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Article ; Online: There are more Hsp90 chaperone mechanisms in heaven and earth, dear reader, than are dreamt of in your philosophy.

Clerico, Eugenia M / Gierasch, Lila M

2022 Volume 82, Issue 8, Page(s) 1403–1404

Abstract: Dahiya et al. (2022) and Biebl et al. (2022) present mechanistic insights into the Hsp40/Hsp70/Hsp90 chaperone teamwork and the co-chaperones that participate in this network. ...

Abstract	Dahiya et al. (2022) and Biebl et al. (2022) present mechanistic insights into the Hsp40/Hsp70/Hsp90 chaperone teamwork and the co-chaperones that participate in this network.
MeSH term(s)	HSP70 Heat-Shock Proteins/genetics ; HSP70 Heat-Shock Proteins/metabolism ; HSP90 Heat-Shock Proteins/genetics ; HSP90 Heat-Shock Proteins/metabolism ; Molecular Chaperones/genetics ; Molecular Chaperones/metabolism ; Philosophy ; Protein Binding
Chemical Substances	HSP70 Heat-Shock Proteins ; HSP90 Heat-Shock Proteins ; Molecular Chaperones
Language	English
Publishing date	2022-04-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Comment
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.03.040
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Article: There are more Hsp90 chaperone mechanisms in heaven and earth, dear reader, than are dreamt of in your philosophy

Clerico, Eugenia M. / Gierasch, Lila M.

Molecular cell. 2022 Apr. 21, v. 82, no. 8

2022

Abstract: Dahiya et al. (2022) and Biebl et al. (2022) present mechanistic insights into the Hsp40/Hsp70/Hsp90 chaperone teamwork and the co-chaperones that participate in this network. ...

Abstract	Dahiya et al. (2022) and Biebl et al. (2022) present mechanistic insights into the Hsp40/Hsp70/Hsp90 chaperone teamwork and the co-chaperones that participate in this network.
Keywords	cells ; philosophy ; teams
Language	English
Dates of publication	2022-0421
Size	p. 1403-1404.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.03.040
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Article ; Online: New insights into the structure and function of the complex between the Escherichia coli Hsp70, DnaK, and its nucleotide-exchange factor, GrpE.

Rossi, Maria-Agustina / Pozhidaeva, Alexandra K / Clerico, Eugenia M / Petridis, Constantine / Gierasch, Lila M

The Journal of biological chemistry

2023 Volume 300, Issue 1, Page(s) 105574

Abstract: The 70 kDa heat shock proteins (Hsp70s) play a pivotal role in many cellular functions using allosteric communication between their nucleotide-binding domain (NBD) and substrate-binding domain, mediated by an interdomain linker, to modulate their ... ...

Abstract	The 70 kDa heat shock proteins (Hsp70s) play a pivotal role in many cellular functions using allosteric communication between their nucleotide-binding domain (NBD) and substrate-binding domain, mediated by an interdomain linker, to modulate their affinity for protein clients. Critical to modulation of the Hsp70 allosteric cycle, nucleotide-exchange factors (NEFs) act by a conserved mechanism involving binding to the ADP-bound NBD and opening of the nucleotide-binding cleft to accelerate the release of ADP and binding of ATP. The crystal structure of the complex between the NBD of the Escherichia coli Hsp70, DnaK, and its NEF, GrpE, was reported previously, but the GrpE in the complex carried a point mutation (G122D). Both the functional impact of this mutation and its location on the NEF led us to revisit the DnaK NBD/GrpE complex structurally using AlphaFold modeling and validation by solution methods that report on protein conformation and mutagenesis. This work resulted in a new model for the DnaK NBD in complex with GrpE in which subdomain IIB of the NBD rotates more than in the crystal structure, resulting in an open conformation of the nucleotide-binding cleft, which now resembles more closely what is seen in other Hsp/NEF complexes. Moreover, the new model is consistent with the increased ADP off-rate accompanying GrpE binding. Excitingly, our findings point to an interdomain allosteric signal in DnaK triggered by GrpE binding.
MeSH term(s)	Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Crystallography, X-Ray ; Escherichia coli/chemistry ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Heat-Shock Proteins/chemistry ; Heat-Shock Proteins/genetics ; Heat-Shock Proteins/metabolism ; HSP70 Heat-Shock Proteins/chemistry ; HSP70 Heat-Shock Proteins/genetics ; HSP70 Heat-Shock Proteins/metabolism ; Mutagenesis ; Point Mutation ; Protein Binding ; Protein Domains ; Reproducibility of Results ; Rotation
Chemical Substances	Adenosine Diphosphate (61D2G4IYVH) ; Adenosine Triphosphate (8L70Q75FXE) ; dnaK protein, E coli (EC 3.6.1.-) ; Escherichia coli Proteins ; GrpE protein, E coli ; Heat-Shock Proteins ; HSP70 Heat-Shock Proteins
Language	English
Publishing date	2023-12-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.105574
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Article ; Online: Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future.

