn about his or her research in a substantive way.
In addition to the formal seminar program and informal faculty dinners, individual faculty hold weekly group meetings in which group members present their own results or plan new projects. These sessions are among the most critical and rigorous aspects of graduate training with much give and take for all participants. Even after completion of their formal rotation schedule, students are encouraged to attend all group meetings of interest.
Journal Club & Research Talks
Mondays at noon, Genentech Hall Room S201
Academic Year 2008: | ||
| Date | Speaker | Topic |
| 9/17/07 | Caleb Bashor | Exploiting a Scaffold Protein as a Platform to Generate Diverse I/O Dynamics in a MAP Kinase Pathway |
| 9/24/07 | Clement Chu | TBA |
| 10/1/07 | Morris Feldman | POSTPONED |
| 10/8/07 | Eli Groban | Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq |
| 10/15/07 | Quincey Justman | TBA |
| 10/22/07 | Sam Pfaff | How to make your very own nuclear pore |
| 11/5/07 | Neema Salimi | New Insights into Alpha-lytic Unfolding |
| 11/19/07 | Jeremy Wilbur | Structure and regulatory roles of clathrin light chain determined by a low resolution crystal structure |
| 11/26/07 | Elizabeth Clarke | A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics |
| 12/10/07 | David Eramian | Can the accuracy of comparative protein structure models be predicted? |
| 12/17/07 | Morris Feldman | ATP competitive inhibition of mTOR |
| 1/14/08 | Anselm Levskaya | Controlling Signaling Pathways with Light |
| 1/28/08 | Arjun Narayanan | AH Bonding at the Helix-Bundle Crossing Controls Gating in Kir Potassium Channels |
| 2/4/08 | Greg Friedland | A simple model of backbone flexibility improves modeling of side-chain conformational variability |
| 2/11/08 | Christian Cunningham | Elephants, Rats, and Bacteria...Oh my! |
| 2/25/08 | Molly Darragh | Designed Protein-Protein Association |
| 3/3/08 | Matt Eames | Post-op introns going under the knife |
| 3/10/08 | Ben Sellers | Synthetic antibodies for specific recognition and crystallization of structured RNA |
| 3/17/08 | Ian Harwood | TBA |
| 3/24/08 | Peretz Partensky | Caught in the act of swapping genetic material: Direct Visualization of Horizontal Gene Transfer |
| 3/31/08 | Bryant Chhun | Microtubule polymerase XMAP215 |
| 4/7/08 | Elisabeth Humphris | Interconversion between two unrelated protein folds in the lymphotactin native state |
| 4/14/08 | Deb Datta | Coiled-coil irregularities and instabilities in group A Streptococcus M1 are required for virulence |
| 4/21/08 | Stephen Floor | Intrinsic motions along an enzymatic reaction trajectory |
| 4/28/08 | Chris McClendon | A Cholesterol Biosynthesis Inhibitor Blocks Staphylococcus aureus Virulence |
| 5/5/08 | Ethan Mirsky | Evolvability and hierarchy in rewired bacterial gene networks |
| 5/12/08 | Liz Montabana | TBA |
| 5/19/08 | Richard Oberdorf | TBA |
| 6/2/08 | Hesper Rego | TBA |
| 6/9/08 | Ben Rhau | TBA |
| 6/16/08 | Charles Biddle-Snead | TBA |
| 6/23/08 | Maya Chandru | TBA |
| 6/30/08 | Rebeca Choy | TBA |
| 7/7/08 | Sheel Dandekar | TBA |
| 7/14/08 | Sai Duriseti | TBA |
| 7/21/08 | David Stanley | TBA |
| 7/28/08 | Laura Lavery | TBA |
| 8/4/08 | Ryan Ritterson | TBA |
| 8/11/08 | Kris Kuchenbecker | TBA |
| 8/18/08 | Reid Williams | TBA |
Academic Year 2007: | ||
| Date | Speaker | Topic |
| 9/25/06 | Chris Farady | The mechanism of inhibition of novel macromolecular inhibitors of membrane-type serine protease 1(MT-SP1) |
| 10/2/06 | Eli Groban | Towards a better understanding of two component systems: A mishmash of protein purification, genetic manipulation, and kinetics |
| 10/9/06 | Quincey Justman | Is bistability necessary to produce sustained oscillations? |
| 10/16/06 | Jeremy Nilmeier | Multiscale Monte Carlo Modeling: theory |
