Structural and dynamical basis for the interaction of HSP70-EEVD with JDP Sis1

Protein folding, refolding and disaggregation are facilitated by the binding and releasing activity of HSP70 proteins. Such activity is aided by J-domain proteins (JDPs, DNAJs or HSP40s) that stimulate the ATPase activity of HSP70 and stabilize complexes between HSP70 and nonnative proteins. The C-terminus EEVD motif of HSP70 interacts with client proteins and with JDPs. Deletion of the EEVD disrupts the ability of HSP70 to associate with class B JDPs. A new understanding of the EEVD interaction with a JDP arises from the results of this work, which gives a detailed NMR characterization of the dynamics and interaction between a class B JDP, Sis1, and the HSP70-EEVD. The EEVD motif binds to multiple sites in Sis1. The interactions at CTDI contribute to the anchoring of HSP70 to Sis1, at site I, and the displacement of the client protein at site II. The competing interaction between the J-domain and the N-terminal boundary of α-helix 6 (at the GF-region) contributes to the interaction of J-domain to HSP70. These results support a mechanism involved in the regulation of the interaction with HSP70 that is autoinhibitory. Finally, a detailed model of the interaction of the EEVD with the J-domain of Sis1 is proposed.

[1]  S. Ovchinnikov,et al.  ColabFold: making protein folding accessible to all , 2022, Nature Methods.

[2]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[3]  Antonio Rosato,et al.  Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem , 2021, Frontiers in Molecular Biosciences.

[4]  E. Chapman,et al.  Function, Therapeutic Potential, and Inhibition of Hsp70 Chaperones. , 2021, Journal of medicinal chemistry.

[5]  J. Kirstein,et al.  J-domain proteins interaction with neurodegenerative disease-related proteins. , 2021, Experimental cell research.

[6]  Nadinath B. Nillegoda,et al.  HSP40 proteins use class-specific regulation to drive HSP70 functional diversity , 2020, Nature.

[7]  V. Kohler,et al.  Hsp70-mediated quality control: should I stay or should I go? , 2020, Biological chemistry.

[8]  Í. Caruso,et al.  The dynamics of free and phosphopeptide-bound Grb2-SH2 reveals two dynamically independent subdomains and an encounter complex with fuzzy interactions , 2020, Scientific Reports.

[9]  Qinglian Liu,et al.  Structural and functional analysis of the Hsp70/Hsp40 chaperone system , 2020, Protein science : a publication of the Protein Society.

[10]  G. Clore,et al.  Unraveling the structure and dynamics of the human DNAJB6b chaperone by NMR reveals insights into Hsp40-mediated proteostasis , 2019, Proceedings of the National Academy of Sciences.

[11]  C. Ramos,et al.  Solution NMR investigation on the structure and function of the isolated J-domain from Sis1: Evidence of transient inter-domain interactions in the full-length protein. , 2019, Archives of biochemistry and biophysics.

[12]  Jason C. Young,et al.  Function, evolution, and structure of J-domain proteins , 2018, Cell Stress and Chaperones.

[13]  C. Ramos,et al.  1H, 15N and 13C resonance assignments of the J-domain of co-chaperone Sis1 from Saccharomyces cerevisiae , 2018, Biomolecular NMR assignments.

[14]  Roman Kityk,et al.  Molecular Mechanism of J-Domain-Triggered ATP Hydrolysis by Hsp70 Chaperones. , 2017, Molecular cell.

[15]  Gabriel Cornilescu,et al.  Broadening the functionality of a J-protein/Hsp70 molecular chaperone system , 2017, PLoS genetics.

[16]  Miron Livny,et al.  NMRbox: A Resource for Biomolecular NMR Computation. , 2017, Biophysical journal.

[17]  R. Clubb,et al.  Nitroxide Labeling of Proteins and the Determination of Paramagnetic Relaxation Derived Distance Restraints for NMR Studies. , 2017, Bio-protocol.

[18]  G C P van Zundert,et al.  The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. , 2016, Journal of molecular biology.

[19]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[20]  C. Simmerling,et al.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. , 2015, Journal of chemical theory and computation.

[21]  Alexey Drozdetskiy,et al.  JPred4: a protein secondary structure prediction server , 2015, Nucleic Acids Res..