Nordquist, Erik B / Clerico, Eugenia M / Chen, Jianhan / Gierasch, Lila M

The journal of physical chemistry. B

2022 Volume 126, Issue 36, Page(s) 6780–6791

Abstract: Hsp70 molecular chaperones play central roles in maintaining a healthy cellular proteome. Hsp70s function by binding to short peptide sequences in incompletely folded client proteins, thus preventing them from misfolding and/or aggregating, and in many ... ...

Abstract	Hsp70 molecular chaperones play central roles in maintaining a healthy cellular proteome. Hsp70s function by binding to short peptide sequences in incompletely folded client proteins, thus preventing them from misfolding and/or aggregating, and in many cases holding them in a state that is competent for subsequent processes like translocation across membranes. There is considerable interest in predicting the sites where Hsp70s may bind their clients, as the ability to do so sheds light on the cellular functions of the chaperone. In addition, the capacity of the Hsp70 chaperone family to bind to a broad array of clients and to identify accessible sequences that enable discrimination of those that are folded from those that are not fully folded, which is essential to their cellular roles, is a fascinating puzzle in molecular recognition. In this article we discuss efforts to harness computational modeling with input from experimental data to develop a predictive understanding of the promiscuous yet selective binding of Hsp70 molecular chaperones to accessible sequences within their client proteins. We trace how an increasing understanding of the complexities of Hsp70-client interactions has led computational modeling to new underlying assumptions and design features. We describe the trend from purely data-driven analysis toward increased reliance on physics-based modeling that deeply integrates structural information and sequence-based functional data with physics-based binding energies. Notably, new experimental insights are adding to our understanding of the molecular origins of "selective promiscuity" in substrate binding by Hsp70 chaperones and challenging the underlying assumptions and design used in earlier predictive models. Taking the new experimental findings together with exciting progress in computational modeling of protein structures leads us to foresee a bright future for a predictive understanding of selective-yet-promiscuous binding exploited by Hsp70 molecular chaperones; the resulting new insights will also apply to substrate binding by other chaperones and by signaling proteins.
MeSH term(s)	HSP70 Heat-Shock Proteins/chemistry ; Humans ; Models, Molecular ; Molecular Chaperones/metabolism ; Protein Binding ; Protein Folding ; Proteome/metabolism
Chemical Substances	HSP70 Heat-Shock Proteins ; Molecular Chaperones ; Proteome
Language	English
Publishing date	2022-08-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.2c03806
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Article: Computationally-Aided Modeling of Hsp70–Client Interactions: Past, Present, and Future

Nordquist, Erik B. / Clerico, Eugenia M. / Chen, Jianhan / Gierasch, Lila M.