| 10/23/06 | Sam Pfaff | Biochemistry and structure of glucocorticoid receptor activation |
| 10/30/06 | Neema Salimi | Promiscuous PolyQ Proteins: Say that three times fast |
| 11/6/06 | Ben Sellers | Improving protein structure prediction using model systems |
| 11/13/06 | Jeremy Wilbur | Clathrin Assembly requires flexibility in the HIPs |
| 11/20/06 | Randy Wu | Nucleosome positions predicted through comparative genomics |
| 12/11/06 | Eli Zunder | A screen in yeast for inhibitor-resistant mutations in the P13K family |
| 12/18/06 | Alan Graves | Probing the boundaries of molecular docking with decoys and model systems |
| 1/8/07 | Caleb Bashor | TBA |
| 1/29/07 | Dave Eramian | Protein model building based on distantly related structures |
| 2/5/07 | Christian Cunningham | A Tale of Two DNAs: Single molecule studies on bacterial chromatin organization by H-NS protein |
| 2/12/07 | Liz Clarke | Getting along: Evolution of species interactions |
| 2/26/07 | Morri Feldman | A Pharmacology of translational balance |
| 3/5/07 | Molly Darragh | Broadening antibody specificity while maintaining optimal affinity |
| 3/12/07 | Peretz Partensky | A "silent" polymorphism in the MDR1 gene changes substrate specificity |
| 3/19/07 | Arjun Narayanan | Quantitative analysis of the activation mechanism of the multicomponent growth-factor receptor Ret |
| 3/26/07 | Greg Friedland | Some predictions left behind: Using computational protein design as input to experimental library selection |
| 4/2/07 | Matt Eames | Kirkland Brand Codons: Why? |
| 4/23/07 | Stephen Floor | Cypoviruses hide inside self-assembling polyhedra waiting for insects |
| 4/30/07 | Anselm Levskaya | Soluble Time: the three-protein circadian clock KaiABC |
| 5/7/07 | Bryant Chhun | Optical interrogation of neural circuitry using light-driven ion pumps |
| 5/14/07 | Deb Datta | An SCN9A channelopathy causes congenital inability to experience pain |
| 5/21/07 | Elisabeth Humphris | Selection Inversion: Forcing Antibiotic Interactions to Select Against Resistance |
| 6/4/07 | Liz Montabana | How Synaptotagmin Promotes Membrane Fusion |
| 6/11/07 | Chris McClendon | Dance of the Pin1 Domains: Dynamical NMR |
| 6/18/07 | Richard Oberdorf | Why Have Costly Sex? |
| 6/25/07 | Hesper Rego | Molecule by molecule: Light microscopy with subdiffraction resolution |
| 7/2/07 | Benjamin Rhau | A universal RNAi-based logic evaluator that operates in mammalian cells |
| 7/9/07 | Ian Harwood | Hooking Up In Sin |
| 7/16/07 | Ethan Mirsky | Advanced Counting |
| 7/23/07 | Charles Biddle-Snead & Maya Chandru | Avoid Probing the Brobe: Delivery of siRNA across the blood-brain barrier (Biddle-Snead) & Are you a Man or a Monkey? A rapidly evolved human RNA gene (Chandru) |
| 7/30/07 | Rebeca Choy & Sheel Dandekar | Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells (Choy) & Experimental and theoretical study of mitotic spindle orientation (Dandekar) |
| 8/6/07 | Sai Duriseti & Kris Kuchenbecker | SP1 as a novel scaffold building block for self-assembly nanofabrication of submicron enzymatic structures (Duriseti) & Picking Up the Pieces: A new fragment-based strategy for small molecule development (Kuchenbecker) |
| 8/13/07 | Laura Lavery & Ryan Ritterson | Probing transcription factor dynamics at the single-molecule level in a living cell (Lavery) & Beyond transfection to trans-speciation: Is your genome all it takes to re-create you? (Ritterson) |
| 8/20/07 | Reid Williams, Lim Lab | Adaptive mutations in bacteria: high rate and small effects |
BBC Journal Club
Academic Year 2008: | |||
| Date | Speaker 1 | Speaker 2 | |
| 10/9/07 | Maya Chandru (Biophysics) | Brianna Burden (CCB) | Details |
Maya Chandru Multi-step pericellular proteolysis controls the transition from individual to collective cancer cell invasion. Wolf et al, Nat Cell Biol 2007 Aug 9 Brianna Burden Aptamer Displacement Identifies Alternative Small-Molecule Target Sites that Escape Viral Resistance amazaki et al, Cell: Chemistry and Biology 14, 804-812, 2007. | |||
