1
|
Hendershot LM, Buck TM, Brodsky JL. The Essential Functions of Molecular Chaperones and Folding Enzymes in Maintaining Endoplasmic Reticulum Homeostasis. J Mol Biol 2024; 436:168418. [PMID: 38143019 DOI: 10.1016/j.jmb.2023.168418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
It has been estimated that up to one-third of the proteins encoded by the human genome enter the endoplasmic reticulum (ER) as extended polypeptide chains where they undergo covalent modifications, fold into their native structures, and assemble into oligomeric protein complexes. The fidelity of these processes is critical to support organellar, cellular, and organismal health, and is perhaps best underscored by the growing number of disease-causing mutations that reduce the fidelity of protein biogenesis in the ER. To meet demands encountered by the diverse protein clientele that mature in the ER, this organelle is populated with a cadre of molecular chaperones that prevent protein aggregation, facilitate protein disulfide isomerization, and lower the activation energy barrier of cis-trans prolyl isomerization. Components of the lectin (glycan-binding) chaperone system also reside within the ER and play numerous roles during protein biogenesis. In addition, the ER houses multiple homologs of select chaperones that can recognize and act upon diverse peptide signatures. Moreover, redundancy helps ensure that folding-compromised substrates are unable to overwhelm essential ER-resident chaperones and enzymes. In contrast, the ER in higher eukaryotic cells possesses a single member of the Hsp70, Hsp90, and Hsp110 chaperone families, even though several homologs of these molecules reside in the cytoplasm. In this review, we discuss specific functions of the many factors that maintain ER quality control, highlight some of their interactions, and describe the vulnerabilities that arise from the absence of multiple members of some chaperone families.
Collapse
Affiliation(s)
- Linda M Hendershot
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
| | - Teresa M Buck
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States
| |
Collapse
|
2
|
Johnson N, Pattinson C, Burgoyne K, Hijazi K, Houssen WE, Milne BF. SARS-CoV-2 Spike Protein-Derived Cyclic Peptides as Modulators of Spike Interaction with GRP78. Chembiochem 2024; 25:e202300789. [PMID: 38613462 DOI: 10.1002/cbic.202300789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024]
Abstract
The human glucose-regulated protein GRP78 is a human chaperone that translocactes to the cell surface when cells are under stress. Theoretical studies suggested it could be involved in SARS-CoV-2 virus entry to cells. In this work, we used in vitro surface plasmon resonance-based assays to show that human GRP78 indeed binds to SARS-CoV-2 spike protein. We have designed and synthesised cyclic peptides based on the loop structure of amino acids 480-488 of the SARS-CoV-2 spike protein S1 domain from the Wuhan and Omicron variants and showed that both peptides bind to GRP78. Consistent with the greater infectiousness of the Omicron variant, the Omicron-derived peptide displays slower dissociation from the target protein. Both peptides significantly inhibit the binding of wild-type S1 protein to the human protein GRP78 suggesting that further development of these cyclic peptide motifs may provide a viable route to novel anti-SARS-CoV-2 agents.
Collapse
Affiliation(s)
- Nicholas Johnson
- Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Aberdeen, AB25 2ZD, UK
| | - Craig Pattinson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Kate Burgoyne
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Karolin Hijazi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Wael E Houssen
- Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Aberdeen, AB25 2ZD, UK
- Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, UK
| | - Bruce F Milne
- Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, UK
- CFisUC, Department of Physics, University of Coimbra, Rua Larga, 3004-516, Coimbra, Portugal
| |
Collapse
|
3
|
Alavi Z, Casanova-Morales N, Quiroga-Roger D, Wilson CAM. Towards the understanding of molecular motors and its relationship with local unfolding. Q Rev Biophys 2024; 57:e7. [PMID: 38715547 DOI: 10.1017/s0033583524000052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Molecular motors are machines essential for life since they convert chemical energy into mechanical work. However, the precise mechanism by which nucleotide binding, catalysis, or release of products is coupled to the work performed by the molecular motor is still not entirely clear. This is due, in part, to a lack of understanding of the role of force in the mechanical-structural processes involved in enzyme catalysis. From a mechanical perspective, one promising hypothesis is the Haldane-Pauling hypothesis which considers the idea that part of the enzymatic catalysis is strain-induced. It suggests that enzymes cannot be efficient catalysts if they are fully complementary to the substrates. Instead, they must exert strain on the substrate upon binding, using enzyme-substrate energy interaction (binding energy) to accelerate the reaction rate. A novel idea suggests that during catalysis, significant strain energy is built up, which is then released by a local unfolding/refolding event known as 'cracking'. Recent evidence has also shown that in catalytic reactions involving conformational changes, part of the heat released results in a center-of-mass acceleration of the enzyme, raising the possibility that the heat released by the reaction itself could affect the enzyme's integrity. Thus, it has been suggested that this released heat could promote or be linked to the cracking seen in proteins such as adenylate kinase (AK). We propose that the energy released as a consequence of ligand binding/catalysis is associated with the local unfolding/refolding events (cracking), and that this energy is capable of driving the mechanical work.
Collapse
Affiliation(s)
- Zahra Alavi
- Department of Physics, Loyola Marymount University, Los Angeles, CA, USA
| | | | - Diego Quiroga-Roger
- Biochemistry and Molecular Biology Department, Faculty of Chemistry and Pharmaceutical Sciences, Universidad de Chile, Santiago, Chile
| | - Christian A M Wilson
- Biochemistry and Molecular Biology Department, Faculty of Chemistry and Pharmaceutical Sciences, Universidad de Chile, Santiago, Chile
| |
Collapse
|
4
|
Sornjai W, Promma P, Priewkhiew S, Ramphan S, Jaratsittisin J, Jinagool P, Wikan N, Greenwood M, Murphy D, Smith DR. The interaction of GRP78 and Zika virus E and NS1 proteins occurs in a chaperone-client manner. Sci Rep 2024; 14:10407. [PMID: 38710792 PMCID: PMC11074156 DOI: 10.1038/s41598-024-61195-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024] Open
Abstract
Glucose regulated protein 78 (GRP78) is a chaperone protein that is a central mediator of the unfolded protein response, a key cellular stress response pathway. GRP78 has been shown to be critically required for infection and replication of a number of flaviviruses, and to interact with both non-structural (NS) and structural flavivirus proteins. However, the nature of the specific interaction between GRP78 and viral proteins remains largely unknown. This study aimed to characterize the binding domain and critical amino acid residues that mediate the interaction of GRP78 to ZIKV E and NS1 proteins. Recombinant EGFP fused GRP78 and individual subdomains (the nucleotide binding domain (NBD) and the substrate binding domain (SBD)) were used as a bait protein and co-expressed with full length or truncated ZIKV E and NS1 proteins in HEK293T/17 cells. Protein-protein interactions were determined by a co-immunoprecipitation assay. From the results, both the NBD and the SBD of GRP78 were crucial for an effective interaction. Single amino acid substitutions in the SBD showed that R492E and T518A mutants significantly reduced the binding affinity of GRP78 to ZIKV E and NS1 proteins. Notably, the interaction of GRP78 with ZIKV E was stably maintained against various single amino acid substitutions on ZIKV E domain III and with all truncated ZIKV E and NS1 proteins. Collectively, the results suggest that the principal binding between GRP78 and viral proteins is mainly a classic canonical chaperone protein-client interaction. The blocking of GRP78 chaperone function effectively inhibited ZIKV infection and replication in neuronal progenitor cells. Our findings reveal that GRP78 is a potential host target for anti-ZIKV therapeutics.
Collapse
Affiliation(s)
- Wannapa Sornjai
- Molecular Pathology Laboratory, Institute of Molecular Biosciences, Mahidol University, 25/25 Phutthamonthon Sai 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Ploenphit Promma
- Molecular Pathology Laboratory, Institute of Molecular Biosciences, Mahidol University, 25/25 Phutthamonthon Sai 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Suphansa Priewkhiew
- Molecular Pathology Laboratory, Institute of Molecular Biosciences, Mahidol University, 25/25 Phutthamonthon Sai 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Suwipa Ramphan
- Molecular Pathology Laboratory, Institute of Molecular Biosciences, Mahidol University, 25/25 Phutthamonthon Sai 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Janejira Jaratsittisin
- Molecular Pathology Laboratory, Institute of Molecular Biosciences, Mahidol University, 25/25 Phutthamonthon Sai 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Pailin Jinagool
- Molecular Pathology Laboratory, Institute of Molecular Biosciences, Mahidol University, 25/25 Phutthamonthon Sai 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Nitwara Wikan
- Molecular Pathology Laboratory, Institute of Molecular Biosciences, Mahidol University, 25/25 Phutthamonthon Sai 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Michael Greenwood
- Molecular Neuroendocrinology Research Group, Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | - David Murphy
- Molecular Neuroendocrinology Research Group, Bristol Medical School, Translational Health Sciences, University of Bristol, Bristol, UK
| | - Duncan R Smith
- Molecular Pathology Laboratory, Institute of Molecular Biosciences, Mahidol University, 25/25 Phutthamonthon Sai 4 Road, Salaya, Nakhon Pathom, 73170, Thailand.
| |
Collapse
|
5
|
Elgharib AM, Elshemey WM, Elfiky AA. Binding site prediction between lysozyme and glucose-regulated protein 78, a hope to fight amyloidosis. J Biomol Struct Dyn 2024:1-12. [PMID: 38393679 DOI: 10.1080/07391102.2024.2321238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
Amyloidosis is an extraordinarily vigorous and heterogeneous group of disorders that causes numerous organ failures due to the precipitation of misfolded proteins. Many of these damaged proteins are discarded before causing any fatal diseases due to the contribution of the protein quality control (PQC) system and its chaperons, including glucose-regulated protein (GRP78). One of the most important enzymatic proteins inside the body is lysozyme, which is reported to have many mutated variants that may cause amyloid fibrils. This study used structural bioinformatics and molecular dynamics simulations to test and suggest binding sites for the human lysozyme protein with GRP78. Multiple sequence alignment (MSA) shows that part of the lysozyme envelope protein (C65-C81 cyclic region) has high similarities (30.77% identity) with the cyclic Pep42. Additionally, the binding between the lysozyme cyclic region (C65-C81) and GRP78 substrate binding domain (SBD) is found favorable. The number and types of interactions vary between each of the mutant isoforms of lysozyme. The more significant the conformational changes in the mutation, the greater its probability of aggregation and the formation of amyloid fibrils. Each mutation leads to different interactions and binding patterns with GRP78. The present computational study suggests a lysozyme-GRP78 binding site, thus paving the way for drug designers to construct suitable carriers that can collect misfolded lysozyme proteins and eliminate them from the body, preventing their aggregation and amyloidogenesis.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ahmed M Elgharib
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Wael M Elshemey
- Department of Physics, Faculty of Science, Islamic University of Madinah, Madinah, Saudi Arabia
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| |
Collapse
|
6
|
Zehe M, Kehrein J, Schollmayer C, Plank C, Kovacs H, Merino Asumendi E, Holzgrabe U, Grimm C, Sotriffer C. Combined In-Solution Fragment Screening and Crystallographic Binding-Mode Analysis with a Two-Domain Hsp70 Construct. ACS Chem Biol 2024; 19:392-406. [PMID: 38317495 DOI: 10.1021/acschembio.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Heat shock protein 70 (Hsp70) isoforms are key players in the regulation of protein homeostasis and cell death pathways and are therefore attractive targets in cancer research. Developing nucleotide-competitive inhibitors or allosteric modulators, however, has turned out to be very challenging for this protein family, and no Hsp70-directed therapeutics have so far become available. As the field could profit from alternative starting points for inhibitor development, we present the results of a fragment-based screening approach on a two-domain Hsp70 construct using in-solution NMR methods, together with X-ray-crystallographic investigations and mixed-solvent molecular dynamics simulations. The screening protocol resulted in hits on both domains. In particular, fragment binding in a deeply buried pocket at the substrate-binding domain could be detected. The corresponding site is known to be important for communication between the nucleotide-binding and substrate-binding domains of Hsp70 proteins. The main fragment identified at this position also offers an interesting starting point for the development of a dual Hsp70/Hsp90 inhibitor.
Collapse
Affiliation(s)
- Markus Zehe
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| | - Josef Kehrein
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| | - Curd Schollmayer
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| | - Christina Plank
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
- University of Würzburg, Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor-Boveri-Institute, Am Hubland, DE-97074 Würzburg, Germany
| | - Helena Kovacs
- Bruker Switzerland AG, Industriestrasse 26, CH-8117 Fällanden, Switzerland
| | - Eduardo Merino Asumendi
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| | - Ulrike Holzgrabe
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| | - Clemens Grimm
- University of Würzburg, Department of Biochemistry and Cancer Therapy Research Center (CTRC), Theodor-Boveri-Institute, Am Hubland, DE-97074 Würzburg, Germany
| | - Christoph Sotriffer
- University of Würzburg, Institute of Pharmacy and Food Chemistry, Am Hubland, DE-97074 Würzburg, Germany
| |
Collapse
|
7
|
Ambrose AJ, Zerio CJ, Sivinski J, Zhu X, Godek J, Sanchez JL, Khanna M, Khanna R, Lairson L, Zhang DD, Chapman E. Human Hsp70 Substrate-Binding Domains Recognize Distinct Client Proteins. Biochemistry 2024; 63:251-263. [PMID: 38243804 DOI: 10.1021/acs.biochem.3c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
The 13 Hsp70 proteins in humans act on unique sets of substrates with diversity often being attributed to J-domain-containing protein (Hsp40 or JDP) cofactors. We were therefore surprised to find drastically different binding affinities for Hsp70-peptide substrates, leading us to probe substrate specificity among the 8 canonical Hsp70s from humans. We used peptide arrays to characterize Hsp70 binding and then mined these data using machine learning to develop an algorithm for isoform-specific prediction of Hsp70 binding sequences. The results of this algorithm revealed recognition patterns not predicted based on local sequence alignments. We then showed that none of the human isoforms can complement heat-shocked DnaK knockout Escherichia coli cells. However, chimeric Hsp70s consisting of the human nucleotide-binding domain and the substrate-binding domain of DnaK complement during heat shock, providing further evidence in vivo of the divergent function of the Hsp70 substrate-binding domains. We also demonstrated that the differences in heat shock complementation among the chimeras are not due to loss of DnaJ binding. Although we do not exclude JDPs as additional specificity factors, our data demonstrate substrate specificity among the Hsp70s, which has important implications for inhibitor development in cancer and neurodegeneration.
Collapse
Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher J Zerio
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jared Sivinski
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Xiaoyi Zhu
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jack Godek
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jonathan L Sanchez
- Department of Pharmacology, College of Medicine, The University of Arizona Health Sciences, Tucson, Arizona 85424, United States
| | - May Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York 10010, United States
| | - Rajesh Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York 10010, United States
| | - Luke Lairson
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Eli Chapman
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| |
Collapse
|
8
|
Lazou M, Hutton JR, Chakravarty A, Joseph-McCarthy D. Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface. J Comput Aided Mol Des 2024; 38:6. [PMID: 38263499 DOI: 10.1007/s10822-023-00546-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/02/2023] [Indexed: 01/25/2024]
Abstract
SARS-CoV-2, the virus that causes COVID-19, led to a global health emergency that claimed the lives of millions. Despite the widespread availability of vaccines, the virus continues to exist in the population in an endemic state which allows for the continued emergence of new variants. Most of the current vaccines target the spike glycoprotein interface of SARS-CoV-2, creating a selection pressure favoring viral immune evasion. Antivirals targeting other molecular interactions of SARS-CoV-2 can help slow viral evolution by providing orthogonal selection pressures on the virus. GRP78 is a host auxiliary factor that mediates binding of the SARS-CoV-2 spike protein to human cellular ACE2, the primary pathway of cell infection. As GRP78 forms a ternary complex with SARS-CoV-2 spike protein and ACE2, disrupting the formation of this complex is expected to hinder viral entry into host cells. Here, we developed a model of the GRP78-Spike RBD-ACE2 complex. We then used that model together with hot spot mapping of the GRP78 structure to identify the putative binding site for spike protein on GRP78. Next, we performed structure-based virtual screening of known drug/candidate drug libraries to identify binders to GRP78 that are expected to disrupt spike protein binding to the GRP78, and thereby preventing viral entry to the host cell. A subset of these compounds has previously been shown to have some activity against SARS-CoV-2. The identified hits are starting points for the further development of novel SARS-CoV-2 therapeutics, potentially serving as proof-of-concept for GRP78 as a potential drug target for other viruses.
Collapse
Affiliation(s)
- Maria Lazou
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Jonathan R Hutton
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | | | | |
Collapse
|
9
|
Mistry AC, Chowdhury D, Chakraborty S, Haldar S. Elucidating the novel mechanisms of molecular chaperones by single-molecule technologies. Trends Biochem Sci 2024; 49:38-51. [PMID: 37980187 DOI: 10.1016/j.tibs.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/20/2023]
Abstract
Molecular chaperones play central roles in sustaining protein homeostasis and preventing protein aggregation. Most studies of these systems have been performed in bulk, providing averaged measurements, though recent single-molecule approaches have provided an in-depth understanding of the molecular mechanisms of their activities and structural rearrangements during substrate recognition. Chaperone activities have been observed to be substrate specific, with some associated with ATP-dependent structural dynamics and others via interactions with co-chaperones. This Review aims to describe the novel mechanisms of molecular chaperones as revealed by single-molecule approaches, and to provide insights into their functioning and its implications for protein homeostasis and human diseases.
Collapse
Affiliation(s)
- Ayush Chandrakant Mistry
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Debojyoti Chowdhury
- Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal 700106, India
| | - Soham Chakraborty
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Shubhasis Haldar
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India; Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal 700106, India; Department of Chemistry, Ashoka University, Sonepat, Haryana 131029, India.
| |
Collapse
|
10
|
Rossi MA, Pozhidaeva AK, Clerico EM, Petridis C, Gierasch LM. New insights into the structure and function of the complex between the Escherichia coli Hsp70, DnaK, and its nucleotide-exchange factor, GrpE. J Biol Chem 2024; 300:105574. [PMID: 38110031 PMCID: PMC10825016 DOI: 10.1016/j.jbc.2023.105574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/18/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023] Open
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.
Collapse
Affiliation(s)
- Maria-Agustina Rossi
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Alexandra K Pozhidaeva
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Eugenia M Clerico
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Constantine Petridis
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Lila M Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA; Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA.
| |
Collapse
|
11
|
Guo W, Wang M, Yang Z, Liu D, Ma B, Zhao Y, Chen Y, Hu Y. Recent advances in small molecule and peptide inhibitors of glucose-regulated protein 78 for cancer therapy. Eur J Med Chem 2023; 261:115792. [PMID: 37690265 DOI: 10.1016/j.ejmech.2023.115792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/18/2023] [Accepted: 09/02/2023] [Indexed: 09/12/2023]
Abstract
Glucose-regulated protein 78 (GRP78) is one of key endoplasmic reticulum (ER) chaperone proteins that regulates the unfolded protein response (UPR) to maintain ER homeostasis. As a core factor in the regulation of the UPR, GRP78 takes a critical part in the cellular processes required for tumorigenesis, such as proliferation, metastasis, anti-apoptosis, immune escape and chemoresistance. Overexpression of GRP78 is closely correlated with tumorigenesis and poor prognosis in various malignant tumors. Targeting GRP78 is regarded as a potentially promising therapeutic strategy for cancer therapy. Although none of the GRP78 inhibitors have been approved to date, there have been several studies of GRP78 inhibitors. Herein, we comprehensively review the structure, physiological functions of GRP78 and the recent progress of GRP78 inhibitors, and discuss the structures, in vitro and in vivo efficacies, and merits and demerits of these inhibitors to inspire further research. Additionally, the feasibility of GRP78-targeting proteolysis-targeting chimeras (PROTACs), disrupting GRP78 cochaperone interactions, or covalent inhibition are also discussed as novel strategies for drugs discovery targeting GRP78, with the hope that these strategies can provide new opportunities for targeted GRP78 antitumor therapy.
Collapse
Affiliation(s)
- Weikai Guo
- The Jointed National Laboratory of Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng, 475004, China
| | - Manjie Wang
- The Jointed National Laboratory of Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng, 475004, China
| | - Zhengfan Yang
- The Jointed National Laboratory of Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng, 475004, China
| | - Danyang Liu
- The Jointed National Laboratory of Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng, 475004, China
| | - Borui Ma
- The Jointed National Laboratory of Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng, 475004, China
| | - Yanqun Zhao
- The Jointed National Laboratory of Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng, 475004, China
| | - Yihua Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Yanzhong Hu
- The Jointed National Laboratory of Antibody Drug Engineering, The First Affiliated Hospital of Henan University, Henan University, Kaifeng, 475004, China.
| |
Collapse
|
12
|
Xue M, Lin Z, Zhang T, Cheng ZJ, Lin R, Guo B, Zeng Y, Hu F, Li F, Zheng P, Huang H, Li N, Zhao Q, Sun B, Tang X. ERC-BiP Functional Protein Pathway for Assessing Endoplasmic Reticulum Stress Induced by SARS-CoV-2 Replication after Cell Invasion. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:7253779. [PMID: 37849973 PMCID: PMC10578982 DOI: 10.1155/2023/7253779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/24/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023]
Abstract
Background SARS-CoV-2 induces apoptosis and amplifies the immune response by continuously stressing the endoplasmic reticulum (ER) after invading cells. This study aimed to establish a protein-metabolic pathway associated with ER dysfunction based on the invasion mechanism of SARS-CoV-2. Methods This study included 17 healthy people and 46 COVID-19 patients, including 38 mild patients and 8 severe patients. Proteomics and metabolomics were measured in the patient plasma collected at admission and one week after admission. The patients were further divided into the aggravation and remission groups based on disease progression within one week of admission. Results Cross-sectional comparison showed that endoplasmic reticulum molecular chaperone-binding immunoglobulin protein (ERC-BiP), angiotensinogen (AGT), ceramide acid (Cer), and C-reactive protein (CRP) levels were significantly increased in COVID-19 patients, while the sphingomyelin (SM) level was significantly decreased (P < 0.05). In addition, longitudinal comparative analysis found that the temporal fold changes of ERC-BiP, AGT, Cer, CRP, and SM were significantly different between the patients in the aggravation and remission groups (P < 0.05). ERC-BiP, AGT, and Cer levels were significantly increased in aggravation patients, while SM was significantly decreased (P < 0.05). Meanwhile, ERC-BiP was significantly correlated with AGT (r = 0.439; P < 0.001). Conclusions ERC-BiP can be used as a core index to reflect the degree of ER stress in COVID-19 patients, which is of great value for evaluating the functional state of cells. A functional pathway for AGT/ERC-BiP/glycolysis can directly assess the activation of unfolded protein reactions. The ERC-BiP pathway is closer to the intracellular replication pathway of SARS-CoV-2 and may help in the development of predictive protocols for COVID-19 exacerbation.