Journal of physical chemistry. 2022 Aug. 30, v. 126, no. 36

2022

Abstract	Hsp70 molecular chaperones play central roles in maintaining a healthy cellular proteome. Hsp70s function by binding to short peptide sequences in incompletely folded client proteins, thus preventing them from misfolding and/or aggregating, and in many cases holding them in a state that is competent for subsequent processes like translocation across membranes. There is considerable interest in predicting the sites where Hsp70s may bind their clients, as the ability to do so sheds light on the cellular functions of the chaperone. In addition, the capacity of the Hsp70 chaperone family to bind to a broad array of clients and to identify accessible sequences that enable discrimination of those that are folded from those that are not fully folded, which is essential to their cellular roles, is a fascinating puzzle in molecular recognition. In this article we discuss efforts to harness computational modeling with input from experimental data to develop a predictive understanding of the promiscuous yet selective binding of Hsp70 molecular chaperones to accessible sequences within their client proteins. We trace how an increasing understanding of the complexities of Hsp70–client interactions has led computational modeling to new underlying assumptions and design features. We describe the trend from purely data-driven analysis toward increased reliance on physics-based modeling that deeply integrates structural information and sequence-based functional data with physics-based binding energies. Notably, new experimental insights are adding to our understanding of the molecular origins of “selective promiscuity” in substrate binding by Hsp70 chaperones and challenging the underlying assumptions and design used in earlier predictive models. Taking the new experimental findings together with exciting progress in computational modeling of protein structures leads us to foresee a bright future for a predictive understanding of selective-yet-promiscuous binding exploited by Hsp70 molecular chaperones; the resulting new insights will also apply to substrate binding by other chaperones and by signaling proteins.
Keywords	peptides ; physical chemistry ; proteome
Language	English
Dates of publication	2022-0830
Size	p. 6780-6791.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.2c03806
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Article ; Online: Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones.

Nordquist, Erik B / English, Charles A / Clerico, Eugenia M / Sherman, Woody / Gierasch, Lila M / Chen, Jianhan

PLoS computational biology

2021 Volume 17, Issue 11, Page(s) e1009567

Abstract: To help cells cope with protein misfolding and aggregation, Hsp70 molecular chaperones selectively bind a variety of sequences ("selective promiscuity"). Statistical analyses from substrate-derived peptide arrays reveal that DnaK, the E. coli Hsp70, ... ...

Abstract	To help cells cope with protein misfolding and aggregation, Hsp70 molecular chaperones selectively bind a variety of sequences ("selective promiscuity"). Statistical analyses from substrate-derived peptide arrays reveal that DnaK, the E. coli Hsp70, binds to sequences containing three to five branched hydrophobic residues, although otherwise the specific amino acids can vary considerably. Several high-resolution structures of the substrate -binding domain (SBD) of DnaK bound to peptides reveal a highly conserved configuration of the bound substrate and further suggest that the substrate-binding cleft consists of five largely independent sites for interaction with five consecutive substrate residues. Importantly, both substrate backbone orientations (N- to C- and C- to N-) allow essentially the same backbone hydrogen-bonding and side-chain interactions with the chaperone. In order to rationalize these observations, we performed atomistic molecular dynamics simulations to sample the interactions of all 20 amino acid side chains in each of the five sites of the chaperone in the context of the conserved substrate backbone configurations. The resulting interaction energetics provide the basis set for deriving a predictive model that we call Paladin (Physics-based model of DnaK-Substrate Binding). Trained using available peptide array data, Paladin can distinguish binders and nonbinders of DnaK with accuracy comparable to existing predictors and further predicts the detailed configuration of the bound sequence. Tested using existing DnaK-peptide structures, Paladin correctly predicted the binding register in 10 out of 13 substrate sequences that bind in the N- to C- orientation, and the binding orientation in 16 out of 22 sequences. The physical basis of the Paladin model provides insight into the origins of how Hsp70s bind substrates with a balance of selectivity and promiscuity. The approach described here can be extended to other Hsp70s where extensive peptide array data is not available.
MeSH term(s)	Binding Sites ; Computational Biology/methods ; Escherichia coli Proteins/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Hydrophobic and Hydrophilic Interactions ; Molecular Dynamics Simulation ; Physical Phenomena ; Protein Binding ; Protein Conformation ; Protein Domains
Chemical Substances	Escherichia coli Proteins ; HSP70 Heat-Shock Proteins ; dnaK protein, E coli (EC 3.6.1.-)
Language	English
Publishing date	2021-11-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1009567
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Article ; Online: Selective promiscuity in the binding of

