Category Archives: Biochemistry

Recommended Readings: Kang Shen, Ph.D.

Posted on by

Friday Lecture Series

Extracellular and Intracellular Mechanisms of Synapse Patterning in C. elegans

Kang Shen, Ph.D., M.P.H., associate professor,

department of biological sciences, Stanford University

 February 22, 2012

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

Caspary Auditorium

Recommended Readings

Allen, P. B., Sgro, A. E., Chao, D. L., Doepker, B. E., Edgar, J. S., Shen, K., & Chiu, D. T. (2008). Single-synapse ablation and long-term imaging in live C. elegans. Journal of Neuroscience Methods, 173(1), 20-26

Crane, M. M., Stirman, J. N., Ou, C. -., Kurshan, P. T., Rehg, J. M., Shen, K., & Lu, H. (2012). Autonomous screening of C. elegans identifies genes implicated in synaptogenesis. Nature Methods, 9(10), 977-980

Klassen, M. P., Wu, Y. E., Maeder, C. I., Nakae, I., Cueva, J. G., Lehrman, E. K., . . . Shen, K. (2010). An arf-like small G protein, ARL-8, promotes the axonal transport of presynaptic cargoes by suppressing vesicle aggregation. Neuron, 66(5), 710-723

Maeder, C. I., & Shen, K. (2011). Genetic dissection of synaptic specificity. Current Opinion in Neurobiology, 21(1), 93-99

Margeta, M. A., Wang, G. J., & Shen, K. (2009). Clathrin adaptor AP-1 complex excludes multiple postsynaptic receptors from axons in C. elegans. Proceedings of the National Academy of Sciences of the United States of America, 106(5), 1632-1637

 

Share

Recommended Readings: Kazuhiro Yamada, PhD October 1, 2012

Posted on by

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

Share

Recommended Readings: Howard C Hang, PhD.

Posted on by
Reply

Chemical Reporters for Exploring Posttranslational

Modifications in Innate Immunity

Howard C Hang, Ph.D.

Laboratory of Chemical Biology and Microbial Pathogenesis

The Rockefeller University

4:00 p.m. Monday, June 4, 2012    Refreshments  3:45  Abby Lounge

Caspary Auditorium

Recommended Readings

Yount JS, Charron G, Hang HC.   2012.  Bioorthogonal proteomics of 15-hexadecynyloxyacetic acid chemical reporter reveals preferential targeting of fatty acid modified proteins and biosynthetis enzymes.    Bioorganic & Medicinal Chemistry.  20(2, S1):650-654.  DOI: 0.1016/j.bmc.2011.03.062

Lei YL, Xie K. et al.  2012.  Chemistry-based functional proteomics to identify novel deubiquitylating enzymes involved in viral infection.   Combinatorial Chemistry & High Throughput Screening.  15(4):316-327.   Please request from Markus Library.

Grammel M, Dossa PD, Taylor-Salmon E, et al.  2012.  II-selective labeling of bacterial proteomes with an  orthogonal phenylalanine amino acid reporter.   Chemical Communications.  48(10):1473-1474.  DOI: 10.1039/c1cc14939c

Aguera-Gonzales S, Gross CC, Fernandez-Messina L, et al.  2011.  Palmitoylation of MICA, a ligand for NKG2D, mediates its recruitment to membrane microdomains and promotes its shedding.    European Journal of Immunology.  41(12):3667-3676.   DOI: 10.1002/eji.20114165

Hao ZY, Hong SL, Chen X, et al.  2011.  Introducing bioorthogonal functionalities into proteins in living cells.  Accounts of Chemical Research   44(9, S1):742-751.   DOI: 10.1021/ar200067r

Hang HC, Linder ME.  2011.  Exploring protein lipidation with chemical biology.  Chemical Reviews.  111(10):6341-6358.   DOI:  10.1021/cr2001977

Yang YY, Hang HC.  2011.  Chemical approaches for the detection and synthesis of acetylated proteins.  Chembiochem.   12(2):314-322.   DOI: 10.1002/cbc.201000558

 

 

 

Share

Recommended Readings: Hugo Bellen, Ph.D., D.V.M.

Posted on by
Reply

Friday Lecture Series

Mitochondria and Neurodegeneration

Hugo Bellen, Ph.D., D.V.M., investigator, Howard Hughes Medical Institute;

professor, departments of molecular and human

genetics and neuroscience, director, Program in Developmental Biology,

Baylor College of Medicine

March 30, 2012

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

Caspary Auditorium

 

Recommended Readings:

Bibliography

Han, S. M., H. Tsuda, Y. Yang, J. Vibbert, P. Cottee, S. -J Lee, J. Winek, C. Haueter, H. J. Bellen, and M. A. Miller. 2012. “Secreted VAPB/ALS8 Major Sperm Protein Domains Modulate Mitochondrial Localization and Morphology Via Growth Cone Guidance Receptors.” Developmental Cell 22 (2): 348-362