[22]  Szymon J. Ciesielski,et al.  Roles of intramolecular and intermolecular interactions in functional regulation of the Hsp70 J-protein co-chaperone Sis1. , 2015, Journal of molecular biology.

[23]  A. Shukla.  Membrane proteins : engineering, purification and crystallization , 2015 .

[24]  B. Kroncke,et al.  Solution NMR Structure Determination of Polytopic α-Helical Membrane Proteins: A Guide to Spin Label Paramagnetic Relaxation Enhancement Restraints. , 2015, Methods in enzymology.

[25]  G. Rivas,et al.  Structural characterization of the substrate transfer mechanism in Hsp70/Hsp90 folding machinery mediated by Hop , 2014, Nature Communications.

[26]  A. Bax,et al.  Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks , 2013, Journal of Biomolecular NMR.

[27]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[28]  R. Konrat,et al.  BEST-TROSY experiments for time-efficient sequential resonance assignment of large disordered proteins , 2013, Journal of biomolecular NMR.

[29]  C. Ramos,et al.  Identification of Regions Involved in Substrate Binding and Dimer Stabilization within the Central Domains of Yeast Hsp40 Sis1 , 2012, PloS one.

[30]  Júlio C. Silva,et al.  Central domain deletions affect the SAXS solution structure and function of Yeast Hsp40 proteins Sis1 and Ydj1 , 2011, BMC Structural Biology.

[31]  C. Ramos,et al.  An overview of the role of molecular chaperones in protein homeostasis. , 2011, Protein and peptide letters.

[32]  Hironori Suzuki,et al.  Peptide-binding sites as revealed by the crystal structures of the human Hsp40 Hdj1 C-terminal domain in complex with the octapeptide from human Hsp70. , 2010, Biochemistry.

[33]  H. Kampinga,et al.  The HSP70 chaperone machinery: J proteins as drivers of functional specificity , 2010, Nature Reviews Molecular Cell Biology.

[34]  C. L. Oliveira,et al.  Conserved central domains control the quaternary structure of type I and type II Hsp40 molecular chaperones. , 2008, Journal of molecular biology.

[35]  A. Brunger.  Version 1.2 of the Crystallography and NMR system , 2007, Nature Protocols.

[36]  Michael Nilges,et al.  ARIA2: Automated NOE assignment and data integration in NMR structure calculation , 2007, Bioinform..

[37]  Gaetano T Montelione,et al.  Evaluating protein structures determined by structural genomics consortia , 2006, Proteins.

[38]  Jingzhi Li,et al.  Crystal structure of yeast Sis1 peptide-binding fragment and Hsp70 Ssa1 C-terminal complex. , 2006, The Biochemical journal.

[39]  David S Wishart,et al.  A simple method to predict protein flexibility using secondary chemical shifts. , 2005, Journal of the American Chemical Society.

[40]  Wayne Boucher,et al.  The CCPN data model for NMR spectroscopy: Development of a software pipeline , 2005, Proteins.

[41]  E. Craig,et al.  In Vivo Bipartite Interaction Between the Hsp40 Sis1 and Hsp70 in Saccharomyces cerevisiae , 2005, Genetics.

[42]  M Nilges,et al.  Automated assignment of ambiguous nuclear overhauser effects with ARIA. , 2001, Methods in enzymology.

[43]  Luis Moroder,et al.  Structure of TPR Domain–Peptide Complexes Critical Elements in the Assembly of the Hsp70–Hsp90 Multichaperone Machine , 2000, Cell.

[44]  J. Hus,et al.  Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data , 2000, Journal of biomolecular NMR.

[45]  D. Cyr,et al.  Protein Folding Activity of Hsp70 Is Modified Differentially by the Hsp40 Co-chaperones Sis1 and Ydj1* , 1998, The Journal of Biological Chemistry.

[46]  W. Kelley,et al.  The J-domain family and the recruitment of chaperone power. , 1998, Trends in biochemical sciences.

[47]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[48]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[49]  A. Caplan,et al.  Characterization of YDJ1: a yeast homologue of the bacterial dnaJ protein , 1991, The Journal of cell biology.

[50]  L. Kay,et al.  Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. , 1989, Biochemistry.

[51]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .