An Interdomain Energetic Tug-of-War Creates the Allosterically Active State in Hsp70 Molecular Chaperones

The allosteric mechanism of Hsp70 molecular chaperones enables ATP binding to the N-terminal nucleotide-binding domain (NBD) to alter substrate affinity to the C-terminal substrate-binding domain (SBD) and substrate binding to enhance ATP hydrolysis. Cycling between ATP-bound and ADP/substrate-bound states requires Hsp70s to visit a state with high ATPase activity and fast on/off kinetics of substrate binding. We have trapped this "allosterically active" state for the E. coli Hsp70, DnaK, and identified how interactions among the NBD, the β subdomain of the SBD, the SBD α-helical lid, and the conserved hydrophobic interdomain linker enable allosteric signal transmission between ligand-binding sites. Allostery in Hsp70s results from an energetic tug-of-war between domain conformations and formation of two orthogonal interfaces: between the NBD and SBD, and between the helical lid and the β subdomain of the SBD. The resulting energetic tension underlies Hsp70 functional properties and enables them to be modulated by ligands and cochaperones and "tuned" through evolution.

[1]  E. Zuiderweg,et al.  High-throughput screen for small molecules that modulate the ATPase activity of the molecular chaperone DnaK. , 2008, Analytical biochemistry.

[2]  L. Kay,et al.  Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy , 2006, Nature Protocols.

[3]  L. Gierasch,et al.  Direct Comparison of a Stable Isolated Hsp70 Substrate-binding Domain in the Empty and Substrate-bound States* , 2006, Journal of Biological Chemistry.

[4]  J. Reinstein,et al.  The second step of ATP binding to DnaK induces peptide release. , 1996, Journal of molecular biology.

[5]  L. Gierasch,et al.  Mutations in the substrate binding domain of the Escherichia coli 70 kDa molecular chaperone, DnaK, which alter substrate affinity or interdomain coupling. , 1999, Journal of molecular biology.

[6]  Lila M. Gierasch,et al.  Sending Signals Dynamically , 2009, Science.

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

[8]  Bernd Bukau,et al.  Allosteric Regulation of Hsp70 Chaperones Involves a Conserved Interdomain Linker* , 2006, Journal of Biological Chemistry.

[9]  Matthias J. Feige,et al.  Substrate discrimination of the chaperone BiP by autonomous and cochaperone-regulated conformational transitions , 2011, Nature Structural &Molecular Biology.

[10]  M. Mayer,et al.  Amide Hydrogen Exchange Reveals Conformational Changes in Hsp70 Chaperones Important for Allosteric Regulation* , 2006, Journal of Biological Chemistry.

[11]  E. Zuiderweg,et al.  Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex employs an unusual dynamic interface , 2011, Proceedings of the National Academy of Sciences.

[12]  K. Flaherty,et al.  Three-dimensional structure of the ATPase fragment of a 70K heat-shock cognate protein , 1990, Nature.

[13]  M. Mayer,et al.  Hsp70 chaperones: Cellular functions and molecular mechanism , 2005, Cellular and Molecular Life Sciences.

[14]  Lila M. Gierasch,et al.  Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones , 2011, Proceedings of the National Academy of Sciences.

[15]  E. Zuiderweg,et al.  Allosteric drugs: the interaction of antitumor compound MKT-077 with human Hsp70 chaperones. , 2011, Journal of molecular biology.

[16]  L. Kay,et al.  Methyl Groups as Probes of Structure and Dynamics in NMR Studies of High‐Molecular‐Weight Proteins , 2005, Chembiochem : a European journal of chemical biology.

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

[18]  Kingshuk Ghosh,et al.  Computing protein stabilities from their chain lengths , 2009, Proceedings of the National Academy of Sciences.

[19]  Craig M. Ogata,et al.  Structural Analysis of Substrate Binding by the Molecular Chaperone DnaK , 1996, Science.

[20]  Najeeb M. Halabi,et al.  Protein Sectors: Evolutionary Units of Three-Dimensional Structure , 2009, Cell.

[21]  J. Reinstein,et al.  Nucleotide-induced Conformational Changes in the ATPase and Substrate Binding Domains of the DnaK Chaperone Provide Evidence for Interdomain Communication (*) , 1995, The Journal of Biological Chemistry.

[22]  Stanislas Leibler,et al.  An interdomain sector mediating allostery in Hsp70 molecular chaperones , 2010, Molecular systems biology.

[23]  Zaida Luthey-Schulten,et al.  MultiSeq: unifying sequence and structure data for evolutionary analysis , 2006, BMC Bioinformatics.

[24]  E. Zuiderweg,et al.  Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate , 2009, Proceedings of the National Academy of Sciences.

[25]  L. Kay,et al.  Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. , 2003, Journal of the American Chemical Society.

[26]  D. Masison,et al.  Single methyl group determines prion propagation and protein degradation activities of yeast heat shock protein (Hsp)-70 chaperones Ssa1p and Ssa2p , 2011, Proceedings of the National Academy of Sciences.

[27]  L. Kay,et al.  Ile, Leu, and Val methyl assignments of the 723-residue malate synthase G using a new labeling strategy and novel NMR methods. , 2003, Journal of the American Chemical Society.

