Recommended Readings: David Julius, Ph.D. Friday February 8, 2019

Friday Lectures

Friday, February 8, 2019  3:45 p.m

Caspary Auditorium

David Julius Ph.D.

Morris Herzstein Chair in Molecular Biology and Medicine

Professor and Chair of Physiology

University of California

Natural Products as Probes of the Pain Pathway: From Physiology to Atomic Structure

Recommended Readings:

Empirical Articles

Gao, Yuan; Cao, Erhu; Julius, David; et al. (2016). TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. NATURE. 534 (7607): 347-+

Paulsen, Candice E.; Armache, Jean-Paul; Gao, Yuan; et al. (2015). Structure of the TRPA1 ion channel suggests regulatory mechanisms. NATURE. 520 (7548): 511-+

Liao, Maofu; Cao, Erhu; Julius, David; et al. (2013). Structure of the TRPV1 ion channel determined by electron cryo-microscopy. NATURE. 504 (7478): 107-+

Cavanaugh, Daniel J.; Chesler, Alexander T.; Jackson, Alexander C.; et al. (2011). Trpv1 Reporter Mice Reveal Highly Restricted Brain Distribution and Functional Expression in Arteriolar Smooth Muscle Cells. JOURNAL OF NEUROSCIENCE. 31 (13): 5067-5077

Cordero-Morales, Julio F.; Gracheva, Elena O.; Julius, David. (2011). Cytoplasmic ankyrin repeats of transient receptor potential A1 (TRPA1) dictate sensitivity to thermal and chemical stimuli. PNAS. 108 (46): E1184-E1191

Cavanaugh, Daniel J.; Chesler, Alexander T.; Braz, Joao M.; et al. (2011). Restriction of Transient Receptor Potential Vanilloid-1 to the Peptidergic Subset of Primary Afferent Neurons Follows Its Developmental Downregulation in Nonpeptidergic Neurons. JOURNAL OF NEUROSCIENCE. 31 (28): 10119-10127

Review Papers

Bohlen, Christopher J.; Julius, David (2012). Receptor-targeting mechanisms of pain-causing toxins: How ow? TOXICON. 60 (3): 254-264

Basbaum, Allan I.; Bautista, Diana M.; Scherrer, Gregory; et al. (2009). Cellular and Molecular Mechanisms of Pain. CELL. 139 (2): 267-284

Book Chapter

Julius, David. (2013). TRP Channels and Pain. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. 29: 355-384

 

Recommended Readings: Tom Muir, Ph.D. Friday January 25, 2019

Friday Lectures

Friday, January 25, 2019  3:45 p.m

Caspary Auditorium

Tom Muir Ph.D.

Professor of Chemistry and Chair

Department of Chemistry

Princeton University

Painting Chromatin with Synthetic Protein Chemistry

 

Recommended Readings:

Empirical Articles

Nacev, B.A., Feng, L., Bagert, J.D. Lemiesz, A., et al. (2019). The expanding landscape of ‘oncohistone’ mutations in human cancers. NATURE, in press

Wojcik, Felix; Dann, Geoffrey P.; Beh, Leslie Y.; et al. (2018). Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants. NATURE COMMUNICATIONS. 9

Lu, Chao; Jain, Siddhant U.; Hoelper, Dominik; et al. (2016). Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape. SCIENCE. 352 (6287): 844-849

Nguyen, Uyen T. T.; Bittoval, Lenka; Mueller, Manuel M.; et al. (2014). Accelerated chromatin biochemistry using DNA-barcoded nucteosome libraries. NATURE METHODS. 11 (8): 834-840

Fierz, Beat; Kilic, Sinan; Hieb, Aaron R.; et al. (2012). Stability of Nucleosomes Containing Homogenously Ubiquitylated H2A and H2B Prepared Using Semisynthesis. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 134 (48): 19548-19551

Review Paper

David, Yael; Muir, Tom W. (2017). Emerging Chemistry Strategies for Engineering Native Chromatin. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 139 (27): 9090-9096

Mueller, Manuel M.; Muir, Tom W. (2015). Histones: At the Crossroads of Peptide and Protein Chemistry. CHEMICAL REVIEWS. 115 (6): 2296-2349

Chatterjee, Champak; Muir, Tom W. (2010). Chemical Approaches for Studying Histone Modifications. JOURNAL OF BIOLOGICAL CHEMISTRY. 285 (15): 11045-11050

Book Chapter

Holt, Matthew; Muir, Tom (2015). Application of the Protein Semisynthesis Strategy to the Generation of Modified Chromatin. ANNUAL REVIEW OF BIOCHEMISTRY. 84: 265-290

McGinty, Robert K.; Chatterjee, Champak; Muir, Tom W. (2009). Semisynthesis of Ubiquitylated Proteins. METHODS IN ENZYMOLOGY: NON-NATURAL AMINO ACIDS. 462: 225-243

Recommended Readings: David Baker, Ph.D. Friday January 11, 2019

Friday Lectures

Friday, January 11, 2018  3:45 p.m

Caspary Auditorium

David Baker Ph.D.

