Meetings: Wednesdays at noon in NHB 4.202
Generally, there is a 30-45 minute presentation on a recent journal paper (or papers) or on the presenter's own research. The emphasis is on structural work but non-structural topics in biochemistry and molecular biology are also welcome. Meetings are open to all who are interested.
Spring 2018 Schedule
February 14 - Mu-Sen Liu - Crystal structures of ternary complexes of archaeal B-family DNA polymerases. H.M. Kropp, K. Betz, J. Wirth, K. Diederichs, A. Marx. PLoS ONE 12, e0188005 (2017).
February 21 - Morgan Gilman - Structure of the mechanically activated ion channel Piezo1. K. Saotome, S.E. Murthy, J.M. Kefauver, T. Whitwam, A. Patapoutian, A.B. Ward. Nature doi: 10.1038/nature25453 [Epub ahead of print] (2017).
February 28 - Jennifer Stamos
March 7 - Daniel Wrapp
March 21 - Nianshuang Wang
March 28 - Harrison Jones
April 4 - Michael Hawkins
April 11 - Alfred Lentzsch
April 18 - Sarah Pattengale
April 25 - Jessica Meinke
May 2 -
Fall 2017 Presentations
October 18 - Aguang Dai - Visualizing the molecular sociology at the HeLa cell nuclear periphery. J. Mahamid, S. Pfeffer, M. Schaffer, E. Villa, R. Danev, L.K. Cuellar, F. Förster, A.A. Hyman, J.M. Plitzko, W. Baumeister. Science 351, 969-972 (2016).
October 25 - Sarah Pattengale - Structural basis for eliciting a cytotoxic effect in HER2-overexpressing cancer cells via binding to the extracellular domain of HER2. C. Jost, J. Schilling, R. Tamaskovic, M. Schwill, A. Honegger, A. Pluckthun. Structure 5, 1979-1991 (2013).
November 1 - Drew Wagner - Structural and functional studies of uncommon polyketide synthase domains
November 15 - Takeshi Miyazawa - Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants. C.A. Schenck, C.K. Holland, M.R. Schneider, Y. Men, S.G. Lee, J.M. Jez, H.A. Maeda. Nat. Chem. Biol. 13, 1029-1035 (2017).
December 6 - Evan Schwartz - Structure basis for directional R-loop formation and substrate handover mechanisms in type I CRISPR-Cas system. Y. Xiao, M. Luo, R.P. Hayes, J. Kim, S. Ng, F. Ding, M. Liao, A. Ke. Cell 170, 48-60 (2017).
Spring 2017 Presentations
April 5 - Jennifer Stamos - The vestigial tail of the spliceosome: the strange connection between Next-Gen RNA-seq and the evolution of eukaryotes
CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast. T.H. Nguyen, W.P. Galej, S.M. Fica, P.C. Lin, A.J. Newman, K. Nagai. Curr. Opin. Struct. Biol. 36, 48-57 (2016).
April 12 - Pat Byrne - Structure of the full-length VEGFR-1 extracellular domain in complex with VEGF-A. S. Markovic-Mueller, E. Stuttfeld, M. Asthana, T. Weinert, S. Bliven, K.N. Goldie, K. Kisko, G. Capitani, K. Ballmer-Hofer. Structure 25, 341-352 (2017).
April 19 - Jessica Meinke - The structure of the pleiotropic transcription regulator CodY provides insight into its GTP-sensing mechanism. A.R. Han, H.R. Kang, J. Son, D.H. Kwon, S. Kim, W.C. Lee, H.K. Song, M.J. Song, K.Y. Hwang. Nucleic Acids Res. 44, 9483-9493 (2016).
April 26 - Tara Shea - Mechanistic basis for the recognition of a misfolded protein by the molecular chaperone Hsp90. J. Oroz, J.H. Kim, B.J. Chang, M. Zweckstetter. Nat. Struct. Mol. Biol. 24, 407–413 (2017).
May 3 - John Cheong - Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis. Y. Gao, W. Yang. Science 352, 1334-1337 (2016).
May 10 - Professor Pinglong Xu - Hippo-sized nucleic acid sensing and antiviral defenses
Hippo signalling governs cytosolic nucleic acid sensing through YAP/TAZ-mediated TBK1 blockade. Q. Zhang, F. Meng, S. Chen, S.W.Plouffe, S. Wu, S. Liu, X. Li, R. Zhou, J. Wang, B. Zhao, J. Liu, J. Qin, J. Zou, X.H. Feng, K.L. Guan, P. Xu. Nat. Cell Biol. 19, 362-374 (2017).