Pesah, Y., T. Pham, H. Burgess, B. Middlebrooks, P. Verstreken, Y. Zhou, M. Harding, H. Bellen, and G. Mardon. 2004. “Drosophila Parkin Mutants have Decreased Mass and Cell Size and Increased Sensitivity to Oxygen Radical Stress.” Development 131 (9): 2183-2194

Romero, E., G. -H Cha, P. Verstreken, C. V. Ly, R. E. Hughes, H. J. Bellen, and J. Botas. 2008. “Suppression of Neurodegeneration and Increased Neurotransmission Caused by Expanded Full-Length Huntingtin Accumulating in the Cytoplasm.” Neuron 57 (1): 27-40

Venken, K. J. T., Y. He, R. A. Hoskins, and H. J. Bellen. 2006. “P[Acman]: A BAC Transgenic Platform for Targeted Insertion of Large DNA Fragments in D. Melanogaster.” Science 314 (5806): 1747-1751

Verstreken, P., C. V. Ly, K. J. T. Venken, T. -W Koh, Y. Zhou, and H. J. Bellen. 2005. “Synaptic Mitochondria are Critical for Mobilization of Reserve Pool Vesicles at Drosophila Neuromuscular Junctions.” Neuron 47 (3): 365-378


Share

Recommended Readings: Hani S. Zaher, PH.D. Monday, March 5, 2012

Posted on by
Reply

Dealing with Mistakes: a New Form of Proofreading on the Ribosome

Hani S. Zaher, Ph.D

Postdoctoral Fellow

Department of Molecular Biology and Genetics

Johns Hopkins School of Medicine

4:00 p.m.  Monday, March 5, 2012   Refreshments at 3:45

Caspary Auditorium

Recommended Readings:

Zaher HS; Shaw JJ; Strobel SA; et al.  2011.  The 2’-OH group of the peptidyl-tRNA stabilizes an active conformation of the ribosomal PTC.  EMBO Journal.   30(12):2445-2453.   DOI:10.1038/emboj.2011.142

Zaher HS; Green R.  2011.  A primary role for release factor 3 in quality control during translation eloncation in Escherichia coli.  CELL.  147(2):396-408.   DOI:10.1016/j.cell.2011.08.45

Zaher HS; Green R.  2010.  Kinetic basis for global loss of fidelity arising from mismatches in the P-site codon:anticodon helix.   RNA-A Publication of the RNA Society.  16(10):1980-1989.  DOI:10.1261/rna.2241810.

Zaher HS; Green R.  2010.  Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRFNA selection.  Molecular Cell   39(1):110-120.   DOI:10.1016/j.molcel.2010.06.009

Zaher HS; Green R. 2009.  Fidelity at the molecular level: lessons from protein synthesis.   CELL.  136(4):746-762.  DOI:10.1016/j.cell.2009.01.036

Zaher HS; Green R.  2009.  Quality control by the ribosome following peptide bond formation.  NATURE.  457(7226):161-U51.   DOI:10.1038/nature07582

Share

Recommended Readings: Karim-Jean Armache Ph.D. Monday February 6, 2012

Posted on by
Reply

Monday lecture Series

Structural Characterization of Silent Chromatin

Karim-Jean Armache

Postdoctoral Fellow

Department of Molecular Biology

  Harvard Medical School and Massachusetts General Hospital

Monday, February 6,  2012

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

Recommended Readings:

 Armache KJ; Garlick JD; Canzio D; et al.  2011.  Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 angstrom resolution.  SCIENCE.  334(6058):877-982.  DOI:10.1126/science.1210915

Kostrewa D; Zeller ME; Armache KJ; et al.  2009.  RNA polymerase II-TFIIB structure and mechanism of transcription initiation.  NATURE.  462(7271):323-330.  DOI:10.1038/nature08548.

Brueckner F; Armache KJ; Cheung A; et al.  2009. Structure-function studies of the RNA polymerase II elongation complex.  Acta Crystallographica Section D-Biological Crystallography.  65:112-120   DOI:10.1107/S0907444908039875

C ramer, P; Armache KJ; Baumli S; et al.  2008.  Structure of eukaryotic RNA polymerases.  Annual Review of Biophysics.  37:337-352.   DOI:10.1146/annurev.biophys.37.032807.130008

Buchberger JR; Onishi M; Li G;  et al.  2008.  Sir3-nucleosome interactions in spreading of silent chromatin in Saccharomyces cerevisiae.  Molecular and Cellular Biology.  28(22):6903-6918.  DOI: 10.1128/MCB.01210-08

Braunstein M; Sobel RE; Allis CD; et al.  1996.  Efficient transcriptional silencing in  Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern.  Molecular and Cellular Biology.  16(8):4349-4356.

Hecht A; Strahl-Bohlsinger S; Grunstein M.  1996.  Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. NATURE.  383(6595):92-96.  DOI:10.1038/383092a0

Share

Recommended Readings: Wayne Hendrickson, Ph.D.