Clerico, Eugenia M / Pozhidaeva, Alexandra K / Jansen, Rachel M / Özden, Can / Tilitsky, Joseph M / Gierasch, Lila M

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 41

Abstract: Heat shock protein 70 (Hsp70) chaperones bind many different sequences and discriminate between incompletely folded and folded clients. Most research into the origins of this "selective promiscuity" has relied on short peptides as substrates to dissect ... ...

Abstract	Heat shock protein 70 (Hsp70) chaperones bind many different sequences and discriminate between incompletely folded and folded clients. Most research into the origins of this "selective promiscuity" has relied on short peptides as substrates to dissect the binding, but much less is known about how Hsp70s bind full-length client proteins. Here, we connect detailed structural analyses of complexes between the
MeSH term(s)	Alkaline Phosphatase/metabolism ; Binding Sites/physiology ; Crystallography, X-Ray ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Models, Molecular ; Molecular Chaperones/metabolism ; Protein Binding/physiology ; Protein Domains/physiology ; Protein Folding
Chemical Substances	Escherichia coli Proteins ; HSP70 Heat-Shock Proteins ; Molecular Chaperones ; Alkaline Phosphatase (EC 3.1.3.1) ; dnaK protein, E coli (EC 3.6.1.-)
Language	English
Publishing date	2021-09-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2016962118
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Article ; Online: Division of Labor: ER-Resident BiP Co-Chaperones Match Substrates to Fates Based on Specific Binding Sequences.

Hebert, Daniel N / Clerico, Eugenia M / Gierasch, Lila M

Molecular cell

2016 Volume 63, Issue 5, Page(s) 721–723

Abstract: In this issue of Molecular Cell, Behnke et al. (2016) describe a novel cell-based peptide-binding assay and use it to analyze the binding specificities of the endoplasmic reticulum Hsp70 chaperone and its co-chaperones and to probe their different roles ... ...

Abstract	In this issue of Molecular Cell, Behnke et al. (2016) describe a novel cell-based peptide-binding assay and use it to analyze the binding specificities of the endoplasmic reticulum Hsp70 chaperone and its co-chaperones and to probe their different roles in protein quality control.
MeSH term(s)	Animals ; Endoplasmic Reticulum/chemistry ; HSP70 Heat-Shock Proteins/analysis ; Heat-Shock Proteins/analysis ; Humans ; Molecular Chaperones/analysis
Chemical Substances	HSP70 Heat-Shock Proteins ; Heat-Shock Proteins ; Molecular Chaperones
Language	English
Publishing date	2016-09-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2016.08.017
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Article ; Online: Allosteric landscapes of eukaryotic cytoplasmic Hsp70s are shaped by evolutionary tuning of key interfaces.

Meng, Wenli / Clerico, Eugenia M / McArthur, Natalie / Gierasch, Lila M

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 47, Page(s) 11970–11975

Abstract: The 70-kDa heat shock proteins (Hsp70s) are molecular chaperones that perform a wide range of critical cellular functions. They assist in the folding of newly synthesized proteins, facilitate assembly of specific protein complexes, shepherd proteins ... ...