Collapse
Affiliation(s)
- Mingshan Xue
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510060, China
- Guangzhou Laboratory, XingDaoHuanBei Road, Guangzhou International Bio-Island, Guangzhou 510005, Guangdong Province, China
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Zhiwei Lin
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Teng Zhang
- Cancer Centre, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Zhangkai J. Cheng
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Runpei Lin
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Baojun Guo
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
- School of Medicine, Henan University, Kaifeng 475000, Henan, China
| | - Yifeng Zeng
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Fengyu Hu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510060, China
| | - Feng Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510060, China
| | - Peiyan Zheng
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Huimin Huang
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Ning Li
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Qi Zhao
- Cancer Centre, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau, China
| | - Baoqing Sun
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Xiaoping Tang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510060, China
- Guangzhou Laboratory, XingDaoHuanBei Road, Guangzhou International Bio-Island, Guangzhou 510005, Guangdong Province, China
| |
Collapse
|
13
|
Abu-Mahfouz A, Ali M, Elfiky A. Anti-breast cancer drugs targeting cell-surface glucose-regulated protein 78: a drug repositioning in silico study. J Biomol Struct Dyn 2023; 41:7794-7808. [PMID: 36129131 DOI: 10.1080/07391102.2022.2125076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/10/2022] [Indexed: 10/14/2022]
Abstract
Breast cancer (BC) is prevalent worldwide and is a leading cause of death among women. However, cell-surface glucose-regulated protein 78 (cs-GRP78) is overexpressed in several types of cancer and during pathogen infections. This study examines two well-known BC drugs approved by the FDA as BC treatments to GRP78. The first type consists of inhibitors of cyclin-based kinases 4/6, including abemaciclib, palbociclib, ribociclib, and dinaciclib. In addition, tunicamycin, and doxorubicin, which are among the most effective anticancer drugs for early and late-stage BC, are tested against GRP78. As (-)-epiGallocatechin gallate inhibits GRP78, it is also being evaluated (used as positive control). Thus, using molecular dynamics simulation approaches, this study aims to examine the advantages of targeting GRP78, which represents a promising cancer therapy regime. In light of recent advances in computational drug response prediction models, this study aimed to examine the benefits of GRP78 targeting, which represents a promising cancer therapy regime, by utilizing combined molecular docking and molecular dynamics simulation approaches. The simulated protein (50 ns) was docked with the drugs, then a second round of dynamics simulation was performed for 100 ns. After that, the binding free energies were calculated from 30 to 100 ns for each complex during the simulation period. These findings demonstrate the efficacy of abemaciclib, ribociclib, and tunicamycin in binding to the nucleotide-binding domain of the GRP78, paving the way for elucidating the mode of interactions between these drugs and cancer (and other stressed) cells that overexpress GRP78.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Alaa Abu-Mahfouz
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Maha Ali
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Abdo Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| |
Collapse
|
14
|
Zhao S, Feng H, Jiang D, Yang K, Wang ST, Zhang YX, Wang Y, Liu H, Guo C, Tang TS. ER Ca 2+ overload activates the IRE1α signaling and promotes cell survival. Cell Biosci 2023; 13:123. [PMID: 37400935 DOI: 10.1186/s13578-023-01062-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/26/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Maintaining homeostasis of Ca2+ stores in the endoplasmic reticulum (ER) is crucial for proper Ca2+ signaling and key cellular functions. Although Ca2+ depletion has been known to cause ER stress which in turn activates the unfolded protein response (UPR), how UPR sensors/transducers respond to excess Ca2+ when ER stores are overloaded remain largely unclear. RESULTS Here, we report for the first time that overloading of ER Ca2+ can directly sensitize the IRE1α-XBP1 axis. The overloaded ER Ca2+ in TMCO1-deficient cells can cause BiP dissociation from IRE1α, promote the dimerization and stability of the IRE1α protein, and boost IRE1α activation. Intriguingly, attenuation of the over-activated IRE1α-XBP1s signaling by a IRE1α inhibitor can cause a significant cell death in TMCO1-deficient cells. CONCLUSIONS Our data establish a causal link between excess Ca2+ in ER stores and the selective activation of IRE1α-XBP1 axis, underscoring an unexpected role of overload of ER Ca2+ in IRE1α activation and in preventing cell death.
Collapse
Affiliation(s)
- Song Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiping Feng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongfang Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keyan Yang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Si-Tong Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Xin Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Caixia Guo
- Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
15
|
Rivera M, Burgos‐Bravo F, Engelberger F, Asor R, Lagos‐Espinoza MIA, Figueroa M, Kukura P, Ramírez‐Sarmiento CA, Baez M, Smith SB, Wilson CAM. Effect of temperature and nucleotide on the binding of BiP chaperone to a protein substrate. Protein Sci 2023; 32:e4706. [PMID: 37323096 PMCID: PMC10303699 DOI: 10.1002/pro.4706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
BiP (immunoglobulin heavy-chain binding protein) is a Hsp70 monomeric ATPase motor that plays broad and crucial roles in maintaining proteostasis inside the cell. Structurally, BiP is formed by two domains, a nucleotide-binding domain (NBD) with ATPase activity connected by a flexible hydrophobic linker to the substrate-binding domain. While the ATPase and substrate binding activities of BiP are allosterically coupled, the latter is also dependent on nucleotide binding. Recent structural studies have provided new insights into BiP's allostery; however, the influence of temperature on the coupling between substrate and nucleotide binding to BiP remains unexplored. Here, we study BiP's binding to its substrate at the single molecule level using thermo-regulated optical tweezers which allows us to mechanically unfold the client protein and explore the effect of temperature and different nucleotides on BiP binding. Our results confirm that the affinity of BiP for its protein substrate relies on nucleotide binding, by mainly regulating the binding kinetics between BiP and its substrate. Interestingly, our findings also showed that the apparent affinity of BiP for its protein substrate in the presence of nucleotides remains invariable over a wide range of temperatures, suggesting that BiP may interact with its client proteins with similar affinities even when the temperature is not optimal. Thus, BiP could play a role as a "thermal buffer" in proteostasis.
Collapse
Affiliation(s)
- Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID–Millennium Science Initiative Program–Millennium Institute for Integrative Biology (iBio)SantiagoChile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Francesca Burgos‐Bravo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
- Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Felipe Engelberger
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID–Millennium Science Initiative Program–Millennium Institute for Integrative Biology (iBio)SantiagoChile
| | - Roi Asor
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordUK
- The Kavli Institute for Nanoscience DiscoveryOxfordUK
| | - Miguel I. A. Lagos‐Espinoza
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Maximiliano Figueroa
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias BiológicasUniversidad de ConcepciónConcepciónChile
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordUK
- The Kavli Institute for Nanoscience DiscoveryOxfordUK
| | - César A. Ramírez‐Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID–Millennium Science Initiative Program–Millennium Institute for Integrative Biology (iBio)SantiagoChile
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | | | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| |
Collapse
|
16
|
Kotler JLM, Street TO. Mechanisms of Protein Quality Control in the Endoplasmic Reticulum by a Coordinated Hsp40-Hsp70-Hsp90 System. Annu Rev Biophys 2023; 52:509-524. [PMID: 37159299 DOI: 10.1146/annurev-biophys-111622-091309] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The Hsp40, Hsp70, and Hsp90 chaperone families are ancient, highly conserved, and critical to cellular protein homeostasis. Hsp40 chaperones can transfer their protein clients to Hsp70, and Hsp70 can transfer clients to Hsp90, but the functional benefits of these transfers are unclear. Recent structural and mechanistic work has opened up the possibility of uncovering how Hsp40, Hsp70, and Hsp90 work together as unified system. In this review, we compile mechanistic data on the ER J-domain protein 3 (ERdj3) (an Hsp40), BiP (an Hsp70), and Grp94 (an Hsp90) chaperones within the endoplasmic reticulum; what is known about how these chaperones work together; and gaps in this understanding. Using calculations, we examine how client transfer could impact the solubilization of aggregates, the folding of soluble proteins, and the triage decisions by which proteins are targeted for degradation. The proposed roles of client transfer among Hsp40-Hsp70-Hsp90 chaperones are new hypotheses, and we discuss potential experimental tests of these ideas.
Collapse
Affiliation(s)
- Judy L M Kotler
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA;
| | - Timothy O Street
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA;
| |
Collapse
|
17
|
SARS-CoV-2 ORF8 Protein Induces Endoplasmic Reticulum Stress-like Responses and Facilitates Virus Replication by Triggering Calnexin: an Unbiased Study. J Virol 2023; 97:e0001123. [PMID: 36877072 PMCID: PMC10062165 DOI: 10.1128/jvi.00011-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the viral pathogen responsible for the worldwide coronavirus disease 2019 (COVID-19) pandemic. The novel SARS-CoV-2 ORF8 protein is not highly homologous with known proteins, including accessory proteins of other coronaviruses. ORF8 contains a 15-amino-acid signal peptide in the N terminus that localizes the mature protein to the endoplasmic reticulum. Oligomannose-type glycosylation has been identified at the N78 site. Here, the unbiased molecular functions of ORF8 are also demonstrated. Via an immunoglobulin-like fold in a glycan-independent manner, both exogenous and endogenous ORF8 interacts with human calnexin and HSPA5. The key ORF8-binding sites of Calnexin and HSPA5 are indicated on the globular domain and the core substrate-binding domain, respectively. ORF8 induces species-dependent endoplasmic reticulum stress-like responses in human cells exclusively via the IRE1 branch, including intensive HSPA5 and PDIA4 upregulation, with increases in other stress-responding effectors, including CHOP, EDEM and DERL3. ORF8 overexpression facilitates SARS-CoV-2 replication. Both stress-like responses and viral replication induced by ORF8 have been shown to result from triggering the Calnexin switch. Thus, ORF8 serves as a key unique virulence gene of SARS-CoV-2, potentially contributing to COVID-19-specific and/or human-specific pathogenesis. IMPORTANCE Although SARS-CoV-2 is basically regarded as a homolog of SARS-CoV, with their genomic structure and the majority of their genes being highly homologous, the ORF8 genes of SARS-CoV and SARS-CoV-2 are distinct. The SARS-CoV-2 ORF8 protein also shows little homology with other viral or host proteins and is thus regarded as a novel special virulence gene of SARS-CoV-2. The molecular function of ORF8 has not been clearly known until now. Our results reveal the unbiased molecular characteristics of the SARS-CoV-2 ORF8 protein and demonstrate that it induces rapidly generated but highly controllable endoplasmic reticulum stress-like responses and facilitates virus replication by triggering Calnexin in human but not mouse cells, providing an explanation for the superficially known in vivo virulence discrepancy of ORF8 between SARS-CoV-2-infected patients and mouse.
Collapse
|
18
|
Elevated human placental heat shock protein 5 is associated with spontaneous preterm birth. Pediatr Res 2023:10.1038/s41390-023-02501-9. [PMID: 36788289 PMCID: PMC9926443 DOI: 10.1038/s41390-023-02501-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 12/28/2022] [Accepted: 01/13/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Specific heat shock proteins are associated with pregnancy complications, including spontaneous preterm birth (SPTB). Placental proteomics and whole exome sequencing recently suggested an association between heat shock protein HSPA5 and uncomplicated SPTB. In the present study, we investigated the localization of and possible roles for HSPA5 in SPTB. METHODS Western blot was performed to validate the result from the previously published proteomic analysis. We used qPCR to assess mRNA expression of genes and immunohistochemistry and immunoelectron microscopy to examine localization of HSPA5 in placental tissue. We silenced the HSPA5 gene in the HTR8/SVneo human trophoblast cell line to investigate possible functions of HSPA5. RESULTS HSPA5 was upregulated in placentas from SPTBs compared to spontaneous term births. We did not observe upregulation of HSPA5 mRNA in placental samples. The protein was localized in placental trophoblast in both spontaneous preterm and term placentas. Gene silencing of HSPA5 in human trophoblast cell culture affected the inflammatory response and decreased the expression of several proinflammatory genes. CONCLUSIONS We suggest that upregulation of HSPA5 in the placenta is associated with spontaneous preterm labor. HSPA5 may promote the inflammatory response and alter the anti-inflammatory state of the placenta which could eventually lead to premature labor. IMPACT We validated upregulation of HSPA5 in placentas from spontaneous preterm birth. HSPA5 was not upregulated at transcriptional level which suggests that it may be regulated post-translationally. Silencing HSPA5 in a human trophoblast-derived cell line suggested that HSPA5 promotes expression of proinflammatory cytokines. The emerging inflammation could lead to spontaneous preterm labor. Identifying inflammatory pathways and factors associated with spontaneous preterm birth increases knowledge of the molecular mechanisms of premature labor. This could provide cues to predict imminent premature labor and lead to information about how to safely maintain pregnancies.
