Yifan Cheng, PhD
Professor
Biochemistry and Biophysics
School of Medicine

A full understanding of the biological functions/processes of any macromolecular complex requires structural information at a wide range of resolutions, including atomic details of its components, spatial arrangements of these components and interactions between them. CryoEM can be used to study macromolecules in their native conformations at a wide resolution range, from sub-nanometer resolution (single particle cryoEM) to the cellular level (electron tomography).

• Single particle electron cryo-microscopy of a mammalian ion channel.
  Current opinion in structural biology 2014 Liao M, Cao E, Julius D, Cheng Y
• Structural mechanism of serum amyloid A-mediated inflammatory amyloidosis.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Lu J, Yu Y, Zhu I, Cheng Y, Sun PD
• CTER-rapid estimation of CTF parameters with error assessment.
  Ultramicroscopy 2014 Penczek PA, Fang J, Li X, Cheng Y, Loerke J, Spahn CM
• Structure of the TRPV1 ion channel determined by electron cryo-microscopy.
  Nature 2013 Liao M, Cao E, Julius D, Cheng Y
• TRPV1 structures in distinct conformations reveal activation mechanisms.
  Nature 2013 Cao E, Liao M, Cheng Y, Julius D
• Self-assembly of VPS41 promotes sorting required for biogenesis of the regulated secretory pathway.
  Developmental cell 2013 Asensio CS, Sirkis DW, Maas JW, Egami K, To TL, Brodsky FM, Shu X, Cheng Y, Edwards RH
• Influence of electron dose rate on electron counting images recorded with the K2 camera.
  Journal of structural biology 2013 Li X, Zheng SQ, Egami K, Agard DA, Cheng Y
• Acetylation-mediated proteasomal degradation of core histones during DNA repair and spermatogenesis.
  Cell 2013 Qian MX, Pang Y, Liu CH, Haratake K, Du BY, Ji DY, Wang GF, Zhu QQ, Song W, Yu Y, Zhang XX, Huang HT, Miao S, Chen LB, Zhang ZH, Liang YN, Liu S, Cha H, Yang D, Zhai Y, Komatsu T, Tsuruta F, Li H, Cao…
• Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.
  Nature methods 2013 Li X, Mooney P, Zheng S, Booth CR, Braunfeld MB, Gubbens S, Agard DA, Cheng Y
• Reconfiguration of the proteasome during chaperone-mediated assembly.
  Nature 2013 Park S, Li X, Kim HM, Singh CR, Tian G, Hoyt MA, Lovell S, Battaile KP, Zolkiewski M, Coffino P, Roelofs J, Cheng Y, Finley D
• A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly.
  Nature 2013 Canzio D, Liao M, Naber N, Pate E, Larson A, Wu S, Marina DB, Garcia JF, Madhani HD, Cooke R, Schuck P, Cheng Y, Narlikar GJ
• Recording high-resolution images of two-dimensional crystals of membrane proteins.
  Methods in molecular biology (Clifton, N.J.) 2013 Avila-Sakar A, Li X, Zheng SQ, Cheng Y
• A method for integrative structure determination of protein-protein complexes.
  Bioinformatics (Oxford, England) 2012 Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A
• Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils.
  Biomacromolecules 2012 Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S
• Fabs enable single particle cryoEM studies of small proteins.
  Structure (London, England : 1993) 2012 Wu S, Avila-Sakar A, Kim J, Booth DS, Greenberg CH, Rossi A, Liao M, Li X, Alian A, Griner SL, Juge N, Yu Y, Mergel CM, Chaparro-Riggers J, Strop P, Tampé R, Edwards RH, Stroud RM, Craik CS, Cheng Y
• Visualizing proteins and macromolecular complexes by negative stain EM: from grid preparation to image acquisition.
  Journal of visualized experiments : JoVE 2011 Booth DS, Avila-Sakar A, Cheng Y
• Self-assembly of amelogenin proteins at the water-oil interface.
  European journal of oral sciences 2011 Martinez-Avila OM, Wu S, Cheng Y, Lee R, Khan F, Habelitz S
• Direct membrane association drives mitochondrial fission by the Parkinson disease-associated protein alpha-synuclein.
  The Journal of biological chemistry 2011 Nakamura K, Nemani VM, Azarbal F, Skibinski G, Levy JM, Egami K, Munishkina L, Zhang J, Gardner B, Wakabayashi J, Sesaki H, Cheng Y, Finkbeiner S, Nussbaum RL, Masliah E, Edwards RH
• A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction.