Professor of Biochemistry and Director of the Institute for Protein Design

University of Washington

The Coming of Age of De Novo Protein Design

 

Recommended Readings:

Science News

Scientists program proteins to pair exactly. December 19, 2018. Science Daily

Empirical Articles

Shen, Hao; Fallas, Jorge A.; Lynch, Eric; et al. (2018). De novo design of self-assembling helical protein filaments. SCIENCE. 362 (6415): 705-709

Marcos, Enrique; Chidyausiku, Tamuka M.; McShan, Andrew C.; et al. (2018). De novo design of a non-local beta-sheet protein with high stability and accuracy. NATURE STRUCTURAL AND MOLECULAR BIOLOGY. 25 (11): 1028-1030

Dou, Jiayi; Vorobieva, Anastassia A.; Sheffler, William; et al. (2018). De novo design of a fluorescence-activating beta-barrel. NATURE. 561 (7724): 485-+

Lu, Peilong; Min, Duyoung; DiMaio, Frank; et al. (2018). Accurate computational design of multipass transmembrane proteins. SCIENCE. 359 (6379): 1042-1046

Hosseinzadeh, Parisa; Bhardwaj, Gaurav; Mulligan, Vikram Khipple; et al. (2017). Comprehensive computational design of ordered peptide macrocycles. SCIENCE. 358 (6369): 1461-1466

Review Paper

Huang, Po-Ssu; Boyken, Scott E.; Baker, David. (2016). The coming of age of de novo protein design. NATURE. 537 (7620): 320-327

Fleishman, Sarel J.; Baker, David. (2012). Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution. CELL. 149 (2): 262-273

Book Chapter

Thyme, Summer; Baker, David. (2014). Redesigning the Specificity of Protein-DNA Interactions with Rosetta. HOMING ENDONUCLEASES: METHODS AND PROTOCOLS. 1123: 265-282

Whitehead, Timothy A.; Baker, David; Fleishman, Sarel J. (2013). Computational Design of Novel Protein Binders and Experimental Affinity Maturation. METHODS IN PROTEIN DESIGN. 523: 1-19

 Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M.; et al. (2011). Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules. METHODS IN ENZYMOLOGY. 487: 545-574

 

Recommended Readings: Jue Chen, Ph.D., Monday December 10, 2018

Monday Lectures

Monday, December 10, 2018  4:00 p.m.

Carson Family Auditorium

Jue Chen, Ph.D.

William E. Ford Professor and Head

Laboratory of Membrane Biology and Biophysics

The Rockefeller University

CFTR, the Odd ABC Transporter Responsible for Cystic Fibrosis

 

Recommended Readings:

Empirical Articles

Kim, Youngjin; Chen, Jue. (2018). Molecular structure of human P-glycoprotein in the ATP-bound, outward-facing conformation. SCIENCE. 359 (6378): 915-919

Zhang, Zhe; Liu, Fangyu; Chen, Jue. (2017). Conformational Changes of CFTR upon Phosphorylation and ATP Binding. CELL. 170 (3): 483-+

Liu, Fangyu; Zhang, Zhe; Csanady, Laszlo; et al. (2017). Molecular Structure of the Human CFTR Ion Channel. CELL. 169 (1): 85-+

Zhang, Zhe; Chen, Jue. (2016). Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator. CELL. 167 (6): 1586-+

Oldham, Michael L.; Davidson, Amy L.; Chen, Jue. (2008). Structural insights into ABC transporter mechanism. CURRENT OPINION IN STRUCTURAL BIOLOGY. 18 (6): 726-733

Review Paper

Davidson, Amy L.; Dassa, Elie; Orelle, Cedric; et al. (2008). Structure, function, and evolution of bacterial ATP-binding cassette systems. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS. 72 (2): 317-364

 

Recommended Readings: Howard C. Hang, Ph.D. Friday October 19, 2018

Friday Lectures

Friday, October 19, 2018  3:45 p.m.

Caspary Auditorium

Howard C. Hang Ph.D.

