Frydman Lab publications at Stanford

  • Lopez T, Dalton K, Frydman J. The Mechanism and Function of Group II Chaperonins. J Mol Biol S0022-2836:00267-3 (2015)
  • Dalton KM, Frydman J, Pande VS. The dynamic conformational cycle of the group I chaperonin C-termini revealed via molecular dynamics simulation. PLoS One 10:e0117724 (2015)
  • Dhungel N, Eleuteri S, Li LB, Kramer NJ, Chartron JW, Spencer B, Kosberg K, Fields JA, Stafa K, Adame A, Lashuel H, Frydman J, Shen K, Masliah E, Gitler AD. Parkinson's disease genes VPS35 and EIF4G1 interact genetically and converge on α-synuclein Neuron 85:76-87 (2015).
  • Freund A, Zhong FL, Venteicher AS, Meng Z, Veenstra TD, Frydman J, Artandi SE. Proteostatic control of telomerase function through TRiC-mediated folding of TCAB1. Cell 159:1389-403 (2014)
  • Neef DW, Jaeger AM, Gomez-Pastor R, Willmund F, Frydman J, Thiele DJ. A direct regulatory interaction between chaperonin TRiC and stress-responsive transcription factor HSF1. Cell Rep 9:955-66 (2014)
  • Pechmann S, Chartron JW, Frydman J. Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo. Nat Struct Mol Biol 21:1100-5 (2014)
  • Joachimiak LA, Walzthoeni T, Liu C, Aebersold R, Frydman J. The structural basis for substrate recognition by the eukaryotic chaperonin TRiC/CCT. Cell 159:1042-55 (2014)
  • Pechmann S, Frydman J. Interplay between chaperones and protein disorder promotes the evolution of protein networks. PLoS Comput Biol 10:e1003674 (2014)
  • Duim WC, Jiang Y, Shen K, Frydman J, Moerner WE. Super-Resolution Fluorescence of Huntingtin Reveals Growth of Globular Species into Short Fibers and Coexistence of Distinct Aggregates. ACS Chem Biol (2014)
  • Leitner A, Joachimiak LA, Unverdorben P, Walzthoeni T, Frydman J, Förster F, Aebersold R. Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes. Proc Natl Acad Sci USA 111:9455-60 (2014)
  • Kasembeli M, Lau WC, Roh SH, Eckols TK, Frydman J, Chiu W, Tweardy DJ. Modulation of STAT3 folding and function by TRiC/CCT chaperonin. PLoS Biol 12:e1001844 (2014)
  • Sontag EM, Vonk WI, Frydman J. Sorting out the trash: the spatial nature of eukaryotic protein quality control. Curr Opin Cell Biol 26:139-46 (2014)
  • Escusa-Toret S, Vonk WI, Frydman J. Spatial sequestration of misfolded proteins by a dynamic chaperone pathway enhances cellular fitness during stress. Nat Cell Biol 15(10):1231-43 (2013).
  • Shahmoradian SH, Galaz-Montoya JG, Schmid MF, Cong Y, Ma B, Spiess C, Frydman J, Ludtke SJ, Chiu W. TRiC's tricks inhibit huntingtin aggregation. Elife 2:e00710 (2013).
  • Duttler S, Pechmann S, Frydman J. Principles of Cotranslational Ubiquitination and Quality Control at the Ribosome Mol Cell 50(3): 379-393 (2013).
  • Lauring AS, Frydman J, Andino R. The role of mutational robustness in RNA virus evolution. Nat Rev Microbiol 11(5):327-36 (2013).
  • Geller R, Andino R, Frydman J Hsp90 Inhibitors Exhibit Resistance-Free Antiviral Activity against Respiratory Syncytial Virus PLoS One 8(2):e56762 (2013).
  • Pechmann S, Willmund W, Frydman J The Ribosome as a Hub for Protein Quality Control Mol Cell 49(3): 411-421 (2013).