| 10/16/07 | Jeremy Phillips (Bioinformatics) | Reid Williams (Biophysics) | Details |
Jeremy Phillips Two distinct modes of guidance signalling during collective migration of border cells. Bianco A, Poukkula M, Cliffe A, Mathieu J, Luque CM, Fulga TA, Rorth P. Nature. 2007 Jul 19;448(7151):362-5. Reid Williams Selection and evolution of enzymes from a partially randomized non-catalytic scaffold Seelig B, Szostak JW. Nature. 2007 Aug 16;448(7155):828-31. | |||
| 10/23/07 | Daniel Gray (CCB) | Rebeca Choy (Biophysics) | Details |
Daniel Gray Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis. Ortlund, Bridgham, Redinbo, Thornton. Science. 2007 Sep 14;317(5844):1544-8. Epub 2007 Aug 16. http://www.nature.com/nsmb/journal/v14/n9/abs/nsmb1280.html Rebeca Choy In vivo dynamics of RNA polymerase II transcription Xavier Darzacq, Yaron Shav-Tal, Valeria de Turris, Yehuda Brody, Shailesh M Shenoy, Robert D Phair & Robert H Singer. Nature Structural & Molecular Biology - 14, 796 - 806 (2007). | |||
| 10/30/07 | Charles Biddle-Snead (Biophysics) | Iana Serafimova (CCB) | Details |
Charles Biddle-Snead Array Tomography: A New Tool for Imaging the Molecular Architecture and Ultrastructure of Neural Circuits Kristina D. Micheva and Stephen J Smith. Neuron 55, 25–36, July 5, 2007 ª2007 Elsevier Inc. 25 Iana Serafimova Splicing factor SF3b as a target of the antitumor natural product pladienolide Yoshihiko Kotake1, Koji Sagane1, Takashi Owa, Yuko Mimori-Kiyosue, Hajime Shimizu, Mai Uesugi, Yasushi Ishihama, Masao Iwata & Yoshiharu Mizui. Nature Chemical Biology, Vol 3, Number 9, September 2007, p570 - 575. | |||
| 11/6/07 | Daniele Canzio (CCB) | David Stanley (Biophysics) | Details |
Daniele Canzio A motor that makes his own track: helicase unwinding of DNA: Single-Molecule Studies Reveal Dynamics of DNA unwinding by the Ring-Shaped T7 Helicase Cell 129, 1299-1309, June 29, 2007 David Stanley Dynamic Scaffolding of a G Protein-Coupled Signaling System Prashant Mishra, Michael Socolich, Mark A. Wall, Jennifer Graves, ZiFen Wang, and Rama Ranganathan. Cell, Vol 131, 80-92, 05 October 2007 | |||
| 11/13/07 | Kris Kuchenbecker (Biophysics) | Details | |
Kris Kuchenbecker Energetics and dynamics of SNAREpin folding across lipid bilayers. Nature Structural and Molecular biology. October 2007. | |||
| 11/20/07 | Laura Lavery (Biophysics) | Sheel Dandekar (Biophysics) | Details |
Laura Lavery High-afinity single-domain binding proteins with a binary-code interface. Akiko Koidea, Ryan N. Gilbreth, Kaori Esaki, Valentina Tershko, Shohei Koide. PNAS, Vol 104, No. 16. April 17, 2007. http://www.pnas.org/cgi/content/full/104/16/6632 Sheel Dandekar Ordered phosphorylation governs oscillation of a three-protein circadian clock Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK. Science. 2007 Nov 2;318(5851):809-12. Epub 2007 Oct 4. | |||
| 1/8/08 | Jonathan Choy (CCB) | Sai Duriseti (Biophysics) | Details |
Jonathan Choy Design of Cyclic Peptides That Bind Protein Surfaces with Antibody-Like Affinity Steven W. Millward, Stephen Fiacco, Ryan J. Austin, and Richard W. Roberts (2007) ACS Chem. Biol. 2, 625-634. Sai Duriseti A Simple DNA-Based Translation System Alejandra V. Garibotti, Shiping Liao, and Nadrian C. Seeman. Nano Letters 2007 Vol. 7, No. 2. 480-483. | |||
| 1/15/08 | Ryan Ritterson (Biophysics) | Charles Kehoe (Bioinformatics) | Details |
Ryan Ritterson Retroposons: DNA parasites or facilitators? A CORE-SINE retroposon as a highly conserved neuronal enhancer. Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene. Santangelo AM, de Souza FSJ, Franchini LF, Bumaschny VF, Low MJ, et al. PLoS Genetics Vol. 3, No. 10, e166doi:10.1371/journal.pgen.0030166 http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0030166 Charles Kehoe Functional specificity among ribosomal proteins regulates gene expression. Komili S, Farny NG, Roth FP, Silver PA.Cell. 2007 Nov 2;131(3):450-1. | |||
