PROTEIN FOLDING IN THE EUKARYOTIC CYTOSOL

Summary

Principal Investigator: J Frydman
Abstract: DESCRIPTION (provided by applicant): The long-term goal of our research is to understand the biochemistry and cell biology of protein folding in eukaryotic cells. The proposed research will focus on folding events as they occur at the ribosome during synthesis of a polypeptide and will examine the role of molecular chaperones in the folding process. The conceptual framework required to understand the folding of proteins as they emerge from the ribosome originates from our previous work, which indicates that folding in the eukaryotic cytosol is mediated by a chaperone network that is physically and functionally linked to translation. The objective of this proposal is to elucidate the mechanism by which chaperones mediate the folding of newly synthesized proteins in eukaryotic cells. To gain insight into this process we identified critical questions that will allow us to understand de novo folding, namely: (i) how and when do chaperones contact the emerging nascent chains?;(ii) what is the relevance of chaperone-binding for de novo folding?;(iii) what is the contribution of different chaperone systems to overall folding in the cell? (iv) how do chaperones interact with the translation machinery? Our general strategy to answer these questions is to combine in vitro and in vivo approaches to obtain mechanistic and functional insights into the role of chaperones in cellular folding. The first two specific aims will analyze the folding of model proteins in vivo and in cell-free translation lysates that faithfully represent the intact cytosol. Since our in vivo analysis indicates that different proteins exhibit distinct chaperone requirements, the third specific aim will examine the contribution of different chaperones to cellular folding and will identify the substrate spectrum of different molecular chaperones. Finally, our fourth specific aim will explore the interaction between chaperones and the translational machinery.
Funding Period: ----------------1997 - ---------------2011-
more information: NIH RePORT

Top Publications

  1. ncbi Chaperonin GroEL and its mutant D87K protect from ischemia in vivo and in vitro
    Lijun Xu
    Department of Anesthesia, Stanford University, Stanford, CA 94305, USA
    Neurobiol Aging 27:562-9. 2006
  2. pmc Principles of cotranslational ubiquitination and quality control at the ribosome
    Stefanie Duttler
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Mol Cell 50:379-93. 2013
  3. pmc Hsp90 inhibitors exhibit resistance-free antiviral activity against respiratory syncytial virus
    Ron Geller
    Department of Biology, Stanford University, Stanford, California, United States of America
    PLoS ONE 8:e56762. 2013
  4. pmc The ribosome as a hub for protein quality control
    Sebastian Pechmann
    Department of Biology, Stanford University, Stanford, CA 94305 5020, USA
    Mol Cell 49:411-21. 2013
  5. pmc The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis
    Felix Willmund
    Department of Biology and BioX Program, Stanford University, Stanford, CA 94305 5430, USA
    Cell 152:196-209. 2013
  6. pmc Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
    Sebastian Pechmann
    Department of Biology, Stanford University, Stanford, California, USA
    Nat Struct Mol Biol 20:237-43. 2013
  7. pmc Systematic functional prioritization of protein posttranslational modifications
    Pedro Beltrao
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94107, USA
    Cell 150:413-25. 2012
  8. pmc Broad action of Hsp90 as a host chaperone required for viral replication
    Ron Geller
    Department of Biology and BioX Program, Stanford University, Stanford, CA, USA
    Biochim Biophys Acta 1823:698-706. 2012
  9. pmc Spatial sequestration of misfolded proteins by a dynamic chaperone pathway enhances cellular fitness during stress
    Stéphanie Escusa-Toret
    Department of Biology, Stanford University, Stanford, California 94305, USA
    Nat Cell Biol 15:1231-43. 2013
  10. ncbi Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches
    Amie J McClellan
    Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
    Cell 131:121-35. 2007