  • Sontag EM, Joachimiak LA, Tan Z, Tomlinson A, Housman DE, Glabe CG, Potkin SG, Frydman J, Thompson LM Exogenous delivery of chaperonin subunit fragment ApiCCT1 modulates mutant Huntingtin cellular phenotypes Proc Natl Acad Sci 110(8):3077-82 (2013).
  • Willmund F, del Alamo M, Pechmann S, Chen T, Albanese V, Dammer EB, Peng J, Frydman J The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis Cell 152:196-209 (2013).
  • Pechmann S & Frydman J Evolutionary conservation of codon optimality reveals hidden signatures of co-translational folding. Nat Struct Mol Biol 20(2):237-43 (2013).
  • Sahl SJ, Weiss LE, Duim WC, Frydman J, Moerner WE Cellular inclusion bodies of mutant huntingtin exon 1 obscure small fibrillar aggregate species Sci Rep. 2:895 (2012).
  • Reissmann S, Joachimiak LA, Chen B, Meyer AS, Nguyen A, Frydman J A gradient of ATP affinities generates an asymmetric power stroke driving the chaperonin TRIC/CCT folding cycle. Cell Rep 2(4):866-77 (2012).
  • Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Fryan J, Krogan NJ Systematic functional prioritization of protein posttranslational modificatios. Cell 150(2):413-25 (2012)
  • Leitner A, Joachimiak LA, Bracher A, Mönkemeyer L, Walzthoeni T, Chen B, Pechmann S, Holmes S, Cong Y, Ma B, Ludtke S, Chiu W, Hartl FU, Aebersold R, Frydman J The Molecular Architecture of the Eukaryotic Chaperonin TRiC/CCT. Structure (2012).
  • Pereira JH, Ralston CY, Douglas NR, Kumar R, Lopez T, McAndrew RP, Knee KM, King JA, Frydman J, Adams PD. Mechanism of nucleotide sensing in group II chaperonins. EMBO J 31(3):731-40 (2011).
  • Geller R, Taguwa S, Frydman J. Broad action of Hsp90 as a host chaperone required for viral replication. Biochim Biophys Acta 1823(3):698-706 (2011).
  • Franzosa EA, Albanèse V, Frydman J, Xia Y, McClellan AJ. Heterozygous yeast deletion collection screens reveal essential targets of Hsp90. PLoS One 6(11):e28211 (2011)
  • Cong Y, Schröder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle EMBO J doi: 10.1038/emboj.2011.366 (2011).
  • Jiang Y, Douglas NR, Conleya NR, Miller EJ, Frydman J, Moerner WE. Sensing cooperativity in ATP hydrolysis for single multisubunit enzymes in solution Proc Natl Acad Sci 108(41):16962-7 (2011).
  • del Alamo M, Hogan DJ, Pechmann S, Albanese V, Brown PO, Frydman J. Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes. PLoS Biol 9(7):e1001100 (2011).
  • Chen B, Retzlaff M, Roos T, Frydman J. Cellular strategies of protein quality control. Cold Spring Harb Perspect Biol 3(8): a004374 (2011).
  • Duim WC, Chen B, Frydman J, Moerner WE. Sub-Diffraction Imaging of Huntingtin Protein Aggregates by Fluorescence Blink-Microscopy and Atomic Force Microscopy. Chemphyschem doi: 10.1002/cphc.201100392 (2011).
  • Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak LA, Baker D, Frydman J, Levitt M, Chiu W. Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure. Structure 19(5):633-9 (2011).
  • Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J. Dual Action of ATP Hydrolysis Couples Lid Closure to Substrate Release into the Group II Chaperonin Chamber. Cell 144:240-52 (2011).
  • Pan X, Reissman S, Douglas NR, Huang Z, Yuan DS, Wang X, McCaffery JM, Frydman J, Boeke JD. Trivalent arsenic inhibits the functions of chaperonin complex. Genetics 186:725-34 (2010).