| 1/22/08 | David Booth (Biophysics) | Details | |
David Booth Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin Abhishek Dey, Francis E. Jenney, Jr., Michael W. W. Adams, Elena Babini, Yasuhiro Takahashi, Keiichi Fukuyama, Keith O. Hodgson, Britt Hedman, Edward I. Solomon, Science, 318, 1464-8, 2007 | |||
| 1/29/08 | Joseph Kliegman (Biophysics) | Michael Lopez (CCB) | Details |
Joseph Kliegman Minor Details of Transcription Factor Specificity Rohit Joshi, Jonathan M. Passner, Remo Rohs, Rinku Jain, Alona Sosinsky, Michael A. Crickmore, Vinitha Jacob, Aneel K. Aggarwal, Barry Honig and Richard S. Mann. Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure, CellVolume 131, Issue 3, , 2 November 2007, Pages 530-543. Michael Lopez A GluR1-cGKII Interaction Regulates AMPA Receptor Trafficking Yafell Serulle, Shuang Zhang, Ipe Ninan, Daniela Puzzo, Maria McCarthy, Latika Khatri, Ottavio Arancio, and Edward B. Ziff Neuron 56, 670�¢ï¿½ï¿½688, November 21, 2007 | |||
| 2/5/08 | Noah Ollikainen (Bioinformatics) | George Masologites (Biophysics) | Details |
Noah Ollikainen Somewhere over the brainbow Jean Livet, Tamily A. Weissman, Hyuno Kang, Ryan W. Draft, Ju Lu, Robyn A. Bennis, Joshua R. Sanes & Jeff W. Lichtman. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature. 450, 56-62 (2007). http://www.nature.com/nature/journal/v450/n7166/abs/nature06293.html George Masologites Nicotinamide Riboside Promotes Sir2 Silencing and Extends Lifespan via Nrk and Urh1/Pnp1/Meu1 Pathways to NAD+ Belenky P, Racette FG, Bogan KL, McClure JM, Smith JS, Brenner C. Cell 129: 473-84 (2007) http://www.cell.com/content/article/abstract?uid=PIIS009286740700390X | |||
| 2/12/08 | Rebecca Maglathlin (CCB) | Heather Newman (Biophysics) | Details |
Rebecca Maglathlin Structural Rearrangements of NR1/NR2A NMDA Receptors during Allosteric Inhibition Marc Gielen, Anne Le Goff, David Stroebel, Jon W. Johnson, Jacques Neyton, and Pierre Paoletti. Neuron 57, 80�93, January 10, 2008 Heather Newman Multicolor Super-Resolution Imagining with Photo-switchable Fluorescent Probes Multicolor Super-Resolution Imagining with Photo-switchable Fluorescent Probes Mark Bates et al., Science 317, 1749 (2007). | |||
| 2/19/08 | Peter Skewes-Cox (Bioinformatics) | David Burkhardt (Biophysics) | Details |
Peter Skewes-Cox Will newly identified host factors exploited by HIV make good drug targets? "Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen," Abraham L. Brass, Derek M. Dykxhoorn, Yair Benita, Nan Yan, Alan Engelman, Ramnik J. Xavier, Judy Lieberman, Stephen J. Elledge. Science, 2008 Jan 10 http://www.sciencemag.org/cgi/content/abstract/1152725v David Burkhardt Switching from repression to activation: microRNAs can up-regulate translation. Vasudevan S, Tong Y, Steitz JA, " Switching from repression to activation: microRNAs can up-regulate translation.", Science 2007 Dec 21 | |||
| 2/26/08 | Hannes Braberg (Biophysics) | Rand Miller (CCB) | Details |
Hannes Braberg High-content single-cell drug screening with phosphospecific flow cytometry Peter O Krutzik, Janelle M Crane, Matthew R Clutter and Garry P Nolan. Nature Chemical Biology 4, 132-142 (2007) doi:10.1038/nchembio.2007.59 Rand Miller Systemic Leukocyte-Directed siRNA Delivery Revealing Cyclin D1 as an Anti-Inflammatory Target Peer, D., Park, E. J., Morishita, Y., Carman, C. V., Shimaoka, M, "Systemic Leukocyte-Directed siRNA Delivery Revealing Cyclin D1 as an Anti-Inflammatory Target," /Science/, 319, 627-630, (2008). DOI: 10.1126/science.1149859 | |||
| 3/4/08 | Nicholas Hertz (CCB) | Elaine Kirschke (Biophysics) | Details |