[28]  Lila M Gierasch,et al.  Hsp70 chaperone ligands control domain association via an allosteric mechanism mediated by the interdomain linker. , 2007, Molecular cell.

[29]  Gregory A Manley,et al.  NMR insights into protein allostery. , 2012, Archives of biochemistry and biophysics.

[30]  A. Hinck,et al.  Structural basis of J cochaperone binding and regulation of Hsp70. , 2007, Molecular cell.

[31]  Wayne A. Hendrickson,et al.  Insights into Hsp70 Chaperone Activity from a Crystal Structure of the Yeast Hsp110 Sse1 , 2007, Cell.

[32]  Tal Pupko,et al.  Structural Genomics , 2005 .

[33]  M. Mayer,et al.  Mechanics of Hsp70 chaperones enables differential interaction with client proteins , 2011, Nature Structural &Molecular Biology.

[34]  B. Bukau,et al.  Mutations altering heat shock specific subunit of RNA polymerase suppress major cellular defects of E. coli mutants lacking the DnaK chaperone. , 1990, The EMBO journal.

[35]  Qinglian Liu,et al.  The four hydrophobic residues on the Hsp70 inter-domain linker have two distinct roles. , 2011, Journal of molecular biology.

[36]  K A Dill,et al.  Stabilization of proteins in confined spaces. , 2001, Biochemistry.

[37]  R. Keller Optimizing the process of nuclear magnetic resonance spectrum analysis and computer aided resonance assignment , 2005 .

[38]  P. Christen,et al.  Sequence-specific rates of interaction of target peptides with the molecular chaperones DnaK and DnaJ. , 1998, Biochemistry.

[39]  Lila M Gierasch,et al.  Segmental isotopic labeling of the Hsp70 molecular chaperone DnaK using expressed protein ligation. , 2010, Biopolymers.

[40]  Bernd Bukau,et al.  Multistep mechanism of substrate binding determines chaperone activity of Hsp70 , 2000, Nature Structural Biology.

[41]  Roman Kityk,et al.  Structure and dynamics of the ATP-bound open conformation of Hsp70 chaperones. , 2012, Molecular cell.

[42]  R. Nussinov,et al.  Induced Fit, Conformational Selection and Independent Dynamic Segments: an Extended View of Binding Events Opinion , 2022 .

[43]  A. Muga,et al.  Ionic Contacts at DnaK Substrate Binding Domain Involved in the Allosteric Regulation of Lid Dynamics* , 2006, Journal of Biological Chemistry.

[44]  E. Zuiderweg,et al.  NMR Study of Nucleotide-induced Changes in the Nucleotide Binding Domain of Thermus thermophilus Hsp70 Chaperone DnaK , 2004, Journal of Biological Chemistry.

[45]  E. Zuiderweg,et al.  Allostery in Hsp70 chaperones is transduced by subdomain rotations. , 2009, Journal of molecular biology.

[46]  A. Muga,et al.  The Lid Subdomain of DnaK Is Required for the Stabilization of the Substrate-binding Site* , 2004, Journal of Biological Chemistry.

[47]  D. Wishart,et al.  The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data , 1994, Journal of biomolecular NMR.

[48]  S. Karamanou,et al.  Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR , 2007, Cell.

[49]  G. Walker,et al.  DnaK as a thermometer: threonine-199 is site of autophosphorylation and is critical for ATPase activity. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[50]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[51]  J. Weigelt Single Scan, Sensitivity- and Gradient-Enhanced TROSY for Multidimensional NMR Experiments , 1998 .

[52]  H. Carlson,et al.  Chemical screens against a reconstituted multiprotein complex: myricetin blocks DnaJ regulation of DnaK through an allosteric mechanism. , 2011, Chemistry & biology.

[53]  Lewis E. Kay,et al.  Methyl groups as probes of supra-molecular structure, dynamics and function , 2010, Journal of biomolecular NMR.

[54]  Andreas Bracher,et al.  Molecular chaperones in protein folding and proteostasis , 2011, Nature.

[55]  F. Hartl,et al.  DnaK functions as a central hub in the E. coli chaperone network. , 2012, Cell reports.

[56]  R. Nussinov,et al.  The origin of allosteric functional modulation: multiple pre-existing pathways. , 2009, Structure.

[57]  K. Hodgson,et al.  Solution small-angle X-ray scattering study of the molecular chaperone Hsc70 and its subfragments. , 1995, Biochemistry.

[58]  J. Rossjohn,et al.  Identification of a membrane-spanning domain of the thiol-activated pore-forming toxin Clostridium perfringens perfringolysin O: an alpha-helical to beta-sheet transition identified by fluorescence spectroscopy. , 1998, Biochemistry.

[59]  Shawn Y. Stevens,et al.  Structural insights into substrate binding by the molecular chaperone DnaK , 2000, Nature Structural Biology.

[60]  C. Seidel,et al.  The conformational dynamics of the mitochondrial Hsp70 chaperone. , 2010, Molecular cell.

[61]  Arturo Muga,et al.  Interdomain interaction through helices A and B of DnaK peptide binding domain , 2003, FEBS letters.

[62]  Charalampos G. Kalodimos,et al.  Protein dynamics and allostery: an NMR view. , 2011, Current opinion in structural biology.

[63]  M. Mayer,et al.  Hsp70 chaperone machines. , 2001, Advances in protein chemistry.

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