Fall 2016 presentations
October 19 - Dan Leahy - Sometimes it is the fifth structure that reveals the key insight
November 2 - Tate Burkholder - Crystal structure of the ectoine hydroxylase, a snapshot of the active site. A. Hoppner, N. Widderich, M. Lenders, E. Bremer, S.H. Smits. J. Biol. Chem. 289, 29570-83 (2014).
Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms. N. Widderich, A. Hoppner, M. Pittelkow, J. Heider, S.H. Smits, E. Bremer. PLoS One 9, e93809 (2014).
November 9 - Jake LeVieux - Structural and kinetic comparison of hydratase-aldolase enzymes involved in bacterial polycyclic aromatic hydrocarbon degradation
November 16 - Drew Wagner - X-ray structure of the mouse serotonin 5-HT3 receptor. G. Hassaine, C. Deluz, L. Grasso, R. Wyss, M.B. Tol, R. Hovius, A. Graff, H. Stahlberg, T. Tomizaki, A. Desmyter, C. Moreau, X.D. Li, F. Poitevin, H. Vogel, H. Nury. Nature 512, 276-281 (2014).
November 30 - David Taylor - Sometimes it’s the fifth structure on a single cryo-EM grid that reveals the key insight
Spring 2016 presentations
March 9 - Jessica Meinke - Structure of the hantavirus nucleoprotein provides insights into the mechanism of RNA encapsidation. D. Olal, O. Daumke. Cell Reports 14, 1-8 (2016).
March 23 - John Cheong - Crystal structure of a substrate-engaged SecY protein-translocation channel. L. Li, E. Park, J.J. Ling, J. Ingram, H. Ploegh, T.A. Rapoport. Nature 531, 395-399 (2016).
March 30 - Yi Kou - How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis. Y.S. Lee, Y. Gao, W. Yang. Nat. Struct. Mol. Biol. 22, 298-303 (2015).
April 6 - Charlie Zogzas - Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport. I.A. Ehrnstorfer, E.R. Geertsma, E. Pardon, J. Steyaert, R. Dutzler. Nat. Struct. Mol. Biol. 21, 990-996 (2014).
April 13 - Wupeng Yan - Molecular basis of substrate-induced permeation by an amino acid antiporter. L. Kowalczyk, M. Ratera, A. Paladino, P. Bartoccioni, E. Errasti-Murugarren, E. Valencia, G. Portella, S. Bial, A. Zorzano, I. Fita, M. Orozco, X. Carpena, J.L. Vázquez-Ibar, M. Palacín. Proc. Nat. Acad. Sci. 108, 2925-3940 (2011).
April 20 - Brenda Medellin - Crystal structures of the PsbS protein essential for photoprotection in plants. M. Fan, M. Li, Z. Liu, P. Cao, X. Pan, H. Zhang, X. Zhao, J. Zhang, W. Chang. Nat. Struct. Mol. Biol. 22, 729-735 (2015).
April 27 - Joshua Mayfield - Structure of BRCA1-BRCT/Abraxas complex reveals phosphorylation-dependent BRCT dimerization at DNA damage sites. Q. Wu, A. Paul, D. Su, S. Mehmood, T.K. Foo, T. Ochi, E.L. Bunting, B. Xia, C.V. Robinson, B. Wang, T.L. Blundell. Mol Cell. 61, 434-448 (2016).
May 4 - Seema Irani - Structure of the sulfoxide synthase EgtB from the ergothioneine biosynthetic pathway. K.V. Goncharenko, A. Vit, W. Blankenfeldt, F.P. Seebeck. Angew Chem Int Ed Engl. 54, 2821-2824 (2015).
Fall 2015 presentations
September 30 - Marvin Hackert - X-ray Crystallography - basics to benefits
October 7 - Connie Bailey - A trans-acyltransferase ketoreductase reveals structural features and sequence signatures of split bimodules
October 14 - Sarah Wong - Structure and functional studies of the PRC1.1 complex
Structure of the Polycomb Group protein PCGF1 (NSPC1) in complex with BCOR reveals basis for binding selectivity of PCGF homologs. S.E. Junco, R. Wang, J.C. Gaipa, A.B. Taylor, V. Schirf, M.D. Gearhart, V..J. Bardwell, B. Demeler, P.J. Hart, C.A. Kim. Structure 21, 665-671 (2013).
October 21 - Jake LeVieux - Structure and function of hydratase-aldolase enzymes in bacterial polycyclic aromatic hydrocarbon degradation
October 28 - Amanda Hughes - Structure and function of the Escherichia coli Tol-Pal stator protein TolR. J.A. Wojdyla, E. Cutts, R. Kaminska, G. Papadakos, J.T.S. Hopper, P.J. Stansfeld, D. Staunton, C.V. Robinson. C. Kleanthous. J. Biol. Chem. epub (2015).