Scientific Experts

  • J Frydman
  • Sebastian Pechmann
  • Véronique Albanèse
  • Ron Geller
  • Felix Willmund
  • Marta del Alamo
  • Yu Xia
  • Amie J McClellan
  • Stefanie Duttler
  • Stéphanie Escusa-Toret
  • Pedro Beltrao
  • Eric A Franzosa
  • Raul Andino
  • Alma Burlingame
  • Daniel Kaganovich
  • Alice Y Yam
  • Mark Gerstein
  • Stephen Tam
  • Lijun Xu
  • Taotao Chen
  • Willianne I M Vonk
  • Eric B Dammer
  • Junmin Peng
  • Lillian R Kenner
  • Wendell A Lim
  • Danielle L Swaney
  • Nevan J Krogan
  • Shuhei Taguwa
  • Judit Villen
  • James S Fraser
  • Patrick O Brown
  • Daniel J Hogan
  • Stefanie Reissmann
  • Hen Tzu Jill Lin
  • Ron Kopito
  • Adam M Deutschbauer
  • Marco Vignuzzi
  • Ron W Davis
  • Christoph Spiess
  • Joshua Baughman
  • Charles Parnot
  • Alice Yen Wen Yam
  • Chin Fen Yang
  • Rona G Giffard
  • Yunjuan Sun
  • Yi Bing Ouyang
  • Manisha Dayal