Posted on by
Reply

Friday Lecture Series

Structural Analysis of SLAC1-family Anion Channel Activity

Wayne Hendrickson, Ph.D.,

professor, department of biochemistry and molecular biophysics,

Columbia University

December 9,  2011

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

Caspary Auditorium

Recommended Readings:

Chen, Y. -H, L. Hu, M. Punta, R. Bruni, B. Hillerich, B. Kloss, B. Rost, J. Love, S. A. Siegelbaum, and W. A. Hendrickson. 2010. Homologue structure of the SLAC1 anion channel for closing stomata in leaves. Nature 467, (7319): 1074-1080

Mancia, F., and W. A. Hendrickson. 2007. Expression of recombinant G-protein coupled receptors for structural biology. Molecular BioSystems 3, (10): 723-734

Williams, J. C., P. L. Roulhac, A. G. Roy, R. B. Vallee, M. C. Fitzgerald, and W. A. Hendrickson. 2007. Structural and thermodynamic characterization of a cytoplasmic dynein light chain-intermediate chain complex. Proceedings of the National Academy of Sciences of the United States of America 104, (24): 10028-10033

Williams, J. C., H. Xie, and W. A. Hendrickson. 2005. Crystal structure of dynein light chain TcTex-1. Journal of Biological Chemistry 280, (23): 21981-21986

Share

Natural Dye Obtained from Lichens May Combat Alzheimer’s Disease

Posted on by
Reply

A red dye derived from lichens that has been used for centuries to color fabrics and food appears to reduce the abundance of small toxic protein aggregates in Alzheimer’s disease. The dye, a compound called orcein, and a related substance, called O4, bind preferentially to small amyloid aggregates that are considered to be toxic and cause neuronal dysfunction and memory impairment in Alzheimer’s disease. O4 binding to small aggregates promotes their conversion into large, mature plaques which researchers assume to be largely non-toxic for neuronal cells.  Read  the full story in NATURE CHEMICAL BIOLOGY.

Share

Yale Scientists Develop Synthetic Biology Approach for Generating Phosphoproteins

Posted on by
Reply

Yale researchers have devised a technique for expressing activated phosphoproteins in Escherichia coli, using it to generate phosphorylated versions of the protein MEK1, a key molecule in cell proliferation, development, differentiation, and oncogenesis. 

According to Yale assistant professor Jesse Rinehart, one of the leaders of the study – which was published in Science – the technique could prove an important source of reagents for phosphoproteomic research and provides an early glimpse of synthetic biology’s potential to aid proteomics more generally.

Share

Recommended Readings: Barry S. Coller M.D. Monday Sept 26 2011

Posted on by
Reply

Monday Lectures

Combing Structure-Based Design and Mass Screening to Probe

 Ligand Binding to Integrin Receptors

Barry S. Coller  M.D.

Vice President for Medical Affairs and Physician-in-Chief

Laboratory of Blood and Vascular Biology

September 26, 2011,  Caspary Auditorium,  4 p.m.

Recommended Readings

Litvinov RI; Barsegov V; Schissler AJ; Fisher AR; Bennett JS; Weisel JW; Shuman H.  2011.  Dissociation of bimolecular αIIβ3-fibrinogen complex under a constant tensile force.   Biophysical Journal.  100(1):165-73.

Lord MS; Cheng B; McCarthy SJ; et al.  2011.  The modulation of platelet adhesion and activation by chitosan through plasma and extracellular matrix proteins.  Biomaterials. 32(28):6655-6662  (Request from Markus Library)

Blue R; Li JH; Steinberg J; et al.  2010.  Effects of limiting extension at the alpha IIb Genu on ligand binding to integrin alpha IIb beta 2.  Journal of Biological Chemistry.  285(23):17604-17613.

Sheldrake HM; Patterson LH.  2009.  Function and antagonism of beta(3) integrins in the development of cancer therapy.  Current Cancer Drug Targets. 9(4):519-540.  (Request from Markus Library)

Basani RB; Zhu H: Thornton MA: et al.  2009.  Species differences in small molecule binding to alpha IIb beta 3 are the result of sequence difference in 2 loops of the alpha IIb beta propeller.   Blood.  113(4):902-910.

Blue R; Kowalska MA; Hirsch J; et al.  2009.  Structural and therapeutic insights from the species specificity and in vivo antithrombotic activity of a novel alpha IIb beta 3 antagonist. Blood  114(1):195-201

Blue R; Murcia M; Karan C; et al.  2008.  Application of high-throughput screening to identify a novel alpha IIb-specific small-molecule inhibitor of alpha IIb 3-mediated platelet interaction with fibrinogen.  Blood.  111(3):1248-1256.

Hynes, RO.  2002.  Integrins: bidirectional, allosteric signaling machines.  Cell. 110(6):673-687.

Share