November 4 - Jia Zeng - Architecture of vertical interactions in trans-AT polyketide synthases
November 11 - Myong Koag - The replication of DNA lesions by human DNA polymerase β
November 18 - Seema Irani - Solving the crystal structure of a novel C-S lyase
December 2 - Drew Wagner - Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya. Nature 473, 55–60 (2011).
Spring 2015 presentations
February 11 - Devinder Ubhi - Characterizing the antifungal drug target Met6p by overcoming three preconceptions: uncrystallizable, undruggable, impossible reaction
February 25 - Nick Marshall - Structure determination for engineered antibody Fc domains with altered receptor specificity
March 4 - Wenzong Li - Studies of the autoprocessing mechanism of human asparaginase-like protein 1
March 11 - Art Monzingo - Novel binding motif and new flexibility revealed by structural analyses of a pyruvate dehydrogenase-dihydrolipoyl acetyltransferase subcomplex from the Escherichia coli pyruvate dehydrogenase multienzyme complex. P. Arjunan, J. Wang, N.S. Nemeria, S. Reynolds, I. Brown, K. Chandrasekhar, G. Calero, F. Jordan, W. Furey. J. Biol. Chem. 289, 30161-30176 (2014).
March 25 - Jessica Meinke - Mechanistic insight from the crystal structure of mitochondrial complex I. V. Zickermann C. Wirth, H. Nasiri, K. Siegmund, H. Schwalbe, C. Hunte, U. Brandt. Science 347, 44-49 (2015).
April 1 - Jake LeVieux - Mechanism and role of NahE in naphthalene degradation
April 8 - Joshua Mayfield - Structural mechanism of laforin function in glycogen dephosphorylation and lafora disease. M. Raththagala, M.K. Brewer, M.W.Parker, A.R. Sherwood, B.K.Wong, S. Hsu, T.M. Bridges, B.C. Paasch, L.M. Hellman, S. Husodo, D.A. Meekins, A.O. Taylor, B.D. Turner, K.D. Auger, V.V. Dukhande, S. Chakravarthy, P. Sanz, V.L. Woods, S. Li, C. W. Vander Kooi, M.S. Gentry. Mol. Cell 57, 261-72 (2015).
April 15 - Wupeng Yan - Endoperoxide formation catalyzed by FtmOx1, an α-ketoglutarate-dependent mononuclear non-heme iron enzyme
April 22 - John Cheong - Crystal structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant. J. Yin, J.C. Mobarec, P. Kolb, D.M. Rosenbaum. Nature 519, 247-250 (2015).
April 29 - Hala Ouzon - Structural basis for mismatch recognition and catalysis by methyl-CpG- binding domain protein 4
May 6 - Ben Gilman - Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog. T. Osawa, H. Inanaga, C. Sato, T. Numata. Mol. Cell epub (2015).
May 13 - Marvin Hackert - Report on the International Year of Crystallography - from Paris to Rabat
Fall 2014 presentations
October 1 - Yi Kou - Role of polymerase β in complementing aprataxin deficiency during abasic-site base excision repair. M. Caglayan, V.K. Batra, A. Sassa, R. Prasad, S.H. Wilson. Nature Structural & Molecular Biology 21, 497-499 (2014).
October 8 - Lilian Lamech - Crystal structure of Cas9 in complex with guide RNA and target DNA. H. Nishimasu, F.A. Ran, P.D. Hsu, S. Konermann, S.I. Shehata, N. Dohmae, R. Ishitani, F. Zhang, O. Nureki. Cell 156, 935-949 (2014).
October 15 - Kevin Entzminger - Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments. H. Chang, J. Jian, H. Hsu, Y. Lee, H. Chen, J. You, S. Hou, C. Shao, Y. Chen, K. Chiu, H. Peng, K. Lee, A. Yang. Structure 22, 9-21 (2014).
October 22 - Anna Mallam - Architecture of the Saccharomyces cerevisiae RNA polymerase I Core Factor complex. B. A. Knutson, J. Luo, J. Ranish, S. Hahn. Nature Structural & Molecular Biology 21, 810-816 (2014).
October 29 - Katy Brown - Biological applications of cryo-soft X-ray tomography. E. Duke, K. Dent, M. Razi, L.M. Collinson. J. Microscopy 255, 65-70 (2014).