Detail Information

Publications19

  1. ncbi Chaperonin GroEL and its mutant D87K protect from ischemia in vivo and in vitro
    Lijun Xu
    Department of Anesthesia, Stanford University, Stanford, CA 94305, USA
    Neurobiol Aging 27:562-9. 2006
    ..This suggests that strategies to maintain protein solubility and inhibit aggregation in the face of acute insults such as stroke may be a useful protective strategy...
  2. pmc Principles of cotranslational ubiquitination and quality control at the ribosome
    Stefanie Duttler
    Department of Biology, Stanford University, Stanford, CA 94305, USA
    Mol Cell 50:379-93. 2013
    ..We find that quality control at the ribosome is achieved through a tiered system wherein nascent polypeptides have a chance to fold before becoming accessible to ubiquitination...
  3. pmc Hsp90 inhibitors exhibit resistance-free antiviral activity against respiratory syncytial virus
    Ron Geller
    Department of Biology, Stanford University, Stanford, California, United States of America
    PLoS ONE 8:e56762. 2013
    ....
  4. pmc The ribosome as a hub for protein quality control
    Sebastian Pechmann
    Department of Biology, Stanford University, Stanford, CA 94305 5020, USA
    Mol Cell 49:411-21. 2013
    ..The tiered and complementary nature of these decision-making processes confers robustness and fidelity to protein homeostasis during protein synthesis...
  5. pmc The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis
    Felix Willmund
    Department of Biology and BioX Program, Stanford University, Stanford, CA 94305 5430, USA
    Cell 152:196-209. 2013
    ..Thus, cotranslationally acting Hsp70 meets the challenge of folding the eukaryotic proteome by stabilizing its longer, more slowly translated, and aggregation-prone nascent polypeptides...
  6. pmc Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
    Sebastian Pechmann
    Department of Biology, Stanford University, Stanford, California, USA
    Nat Struct Mol Biol 20:237-43. 2013
    ..These findings establish how mRNA sequences are generally under selection to optimize the cotranslational folding of corresponding polypeptides...
  7. pmc Systematic functional prioritization of protein posttranslational modifications
    Pedro Beltrao
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94107, USA
    Cell 150:413-25. 2012
    ..Finally, our analysis of the evolution of PTM regulation highlights potential routes for neutral drift in regulatory interactions and suggests that only a fraction of modification sites are likely to have a significant biological role...
  8. pmc Broad action of Hsp90 as a host chaperone required for viral replication
    Ron Geller
    Department of Biology and BioX Program, Stanford University, Stanford, CA, USA
    Biochim Biophys Acta 1823:698-706. 2012
    ..The major developments in this emerging field are hereby discussed. This article is part of a Special Issue entitled: Heat Shock Protein 90 (HSP90)...
  9. pmc Spatial sequestration of misfolded proteins by a dynamic chaperone pathway enhances cellular fitness during stress
    Stéphanie Escusa-Toret
    Department of Biology, Stanford University, Stanford, California 94305, USA
    Nat Cell Biol 15:1231-43. 2013
    ..We conclude that spatial sequestration of misfolded proteins in Q-bodies is an early quality control strategy occurring synchronously with degradation to clear the cytoplasm of potentially toxic species. ..
  10. ncbi Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches
    Amie J McClellan
    Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
    Cell 131:121-35. 2007
    ..Importantly, biochemical and cell biological analyses validated several of these Hsp90-dependent functions, highlighting the potential of our integrated global approach to uncover chaperone functions in the cell...
  11. ncbi Systems analyses reveal two chaperone networks with distinct functions in eukaryotic cells
    Véronique Albanèse
    Department of Biological Sciences and BioX Program, Stanford University, Stanford, CA 94305, USA
    Cell 124:75-88. 2006
    ..The emergence of a translation-linked chaperone network likely underlies the elaborate cotranslational folding process necessary for the evolution of larger multidomain proteins characteristic of eukaryotic cells...
  12. pmc The chaperonin TRiC controls polyglutamine aggregation and toxicity through subunit-specific interactions
    Stephen Tam
    Biophysics Graduate Program, Stanford University, Stanford, California 94305, USA
    Nat Cell Biol 8:1155-62. 2006
    ..Based on the specificity of the Htt-CCT1 interaction, the CCT1 substrate-binding domain may provide a versatile scaffold for therapeutic inhibitors of neurodegenerative disease...
  13. pmc Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies
    Alice Y Yam
    Department of Biology and BioX Program, E200A James Clark Center, 318 Campus Drive, Stanford University, Stanford, California 94043, USA
    Nat Struct Mol Biol 15:1255-62. 2008
    ..Thus, TRiC may have evolved to protect complex protein topologies within its central cavity during biosynthesis and folding...
  14. pmc Misfolded proteins partition between two distinct quality control compartments
    Daniel Kaganovich
    Department of Biology and BioX Program, Stanford University, Stanford, California 94305, USA
    Nature 454:1088-95. 2008
    ..Our findings provide a framework for understanding the preferential accumulation of amyloidogenic proteins in inclusions linked to human disease...
  15. pmc Evolutionary constraints on chaperone-mediated folding provide an antiviral approach refractory to development of drug resistance
    Ron Geller
    Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
    Genes Dev 21:195-205. 2007
    ..We propose that targeting folding of viral proteins may provide a general antiviral strategy that is refractory to development of drug resistance...
  16. pmc A ribosome-anchored chaperone network that facilitates eukaryotic ribosome biogenesis
    Véronique Albanèse
    Department of Biology, Stanford University, Palo Alto, CA 94305, USA
    J Cell Biol 189:69-81. 2010
    ..Our results demonstrate that, in addition to their known cytoplasmic roles in de novo protein folding, some ribosome-anchored CLIPS chaperones play a critical role in nuclear steps of ribosome biogenesis...
  17. pmc Heterozygous yeast deletion collection screens reveal essential targets of Hsp90
    Eric A Franzosa
    Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
    PLoS ONE 6:e28211. 2011
    ..Altogether, these novel contributions enable a more complete picture of essential Hsp90 functions...
  18. pmc Defining the specificity of cotranslationally acting chaperones by systematic analysis of mRNAs associated with ribosome-nascent chain complexes
    Marta del Alamo
    Department of Biology and BioX Program, Stanford University, Stanford, California, United States of America
    PLoS Biol 9:e1001100. 2011
    ..The strategy we used should be generally applicable to mapping the specificity, interplay, and dynamics of the cotranslational protein homeostasis network...