  • Kim SY, Miller EJ, Frydman J, Moerner WE. Action of the chaperonin GroEL/ES on a non-native substrate observed with single-molecule FRET. J Mol Biol 401:553-63 (2010).
  • Pereira JH, Ralston CY, Douglas NR, Meyer D, Knee KM, Goulet DR, King JA, Frydman J, Adams PD. Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J Biol Chem 285:27958-66 (2010).
  • Albanese V, Reissmann S, Frydman J. A ribosome-anchored chaperone network that facilitates eukaryotic ribosome biogenesis. J Cell Biol 189:69-81 (2010).
  • Cong Y, Baker ML, Jakana J, Woolford D, Miller EJ, Reissmann S, Kumar RN, Redding-Johanson AM, Batth TS, Mukhopadhyay A, Ludtke SJ, Frydman J, Chiu W. 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Proc Natl Acad Sci 107:4967-72 (2010)
  • Zhang J, Baker ML, Schröder GF, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W. Mechanism of folding chamber closure in a group II chaperonin. Nature 463:379-83 (2010)
  • Tam S, Spiess C, Auyeung W, Joachimiak L, Chen B, Poirier MA, Frydman J. The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation. Nat Struct Mol Biol 16:1279-85 (2009)
  • Kelley NW, Huang X, Tam S, Spiess C, Frydman J, Pande VS. The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation. J Mol Biol 388:919-27 (2009)
  • Mayer MP, Prodromou C, Frydman J. The Hsp90 mosaic: a picture emerges. Nat Struct Mol Biol 16:2-6 (2009)
  • Yam AY, Xia Y, Lin HT, Burlingame A, Gerstein M, Frydman J. Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nat Struct Mol Biol 15:1255-62 (2008)
  • Kaganovich D, Kopito R, Frydman J. Misfolded proteins partition between two distinct quality control compartments. Nature 454:1088-95 (2008)
  • Jiang Y, Wang Q, Cohen AE, Douglas N, Frydman J, Moerner WE. Hardware-based anti-Brownian electrokinetic trap (ABEL trap) for single molecules: Control loop simulations and application to ATP binding stoichiometry in multi-subunit enzymes. Proc Soc Photo Opt Instrum Eng 7038:1-12 (2008)
  • Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, Frydman J. Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nat Struct Mol Biol 15:746-53 (2008)
  • McClellan AJ, Xia Y, Deutschbauer AM, Davis RW, Gerstein M, Frydman J. Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell 131:121-35 (2007)
  • Reissmann S, Parnot C, Booth CR, Chiu W, Frydman J. Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins. Nat Struct Mol Biol14:432-40 (2007)
  • Geller R, Vignuzzi M, Andino R, Frydman J. Evolutionary constraints on chaperone-mediated folding provide an antiviral approach refractory to development of drug resistance. Genes Dev 21:195-205 (2007)
  • Spiess C, Miller EJ, McClellan AJ, Frydman J. Identification of the TRiC/CCT substrate binding sites uncovers the function of subunit diversity in eukaryotic chaperonins. Mol Cell 24:25-37 (2006)
  • Tam S, Geller R, Spiess C, Frydman J. The chaperonin TRiC controls polyglutamine aggregation and toxicity through subunit-specific interactions. Nat Cell Biol 8:1155-62 (2006)
  • Miller EJ, Meyer AS, Frydman J. Modeling of possible subunit arrangements in the eukaryotic chaperonin TRiC. Protein Sci 15:1522-6 (2006)
  • Albanèse V, Yam AY, Baughman J, Parnot C, Frydman J. Systems analyses reveal two chaperone networks with distinct functions in eukaryotic cells. Cell 124:75-88 (2006)
  • Kim SY, Semyonov AN, Twieg RJ, Horwich AL, Frydman J, Moerner WE. Probing the sequence of conformationally induced polarity changes in the molecular chaperonin GroEL with fluorescence spectroscopy. J Phys Chem B 109:24517-25 (2005)