Abstract	The 70-kDa heat shock proteins (Hsp70s) are molecular chaperones that perform a wide range of critical cellular functions. They assist in the folding of newly synthesized proteins, facilitate assembly of specific protein complexes, shepherd proteins across membranes, and prevent protein misfolding and aggregation. Hsp70s perform these functions by a conserved mechanism that relies on allosteric cycles of nucleotide-modulated binding and release of client proteins. Current models for Hsp70 allostery have come from extensive study of the bacterial Hsp70, DnaK. Extending our understanding to eukaryotic Hsp70s is extremely important not only in providing a likely common mechanistic framework but also because of their central roles in cellular physiology. In this study, we examined the allosteric behaviors of the eukaryotic cytoplasmic Hsp70s, HspA1 and Hsc70, and found significant differences from that of DnaK. We found that HspA1 and Hsc70 favor a state in which the nucleotide-binding domain (NBD) and substrate-binding domain (SBD) are intimately docked significantly more as compared to DnaK. Past work established that the NBD-SBD interface and the helical lid-β-SBD interface govern the allosteric landscape of DnaK. Here, we identified sites on these interfaces that differ between eukaryotic cytoplasmic Hsp70s and DnaK. Our mutational analysis has revealed key evolutionary variations that account for the population shifts between the docked and undocked conformations. These results underline the tunability of Hsp70 functions by modulation of allosteric interfaces through evolutionary diversification and also suggest sites where the binding of small-molecule modulators could influence Hsp70 function.
MeSH term(s)	Allosteric Regulation/genetics ; Allosteric Site/genetics ; Animals ; Computational Biology/methods ; Cytoplasm/metabolism ; Cytosol/metabolism ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Eukaryota/genetics ; Eukaryota/metabolism ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; HSC70 Heat-Shock Proteins/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Heat-Shock Proteins/genetics ; Heat-Shock Proteins/metabolism ; Humans ; Models, Molecular ; Protein Conformation ; Protein Domains
Chemical Substances	Escherichia coli Proteins ; HSC70 Heat-Shock Proteins ; HSP70 Heat-Shock Proteins ; HSPA1A protein, human ; Heat-Shock Proteins ; dnaK protein, E coli (EC 3.6.1.-)
Language	English
Publishing date	2018-11-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1811105115
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Article ; Online: Hsp70 molecular chaperones: multifunctional allosteric holding and unfolding machines.

Clerico, Eugenia M / Meng, Wenli / Pozhidaeva, Alexandra / Bhasne, Karishma / Petridis, Constantine / Gierasch, Lila M

The Biochemical journal

2019 Volume 476, Issue 11, Page(s) 1653–1677

Abstract: The Hsp70 family of chaperones works with its co-chaperones, the nucleotide exchange factors and J-domain proteins, to facilitate a multitude of cellular functions. Central players in protein homeostasis, these jacks-of-many-trades are utilized in a ... ...

Abstract	The Hsp70 family of chaperones works with its co-chaperones, the nucleotide exchange factors and J-domain proteins, to facilitate a multitude of cellular functions. Central players in protein homeostasis, these jacks-of-many-trades are utilized in a variety of ways because of their ability to bind with selective promiscuity to regions of their client proteins that are exposed when the client is unfolded, either fully or partially, or visits a conformational state that exposes the binding region in a regulated manner. The key to Hsp70 functions is that their substrate binding is transient and allosterically cycles in a nucleotide-dependent fashion between high- and low-affinity states. In the past few years, structural insights into the molecular mechanism of this allosterically regulated binding have emerged and provided deep insight into the deceptively simple Hsp70 molecular machine that is so widely harnessed by nature for diverse cellular functions. In this review, these structural insights are discussed to give a picture of the current understanding of how Hsp70 chaperones work.
MeSH term(s)	Allosteric Site ; Binding Sites ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; HSP70 Heat-Shock Proteins/chemistry ; HSP70 Heat-Shock Proteins/metabolism ; Humans ; Models, Molecular ; Protein Aggregates ; Protein Folding ; Protein Transport ; Proteolysis
Chemical Substances	Escherichia coli Proteins ; HSP70 Heat-Shock Proteins ; Protein Aggregates ; dnaK protein, E coli (EC 3.6.1.-)
Language	English
Publishing date	2019-06-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BCJ20170380
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