Collapse
|
19
|
Schneider M, Antes I. Comparison of allosteric signaling in DnaK and BiP using mutual information between simulated residue conformations. Proteins 2023; 91:237-255. [PMID: 36111439 DOI: 10.1002/prot.26425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/06/2022] [Accepted: 09/13/2022] [Indexed: 01/13/2023]
Abstract
The heat shock protein 70 kDa (Hsp70) chaperone system serves as a critical component of protein quality control across a wide range of prokaryotic and eukaryotic organisms. Divergent evolution and specialization to particular organelles have produced numerous Hsp70 variants which share similarities in structure and general function, but differ substantially in regulatory aspects, including conformational dynamics and activity modulation by cochaperones. The human Hsp70 variant BiP (also known as GRP78 or HSPA5) is of therapeutic interest in the context of cancer, neurodegenerative diseases, and viral infection, including for treatment of the pandemic virus SARS-CoV-2. Due to the complex conformational rearrangements and high sequential variance within the Hsp70 protein family, it is in many cases poorly understood which amino acid mutations are responsible for biochemical differences between protein variants. In this study, we predicted residues associated with conformational regulation of human BiP and Escherichia coli DnaK. Based on protein structure networks obtained from molecular dynamics simulations, we analyzed the shared information between interaction timelines to highlight residue positions with strong conformational coupling to their environment. Our predictions, which focus on the binding processes of the chaperone's substrate and cochaperones, indicate residues filling potential signaling roles specific to either DnaK or BiP. By combining predictions of individual residues into conformationally coupled chains connecting ligand binding sites, we predict a BiP specific secondary signaling pathway associated with substrate binding. Our study sheds light on mechanistic differences in signaling and regulation between Hsp70 variants, which provide insights relevant to therapeutic applications of these proteins.
Collapse
Affiliation(s)
- Markus Schneider
- TUM Center for Functional Protein Assemblies and TUM School of Life Sciences, Technische Universität München, Freising, Bavaria, Germany
| | - Iris Antes
- TUM Center for Functional Protein Assemblies and TUM School of Life Sciences, Technische Universität München, Freising, Bavaria, Germany
| |
Collapse
|
20
|
Ambrose AJ, Sivinski J, Zerio CJ, Zhu X, Godek J, Kumirov VK, Coma Brujas T, Torra Garcia J, Annadurai A, Schmidlin CJ, Werner A, Shi T, Zavareh RB, Lairson L, Zhang DD, Chapman E. Discovery and Development of a Selective Inhibitor of the ER Resident Chaperone Grp78. J Med Chem 2023; 66:677-694. [PMID: 36516003 DOI: 10.1021/acs.jmedchem.2c01631] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A recent study illustrated that a fluorescence polarization assay can be used to identify substrate-competitive Hsp70 inhibitors that can be isoform-selective. Herein, we use that assay in a moderate-throughput screen and report the discovery of a druglike amino-acid-based inhibitor with reasonable specificity for the endoplasmic reticular Hsp70, Grp78. Using traditional medicinal chemistry approaches, the potency and selectivity were further optimized through structure-activity relationship (SAR) studies in parallel assays for six of the human Hsp70 isoforms. The top compounds were all tested against a panel of cancer cell lines and disappointingly showed little effect. The top-performing compound, 8, was retested using a series of endoplasmic reticulum (ER) stress-inducing agents and found to synergize with these agents. Finally, 8 was tested in a spheroid tumor model and found to be more potent than in two-dimensional models. The optimized Grp78 inhibitors are the first reported isoform-selective small-molecule-competitive inhibitors of an Hsp70-substrate interaction.
Collapse
Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Jared Sivinski
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Christopher J Zerio
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Xiaoyi Zhu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Jack Godek
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Vlad K Kumirov
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona85719, United States
| | - Teresa Coma Brujas
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Joan Torra Garcia
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Anandhan Annadurai
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Cody J Schmidlin
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Alyssa Werner
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Taoda Shi
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Reza Beheshti Zavareh
- Department of Chemistry, The Scripps Research Institute, La Jolla, California92037, United States
| | - Luke Lairson
- Department of Chemistry, The Scripps Research Institute, La Jolla, California92037, United States
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| | - Eli Chapman
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona85721, United States
| |
Collapse
|
21
|
Elfiky AA, Ibrahim IM, Ibrahim MN, Elshemey WM. Host-cell recognition of SARS-CoV-2 spike receptor binding domain from different variants. J Infect 2022; 85:702-769. [PMID: 36220503 PMCID: PMC9547754 DOI: 10.1016/j.jinf.2022.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt,Corresponding author
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Mohamed N Ibrahim
- Clinical Laboratories Department, College of Applied Medical Sciences, Jouf University, Sakakah, Saudi Arabia
| | - Wael M Elshemey
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt,Department of Physics, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
| |
Collapse
|
22
|
Yokoyama T, Fujii S, Ostermann A, Schrader TE, Nabeshima Y, Mizuguchi M. Neutron crystallographic analysis of the nucleotide-binding domain of Hsp72 in complex with ADP. IUCRJ 2022; 9:562-572. [PMID: 36071806 PMCID: PMC9438496 DOI: 10.1107/s2052252522006297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
The 70 kDa heat-shock proteins (Hsp70s) are ATP-dependent molecular chaperones that contain an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain. Hsp70s bind to misfolded/unfolded proteins and thereby prevent their aggregation. The ATP hydrolysis reaction in the NBD plays a key role in allosteric control of the binding of substrate proteins. In the present study, the neutron crystal structure of the NBD of Hsp72, a heat-inducible Hsp70 family member, was solved in complex with ADP in order to study the structure-function relationship with a focus on hydrogens. ADP bound to Hsp72 was fully deprotonated, and the catalytically important residues, including Asp10, Asp199 and Asp206, are also deprotonated. Neutron analysis also enabled the characterization of the water clusters in the NBD. Enzymatic assays and X-ray crystallographic analysis revealed that the Y149A mutation exhibited a higher ATPase activity and caused disruption of the water cluster and incorporation of an additional magnesium ion. Tyr149 was suggested to contribute to the low intrinsic ATPase activity and to stabilize the water cluster. Collectively, these structural studies will help to elucidate the molecular basis of the function of Hsp72.
Collapse
Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugkitani, Toyama 930-0914, Japan
| | - Shiho Fujii
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugkitani, Toyama 930-0914, Japan
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universtät München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Tobias E. Schrader
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugkitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugkitani, Toyama 930-0914, Japan
| |
Collapse
|
23
|
Elfiky AA, Ibrahim IM, Elgohary AM. SARS-CoV-2 Delta Variant is Recognized Through GRP78 Host-Cell Surface Receptor, In Silico Perspective. Int J Pept Res Ther 2022; 28:146. [PMID: 36034049 PMCID: PMC9395890 DOI: 10.1007/s10989-022-10450-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2022] [Indexed: 12/30/2022]
Abstract
Different SARS-CoV-2 new variants emerged and spread during the past few months, sparking infections and death counts. The new variant B.1.617 (delta variant) sparked in India in the past few months, causing the highest records. The B.1.617 variant of SARS-CoV-2 has the double mutations E484Q and L452R on its spike Receptor Binding Domain (RBD). The first mutation is like the reported South African and the Brazilian variants (501.V2 and B.1.1.248). This mutation lies in the region C480-C488, which we predicted before to be recognized by the host-cell receptor; Glucose Regulated Protein 78 (GRP78). In the current study, we test the binding affinity of the host-cell receptor GRP78 to the delta variant spike RBD using molecular docking and molecular dynamics simulations of up to 100 ns. Additionally, the ACE2-RBD is tested by protein–protein docking. The results reveal equal average binding affinities of the GRP78 against wildtype and delta variant spikes. This supports our previous predictions of the contribution of GRP78 in SARS-CoV-2 spike recognition as an auxiliary route for entry.
Collapse
Affiliation(s)
- Abdo A. Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Ibrahim M. Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Alaa M. Elgohary
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| |
Collapse
|
24
|
Iraci N, Corsaro C, Giofrè SV, Neri G, Mezzasalma AM, Vacalebre M, Speciale A, Saija A, Cimino F, Fazio E. Nanoscale Technologies in the Fight against COVID-19: From Innovative Nanomaterials to Computer-Aided Discovery of Potential Antiviral Plant-Derived Drugs. Biomolecules 2022; 12:1060. [PMID: 36008954 PMCID: PMC9405735 DOI: 10.3390/biom12081060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
The last few years have increasingly emphasized the need to develop new active antiviral products obtained from artificial synthesis processes using nanomaterials, but also derived from natural matrices. At the same time, advanced computational approaches have found themselves fundamental in the repurposing of active therapeutics or for reducing the very long developing phases of new drugs discovery, which represents a real limitation, especially in the case of pandemics. The first part of the review is focused on the most innovative nanomaterials promising both in the field of therapeutic agents, as well as measures to control virus spread (i.e., innovative antiviral textiles). The second part of the review aims to show how computer-aided technologies can allow us to identify, in a rapid and therefore constantly updated way, plant-derived molecules (i.e., those included in terpenoids) potentially able to efficiently interact with SARS-CoV-2 cell penetration pathways.
Collapse
Affiliation(s)
- Nunzio Iraci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy; (N.I.); (S.V.G.); (G.N.); (A.S.); (A.S.)
| | - Carmelo Corsaro
- Department of Mathematical and Computational Sciences, Physics Science and Earth Science, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy; (A.M.M.); (M.V.); (E.F.)
| | - Salvatore V. Giofrè
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy; (N.I.); (S.V.G.); (G.N.); (A.S.); (A.S.)
| | - Giulia Neri
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy; (N.I.); (S.V.G.); (G.N.); (A.S.); (A.S.)
| | - Angela Maria Mezzasalma
- Department of Mathematical and Computational Sciences, Physics Science and Earth Science, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy; (A.M.M.); (M.V.); (E.F.)
| | - Martina Vacalebre
- Department of Mathematical and Computational Sciences, Physics Science and Earth Science, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy; (A.M.M.); (M.V.); (E.F.)
| | - Antonio Speciale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy; (N.I.); (S.V.G.); (G.N.); (A.S.); (A.S.)
| | - Antonina Saija
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy; (N.I.); (S.V.G.); (G.N.); (A.S.); (A.S.)
| | - Francesco Cimino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy; (N.I.); (S.V.G.); (G.N.); (A.S.); (A.S.)
| | - Enza Fazio
- Department of Mathematical and Computational Sciences, Physics Science and Earth Science, University of Messina, Viale F. Stagno D’Alcontres 31, I-98166 Messina, Italy; (A.M.M.); (M.V.); (E.F.)
| |
Collapse
|
25
|
Amankwah YS, Collins P, Fleifil Y, Unruh E, Ruiz Márquez KJ, Vitou K, Kravats AN. Grp94 works upstream of BiP in protein remodeling under heat stress. J Mol Biol 2022; 434:167762. [PMID: 35905823 DOI: 10.1016/j.jmb.2022.167762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/28/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
Abstract
Hsp90 and Hsp70 are highly conserved molecular chaperones that promote the proper folding and activation of substrate proteins that are often referred to as clients. The two chaperones functionally collaborate to fold specific clients in an ATP-dependent manner. In eukaryotic cytosol, initial client folding is done by Hsp70 and its co-chaperones, followed by a direct transfer of client refolding intermediates to Hsp90 for final client processing. However, the mechanistic details of collaboration of organelle specific Hsp70 and Hsp90 are lacking. This work investigates the collaboration of the endoplasmic reticulum (ER) Hsp70 and Hsp90, BiP and Grp94 respectively, in protein remodeling using in vitro refolding assays. We show that under milder denaturation conditions, BiP collaborates with its co-chaperones to refold misfolded proteins in an ATP-dependent manner. Grp94 does not play a major role in this refolding reaction. However, under stronger denaturation conditions that favor aggregation, Grp94 works in an ATP-independent manner to bind and hold misfolded clients in a folding competent state for subsequent remodeling by the BiP system. We also show that the collaboration of Grp94 and BiP is not simply a reversal of the eukaryotic refolding mechanism since a direct interaction of Grp94 and BiP is not required for client transfer. Instead, ATP binding but not hydrolysis by Grp94 facilitates the release of the bound client, which is then picked up by the BiP system for subsequent refolding in a Grp94-independent manner.