Nicholas Hertz A Comprehensive Profile of Brain Enzymes that Hydrolyze the Endocannabinoid 2-Arachidonoylglycerol Blankman, J.L., Simon, G.M., Cravatt, B.F. (2007). A Comprehensive Profile of Brain Enzymes that Hydrolyze the Endocannabinoid 2-Arachidonoylglycerol. Chem. Biol. 14, 1347-1356 Elaine Kirschke Activation of the Chaperone Hsp26 Is Controlled by the Rearrangement of Its Thermosensor Domain T. Franzmann, P. Menhorn, S. Walter, and J. Buchner. (2008) Activation of the Chaperone Hsp26 Is Controlled by the Rearrangement of Its Thermosensor Domain. Molecular Cell, Vol 29, 207-216, 01 | |||
| 3/11/08 | Bethany Simmons (Bioinformatics) | Kiyoshi Egami (Biophysics) | Details |
Bethany Simmons Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Lecuyer E, Yoshida H, ..., Tomancak P, Krause HM Cell 2007 Oct 5 131(1):174-87 Kiyoshi Egami Glycan topology determines human adaptation of avian H5N1 virus hemagglutinin. Chandrasekaran A, Srinivasan A, Raman R, Viswanathan K, Raguram S, Tumpey TM, Sasisekharan V, Sasisekharan R. Nat Biotechnol. 2008 Jan;26(1):107-13. Epub 2008 Jan 6. | |||
| 4/1/08 | Brandon Butler (CCB) | Jaline Gerardin (Biophysics) | Details |
Brandon Butler A beta-arrestin 2 Signalling Complex Mediates Lithium Action on Behavior Jean-Martin Beaulieu et al. Cell, 132, 125-136, Jan 11, 2008. Jaline Gerardin Direct observation of hierarchical folding in single riboswitch aptamers Greenleaf WJ, Frieda KL, Foster DAN, Woodside MT, Block SM. Direct observation of hierarchical folding in single riboswitch aptamers. Science. 2008 Feb 1;319(5863):630-3. | |||
| 4/8/08 | Carrie Shiau (CCB) | Adam Marko (Bioinformatics) | Details |
Carrie Shiau Transcriptional repression mediated by repositioning of genes to the nuclear lamina Reddy, K. L. et al. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452, 243 – 247 (2008). Adam Marko Computational Enzyme Design Lin Jiang, Eric A. Althoff, Fernando R. Clemente, Lindsey Doyle, Daniela Röthlisberger, Alexandre Zanghellini, Jasmine L. Gallaher, Jamie L. Betker, Fujie Tanaka, Carlos F. Barbas, III, Donald Hilvert, Kendall N. Houk, Barry L. Stoddard, David Baker. De Novo Computational Design of Retro-Aldol Enzymes. Science 7 March 2008: Vol. 319. no. 5868, pp. 1387 - 139. DOI: 10.1126/science.1152692 | |||
| 4/15/08 | Jennifer Hsiao (Biophysics) | Jennifer Liu (CCB) | Details |
Jennifer Hsiao Hydrodynamic Flow-Mediated Protein Sorting on the Cell Surface of Trypanosomes Markus Engstler, Thomas Pfohl, Stephan Herminghaus, Michael Boshart, Geert Wiegertjes, Niko Heddergott, and Peter Overath. Cell 131, 505–515, November 2, 2007 Jennifer Liu Preserving cell shape under environmental stress Boaz Cook, Robert W Hardy, William B McConnaughey, Charles S Zuker. Nature 452, 361-364 (20 March 2008), doi:10.1038/nature06603 | |||
| 4/22/08 | Gabriel Rocklin (Biophysics) | Cheryl Tajon (CCB) | Details |
Gabriel Rocklin Integrating high-content screening and ligand-target prediction to identify mechanism of action Young, DW et al. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nature Chemical Biology 4:1 Jan 2008 Cheryl Tajon Near-Infrared Resonant Nanoshells for Combined Optical Imaging and Photothermal Cancer Therapy Andre´ M. Gobin, Min Ho Lee, Naomi J. Halas, William D. James, Rebekah A. Drezek, and Jennifer L. West. Near-Infrared Resonant Nanoshells for Combined Optical Imaging and Photothermal Cancer Therapy. Nano Letters, 2007, vol. 7, no. 7, 1929-34. | |||
| 4/29/08 | Brittany Belin (Biophysics) | Xiu Ming Wong (CCB) | Details |
Brittany Belin Structural basis of membrane invagination by F-BAR domains Frost A, Perera R, Roux A, Spasov K, Destaing O, Egelman EH, De Camilli P, Unger VM. (2008) Structural basis of membrane invagination by F-BAR domains. Cell 132(5):807-17. Xiu Ming Wong Ran-Binding Protein 3 Phosphorylation Links the Ras and PI3-Kinase Pathways to Nucleocytoplasmic Transport. Sang-Oh Yoon, Sejeong Shin, Yuzhen Liu, Bryan A. Ballif, Michele S. Woo, Steven P. Gygi, and John Blenis, Ran-Binding Protein 3 Phosphorylation Links the Ras and PI3-Kinase Pathways to Nucleocytoplasmic Transport. Molecular Cell, Volume 29, Issue 3, 15 February 2008, Pages 362-375. | |||