Richard E. Salomon Family Associate Professor and Head

Laboratory of Chemical Biology and Microbial Pathogenesis

The Rockefeller University

Chemical Dissection of Host-Microbe Interactions

Recommended Readings:

Empirical Articles

Liu W, Zhou Y, Peng T, Zhou P, Ding X, Li Z, Zhong H, Xu Y, Chen S, Hang HC, Shao F. (2018). Nε-fatty acylation of multiple membrane-associated proteins by Shigella IcsB effector to modulate host function. NATURE MICROBIOLOGY. 3 (9): 996-1009

Thinon, Emmanuelle; Fernandez, Joseph P.; Molina, Henrik; et al. (2018). Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites. JOURNAL OF PROTEOME RESEARCH. 17 (5): 1907-1922

Westcott N, Fernandez JP, Molina H, Hang HC. (2017). Chemical proteomics reveals ADP-ribosylation of small GTPases during oxidative stress. NATURE CHEMICAL BIOLOGY. 13 (3): 302-308

Peng T, Hang HC. (2016). Site-Specific Bioorthogonal Labeling for Fluorescence Imaging of Intracellular Proteins in Living Cells. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 138 (43): 14423-14433

Rangan, Kavita J.; Pedicord, Virginia A.; Wang, Yen-Chih; et al. (2016). A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens. SCIENCE. 353 (6306): 1434-1437

Percher, Avital; Ramakrishnan, Srinivasan; Thinon, Emmanuelle; et al. (2016). Mass-tag labeling reveals site-specific and endogenous levels of protein S-fatty acylation. PNAS. 113 (16): 4302-7

Review Paper

Peng, Tao; Thinon, Emmanuelle; Hang, Howard C. (2016). Proteomic analysis of fatty-acylated proteins. CURRENT OPINION IN CHEMICAL BIOLOGY. 30: 77-86

Westcott, Nathan P.; Hang, Howard C. (2014). Chemical reporters for exploring ADP-ribosylation and AMPylation at the host-pathogen interface.  CURRENT OPINION IN CHEMICAL BIOLOGY. 23: 56-62

Grammel, Markus; Hang, Howard C. (2013). Chemical reporters for biological discovery. NATURE CHEMICAL BIOLOGY. 9 (8): 475-484

Recommended Readings: David Pellman, M.D. Friday June 1, 2018

Friday Lectures

Friday, June 1, 2018  3:45 p.m.

Caspary Auditorium

David Pellman M.D.

Margaret M. Dyson Professor

Department of Cell Biology

Harvard Medical School

Mechanisms of Rapid Genome Evolution

Recommended Readings:

Science News

Dana-Farber Cancer Institute. Researchers identify origin of chromosomal oddity in some cancer cells. May 27, 2015. EurekAlert

Empirical Articles

Marteil, Gaelle; Guerrero, Adan; Vieira, Andre F.; et al. (2018). Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation. NATURE COMMUNICATIONS. 9    

Zhang, Cheng-Zhong; Spektor, Alexander; Cornils, Hauke; et al. (2015). Chromothripsis from DNA damage in micronuclei. NATURE. 522 (7555): 179-+

Selmecki, Anna M.; Maruvka, Yosef E.; Richmond, Phillip A.; et al. (2015). Polyploidy can drive rapid adaptation in yeast. NATURE. 519 (7543): 349-+

Crasta, Karen; Ganem, Neil J.; Dagher, Regina; et al. (2012). DNA breaks and chromosome pulverization from errors in mitosis. NATURE. 482 (7383): 53-U70

Carter, Scott L.; Cibulskis, Kristian; Helman, Elena; et al. (2012). Absolute quantification of somatic DNA alterations in human cancer. NATURE BIOTECHNOLOGY. 30 (5): 413-+

Ganem, Neil J.; Godinho, Susana A.; Pellman, David. (2009). A mechanism linking extra centrosomes to chromosomal instability. NATURE. 460 (7252): 278-U146

Review Paper

Zhang, Cheng-Zhong; Leibowitz, Mitchell L.; Pellman, David. (2013). Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements. GENES AND DEVELOPMENT. 27 (23): 2513-2530   

Gordon, David J.; Resio, Benjamin; Pellman, David. (2012). Causes and consequences of aneuploidy in cancer. NATURE REVIEWS GENETICS. 13 (3): 189-203

Book Chapter

Leibowitz, Mitchell L.; Zhang, Cheng-Zhong; Pellman, David. (2015). Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. ANNUAL REVIEW OF GENETICS. 49: 183-211

Recommended Readings: Stephen Elledge, Ph.D. Friday May 18, 2018

Friday Lectures

Friday, May 18, 2018  3:45 p.m.