Collapse
Affiliation(s)
- Yaa S Amankwah
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - Preston Collins
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - Yasmeen Fleifil
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - Erin Unruh
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | | | - Katherine Vitou
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - Andrea N Kravats
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056.
| |
Collapse
|
26
|
Xu H. Non-Equilibrium Protein Folding and Activation by ATP-Driven Chaperones. Biomolecules 2022; 12:biom12060832. [PMID: 35740957 PMCID: PMC9221429 DOI: 10.3390/biom12060832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/14/2022] Open
Abstract
Recent experimental studies suggest that ATP-driven molecular chaperones can stabilize protein substrates in their native structures out of thermal equilibrium. The mechanism of such non-equilibrium protein folding is an open question. Based on available structural and biochemical evidence, I propose here a unifying principle that underlies the conversion of chemical energy from ATP hydrolysis to the conformational free energy associated with protein folding and activation. I demonstrate that non-equilibrium folding requires the chaperones to break at least one of four symmetry conditions. The Hsp70 and Hsp90 chaperones each break a different subset of these symmetries and thus they use different mechanisms for non-equilibrium protein folding. I derive an upper bound on the non-equilibrium elevation of the native concentration, which implies that non-equilibrium folding only occurs in slow-folding proteins that adopt an unstable intermediate conformation in binding to ATP-driven chaperones. Contrary to the long-held view of Anfinsen’s hypothesis that proteins fold to their conformational free energy minima, my results predict that some proteins may fold into thermodynamically unstable native structures with the assistance of ATP-driven chaperones, and that the native structures of some chaperone-dependent proteins may be shaped by their chaperone-mediated folding pathways.
Collapse
Affiliation(s)
- Huafeng Xu
- Roivant Sciences, New York, NY 10036, USA
| |
Collapse
|
27
|
Elshemey WM, Elfiky AA, Ibrahim IM, Elgohary AM. Interference of Chaga mushroom terpenoids with the attachment of SARS-CoV-2; in silico perspective. Comput Biol Med 2022; 145:105478. [PMID: 35421790 PMCID: PMC8988443 DOI: 10.1016/j.compbiomed.2022.105478] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023]
Abstract
Finding a potent inhibitor to the pandemic SARS-CoV-2 is indispensable nowadays. Currently, in-silico methods work as expeditious investigators to screen drugs for possible repurposing or design new ones. Targeting one of the possible SARS-CoV-2 attachment and entry receptors, Glucose-regulated protein 78 (GRP78), is an approach of major interest. Recently, GRP78 was reported as a recognized representative in recognition of the latest variants of SARS-CoV-2. In this work, molecular docking and molecular dynamics simulations were performed on the host cell receptor GRP78. With its many terpenoid compounds, Chaga mushroom was tested as a potential therapeutic against the SARS-CoV-2 receptor, GRP78. Results revealed low binding energies (high affinities) toward the GRP78 substrate-binding domain β (SBDβ) of Chaga mushroom terpenoids. Even the highly specific cyclic peptide Pep42, which selectively targeted GRP78 over cancer cells in vivo, showed lower binding affinity against GRP78 SBDβ compared to the binding affinities of terpenoids. These are auspicious results that need to be tested experimentally. Intriguingly, terpenoids work as a double sword as they can be used to interfere with VUI 202,012/01, 501.V2, and B.1.1.248 variants of SARS-CoV-2 spike recognition.
Collapse
Affiliation(s)
- Wael M. Elshemey
- Physics Department, Faculty of Science, Islamic University of Madinah, Madinah, Saudi Arabia,Corresponding author
| | - Abdo A. Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Ibrahim M. Ibrahim
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Alaa M. Elgohary
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| |
Collapse
|
28
|
Shen J, Wang L, Wang X, Xie J, Yao T, Yu Y, Wang Q, Ding Z, Zhang J, Zhang M, Xu L. Cypermethrin induces apoptosis of Sertoli cells through the endoplasmic reticulum pathway. Toxicol Ind Health 2022; 38:399-407. [PMID: 35610186 DOI: 10.1177/07482337221104905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Cypermethrin, an extensively used pyrethroid pesticide, is regarded as one of many endocrine-disrupting chemicals (EDCs) with anti-androgenic activity to damage male reproductive systems. We previously found cypermethrin-induced apoptosis in mouse Sertoli cells TM4. We hypothesized cypermethrin-induced TM4 apoptosis by the endoplasmic reticulum (ER) pathway. This study aimed to explore the roles of the ER pathway in cypermethrin-induced apoptosis in TM4 cells. The cells were treated with cypermethrin for 24 h at various concentrations (0 µM, 10 µM, 20 µM, 40 µM, and 80 µM). Flow cytometry was used to test for apoptosis. Western blot was used to test protein expressions in the ER stress pathway. The results showed that the apoptosis rate of TM4 cells increased with increased concentrations of cypermethrin, and a significant difference was detected in the 80-μM group. The protein expressions of glucose-regulated protein 78 (GRP78), protein kinase R (PKR)-like ER kinase (PERK), p-PERK, α subunit of eukaryotic initiation factor (eIF2α), p-eIF2α, activating transcription factor 4 (ATF4), C/EBP homologous protein (CHOP), caspase-12, caspase-9, and caspase-3 increased with increased concentrations of cypermethrin . The results suggested cypermethrin-induced apoptosis in TM4 cells regulated by the ER pathway involving PERK-eIF2α-ATF4-CHOP. The study provides a new insight into cypermethrin-induced apoptosis in Sertoli cells.
Collapse
Affiliation(s)
- Junyu Shen
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| | - Lushan Wang
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| | - Xuxu Wang
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| | - Jiafei Xie
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| | - Tingting Yao
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| | - Yue Yu
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| | - Qi Wang
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| | - Zhen Ding
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| | - Jinpeng Zhang
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| | - Meirong Zhang
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| | - Lichun Xu
- Key Lab of Environment and Health, Key Laboratory of Human Genetics and Environmental Medicine, School of Public Health, 38044Xuzhou Medical University, Xuzhou, China
| |
Collapse
|
29
|
Deans EE, Kotler JLM, Wei WS, Street TO. Electrostatics drive the molecular chaperone BiP to preferentially bind oligomerized states of a client protein. J Mol Biol 2022; 434:167638. [PMID: 35597552 DOI: 10.1016/j.jmb.2022.167638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/26/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
Abstract
Hsp70 chaperones bind short monomeric peptides with a weak characteristic affinity in the low micromolar range, but can also bind some aggregates, fibrils, and amyloids, with low nanomolar affinity. While this differential affinity enables Hsp70 to preferentially target potentially toxic aggregates, it is unknown how a chaperone can differentiate between monomeric and aggregated states of a client protein and why preferential binding is only observed for some aggregated clients but not others. Here we examine the interaction of BiP (the Hsp70 paralog in the endoplasmic reticulum) with the client proIGF2, the pro-protein form of IGF2 that includes a long and mostly disordered E-peptide region that promotes proIGF2 oligomerization. By dissecting the mechanism by which BiP targets proIGF2 and E-peptide oligomers we discover that electrostatic attraction is a powerful driving force for oligomer recognition. We identify the specific BiP binding sites on proIGF2 and as monomers they bind BiP with characteristically weak affinity in the low micromolar range, but electrostatic attraction to E-peptide oligomers boosts the affinity to the low nanomolar level. The dominant role of electrostatics is manifested kinetically as a steering force that accelerates the binding of BiP to E-peptide oligomers by approximately two orders of magnitude as compared against monomeric peptides. Electrostatic targeting of Hsp70 provides an explanation for why preferential binding has been observed for some aggregated clients but not others, as all the currently-documented cases in which Hsp70 binds aggregates with high-affinity involve clients that have an opposite charge to Hsp70.
Collapse
Affiliation(s)
- Erin E Deans
- Departments of Biochemistry, Brandeis University, Waltham, Massachusetts 02453
| | - Judy L M Kotler
- Departments of Biochemistry, Brandeis University, Waltham, Massachusetts 02453
| | - Wei-Shao Wei
- Departments of Physics, Brandeis University, Waltham, Massachusetts 02453
| | - Timothy O Street
- Departments of Biochemistry, Brandeis University, Waltham, Massachusetts 02453
| |
Collapse
|
30
|
Lebeau PF, Byun JH, Platko K, Saliba P, Sguazzin M, MacDonald ME, Paré G, Steinberg GR, Janssen LJ, Igdoura SA, Tarnopolsky MA, Wayne Chen SR, Seidah NG, Magolan J, Austin RC. Caffeine blocks SREBP2-induced hepatic PCSK9 expression to enhance LDLR-mediated cholesterol clearance. Nat Commun 2022; 13:770. [PMID: 35140212 PMCID: PMC8828868 DOI: 10.1038/s41467-022-28240-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/05/2022] [Indexed: 01/06/2023] Open
Abstract
Evidence suggests that caffeine (CF) reduces cardiovascular disease (CVD) risk. However, the mechanism by which this occurs has not yet been uncovered. Here, we investigated the effect of CF on the expression of two bona fide regulators of circulating low-density lipoprotein cholesterol (LDLc) levels; the proprotein convertase subtilisin/kexin type 9 (PCSK9) and the low-density lipoprotein receptor (LDLR). Following the observation that CF reduced circulating PCSK9 levels and increased hepatic LDLR expression, additional CF-derived analogs with increased potency for PCSK9 inhibition compared to CF itself were developed. The PCSK9-lowering effect of CF was subsequently confirmed in a cohort of healthy volunteers. Mechanistically, we demonstrate that CF increases hepatic endoplasmic reticulum (ER) Ca2+ levels to block transcriptional activation of the sterol regulatory element-binding protein 2 (SREBP2) responsible for the regulation of PCSK9, thereby increasing the expression of the LDLR and clearance of LDLc. Our findings highlight ER Ca2+ as a master regulator of cholesterol metabolism and identify a mechanism by which CF may protect against CVD.