  • Xu L, Dayal M, Ouyang YB, Sun Y, Yang CF, Frydman J, Giffard RG. Chaperonin GroEL and its mutant D87K protect from ischemia in vivo and in vitro. Neurobiol Aging 27:562-9 (2006)
  • Yam AY, Albanèse V, Lin HT, Frydman J. Hsp110 cooperates with different cytosolic HSP70 systems in a pathway for de novo folding. J Biol Chem 280:41252-61 (2005)
  • McClellan AJ, Tam S, Kaganovich D, Frydman J. Protein quality control: chaperones culling corrupt conformations. Nat Cell Biol 7:736-41 (2005)
  • McClellan AJ, Scott MD, Frydman J. Folding and quality control of the VHL tumor suppressor proceed through distinct chaperone pathways. Cell 121:739-48 (2005)
  • Etchells SA, Meyer AS, Yam AY, Roobol A, Miao Y, Shao Y, Carden MJ, Skach WR, Frydman J, Johnson AE. The cotranslational contacts between ribosome-bound nascent polypeptides and the subunits of the hetero-oligomeric chaperonin TRiC probed by photocross-linking. J Biol Chem 280:28118-26 (2005)
  • Vang S, Corydon TJ, Børglum AD, Scott MD, Frydman J, Mogensen J, Gregersen N, Bross P. Actin mutations in hypertrophic and dilated cardiomyopathy cause inefficient protein folding and perturbed filament formation. FEBS J 272:2037-49 (2005)
  • Spiess C, Meyer AS, Reissmann S, Frydman J. Mechanism of the eukaryotic chaperonin: protein folding in the chamber of secrets. Trends Cell Biol 14:598-604 (2004)
  • Feldman DE, Spiess C, Howard DE, Frydman J. Tumorigenic mutations in VHL disrupt folding in vivo by interfering with chaperonin binding. Mol Cell 12:1213-24 (2003)
  • Scott MD, Frydman J. Aberrant protein folding as the molecular basis of cancer. Methods Mol Biol 232:67-76 (2003)
  • Meyer AS, Gillespie JR, Walther D, Millet IS, Doniach S, Frydman J. Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis. Cell 113:369-81 (2003)
  • Melville MW, McClellan AJ, Meyer AS, Darveau A, Frydman J. The Hsp70 and TRiC/CCT chaperone systems cooperate in vivo to assemble the von Hippel-Lindau tumor suppressor complex. Mol Cell Biol 23:3141-51 (2003)
  • Albanèse V, Frydman J. Where chaperones and nascent polypeptides meet. Nat Struct Biol 9:716-8 (2002)
  • Dunn AY, Melville MW, Frydman J. Review: cellular substrates of the eukaryotic chaperonin TRiC/CCT. J Struct Biol 135:176-84 (2001)
  • Thulasiraman V, Ferreyra RG, Frydman J. Folding assays. Assessing the native conformation of proteins. Methods Mol Biol 140:169-77 (2000)
  • Thulasiraman V, Ferreyra RG, Frydman J. Monitoring actin folding. Purification protocols for labeled proteins and binding to DNase I-sepharose beads. Methods Mol Biol 140:161-7 (2000)
  • Ferreyra RG, Frydman J. Purification of the cytosolic chaperonin TRiC from bovine testis. Methods Mol Biol 140:153-60 (2000)
  • Frydman J. Folding of newly translated proteins in vivo: the role of molecular chaperones. Annu Rev Biochem 70:603-47 (2001)
  • McClellan AJ, Frydman J. Molecular chaperones and the art of recognizing a lost cause. Nat Cell Biol 3:E51-3 (2001)
  • McCallum CD, Do H, Johnson AE, Frydman J. The interaction of the chaperonin tailless complex polypeptide 1 (TCP1) ring complex (TRiC) with ribosome-bound nascent chains examined using photo-cross-linking. J Cell Biol 149:591-602 (2000)
  • Feldman DE, Frydman J. Protein folding in vivo: the importance of molecular chaperones. Curr Opin Struct Biol 10:26-33 (2000)
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