  Ultramicroscopy 2011 Zheng SQ, Branlund E, Kesthelyi B, Braunfeld MB, Cheng Y, Sedat JW, Agard DA
• Self-aligning amelogenin nanoribbons in oil-water system.
  Journal of structural biology 2010 He X, Wu S, Martinez-Avila O, Cheng Y, Habelitz S
• Structure characterization of the 26S proteasome.
  Biochimica et biophysica acta 2010 Kim HM, Yu Y, Cheng Y
• HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes.
  Proceedings of the National Academy of Sciences of the United States of America 2010 Daugherty MD, Booth DS, Jayaraman B, Cheng Y, Frankel AD
• GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors.
  Journal of structural biology 2010 Li X, Grigorieff N, Cheng Y
• Collecting electron crystallographic data of two-dimensional protein crystals.
  Methods in enzymology 2010 Hite RK, Schenk AD, Li Z, Cheng Y, Walz T
• HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells.
  Traffic (Copenhagen, Denmark) 2010 Lenassi M, Cagney G, Liao M, Vaupotic T, Bartholomeeusen K, Cheng Y, Krogan NJ, Plemenitas A, Peterlin BM
• The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes.
  Nature 2009 Racki LR, Yang JG, Naber N, Partensky PD, Acevedo A, Purcell TJ, Cooke R, Cheng Y, Narlikar GJ
• Interactions of PAN's C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome-ATPase interactions.
  The EMBO journal 2009 Yu Y, Smith DM, Kim HM, Rodriguez V, Goldberg AL, Cheng Y
• Evaluation of imaging plates as recording medium for images of negatively stained single particles and electron diffraction patterns of two-dimensional crystals.
  Journal of electron microscopy 2009 Li Z, Hite RK, Cheng Y, Walz T
• Toward an atomic model of the 26S proteasome.
  Current opinion in structural biology 2009 Cheng Y
• A designed angiopoietin-2 variant, pentameric COMP-Ang2, strongly activates Tie2 receptor and stimulates angiogenesis.
  Biochimica et biophysica acta 2009 Kim HZ, Jung K, Kim HM, Cheng Y, Koh GY
• The advent of near-atomic resolution in single-particle electron microscopy.
  Annual review of biochemistry 2009 Cheng Y, Walz T
• Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases.
  Molecular cell 2008 Rabl J, Smith DM, Yu Y, Chang SC, Goldberg AL, Cheng Y
• A fusion-intermediate state of HIV-1 gp41 targeted by broadly neutralizing antibodies.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Frey G, Peng H, Rits-Volloch S, Morelli M, Cheng Y, Chen B
• In vitro self-assembly of tailorable nanotubes from a simple protein building block.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Ballister ER, Lai AH, Zuckermann RN, Cheng Y, Mougous JD
• Structural organization of the anaphase-promoting complex bound to the mitotic activator Slp1.
  Molecular cell 2007 Ohi MD, Feoktistova A, Ren L, Yip C, Cheng Y, Chen JS, Yoon HJ, Wall JS, Huang Z, Penczek PA, Gould KL, Walz T
• Polymorphic assemblies and crystalline arrays of lens tetraspanin MP20.
  Journal of molecular biology 2007 Gonen T, Hite RK, Cheng Y, Petre BM, Kistler J, Walz T
• Docking of the proteasomal ATPases' carboxyl termini in the 20S proteasome's alpha ring opens the gate for substrate entry.
  Molecular cell 2007 Smith DM, Chang SC, Park S, Finley D, Cheng Y, Goldberg AL
• Reconstructing the endocytotic machinery.
  Methods in cell biology 2007 Cheng Y, Walz T
• Cryo-electron tomography of clathrin-coated vesicles: structural implications for coat assembly.
  Journal of molecular biology 2006 Cheng Y, Boll W, Kirchhausen T, Harrison SC, Walz T
• Activation of leukocyte beta2 integrins by conversion from bent to extended conformations.
  Immunity 2006 Nishida N, Xie C, Shimaoka M, Cheng Y, Walz T, Springer TA
• Electron tomography of swollen rigor fibers of insect flight muscle reveals a short and variably angled S2 domain.