Caspary Auditorium

Stephen J. Elledge Ph.D.

Gregor Mendel Professor

Department of Genetics

Harvard Medical School

Microgenetics: What We Can Learn About Protein Degradation from Bits of Genes

Recommended Readings:

Science News

Your viral infection history in a single drop of blood. June 4, 2015. ScienceDaily

Empirical Articles

Sack, Laura Magill; Davoli, Teresa; Li, Mamie Z.; et al. (2018). Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns. CELL. 173 (2): 499-+

Liao, Sida; Davoli, Teresa; Leng, Yumei; et al. (2017). A genetic interaction analysis identifies cancer drivers that modify EGFR dependency. GENES AND DEVELOPMENT. 31 (2): 184-196

Xu, George J.; Kula, Tomasz; Xu, Qikai; et al. (2015). Comprehensive serological profiling of human populations using a synthetic human virome. SCIENCE. 348 (6239)

Emanuele, Michael J.; Elia, Andrew E. H.; Xu, Qikai; et al. (2011). Global Identification of Modular Cullin-RING Ligase Substrates. CELL. 147 (2): 459-474

Larman, H. Benjamin; Zhao, Zhenming; Laserson, Uri; et al. (2011). Autoantigen discovery with a synthetic human peptidome. NATURE BIOTECHNOLOGY. 29 (6): 535-U101

Yen, Hsueh-Chi Sherry; Xu, Qikai; Chou, Danny M.; et al. (2008). Global Protein Stability Profiling in Mammalian Cells. SCIENCE. 322 (5903): 918-923

Yen, Hsueh-Chi Sherry; Elledge, Stephen J. (2008). Identification of SCF Ubiquitin Ligase Substrates by Global Protein Stability Profiling. SCIENCE. 322 (5903): 923-929

Review Paper

Ciccia, Alberto; Elledge, Stephen J. (2010). The DNA Damage Response: Making It Safe to Play with Knives. MOLECULAR CELL. 40 (2): 179-204

Luo, Ji; Solimini, Nicole L.; Elledge, Stephen J. (2009). Principles of Cancer Therapy: Oncogene and Non-oncogene Addiction. CELL. 136 (5): 823-837

 

Recommended Readings: Stephen Goff, Ph.D. Friday May 11, 2018

Friday Lectures

Friday, May 11, 2018  3:45 p.m.

Caspary Auditorium

Stephen Goff Ph.D.

Higgins Professor

Department of Biochemistry and Molecular Biophysics

Columbia University College of Physicians and Surgeons

Quiet, Please: Silencing Retroviral DNAs

Recommended Readings:

Empirical Articles

Lee, Andreia; CingOz, Oya; Sabo, Yosef; et al. (2018). Characterization of interaction between Trim28 and YY1 in silencing proviral DNA of Moloney murine leukemia virus. VIROLOGY. 516: 165-175

Geis, Franziska K.; Galla, Melanie; Hoffmann, Dirk; et al. (2017). Potent and reversible lentiviral vector restriction in murine induced pluripotent stem cells. RETROVIROLOGY. 14

Wang, Gary Z.; Goff, Stephen P. (2017). Transcriptional Silencing of Moloney Murine Leukemia Virus in Human Embryonic Carcinoma Cells. JOURNAL OF VIROLOGY. 91 (1)

Wang, Cheng; Goff, Stephen P. (2017). Differential control of retrovirus silencing in embryonic cells by proteasomal regulation of the ZFP809 retroviral repressor. PNAS. 114 (6): E922-E930

Wang, Gary Z.; Wang, Ying; Goff, Stephen P. (2016). Histones Are Rapidly Loaded onto Unintegrated Retroviral DNAs Soon after Nuclear Entry. CELL HOST MICROBE.  20 (6): 798-809

Griffin, Daniel O.; Goff, Stephen P. (2015). HIV-1 Is Restricted prior to Integration of Viral DNA in Primary Cord-Derived Human CD34(+) Cells. JOURNAL OF VIROLOGY. 89 (15): 8096-8100

Yang, Bin Xia; El Farran, Chadi A.; Guo, Hong Chao; et al. (2015). Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells. CELL. 163 (1): 230-245

Review Paper

Schlesinger, Sharon; Goff, Stephen P. (2015). Retroviral Transcriptional Regulation and Embryonic Stem Cells: War and Peace. MOLECULAR AND CELLULAR BIOLOGY. 35 (5): 770-777

Studamire, Barbara; Goff, Stephen P. (2010). Interactions of Host Proteins with the Murine Leukemia Virus Integrase. VIRUSES. 2 (5): 1110-1145


Recommended Readings: Michael P. Rout, Ph.D. Monday April 2, 2018

Monday Lectures

Monday, April 2, 2018  4:00 p.m.