Collapse
Affiliation(s)
- Paul F Lebeau
- Department of Medicine, Division of Nephrology, McMaster University, The Research Institute of St. Joe's Hamilton and the Hamilton Center for Kidney Research, Hamilton, ON, L8N 4A6, Canada
| | - Jae Hyun Byun
- Department of Medicine, Division of Nephrology, McMaster University, The Research Institute of St. Joe's Hamilton and the Hamilton Center for Kidney Research, Hamilton, ON, L8N 4A6, Canada
| | - Khrystyna Platko
- Department of Medicine, Division of Nephrology, McMaster University, The Research Institute of St. Joe's Hamilton and the Hamilton Center for Kidney Research, Hamilton, ON, L8N 4A6, Canada
| | - Paul Saliba
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Matthew Sguazzin
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Melissa E MacDonald
- Department of Medicine, Division of Nephrology, McMaster University, The Research Institute of St. Joe's Hamilton and the Hamilton Center for Kidney Research, Hamilton, ON, L8N 4A6, Canada
| | - Guillaume Paré
- Population Health Research Institute, McMaster University, Hamilton, ON, L8L 2X2, Canada.,The Departments of Medicine, Epidemiology and Pathology, McMaster University, Hamilton, ON, L8L 2X2, Canada.,The Thrombosis and Atherosclerosis Research Institute (TaARI), Department of Medicine, David Braley Research Institute, McMaster University, Hamilton, L8L 2X2, Canada
| | - Gregory R Steinberg
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada.,Centre for Metabolism, Obesity and Diabetes Research, Department of Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Luke J Janssen
- Firestone Institute for Respiratory Health, St. Joseph's Hospital, Hamilton, ON, L8S 4K1, Canada
| | - Suleiman A Igdoura
- Department of Biology and Pathology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Mark A Tarnopolsky
- Department of Medicine/Neurology, McMaster University, Hamilton, ON, L8N 3Z5, Canada.,Department of Pediatrics, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - S R Wayne Chen
- Libin Cardiovascular Institute of Alberta, Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, T2N 2T9, Canada
| | - Nabil G Seidah
- Laboratory of Biochemical Neuroendocrinology, Clinical Research Institute of Montreal, affiliated to the University of Montreal, Montreal, QC, H2W 1R7, Canada
| | - Jakob Magolan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Richard C Austin
- Department of Medicine, Division of Nephrology, McMaster University, The Research Institute of St. Joe's Hamilton and the Hamilton Center for Kidney Research, Hamilton, ON, L8N 4A6, Canada. .,The Thrombosis and Atherosclerosis Research Institute (TaARI), Department of Medicine, David Braley Research Institute, McMaster University, Hamilton, L8L 2X2, Canada.
| |
Collapse
|
31
|
The endoplasmic reticulum chaperone BiP is a closure-accelerating cochaperone of Grp94. Proc Natl Acad Sci U S A 2022; 119:2118793119. [PMID: 35078937 PMCID: PMC8812556 DOI: 10.1073/pnas.2118793119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2021] [Indexed: 01/19/2023] Open
Abstract
The endoplasmic reticulum (ER) is the site at which secreted proteins (such as the hormone insulin) and membrane-bound proteins are folded. ATP-dependent chaperones within the ER help proteins fold. This study describes how two key ER chaperones, BiP and Grp94, work together at a molecular level. BiP binds to Grp94, which enables Grp94 to change conformation and hydrolyze ATP. In short, BiP provides a signal to switch on Grp94 conformational changes that are required to help other proteins fold. This finding helps explain how two chaperones can work together collaboratively in protein folding. Because BiP and Grp94 are members of highly conserved chaperone families, these findings may provide insight into chaperone-assisted protein folding beyond the ER. Hsp70 and Hsp90 chaperones provide protein quality control to the cytoplasm, endoplasmic reticulum (ER), and mitochondria. Hsp90 activity is often enhanced by cochaperones that drive conformational changes needed for ATP-dependent closure and capture of client proteins. Hsp90 activity is also enhanced when working with Hsp70, but, in this case, the underlying mechanistic explanation is poorly understood. Here we examine the ER-specific Hsp70/Hsp90 paralogs (BiP/Grp94) and discover that BiP itself acts as a cochaperone that accelerates Grp94 closure. The BiP nucleotide binding domain, which interacts with the Grp94 middle domain, is responsible for Grp94 closure acceleration. A client protein initiates a coordinated progression of steps for the BiP/Grp94 system, in which client binding to BiP causes a conformational change that enables BiP to bind to Grp94 and accelerate its ATP-dependent closure. Single-molecule fluorescence resonance energy transfer measurements show that BiP accelerates Grp94 closure by stabilizing a high-energy conformational intermediate that otherwise acts as an energetic barrier to closure. These findings provide an explanation for enhanced activity of BiP and Grp94 when working as a pair, and demonstrate the importance of a high-energy conformational state in controlling the timing of the Grp94 conformational cycle. Given the high conservation of the Hsp70/Hsp90 system, other Hsp70s may also serve dual roles as both chaperones and closure-accelerating cochaperones to their Hsp90 counterparts.
Collapse
|
32
|
Ghasemitarei M, Privat-Maldonado A, Yusupov M, Rahnama S, Bogaerts A, Ejtehadi MR. Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations. J Chem Inf Model 2022; 62:129-141. [PMID: 34965734 PMCID: PMC8751020 DOI: 10.1021/acs.jcim.1c00853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 12/15/2022]
Abstract
Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.
Collapse
Affiliation(s)
- Maryam Ghasemitarei
- Department
of Physics, Sharif University of Technology, Tehran 14588-89694, Iran
- Research
Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Angela Privat-Maldonado
- Research
Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Maksudbek Yusupov
- Research
Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
- Laboratory
of Thermal Physics of Multiphase Systems, Arifov Institute of Ion-Plasma
and Laser Technologies, Academy of Sciences
of Uzbekistan, Durmon
yuli str. 33, 100125 Tashkent, Uzbekistan
| | - Shadi Rahnama
- Institute
for Nanoscience & Nanotechnology (INST), Sharif University of Technology, Azadi Avenue, Tehran 14588-89694, Iran
| | - Annemie Bogaerts
- Research
Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | | |
Collapse
|
33
|
Ghosh D, Dey S, Chakraborty H, Mukherjee S, Halder A, Sarkar A, Chakraborty P, Ghosh R, Sarkar J. Mucormycosis: A new threat to Coronavirus disease 2019 with special emphasis on India. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2022; 15:101013. [PMID: 35342843 PMCID: PMC8934183 DOI: 10.1016/j.cegh.2022.101013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/10/2021] [Accepted: 03/10/2022] [Indexed: 01/03/2023] Open
Abstract
The main reason for the growth of mucormycosis in people with Coronavirus disease-2019 (COVID-19) is mainly produced by Rhizopus spp. The infective mechanisms and issues recognized in Rhizopus spp. are the cell wall, germination proteins, and enzymes assisted to iron sequestration, CotH protein, and positive regulation of the GRP78 cell receptor. Mucormycosis is mainly caused by the Rhizopus spp. such as R. oryzae, R. microsporus, R. arrhizus, R. homothallicus, etc. that are gifted to numerous host defense mechanisms and attribute to the endothelium via specific receptors, GRP78 simplifying their endocytosis and angio-invasion. Factors such as hyperglycemia, elevated iron concentrations, and ketoacidosis have been shown to contribute to the pathogenesis in the tentative situation. The analytical data of 'black fungus disease' or 'mucormycosis', specify India reported for about 42.3% of published cases, followed by the USA about 16.9%, Iraq, Bangladesh, Iran, Paraguay, and 1 case each from Brazil, Mexico, Italy, UK, China, France, Uruguay, Turkey, and Austria. The COVID-19 infection is maybe a predisposing factor for mucormycosis and is related to a high mortality rate. Early recognition and restriction of hyperglycemia, liposomal amphotericin B, and surgical debridement are the bases in the successful managing of mucormycosis.
Collapse
Affiliation(s)
- Deganta Ghosh
- Department of Botany, Dinabandhu Andrews College, Garia, Kolkata, West Bengal, India, 700084
| | - Sagardeep Dey
- Department of Botany, Dinabandhu Andrews College, Garia, Kolkata, West Bengal, India, 700084
| | - Himanko Chakraborty
- Department of Botany, Dinabandhu Andrews College, Garia, Kolkata, West Bengal, India, 700084
| | - Sneha Mukherjee
- Department of Botany, Dinabandhu Andrews College, Garia, Kolkata, West Bengal, India, 700084
| | - Ankita Halder
- Department of Botany, Dinabandhu Andrews College, Garia, Kolkata, West Bengal, India, 700084
| | - Akash Sarkar
- Department of Botany, Dinabandhu Andrews College, Garia, Kolkata, West Bengal, India, 700084
| | - Pallab Chakraborty
- Department of Botany, Acharya Prafulla Chandra College, New Barrakpur, Kolkata, West Bengal, India, 700131
| | - Rajdeep Ghosh
- GSL Medical College and General Hospital, Rajahmundry, Andhra Pradesh, India, 533296
| | - Joy Sarkar
- Department of Botany, Dinabandhu Andrews College, Garia, Kolkata, West Bengal, India, 700084,Corresponding author
| |
Collapse
|
34
|
Li H, Musayev FN, Yang J, Su J, Liu Q, Wang W, Fang X, Zhou L, Liu Q. A novel and unique ATP hydrolysis to AMP by a human Hsp70 Binding immunoglobin protein (BiP). Protein Sci 2021; 31:797-810. [PMID: 34941000 DOI: 10.1002/pro.4267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 11/07/2022]
Abstract
Hsp70s are ubiquitous and highly conserved molecular chaperones. They play crucial roles in maintaining cellular protein homeostasis. It is well established that Hsp70s use the energy of ATP hydrolysis to ADP to power the chaperone activity regardless of the cellular locations and isoforms. Binding immunoglobin protein (BiP), the major member of Hsp70s in the endoplasmic reticulum, is essential for protein folding and quality control. Unexpectedly, our structural analysis of BiP demonstrated a novel ATP hydrolysis to AMP during crystallization under the acidic conditions. Our biochemical studies confirmed this newly discovered ATP to AMP hydrolysis in solutions. Unlike the canonical ATP to ADP hydrolysis observed for Hsp70s, this ATP hydrolysis to AMP depends on the substrate-binding domain of BiP and is inhibited by the binding of a peptide substrate. Intriguingly, this ATP to AMP hydrolysis is unique to BiP, not shared by two representative Hsp70 proteins from the cytosol. Taken together, this novel and unique ATP to AMP hydrolysis may provide a potentially new direction for understanding the activity and cellular function of BiP.
Collapse
Affiliation(s)
- Hongtao Li
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Faik N Musayev
- Department of Medicinal Chemistry, The Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jiao Yang
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jiayue Su
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Qingdai Liu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Wei Wang
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Xianjun Fang
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Lei Zhou
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Qinglian Liu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| |
Collapse
|
35
|
Calvaresi V, Truelsen LT, Larsen SB, Petersen NHT, Kirkegaard T, Rand KD. Conformational dynamics of free and membrane-bound human Hsp70 in model cytosolic and endo-lysosomal environments. Commun Biol 2021; 4:1369. [PMID: 34876699 PMCID: PMC8651726 DOI: 10.1038/s42003-021-02892-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 11/10/2021] [Indexed: 11/21/2022] Open
Abstract
The binding of the major stress-inducible human 70-kDa heat shock protein (Hsp70) to the anionic phospholipid bis-(monoacylglycero)-phosphate (BMP) in the lysosomal membrane is crucial for its impact on cellular pathology in lysosomal storage disorders. However, the conformational features of this protein-lipid complex remain unclear. Here, we apply hydrogen-deuterium exchange mass spectrometry (HDX-MS) to describe the dynamics of the full-length Hsp70 in the cytosol and its conformational changes upon translocation into lysosomes. Using wild-type and W90F mutant proteins, we also map and discriminate the interaction of Hsp70 with BMP and other lipid components of the lysosomal membrane. We identify the N-terminal of the nucleotide binding domain (residues 87-118) as the primary orchestrator of BMP interaction. We show that the conformation of this domain is significantly reorganized in the W90F mutant, explaining its inability to stabilize lysosomal membranes. Overall, our results reveal important new molecular details of the protective effect of Hsp70 in lysosomal storage diseases, which, in turn, could guide future drug development.