November 12 - Charlie Zogzas - Metal homeostasis: Elucidation of an ion binding site in SLC30A10
SLC30A10 Is a cell surface-localized manganese efflux transporter, and Parkinsonism-causing mutations block its intracellular trafficking and efflux activity. D. Leyva-Illades, P. Chen, C.E. Zogzas, S. Hutchens, J.M. Mercado, C.D. Swaim, R.A. Morrisett, A.B. Bowman, M. Aschner, S. Mukhopadhyay. J. Neuroscience 34, 14079-14095 (2014).
Structure of the zinc transporter YiiP. M. Lu, D. Fu. Science 317, 1746-1748 (2007).
November 19 - Drew Wagner - Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. R.K. McGinty, R.C. Henrici, S. Tan. Nature 514, 591-596 (2014).
December 3 - Nancy Yuan - Using MismatCHA to detect ricin-generated apurinic sites
Mismatches improve the performance of strand-displacement nucleic acid circuits. Y.S. Jiang, S. Bhadra, B. Li, A.D. Ellington. Angew. Chem. Int. Ed. Engl. 53, 1845-1848 (2014).
Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. B. Li, A.D. Ellington, X. Chen. Nucl. Acids Res. 39, e110 (2011).
Spring 2014 presentations
February 26 - S.D. "Yogi" Yogesha - Improved crystallographic structures using extensive combinatorial refinement. J.C. Nwachukwu, M.R. Southern, J.R. Kiefer, P.V. Afonine, P.D. Adams, T.C. Terwilliger, K.W. Nettles. Structure 21, 1923-1930 (2013).
March 5 - Darren Gay - Crystal structure of botulinum neurotoxin DC in complex with its protein receptors Synaptotagmin I and II. R.P-A. Berntsson, L. Peng, L.M. Svensson, M. Dong, P. Stenmark. Structure 21, 1602-1611 (2013).
March 19 - Wenzong Li - Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. L. Redecke, K. Nass, D.P. DePonte, et al. Science 339, 227-230 (2013).
March 26 - Nick Marshall - Architecture and active site of particulate methane monooxygenase. M.A. Culpepper, A.C. Rosenzweig. Critical Reviews in Biochemistry and Molecular Biology 47, 483-492 (2012).
April 2 - Som Mukhopadhyay - Intracellular trafficking of Shiga toxin: mechanisms to therapeutics.
April 9 - Seongmin Lee - Alkylation damage and DNA replication.
Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta. M.-C. Koag, S. Lee. J. Am. Chem. Soc. e-pub (2014).
April 16 - Joshua Mayfield - Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Q. Li, S. Wanderling, M. Paduch, D. Medovoy, A. Singharoy, R. McGreevy, C.A. Villalba-Galea, R.E. Hulse, B. Roux, K. Schulten, A. Kossiakoff, E. Perozo. Nat. Struct. Mol. Biol. 21, 244-252 (2014).
April 23 - Dusty Brown - Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1. J.L. Parker, S. Newstead. Nature 507, 68-72 (2014).
April 30 - Katy Brown - De novo protein crystal structure determination from X-ray free-electron laser data. T.R.M. Barends, L. Foucar, S. Botha, R.B. Doak, R.L. Shoeman, K. Nass, J.E. Koglin, G.J. Williams, S. Boutet, M. Messerschmidt, I. Schlichting. Nature 505, 244-247 (2014).
May 7 - Devinder Ubhi - Structure and alternative conformations of dihydrofolate reductase.
Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. M.R. Sawaya, J. Kraut. Biochemistry 36, 586-603 (1997).
Structure, dynamics, and catalytic function of dihydrofolate reductase. J.R. Schnell, H.J. Dyson, P.E. Wright. Annual Review of Biophysics and Biomolecular Structure 33, 119-140 (2004).
Fall 2013 presentations
October 2 - Kevin Entzminger - Computational design of ligand-binding proteins with high affinity and selectivity. C.E. Tinberg, S.D. Khare, J. Dou, L. Doyle, J.W. Nelson, A Schena, W. Jankowski, C.G. Kalodimos, K. Johnsson, B.L. Stoddard, D. Baker. Nature 501, 212-216 (2013).
October 9 - Brent Halling - Calcium dependent stoichiometries of the SK intracellular domain/complex in solution.
October 16 - Drew Wagner - Crystallographic interrogation of bacillaene ketosynthase 6.
October 23 - Myong Koag - Structural basis for slow preferential misincorporation of dTTP opposite O6-methylguanine by human DNA polymerase ß.
October 30 - Marvin Hackert - IYCr2014 – Celebrating 100 years of X-ray crystallography.