| 5/6/08 | Monica Tremont (Biophysics) | Christopher Wen (Bioinformatics) | Details |
Monica Tremont Allosteric cooperativity in protein kinase A Masterson, L. Rl et al. Allosteric cooperativity in protein kinase A. Proc. Nat. Acad. Sci. U.S.A. 105(2), 506-511 (2008). http://www.pnas.org/cgi/reprint/105/2/506 Christopher Wen 1. Membrane proteins of the endoplasmic reticulum induce high-curvature tubules. Hu J, Shibata Y, Voss C, Shemesh T, Li Z, Coughlin M, Kozlov MM, Rapoport TA, Prinz WA. Membrane proteins of the endoplasmic reticulum induce high-curvature tubules. Science. 2008 Feb 29;319(5867):1247-50 | |||
| 5/13/08 | Marlisa Pillsbury (CCB) | Robin Aglietti (CCB) | Details |
Marlisa Pillsbury Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter Karpova,T, Kim, MJ, Spriet, C, Nalley, K, Stasevich, TJ, Kherrouche, Z, Heliot, L, McNally JG. Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter. Science 25 January 2008: Vol. 319. no. 5862, pp. 466 - 469. DOI: 10.1126/science.1150559 Robin Aglietti Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR Ioannis Gelis, Alexandre M.J.J. Bonvin, Dimitra Keramisanou, Marina Koukaki, Giorgos Gouridis, Spyridoula Karamanou, Anastassios Economou, and Charalampos G. Kalodimos. Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR. Cell, Vol 131, 756-769, 16 November 2007 | |||
Academic Year 2007: | |||
| Date | Speaker 1 | Speaker 2 | |
| 10/10/06 | Segun Williams (CCB) | Stephen Floor (Biophysics) | |
| 10/17/06 | Michelle Dimon (Bioinformatics) | Ethan Mirsky (Biophysics) | Details |
Michelle Dimon DNA Sequences Predict Packaging Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom AC, Field Y, Moore IK, Wang JPZ, Widome J. A genomic code for nucleosome positioning. Nature 17:442 (7104), 772 (2006) Ethan Mirsky Oceanic Gene Pooling Lindell, D. et al. Photosynthesis genes in marine viruses yield proteins during host infection. Nature. 438(7064): 86 (2005) | |||
| 10/24/06 | Hesper Rego (Biophysics) | Karin Buser (CCB) | |
| 10/31/06 | Rafaela Ferreira (CCB) | Michael Cary (Bioinformatics) | Details |
Michael Cary The first genome-wide map of DNA methylation Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126(6): 1189 (2006) | |||
| 11/7/06 | Benjamin Rhau (Biophysics) | Andy MacKinnon (CCB) | Details |
Benjamin Rhau Computational redesign of endonuclease DNA binding and cleavage specificity. Ashworth J, Hayranek JJ, Duarte CM, Sussman D, Monnat RJ Jr., Stoddard BL, Baker D. Nature. 2006 Jun 1;441(7093):656-9. Andy MacKinnon A Proposed Twisting Mechanism of Dynamin During Membrane Fission Roux, Aurelien, Uyhazi, Katherine, Frost, Adam, De Camilli, Pietro. GTP-dependent twisting of dynamin implicates constriction and tension in membrane fission. Nature.  441: 528 (2006) | |||
| 11/14/06 | Colin Smith (Bioinformatics) | Bryant Chhun (Biophysics) | Details |
Colin Smith Taking turns with the whip Leake MC, Chandler JH, Wadhams GH, Bai F, Berry RM, Armitage JP. Stoichiometry and turnover in single, functioning membrane protein complexes. Nature 443(7109):355 (2006) | |||
| 11/21/06 | Chris McClendon (Biophysics) | Mark Borja (CCB) | |
| 1/9/07 | Liz Montabana (Biophysics) | David Barkan (Bioinformatics) | Details |
David Barkan Imitation by epidermal growth factor receptor is the sincerest form of flattery Zhang et al. An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell. 125 (6):1137-49. (2006) | |||
| 1/16/07 | Julie Zorn (CCB) | Richard Oberdorf (Biophysics) | |
| 1/23/07 | Deb Datta (Biophysics) | Brandon Tavshanjian (CCB) | |
| 1/30/07 | Beth Apsel (CCB) | Leonard Apeltsin (Bioinformatics) | Details |