Collapse
Affiliation(s)
- Valeria Calvaresi
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Line T. Truelsen
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Sidsel B. Larsen
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | | | | | - Kasper D. Rand
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| |
Collapse
|
36
|
Wang W, Liu Q, Liu Q, Hendrickson WA. Conformational equilibria in allosteric control of Hsp70 chaperones. Mol Cell 2021; 81:3919-3933.e7. [PMID: 34453889 DOI: 10.1016/j.molcel.2021.07.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/04/2021] [Accepted: 07/28/2021] [Indexed: 01/16/2023]
Abstract
Heat-shock proteins of 70 kDa (Hsp70s) are vital for all life and are notably important in protein folding. Hsp70s use ATP binding and hydrolysis at a nucleotide-binding domain (NBD) to control the binding and release of client polypeptides at a substrate-binding domain (SBD); however, the mechanistic basis for this allostery has been elusive. Here, we first characterize biochemical properties of selected domain-interface mutants in bacterial Hsp70 DnaK. We then develop a theoretical model for allosteric equilibria among Hsp70 conformational states to explain the observations: a restraining state, Hsp70R-ATP, restricts ATP hydrolysis and binds peptides poorly, whereas a stimulating state, Hsp70S-ATP, hydrolyzes ATP rapidly and has high intrinsic substrate affinity but rapid binding kinetics. We support this model for allosteric regulation with DnaK structures obtained in the postulated stimulating state S with biochemical tests of the S-state interface and with improved peptide-binding-site definition in an R-state structure.
Collapse
Affiliation(s)
- Wei Wang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Qinglian Liu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
37
|
Fernandez RA, Quimque MT, Notarte KI, Manzano JA, Pilapil DY, de Leon VN, San Jose JJ, Villalobos O, Muralidharan NH, Gromiha MM, Brogi S, Macabeo APG. Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. J Biomol Struct Dyn 2021; 40:12209-12220. [PMID: 34463219 PMCID: PMC8436362 DOI: 10.1080/07391102.2021.1969281] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/12/2021] [Indexed: 12/24/2022]
Abstract
The severity of the COVID-19 pandemic has necessitated the search for drugs against SARS-CoV-2. In this study, we explored via in silico approaches myxobacterial secondary metabolites against various receptor-binding regions of SARS-CoV-2 spike which are responsible in recognition and attachment to host cell receptors mechanisms, namely ACE2, GRP78, and NRP1. In general, cyclic depsipeptide chondramides conferred high affinities toward the spike RBD, showing strong binding to the known viral hot spots Arg403, Gln493 and Gln498 and better selectivity compared to most host cell receptors studied. Among them, chondramide C3 (1) exhibited a binding energy which remained relatively constant when docked against most of the spike variants. Chondramide C (2) on the other hand exhibited strong affinity against spike variants identified in the United Kingdom (N501Y), South Africa (N501Y, E484K, K417N) and Brazil (N501Y, E484K, K417T). Chondramide C6 (9) showed highest BE towards GRP78 RBD. Molecular dynamics simulations were also performed for chondramides 1 and 2 against SARS-CoV-2 spike RBD of the Wuhan wild-type and the South African variant, respectively, where resulting complexes demonstrated dynamic stability within a 120-ns simulation time. Protein-protein binding experiments using HADDOCK illustrated weaker binding affinity for complexed chondramide ligands in the RBD against the studied host cell receptors. The chondramide derivatives in general possessed favorable pharmacokinetic properties, highlighting their potential as prototypic anti-COVID-19 drugs limiting viral attachment and possibly minimizing viral infection.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Rey Arturo Fernandez
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Mark Tristan Quimque
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Chemistry Department, College of Science and Mathematics, Mindanao State University – Iligan Institute of Technology, Tibanga, Iligan City, Philippines
| | - Kin Israel Notarte
- Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines
| | - Joe Anthony Manzano
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Delfin Yñigo Pilapil
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Von Novi de Leon
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - John Jeric San Jose
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Omar Villalobos
- Department of Pharmacy, Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Nisha Harur Muralidharan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Allan Patrick G. Macabeo
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| |
Collapse
|
38
|
Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD. Nat Commun 2021; 12:5004. [PMID: 34408154 PMCID: PMC8373988 DOI: 10.1038/s41467-021-25076-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/15/2021] [Indexed: 12/22/2022] Open
Abstract
The endoplasmic reticulum (ER) Hsp70 chaperone BiP is regulated by AMPylation, a reversible inactivating post-translational modification. Both BiP AMPylation and deAMPylation are catalysed by a single ER-localised enzyme, FICD. Here we present crystallographic and solution structures of a deAMPylation Michaelis complex formed between mammalian AMPylated BiP and FICD. The latter, via its tetratricopeptide repeat domain, binds a surface that is specific to ATP-state Hsp70 chaperones, explaining the exquisite selectivity of FICD for BiP’s ATP-bound conformation both when AMPylating and deAMPylating Thr518. The eukaryotic deAMPylation mechanism thus revealed, rationalises the role of the conserved Fic domain Glu234 as a gatekeeper residue that both inhibits AMPylation and facilitates hydrolytic deAMPylation catalysed by dimeric FICD. These findings point to a monomerisation-induced increase in Glu234 flexibility as the basis of an oligomeric state-dependent switch between FICD’s antagonistic activities, despite a similar mode of engagement of its two substrates — unmodified and AMPylated BiP. The ER chaperone BiP is regulated by FICD-mediated AMPylation and deAMPylation. Here, the authors characterise the structure of mammalian AMPylated BiP bound to FICD, by X-ray crystallography and neutron scattering, providing insights into the mechanism of BiP AMPylation and deAMPylation.
Collapse
|
39
|
Li H, Hu L, Cuffee CW, Mohamed M, Li Q, Liu Q, Zhou L, Liu Q. Interdomain interactions dictate the function of the Candida albicans Hsp110 protein Msi3. J Biol Chem 2021; 297:101082. [PMID: 34403698 PMCID: PMC8424595 DOI: 10.1016/j.jbc.2021.101082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/29/2021] [Accepted: 08/13/2021] [Indexed: 01/27/2023] Open
Abstract
Heat shock proteins of 110 kDa (Hsp110s), a unique class of molecular chaperones, are essential for maintaining protein homeostasis. Hsp110s exhibit a strong chaperone activity preventing protein aggregation (the "holdase" activity) and also function as the major nucleotide-exchange factor (NEF) for Hsp70 chaperones. Hsp110s contain two functional domains: a nucleotide-binding domain (NBD) and substrate-binding domain (SBD). ATP binding is essential for Hsp110 function and results in close contacts between the NBD and SBD. However, the molecular mechanism of this ATP-induced allosteric coupling remains poorly defined. In this study, we carried out biochemical analysis on Msi3, the sole Hsp110 in Candida albicans, to dissect the unique allosteric coupling of Hsp110s using three mutations affecting the domain-domain interface. All the mutations abolished both the in vivo and in vitro functions of Msi3. While the ATP-bound state was disrupted in all mutants, only mutation of the NBD-SBDβ interfaces showed significant ATPase activity, suggesting that the full-length Hsp110s have an ATPase that is mainly suppressed by NBD-SBDβ contacts. Moreover, the high-affinity ATP-binding unexpectedly appears to require these NBD-SBD contacts. Remarkably, the "holdase" activity was largely intact for all mutants tested while NEF activity was mostly compromised, although both activities strictly depended on the ATP-bound state, indicating different requirements for these two activities. Stable peptide substrate binding to Msi3 led to dissociation of the NBD-SBD contacts and compromised interactions with Hsp70. Taken together, our data demonstrate that the exceptionally strong NBD-SBD contacts in Hsp110s dictate the unique allosteric coupling and biochemical activities.
Collapse
Affiliation(s)
- Hongtao Li
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Liqing Hu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA,Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Crist William Cuffee
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Mahetab Mohamed
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Qianbin Li
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Qingdai Liu
- Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
| | - Lei Zhou
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Qinglian Liu
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia, USA,For correspondence: Qinglian Liu
| |
Collapse
|
40
|
Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET. Proc Natl Acad Sci U S A 2021; 118:2025578118. [PMID: 34389669 DOI: 10.1073/pnas.2025578118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cellular function depends on the correct folding of proteins inside the cell. Heat-shock proteins 70 (Hsp70s), being among the first molecular chaperones binding to nascently translated proteins, aid in protein folding and transport. They undergo large, coordinated intra- and interdomain structural rearrangements mediated by allosteric interactions. Here, we applied a three-color single-molecule Förster resonance energy transfer (FRET) combined with three-color photon distribution analysis to compare the conformational cycle of the Hsp70 chaperones DnaK, Ssc1, and BiP. By capturing three distances simultaneously, we can identify coordinated structural changes during the functional cycle. Besides the known conformations of the Hsp70s with docked domains and open lid and undocked domains with closed lid, we observed additional intermediate conformations and distance broadening, suggesting flexibility of the Hsp70s in adopting the states in a coordinated fashion. Interestingly, the difference of this distance broadening varied between DnaK, Ssc1, and BiP. Study of their conformational cycle in the presence of substrate peptide and nucleotide exchange factors strengthened the observation of additional conformational intermediates, with BiP showing coordinated changes more clearly compared to DnaK and Ssc1. Additionally, DnaK and BiP were found to differ in their selectivity for nucleotide analogs, suggesting variability in the recognition mechanism of their nucleotide-binding domains for the different nucleotides. By using three-color FRET, we overcome the limitations of the usual single-distance approach in single-molecule FRET, allowing us to characterize the conformational space of proteins in higher detail.
Collapse
|
41
|
Sanyal A, Zbornik EA, Watson BG, Christoffer C, Ma J, Kihara D, Mattoo S. Kinetic and structural parameters governing Fic-mediated adenylylation/AMPylation of the Hsp70 chaperone, BiP/GRP78. Cell Stress Chaperones 2021; 26:639-656. [PMID: 33942205 PMCID: PMC8275707 DOI: 10.1007/s12192-021-01208-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
Abstract
Fic (filamentation induced by cAMP) proteins regulate diverse cell signaling events by post-translationally modifying their protein targets, predominantly by the addition of an AMP (adenosine monophosphate). This modification is called Fic-mediated adenylylation or AMPylation. We previously reported that the human Fic protein, HYPE/FicD, is a novel regulator of the unfolded protein response (UPR) that maintains homeostasis in the endoplasmic reticulum (ER) in response to stress from misfolded proteins. Specifically, HYPE regulates UPR by adenylylating the ER chaperone, BiP/GRP78, which serves as a sentinel for UPR activation. Maintaining ER homeostasis is critical for determining cell fate, thus highlighting the importance of the HYPE-BiP interaction. Here, we study the kinetic and structural parameters that determine the HYPE-BiP interaction. By measuring the binding and kinetic efficiencies of HYPE in its activated (Adenylylation-competent) and wild type (de-AMPylation-competent) forms for BiP in its wild type and ATP-bound conformations, we determine that HYPE displays a nearly identical preference for the wild type and ATP-bound forms of BiP in vitro and preferentially de-AMPylates the wild type form of adenylylated BiP. We also show that AMPylation at BiP's Thr366 versus Thr518 sites differentially affect its ATPase activity, and that HYPE does not adenylylate UPR accessory proteins like J-protein ERdJ6. Using molecular docking models, we explain how HYPE is able to adenylylate Thr366 and Thr518 sites in vitro. While a physiological role for AMPylation at both the Thr366 and Thr518 sites has been reported, our molecular docking model supports Thr518 as the structurally preferred modification site. This is the first such analysis of the HYPE-BiP interaction and offers critical insights into substrate specificity and target recognition.
Collapse
Affiliation(s)
- Anwesha Sanyal
- From the Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN, 47907, USA
| | - Erica A Zbornik
- From the Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN, 47907, USA
| | - Ben G Watson
- From the Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN, 47907, USA
| | - Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Jia Ma
- Bindley Biosciences Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Daisuke Kihara
- From the Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN, 47907, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Seema Mattoo
- From the Department of Biological Sciences, Purdue University, 915 W. State St., LILY G-227, West Lafayette, IN, 47907, USA.
| |
Collapse
|
42
|
Kohler V, Andréasson C. Hsp70-mediated quality control: should I stay or should I go? Biol Chem 2021; 401:1233-1248. [PMID: 32745066 DOI: 10.1515/hsz-2020-0187] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/11/2020] [Indexed: 12/30/2022]
Abstract
Chaperones of the 70 kDa heat shock protein (Hsp70) superfamily are key components of the cellular proteostasis system. Together with its co-chaperones, Hsp70 forms proteostasis subsystems that antagonize protein damage during physiological and stress conditions. This function stems from highly regulated binding and release cycles of protein substrates, which results in a flow of unfolded, partially folded and misfolded species through the Hsp70 subsystem. Specific factors control how Hsp70 makes decisions regarding folding and degradation fates of the substrate proteins. In this review, we summarize how the flow of Hsp70 substrates is controlled in the cell with special emphasis on recent advances regarding substrate release mechanisms.