November 6 - Wupeng Yan - Structure determination of the non-heme binding alpha-ketoglutarate-dependent dioxygenase FtmOX1 and cystathionine gamma-lyase.
November 13 - Chris Fage - BktB: The tale of a twinned thiolase.
November 20 - Lilian Lamech - Mitochondrial TyrRS: Evolving a function beyond translation.
December 4 - Yi Kou - Initial study of N7mG lesion with DNA polymerase beta.
Spring 2013 presentations
February 20 - Art Monzingo - Crystal structure of Prp8 reveals active site cavity of the spliceosome. W.P. Galej, C. Oubridge, A.J. Newman, K. Nagai. Nature 493, 638-644 (2013).
February 27 - Wenzong Li - Structure of a presenilin family intramembrane aspartate protease. X. Li, S. Dang, C. Yan, X. Gong, J. Wang, Y. Shi. Nature 493, 58-61 (2013).
March 6 - Eta Isiorho - Structural studies of the spinosyn rhamnosyltransferase, SpnG. E.A. Isiorho, H.W. Liu, A.T. Keatinge-Clay. Biochemistry 51, 1213-1222 (2012).
March 20 - Mark Collins - Two-color selection for amplified co-production of proteins in mammalian cells. Z. Assura, I. Schieren, W.A. Hendrickson, F. Mancia. Protein Expression and Purification 55, 319-324 (2007).
Detection and prevention of protein aggregation before, during, and after purification. S.E. Bondos, A. Bicknell. Analytical Biochemistry 316, 223-231 (2003).
March 27 - Rick Russell - RNA folding and ATP-dependent chaperone proteins monitored by SAXS.
April 3 - Adrian Keatinge-Clay - Piecing together the modular polyketide synthase puzzle.
April 10 - Darren Gay - Is a ketosynthase from a trans-AT polyketide synthase a trans-former?
April 17 - Katy Brown - Four distinct structural domains in Clostridium difficile toxin B visualized using SAXS. D. Albesa-Jové, T. Bertrand, E.P. Carpenter, G.V. Swain, J. Lim, J. Zhang, L.F. Haire, N. Vasisht, V. Braun, A. Lange, C. von Eichel-Streiber, D.I. Svergun, N.F. Fairweather, K.A. Brown. J. Mol. Biol. 396, 1260-1270 (2010).
April 24 - Devinder Ubhi - Discovering inhibitors against the fungal Met6p enzyme using X-ray crystallography, differential scanning fluorimetry and enzyme kinetics.
May 1 - Anna Mallam - Crystal structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p. A.L. Mallam, M. Del Campo, B. Gilman, D.J. Sidote, A.M. Lambowitz. Nature 490, 121-125 (2012).
David Hofmann's suggestions for Journal Club presentations
- Create an introduction that provides a broad perspective for the specific work being presented. For example, if you are presenting a paper on a new reverse transcriptase (RT) structure, you should provide some background on RTs in general. Don't assume that everyone in your audience knows the background. Provide historical perspective, such as when was the first RT discovered? When was the first structure of a member of the RT family solved? Why do we care about RT? This will provide a context for introducing what is special about the paper you are presenting. Also, explain enough about the work that came immediately before your paper (often from the same research group) so that your audience understands the starting point for the paper you are presenting.
- Explain why you chose the paper you did. What do you find most interesting about it? Why is it important? Also, why is the topic interesting and important?
- Instead of simply describing the methods used, look at the methods critically, with an eye for anything interesting or unusual. Point out anything that might be generally useful. For example, did the authors use any unusual purification or expression tricks? The people in your audience, many of whom are struggling with purification and expression, may find this helpful.
- What is the most significant contribution of the specific work to the field in general?
- As much as possible, make your own cartoons and schematic diagrams - don't copy these from the paper. When you make your own figure, you can be sure that it makes exactly the points you want, no more and no less.
- Do the results suggest any additional experiments to answer any new questions raised by the work? Hint for 2nd year grad students: These presentations can be a good source of ideas for qualifying exam topics.
- Clearly explain the significance of the results. Results by themselves are dull, unless they have significance. The significance may not be obvious to the audience, so point it out specifically. Also, try to think critically about the author's work. For example, are there any possible alternative interpretations of the results?
- Try to appear truly interested (even excited!) about the work you are presenting. Enthusiasm is contagious, and keeps your audience interested. Can you think of anything to make your presentation unique? An unusual prop or visual aid? Make your presentation "professional". That means, stand up in front, look directly at your audience, and don't "read" your slides.
- Arrive at the conference room early. Make sure you can get into the room. Make sure you can make the projector work, and make sure you have everything you need for your presentation, such as a pointer.
- Practice your talk!