Carson Family Auditorium

Michael P. Rout, Ph.D.

Professor

Laboratory of Cellular and Structural Biology

The Rockefeller University

A Hole New View: Structure-Function Mapping of the Nuclear Pore Complex

Recommended Readings:

Science News

March 15, 2018. Scientists map the portal to the cell’s nucleus. Science Daily.

Empirical Articles

Upla, Paula; Kim, Seung Joong; Sampathkumar, Parthasarathy; et al. (2017). Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. STRUCTURE. 25 (3): 434-445

Hayama, Ryo; Rout, Michael P.; Fernandez-Martinez, Javier. (2017). The nuclear pore complex core scaffold and permeability barrier: variations of a common theme. CURRENT OPINION IN CELL BIOLOGY. 46: 110-118

Fernandez-Martinez, Javier; Kim, Seung Joong; Shi, Yi; et al. (2016). Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. CELL. 167 (5): 1215-+

Raveh, Barak; Karp, Jerome M.; Sparks, Samuel; et al. (2016). Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. PNAS. 113 (18): E2489-E2497

Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; et al. (2014). Integrative Structure-Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex. MOLECULAR & CELLULAR PROTEOMICS. 13 (11): 2911-2926

Wente, Susan R.; Rout, Michael P. (2010). The Nuclear Pore Complex and Nuclear Transport. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY. 2 (10)

Review Papers

Field, Mark C.; Koreny, Ludek; Rout, Michael P. (2014). Enriching the Pore: Splendid Complexity from Humble Origins. TRAFFIC. 15 (2): 141-156

Strambio-De-Castillia, Caterina; Niepel, Mario; Rout, Michael P. (2010). The nuclear pore complex: bridging nuclear transport and gene regulation. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 11 (7): 490-501

Book Chapter

Jovanovic-Talisman, Tijana; Chait, Brian T.; Rout, Michael P. (2014). NPC Mimics: Probing the Mechanism of Nucleocytoplasmic Transport. METHODS IN CELL BIOLOGY. 122: 379-393  

Recommended Readings: Edward H. Egelman, Ph.D. Friday January 19th, 2018

Friday Lectures

Friday, January 19, 2018  3:45 p.m.

Caspary Auditorium

Edward Egelman, Ph.D.

Harrison Distinguished Professor

Biochemistry and Molecular Genetics

University of Virginia Medical School

Cryo-EM of Protein and Nucleoprotein Polymers at Near-Atomic Resolution

Recommended Readings:

Science News

Kenny Walter. Virus Holds Key to Durable Material. (2017, Jul 20). Virus Holds Key to Durable Material. R&D Magazine

Empirical Articles

Egelman, Edward H. (2017). Cryo-EM of bacterial pili and archaeal flagellar filaments. CURRENT OPINION IN STRUCTURAL BIOLOGY. 46: 31-37

Wang, Fengbin; Burrage, Andrew M.; Postel, Sandra; et al. (2017). A structural model of flagellar filament switching across multiple bacterial species. NATURE COMMUNICATIONS. 8: 960

Wang, Fengbin; Coureuil, Mathieu; Osinski, Tomasz; et al. (2017). Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution. STRUCTURE. 25 (9): 1423-+

Kasson, Peter; DiMaio, Frank; Yu, Xiong; et al. (2017). Model for a novel membrane envelope in a filamentous hyperthermophilic virus. ELIFE. 6  

Kolappan, Subramania; Coureuil, Mathieu; Yu, Xiong; et al. (2016). Structure of the Neisseria meningitidis Type IV pilus. NATURE COMMUNICATIONS. 7: 13015

Braun, Tatjana; Vos, Matthijn R.; Kalisman, Nir; et al. (2016). Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain. PNAS. 113 (37): 10352-10357

Egelman, Edward H. (2016). The Current Revolution in Cryo-EM. BIOPHYSICAL JOURNAL. 110 (5): 1008-1012

Wang, Ray Yu-Ruei; Kudryashev, Mikhail; Li, Xueming; et al. (2015). De novo protein structure determination from near-atomic-resolution cryo-EM maps. NATURE METHODS. 12 (4): 335-U84

DiMaio, Frank; Yu, Xiong; Rensen, Elena; et al. (2015). A virus that infects a hyperthermophile encapsidates A-form DNA. SCIENCE. 348 (6237): 914-917

Review Papers

Egelman, Edward H. (2015). Three-dimensional reconstruction of helical polymers. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS. 581: 54-58