Leonard Apeltsin Computer Tobacco Mosaic Viruses: Engineering a Digital Memory Device from Biological Parts Tseng, R.J. Tsai, C. Ma, L. Ouyang, J. Ozkan C.S. Yang, Y. Digitalmemory device based on tobacco mosaic virus conjugated with nanoparticles. Nature Nanotechnology. 1, 72-77. (2006) | |||
| 2/6/07 | Emily Crawford (CCB) | Charles Biddle-Snead (Biophysics) | |
| 2/13/07 | Jeremy Phillips (Bioinformatics) | Maya Chandru (Biophysics) | Details |
Jeremy Phillips A noise-excitable circuit induces competence in B. subtilis Suel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB. An excitable gene regulatory circuit induces transient cellular differentiation. Nature. 440(7083):545-50. (2006) | |||
| 2/20/07 | Ryan Ritterson (Biophysics) | Briana Burden (CCB) | |
| 2/27/07 | Daniel Gray (CCB) | David Stanley (Biophysics) | |
| 3/6/07 | Marlisa Pillsbury (CCB) | David Stanley (Biophysics) | |
| 3/13/07 | Reid Williams (Biophysics) | Daniele Canzio (CCB) | |
| 3/20/07 | Laura Lavery (Biophysics) | Kimberly Erickson (CCB) | |
| 4/3/07 | Iana Serafimova (CCB) | Kris Kuchenbecker (Biophysics) | Details |
Iana Serafimova Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B. Yudushkin IA, Schleifenbaum A., Kinkhabwala A, Neel BG, Schultz C, Bastiaens PI. European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany. Kris Kuchenbecker Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Boudker O, Ryan RM, Yernool D, Shimamoto K, Gouaux E. Science. 2007 Jan 5;315(5808):115-9. | |||
| 4/10/07 | Sheel Dandekar (Biophysics) | Rebeca Choy (Biophysics) | Details |
Rebeca Choy From Swimming to Walking with a Salamander Robot Driven by a Spinal Cord Model Auke Jan Ijspeert,1* Alessandro Crespi,1 Dimitri Ryczko,2,3 Jean-Marie Cabelguen2,3. Science 9 March 2007: Vol. 315. no. 5817, pp. 1416 - 1420 DOI: 10.1126/science.1138353 | |||
Biophysics / CCB Formal Seminars
Thursdays, GH Auditorium 12:00-1:00, Simulcast to S161 Parnassus
Academic Year 2008: | |||
| Date | Speaker | Topic | Host |
| 10/11/07 | Nick Endres, UC Berkeley | Clements Talk: Using artificial lipid membranes to gain insights into the structure and function of signaling proteins in the EGFR/Ras signaling network | D. Agard |
| 10/18/07 | Justin Gallivan, Emory University | Reprogramming Bacteria with Small Molecules and RNA | P. England |
| 10/25/07 | Jack Szostak, Harvard Medical School |
Braisted Lecture: Towards the Design and Synthesis of an Artificial Cell Please note: this talk will be held at 4:00pm |
C. Craik and J. Wells |
| 11/1/07 | Peter Wright, Scripps | Exploring the protein energy landscape: Disorder, dynamics, and protein function | S. Miller |
| 11/15/07 | Paul Hergenrother, University of Illinois | Using small molecules to identify novel targets for the treatment of cancer | J. Taunton |
| 11/29/07 | David Baker, U Washington | Novel enzyme catalysts, rapid structure determination, and pushing the limits of folding and design with a multiplayer online computer game | J. Wells |
| 12/13/07 | David Deamer, UC Santa Cruz | Nanopore analysis of DNA | K. Dill |
| 12/20/07 | Lewis Kay, University of Toronto | Seeing the invisible by solution NMR spectroscopy | T. James |
| 1/3/08 | Rob Phillips, Caltech | How Cells Decide What to Eat and Where to Go | W. Marshall |
| 1/10/08 | Tom Knight, MIT | TBA | R. Williams |
| 1/17/08 | Tom Wandless, Stanford | A General Solution to the "Problem" of Chemical Genetics | J. Taunton |
| 1/24/08 | Gaudenz Danuser, Scripps | Integration of mechanical and chemical signals in cell migration deciphered by global fluctuation analysis | W. Marshall |
| 2/14/08 | Eric Siggia, Rockefeller University | Predicting the course of evolution | H. Li |
| 2/21/08 | Susan Marqusee, UC Berkeley | TBA | K. Dill |
| 2/28/08 | James Inglese, NIH Chemical Genomics Center | Integrative Technologies Enabling Chemistry and Biology as a Public Resource for Chemical Probe and Drug Discovery | B. Shoichet |