Collapse
Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
| |
Collapse
|
43
|
Inhibition of the Human Hsc70 System by Small Ligands as a Potential Anticancer Approach. Cancers (Basel) 2021; 13:cancers13122936. [PMID: 34208232 PMCID: PMC8230956 DOI: 10.3390/cancers13122936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary High levels of Heat shock proteins (Hsps) in specific cancers are usually linked to a poor prognosis, tumor progression, invasiveness, and resistance to treatment. Chaperone inhibition could therefore be toxic for cancer cells due to their high dependence on chaperone activity to survive. This study shows the potential to repurpose the small chemical compound pinaverium bromide, currently used to treat functional gastrointestinal disorders, as a possible antitumor drug since it displays a marked toxicity against two melanoma cell lines without affecting the viability of fibroblast and primary melanocytes. This compound interacts with structural regions shared by representatives of the Hsp70 and Hsp110 families, inhibiting the substrate remodeling ability of the Hsp70 system in vitro and in a cellular context. Abstract Heat shock protein (Hsp) synthesis is upregulated in a wide range of cancers to provide the appropriate environment for tumor progression. The Hsp110 and Hsp70 families have been associated to cancer cell survival and resistance to chemotherapy. In this study, we explore the strategy of drug repurposing to find new Hsp70 and Hsp110 inhibitors that display toxicity against melanoma cancer cells. We found that the hits discovered using Apg2, a human representative of the Hsp110 family, as the initial target bind also to structural regions present in members of the Hsp70 family, and therefore inhibit the remodeling activity of the Hsp70 system. One of these compounds, the spasmolytic agent pinaverium bromide used for functional gastrointestinal disorders, inhibits the intracellular chaperone activity of the Hsp70 system and elicits its cytotoxic activity specifically in two melanoma cell lines by activating apoptosis. Docking and molecular dynamics simulations indicate that this compound interacts with regions located in the nucleotide-binding domain and the linker of the chaperones, modulating their ATPase activity. Thus, repurposing of pinaverium bromide for cancer treatment appears as a promising novel therapeutic approach.
Collapse
|
44
|
Mayer MP. The Hsp70-Chaperone Machines in Bacteria. Front Mol Biosci 2021; 8:694012. [PMID: 34164436 PMCID: PMC8215388 DOI: 10.3389/fmolb.2021.694012] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/20/2021] [Indexed: 12/02/2022] Open
Abstract
The ATP-dependent Hsp70s are evolutionary conserved molecular chaperones that constitute central hubs of the cellular protein quality surveillance network. None of the other main chaperone families (Tig, GroELS, HtpG, IbpA/B, ClpB) have been assigned with a comparable range of functions. Through a multitude of functions Hsp70s are involved in many cellular control circuits for maintaining protein homeostasis and have been recognized as key factors for cell survival. Three mechanistic properties of Hsp70s are the basis for their high versatility. First, Hsp70s bind to short degenerate sequence motifs within their client proteins. Second, Hsp70 chaperones switch in a nucleotide-controlled manner between a state of low affinity for client proteins and a state of high affinity for clients. Third, Hsp70s are targeted to their clients by a large number of cochaperones of the J-domain protein (JDP) family and the lifetime of the Hsp70-client complex is regulated by nucleotide exchange factors (NEF). In this review I will discuss advances in the understanding of the molecular mechanism of the Hsp70 chaperone machinery focusing mostly on the bacterial Hsp70 DnaK and will compare the two other prokaryotic Hsp70s HscA and HscC with DnaK.
Collapse
Affiliation(s)
- Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, Heidelberg, Germany
| |
Collapse
|
45
|
Ibrahim IM, Elfiky AA, Elgohary AM. Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. Biochem Biophys Res Commun 2021; 562:89-93. [PMID: 34049205 PMCID: PMC8139235 DOI: 10.1016/j.bbrc.2021.05.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 12/28/2022]
Abstract
New SARS-CoV-2 variants emerged in the United Kingdom and South Africa in December 2020 in concomitant with the Brazillian variant in February 2021 (B.1.1.248 lineage) and currently sparking worldwide during the last few months. The new strain 501.V2 in South Africa bears three mutations in the spike receptor-binding domain (RBD); K417 N, E484K, and N501Y, while the Brazilian B.1.1.248 lineage has 12 mutations. In the current study, we simulate the complex ACE2-SARS-CoV-2 spike RBD system in which the RBD is in the wild-type and mutated isoforms. Additionally, the cell-surface Glucose Regulated Protein 78 (CS-GRP78) associated with the ACE2-SARS-CoV-2 spike RBD complex (ACE2-S RBD) is modeled at the presence of these mutant variants of the viral spike. The results showed that E484K and N501Y are critical in viral spike recognition through either ACE2 or CS-GRP78. The mutated variants (the UK, South African, and Brazilian) of the spike RBD tightly bind to GRP78 more than in the case of the wild-type RBD. These results point to the potent role of GRP78 with ACE2 in the attachment of the new variants, which could be a key for the design of inhibitors to block SARS-CoV-2 attachment and entry to the host cell.
Collapse
Affiliation(s)
- Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt.
| | - Alaa M Elgohary
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| |
Collapse
|
46
|
Ambrose AJ, Chapman E. Function, Therapeutic Potential, and Inhibition of Hsp70 Chaperones. J Med Chem 2021; 64:7060-7082. [PMID: 34009983 DOI: 10.1021/acs.jmedchem.0c02091] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hsp70s are among the most highly conserved proteins in all of biology. Through an iterative binding and release of exposed hydrophobic residues on client proteins, Hsp70s can prevent aggregation and promote folding to the native state of their client proteins. The human proteome contains eight canonical Hsp70s. Because Hsp70s are relatively promiscuous they play a role in folding a large proportion of the proteome. Hsp70s are implicated in disease through their ability to regulate protein homeostasis. In recent years, researchers have attempted to develop selective inhibitors of Hsp70 isoforms to better understand the role of individual isoforms in biology and as potential therapeutics. Selective inhibitors have come from rational design, forced localization, and serendipity, but the development of completely selective inhibitors remains elusive. In the present review, we discuss the Hsp70 structure and function, the known Hsp70 client proteins, the role of Hsp70s in disease, and current efforts to discover Hsp70 modulators.
Collapse
Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| |
Collapse
|
47
|
Chatterjee BK, Truttmann MC. Fic and non-Fic AMPylases: protein AMPylation in metazoans. Open Biol 2021; 11:210009. [PMID: 33947243 PMCID: PMC8097203 DOI: 10.1098/rsob.210009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Protein AMPylation refers to the covalent attachment of an AMP moiety to the amino acid side chains of target proteins using ATP as nucleotide donor. This process is catalysed by dedicated AMP transferases, called AMPylases. Since this initial discovery, several research groups have identified AMPylation as a critical post-translational modification relevant to normal and pathological cell signalling in both bacteria and metazoans. Bacterial AMPylases are abundant enzymes that either regulate the function of endogenous bacterial proteins or are translocated into host cells to hijack host cell signalling processes. By contrast, only two classes of metazoan AMPylases have been identified so far: enzymes containing a conserved filamentation induced by cAMP (Fic) domain (Fic AMPylases), which primarily modify the ER-resident chaperone BiP, and SelO, a mitochondrial AMPylase involved in redox signalling. In this review, we compare and contrast bacterial and metazoan Fic and non-Fic AMPylases, and summarize recent technological and conceptual developments in the emerging field of AMPylation.
Collapse
Affiliation(s)
- Bhaskar K Chatterjee
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthias C Truttmann
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.,Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
48
|
Specificity of AMPylation of the human chaperone BiP is mediated by TPR motifs of FICD. Nat Commun 2021; 12:2426. [PMID: 33893288 PMCID: PMC8065156 DOI: 10.1038/s41467-021-22596-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
To adapt to fluctuating protein folding loads in the endoplasmic reticulum (ER), the Hsp70 chaperone BiP is reversibly modified with adenosine monophosphate (AMP) by the ER-resident Fic-enzyme FICD/HYPE. The structural basis for BiP binding and AMPylation by FICD has remained elusive due to the transient nature of the enzyme-substrate-complex. Here, we use thiol-reactive derivatives of the cosubstrate adenosine triphosphate (ATP) to covalently stabilize the transient FICD:BiP complex and determine its crystal structure. The complex reveals that the TPR-motifs of FICD bind specifically to the conserved hydrophobic linker of BiP and thus mediate specificity for the domain-docked conformation of BiP. Furthermore, we show that both AMPylation and deAMPylation of BiP are not directly regulated by the presence of unfolded proteins. Together, combining chemical biology, crystallography and biochemistry, our study provides structural insights into a key regulatory mechanism that safeguards ER homeostasis.
Collapse
|
49
|
Samanta S, Yang S, Debnath B, Xue D, Kuang Y, Ramkumar K, Lee AS, Ljungman M, Neamati N. The Hydroxyquinoline Analogue YUM70 Inhibits GRP78 to Induce ER Stress-Mediated Apoptosis in Pancreatic Cancer. Cancer Res 2021; 81:1883-1895. [PMID: 33531374 PMCID: PMC8137563 DOI: 10.1158/0008-5472.can-20-1540] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/27/2020] [Accepted: 01/28/2021] [Indexed: 11/16/2022]
Abstract
GRP78 (glucose-regulated protein, 78 kDa) is a key regulator of endoplasmic reticulum (ER) stress signaling. Cancer cells are highly proliferative and have high demand for protein synthesis and folding, which results in significant stress on the ER. To respond to ER stress and maintain cellular homeostasis, cells activate the unfolded protein response (UPR) that promotes either survival or apoptotic death. Cancer cells utilize the UPR to promote survival and growth. In this study, we describe the discovery of a series of novel hydroxyquinoline GRP78 inhibitors. A representative analogue, YUM70, inhibited pancreatic cancer cell growth in vitro and showed in vivo efficacy in a pancreatic cancer xenograft model with no toxicity to normal tissues. YUM70 directly bound GRP78 and inactivated its function, resulting in ER stress-mediated apoptosis. A YUM70 analogue conjugated with BODIPY showed colocalization of the compound with GRP78 in the ER. Moreover, a YUM70-PROTAC (proteolysis targeting chimera) was synthesized to force degradation of GRP78 in pancreatic cancer cells. YUM70 showed a strong synergistic cytotoxicity with topotecan and vorinostat. Together, our study demonstrates that YUM70 is a novel inducer of ER stress, with preclinical efficacy as a monotherapy or in combination with topoisomerase and HDAC inhibitors in pancreatic cancer. SIGNIFICANCE: This study identifies a novel ER stress inducer that binds GRP78 and inhibits pancreatic cancer cell growth in vitro and in vivo, demonstrating its potential as a therapeutic agent for pancreatic cancer.
Collapse
Affiliation(s)
- Soma Samanta
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Suhui Yang
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Bikash Debnath
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Ding Xue
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Yuting Kuang
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Kavya Ramkumar
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California
| | - Amy S Lee
- Department of Biochemistry and Molecular Medicine, University of Southern California, Keck School of Medicine, USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Mats Ljungman
- Department of Radiation Oncology, Rogel Cancer Center, Center for RNA Biomedicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan.
| |
Collapse
|
50
|
Lotfi M, Ghafouri H, Sarikhan S, Shahangian SS, Darvishi R. Cloning, prokaryotic expression, and functional characterization of a novel 70-kDa heat shock protein (DnaK) from Bacillus persicus. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|