  Journal of molecular biology 2006 Liu J, Wu S, Reedy MC, Winkler H, Lucaveche C, Cheng Y, Reedy MK, Taylor KA
• Structure determination of clathrin coats to subnanometer resolution by single particle cryo-electron microscopy.
  Journal of structural biology 2006 Fotin A, Kirchhausen T, Grigorieff N, Harrison SC, Walz T, Cheng Y
• Three-dimensional structure of an AMPA receptor without associated stargazin/TARP proteins.
  Biological chemistry 2006 Nakagawa T, Cheng Y, Sheng M, Walz T
• ATP binding to PAN or the 26S ATPases causes association with the 20S proteasome, gate opening, and translocation of unfolded proteins.
  Molecular cell 2005 Smith DM, Kafri G, Cheng Y, Ng D, Walz T, Goldberg AL
• Lipid-protein interactions in double-layered two-dimensional AQP0 crystals.
  Nature 2005 Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T
• Single particle reconstruction of the human apo-transferrin-transferrin receptor complex.
  Journal of structural biology 2005 Cheng Y, Zak O, Aisen P, Harrison SC, Walz T
• Single particle reconstructions of the transferrin-transferrin receptor complex obtained with different specimen preparation techniques.
  Journal of molecular biology 2005 Cheng Y, Wolf E, Larvie M, Zak O, Aisen P, Grigorieff N, Harrison SC, Walz T
• Structure and different conformational states of native AMPA receptor complexes.
  Nature 2005 Nakagawa T, Cheng Y, Ramm E, Sheng M, Walz T
• Molecular model for a complete clathrin lattice from electron cryomicroscopy.
  Nature 2004 Fotin A, Cheng Y, Sliz P, Grigorieff N, Harrison SC, Kirchhausen T, Walz T
• Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating.
  Nature 2004 Fotin A, Cheng Y, Grigorieff N, Walz T, Harrison SC, Kirchhausen T
• Aquaporin-0 membrane junctions form upon proteolytic cleavage.
  Journal of molecular biology 2004 Gonen T, Cheng Y, Kistler J, Walz T
• Aquaporin-0 membrane junctions reveal the structure of a closed water pore.
  Nature 2004 Gonen T, Sliz P, Kistler J, Cheng Y, Walz T
• A chimeric protein of simian immunodeficiency virus envelope glycoprotein gp140 and Escherichia coli aspartate transcarbamoylase.
  Journal of virology 2004 Chen B, Cheng Y, Calder L, Harrison SC, Reinherz EL, Skehel JJ, Wiley DC
• Negative Staining and Image Classification - Powerful Tools in Modern Electron Microscopy.
  Biological procedures online 2004 Ohi M, Li Y, Cheng Y, Walz T
• Structure of the human transferrin receptor-transferrin complex.
  Cell 2004 Cheng Y, Zak O, Aisen P, Harrison SC, Walz T
• The crystal structure of the bifunctional primase-helicase of bacteriophage T7.
  Molecular cell 2003 Toth EA, Li Y, Sawaya MR, Cheng Y, Ellenberger T
• Structure of the Sec23p/24p and Sec13p/31p complexes of COPII.
  Proceedings of the National Academy of Sciences of the United States of America 2001 Lederkremer GZ, Cheng Y, Petre BM, Vogan E, Springer S, Schekman R, Walz T, Kirchhausen T
• The three-dimensional map of microsomal glutathione transferase 1 at 6 A resolution.
  The EMBO journal 2000 Schmidt-Krey I, Mitsuoka K, Hirai T, Murata K, Cheng Y, Fujiyoshi Y, Morgenstern R, Hebert H
• The projection structure of the membrane protein microsomal glutathione transferase at 3 A resolution as determined from two-dimensional hexagonal crystals.
  Journal of molecular biology 1999 Schmidt-Krey I, Murata K, Hirai T, Mitsuoka K, Cheng Y, Morgenstern R, Fujiyoshi Y, Hebert H
• Influence of various nucleotides on the in situ crystallization of Ca2+-ATPase.
  Biochimica et biophysica acta 1999 Hiroaki Y, Mitsuoka K, Cheng Y, Hiroaki H, Fujiyoshi Y
• Characterization of the low magnification performance of a Philips CM300-FEG.
  Ultramicroscopy 1998 Cheng Y, Taylor KA
• The use of electron tomography for structural analysis of disordered protein arrays.
  Journal of structural biology 1997 Taylor KA, Tang J, Cheng Y, Winkler H