| 3/13/08 | Gavin MacBeath, Harvard University | TBA | TBA |
| 3/20/08 | Ned Wingreen, Princeton | Modeling the chemotaxis network of E. coli | C. Tang |
| 4/17/08 | Tudor Oprea, University of New Mexico | From Digital to Experimental Bioactivity: Exploring novel estrogen receptors | B. Shoichet |
| 4/24/08 | Richard Ebright, Rutgers | Single-molecule analysis of transcription | G. Narlikar |
| 5/1/08 | Vishva Dixit, Genentech, Inc. | The Inflammasome & Deubiquitinases in Innate Immune Signaling | J. Wells |
| 5/15/08 | Rachel Brem, UC Berkeley | Expression variation and regulatory feedback | K. Dill |
| 5/22/08 | Jagesh Shah, Harvard Medical School | Biophysical measurements of mitotic checkpoint signaling: How cells prevent chromosome loss | W. Marshall |
| 5/27/08 | Gary Ruvkun, Harvard University | TBA | TBA |
| 5/29/08 | Brian Chait, Rockefeller University | Protein Interactions as a Window into Cellular Function | A. Krutchinsky |
| 6/5/08 | Gerald Crabtree, Stanford | Designing small molecules to regulate protein interactions | TBA |
Academic Year 2007: | |||
| Date | Speaker | Topic | Host |
| 10/12/06 | Mathew Francis, UC Berkeley | New chemical tools for site-selective protein modification | P. England |
| 10/19/06 | Adrian Keatinge-Clay, UCSF | Dissecting, deciphering, and designing polyketide assembly lines | R. Stroud |
| 10/26/06 | Christopher Walsh, Harvard | Andrew Braisted Lecture, Halogenases: Natural product tailoring enzymes | C. Craik |
| 11/2/06 | Ron Weiss, Princeton | Synthetic biology: from bacteria to stem cells | C. Voigt |
| 11/16/06 | Jay Keasling, UC Berkeley | Engineering microorganisms for production of inexpensive, effective, anti-malarial drugs | C. Craik |
| 11/30/06 | Sarah O'Connor, MIT | Biosynthesis of new alkaloids in periwinkle | K. Shokat |
| 12/14/06 | Maurizio Pellecchia, Burnham Institute | A million little pieces: Fragment based approaches to drug discovery | M. Jacobson |
| 1/11/07 | David Weitz, Harvard | Reconstituted networks as models of cell mechanics | W. Marshall |
| 1/18/07 | Richard H. Kramer, UC Berkeley | Engineering light-activated ion channels for remote control of neuronal activity | R. Edwards |
| 1/25/07 | Edward Egelman, University of Virginia | Polymorphic perversity in polymers: The biological role of multiple subunit interfaces in helical filaments | D. Mullins |
| 2/1/07 | Christina Smolke, Caltech | Engineering molecular sensors for probing and programming cellular systems | H. El-Samad |
| 2/22/07 | Alice Ting, MIT | New protein labeling methodology and application to single molecule imaging of receptor trafficking with quantum dots | J. Wells |
| 3/1/07 | Lorena Beese, Duke | An integrated view of DNA polymerization and repair | R. Stroud |
| 3/15/07 | Wilfred van der Donk, University of Illinois | Chemistry and biology of ianthionine synthesis | J. Taunton |
| 4/12/07 | David Tirrell, California Institute of Technology | Non-canonical amino acids in protein engineering and proteomic analysis | P. England |
| 4/19/07 | Brenda Bass, University of Utah | dsRNA binding proteins in RNA editing and RNA interference | J. Gross |
| 4/26/07 | Adrian Gross, Northwestern | Structural aspects of potassium channel function | B. Shoichet |
| 5/10/07 | Pei Zhou, Duke University Medical Center | From novel antibiotics to fast NMR | J. Gross |
| 5/17/07 | Melissa Jurica, UCSC | Spliceosome structure by cryo-EM reconstruction | G. Narlikar |
| 5/24/07 | Phil Baran, Scripps | The catalytic cycle of discovery in total synthesis | A. Renslo |
| 5/31/07 | William Bialek, Princeton | Physics problems in early embryonic development | R. Fletterick |
| 6/7/07 | Luc Jaeger, UC Santa Barbara | Exploring folding, assembly and design principles of RNA as a proto-language | A. Frankel |